From c2f95a6be5e18cca587084763f384a4302c482dc Mon Sep 17 00:00:00 2001 From: Remi Gau Date: Mon, 20 May 2024 19:56:18 -0400 Subject: [PATCH 01/31] refactor and deal with simple visbility --- .pre-commit-config.yaml | 10 +- ui/forms.py | 235 ++++++++++++++++++ ui/modules.py | 28 +++ ui/neurovault/README_eCOBIDAS-en.html | 139 +++++++++++ .../experimental_design_schema.jsonld | 129 ++++++++++ .../items/length_of_blocks.jsonld | 28 +++ .../items/length_of_runs.jsonld | 28 +++ .../items/length_of_trials.jsonld | 28 +++ .../items/number_of_experimental_units.jsonld | 20 ++ .../items/number_of_imaging_runs.jsonld | 20 ++ .../items/optimization.jsonld | 23 ++ .../items/optimization_method.jsonld | 17 ++ .../items/type_of_design.jsonld | 42 ++++ .../group_inference_schema.jsonld | 64 +++++ .../items/group_smoothness_fwhm.jsonld | 20 ++ .../items/group_statistic_parameters.jsonld | 20 ++ .../items/group_statistic_type.jsonld | 66 +++++ .../group_modeling_schema.jsonld | 116 +++++++++ .../items/group_estimation_type.jsonld | 36 +++ .../items/group_inference_type.jsonld | 42 ++++ .../items/group_model_multilevel.jsonld | 17 ++ .../items/group_model_type.jsonld | 30 +++ .../items/group_modeling_software.jsonld | 23 ++ .../items/group_repeated_measures.jsonld | 23 ++ .../group_repeated_measures_method.jsonld | 17 ++ .../individual_subject_modeling_schema.jsonld | 220 ++++++++++++++++ .../items/autocorrelation_model.jsonld | 17 ++ .../items/contrast_definition.jsonld | 17 ++ .../items/contrast_definition_cogatlas.jsonld | 17 ++ .../hemodynamic_response_function.jsonld | 42 ++++ .../items/high_pass_filter_method.jsonld | 17 ++ .../items/intrasubject_estimation_type.jsonld | 36 +++ .../items/intrasubject_model_type.jsonld | 30 +++ .../intrasubject_modeling_software.jsonld | 23 ++ .../orthogonalization_description.jsonld | 17 ++ .../items/used_dispersion_derivatives.jsonld | 23 ++ .../items/used_high_pass_filter.jsonld | 23 ++ .../items/used_motion_regressors.jsonld | 23 ++ .../items/used_orthogonalization.jsonld | 23 ++ .../items/used_reaction_time_regressor.jsonld | 23 ++ .../items/used_temporal_derivatives.jsonld | 23 ++ .../intersubject_registration_schema.jsonld | 233 +++++++++++++++++ .../items/coordinate_space.jsonld | 42 ++++ ...nctional_coregistered_to_structural.jsonld | 23 ++ .../functional_coregistration_method.jsonld | 17 ++ .../items/interpolation_method.jsonld | 23 ++ .../intersubject_registration_software.jsonld | 23 ++ .../intersubject_transformation_type.jsonld | 36 +++ .../items/nonlinear_transform_type.jsonld | 17 ++ .../items/object_image_type.jsonld | 17 ++ .../items/resampled_voxel_size.jsonld | 20 ++ .../items/smoothing_fwhm.jsonld | 28 +++ .../items/smoothing_type.jsonld | 21 ++ .../items/target_resolution.jsonld | 28 +++ .../items/target_template_image.jsonld | 17 ++ .../items/transform_similarity_metric.jsonld | 17 ++ .../used_intersubject_registration.jsonld | 23 ++ .../items/used_smoothing.jsonld | 23 ++ .../mri_acquisition/items/EchoTime.jsonld | 28 +++ .../mri_acquisition/items/FlipAngle.jsonld | 28 +++ .../items/MagneticFieldStrength.jsonld | 28 +++ .../mri_acquisition/items/Manufacturer.jsonld | 42 ++++ .../items/ManufacturersModelName.jsonld | 17 ++ .../items/PulseSequenceType.jsonld | 60 +++++ .../items/RepetitionTime.jsonld | 28 +++ .../mri_acquisition/items/SliceTiming.jsonld | 42 ++++ .../items/acquisition_orientation.jsonld | 42 ++++ .../items/field_of_view.jsonld | 28 +++ .../mri_acquisition/items/matrix_size.jsonld | 20 ++ .../items/parallel_imaging.jsonld | 17 ++ .../mri_acquisition/items/skip_factor.jsonld | 28 +++ .../items/slice_thickness.jsonld | 28 +++ .../mri_acquisition_schema.jsonld | 207 +++++++++++++++ .../items/group_comparison.jsonld | 23 ++ .../items/group_description.jsonld | 17 ++ .../participants/items/handedness.jsonld | 42 ++++ .../items/inclusion_exclusion_criteria.jsonld | 17 ++ .../items/number_of_rejected_subjects.jsonld | 20 ++ .../items/number_of_subjects.jsonld | 20 ++ .../items/proportion_male_subjects.jsonld | 145 +++++++++++ .../participants/items/subject_age_max.jsonld | 20 ++ .../items/subject_age_mean.jsonld | 20 ++ .../participants/items/subject_age_min.jsonld | 20 ++ .../participants/participants_schema.jsonld | 155 ++++++++++++ .../preprocessing/items/SoftwareName.jsonld | 23 ++ .../items/SoftwareVersion.jsonld | 17 ++ .../items/b0_unwarping_software.jsonld | 23 ++ .../motion_correction_interpolation.jsonld | 23 ++ .../items/motion_correction_metric.jsonld | 23 ++ .../items/motion_correction_reference.jsonld | 17 ++ .../items/motion_correction_software.jsonld | 23 ++ .../order_of_preprocessing_operations.jsonld | 17 ++ .../items/quality_control.jsonld | 17 ++ .../slice_timing_correction_software.jsonld | 17 ++ .../items/used_b0_unwarping.jsonld | 23 ++ .../items/used_motion_correction.jsonld | 23 ++ ...sed_motion_susceptibiity_correction.jsonld | 23 ++ .../items/used_slice_timing_correction.jsonld | 23 ++ .../preprocessing/preprocessing_schema.jsonld | 207 +++++++++++++++ .../protocols/neurovault_schema.jsonld | 133 ++++++++++ ui/requirements.txt | 3 + ui/templates/404.html | 14 ++ ui/templates/500.html | 14 ++ ui/templates/about.html | 1 + ui/templates/activity.html | 14 ++ ui/templates/base.html | 52 ++++ ui/templates/index.html | 18 ++ 107 files changed, 4292 insertions(+), 1 deletion(-) create mode 100644 ui/forms.py create mode 100644 ui/modules.py create mode 100644 ui/neurovault/README_eCOBIDAS-en.html create mode 100644 ui/neurovault/activities/experimental_design/experimental_design_schema.jsonld create mode 100644 ui/neurovault/activities/experimental_design/items/length_of_blocks.jsonld create mode 100644 ui/neurovault/activities/experimental_design/items/length_of_runs.jsonld create mode 100644 ui/neurovault/activities/experimental_design/items/length_of_trials.jsonld create mode 100644 ui/neurovault/activities/experimental_design/items/number_of_experimental_units.jsonld create mode 100644 ui/neurovault/activities/experimental_design/items/number_of_imaging_runs.jsonld create mode 100644 ui/neurovault/activities/experimental_design/items/optimization.jsonld create mode 100644 ui/neurovault/activities/experimental_design/items/optimization_method.jsonld create mode 100644 ui/neurovault/activities/experimental_design/items/type_of_design.jsonld create mode 100644 ui/neurovault/activities/group_inference/group_inference_schema.jsonld create mode 100644 ui/neurovault/activities/group_inference/items/group_smoothness_fwhm.jsonld create mode 100644 ui/neurovault/activities/group_inference/items/group_statistic_parameters.jsonld create mode 100644 ui/neurovault/activities/group_inference/items/group_statistic_type.jsonld create mode 100644 ui/neurovault/activities/group_modeling/group_modeling_schema.jsonld create mode 100644 ui/neurovault/activities/group_modeling/items/group_estimation_type.jsonld create mode 100644 ui/neurovault/activities/group_modeling/items/group_inference_type.jsonld create mode 100644 ui/neurovault/activities/group_modeling/items/group_model_multilevel.jsonld create mode 100644 ui/neurovault/activities/group_modeling/items/group_model_type.jsonld create mode 100644 ui/neurovault/activities/group_modeling/items/group_modeling_software.jsonld create mode 100644 ui/neurovault/activities/group_modeling/items/group_repeated_measures.jsonld create mode 100644 ui/neurovault/activities/group_modeling/items/group_repeated_measures_method.jsonld create mode 100644 ui/neurovault/activities/individual_subject_modeling/individual_subject_modeling_schema.jsonld create mode 100644 ui/neurovault/activities/individual_subject_modeling/items/autocorrelation_model.jsonld create mode 100644 ui/neurovault/activities/individual_subject_modeling/items/contrast_definition.jsonld create mode 100644 ui/neurovault/activities/individual_subject_modeling/items/contrast_definition_cogatlas.jsonld create mode 100644 ui/neurovault/activities/individual_subject_modeling/items/hemodynamic_response_function.jsonld create mode 100644 ui/neurovault/activities/individual_subject_modeling/items/high_pass_filter_method.jsonld create mode 100644 ui/neurovault/activities/individual_subject_modeling/items/intrasubject_estimation_type.jsonld create mode 100644 ui/neurovault/activities/individual_subject_modeling/items/intrasubject_model_type.jsonld create mode 100644 ui/neurovault/activities/individual_subject_modeling/items/intrasubject_modeling_software.jsonld create mode 100644 ui/neurovault/activities/individual_subject_modeling/items/orthogonalization_description.jsonld create mode 100644 ui/neurovault/activities/individual_subject_modeling/items/used_dispersion_derivatives.jsonld create mode 100644 ui/neurovault/activities/individual_subject_modeling/items/used_high_pass_filter.jsonld create mode 100644 ui/neurovault/activities/individual_subject_modeling/items/used_motion_regressors.jsonld create mode 100644 ui/neurovault/activities/individual_subject_modeling/items/used_orthogonalization.jsonld create mode 100644 ui/neurovault/activities/individual_subject_modeling/items/used_reaction_time_regressor.jsonld create mode 100644 ui/neurovault/activities/individual_subject_modeling/items/used_temporal_derivatives.jsonld create mode 100644 ui/neurovault/activities/intersubject_registration/intersubject_registration_schema.jsonld create mode 100644 ui/neurovault/activities/intersubject_registration/items/coordinate_space.jsonld create mode 100644 ui/neurovault/activities/intersubject_registration/items/functional_coregistered_to_structural.jsonld create mode 100644 ui/neurovault/activities/intersubject_registration/items/functional_coregistration_method.jsonld create mode 100644 ui/neurovault/activities/intersubject_registration/items/interpolation_method.jsonld create mode 100644 ui/neurovault/activities/intersubject_registration/items/intersubject_registration_software.jsonld create mode 100644 ui/neurovault/activities/intersubject_registration/items/intersubject_transformation_type.jsonld create mode 100644 ui/neurovault/activities/intersubject_registration/items/nonlinear_transform_type.jsonld create mode 100644 ui/neurovault/activities/intersubject_registration/items/object_image_type.jsonld create mode 100644 ui/neurovault/activities/intersubject_registration/items/resampled_voxel_size.jsonld create mode 100644 ui/neurovault/activities/intersubject_registration/items/smoothing_fwhm.jsonld create mode 100644 ui/neurovault/activities/intersubject_registration/items/smoothing_type.jsonld create mode 100644 ui/neurovault/activities/intersubject_registration/items/target_resolution.jsonld create mode 100644 ui/neurovault/activities/intersubject_registration/items/target_template_image.jsonld create mode 100644 ui/neurovault/activities/intersubject_registration/items/transform_similarity_metric.jsonld create mode 100644 ui/neurovault/activities/intersubject_registration/items/used_intersubject_registration.jsonld create mode 100644 ui/neurovault/activities/intersubject_registration/items/used_smoothing.jsonld create mode 100644 ui/neurovault/activities/mri_acquisition/items/EchoTime.jsonld create mode 100644 ui/neurovault/activities/mri_acquisition/items/FlipAngle.jsonld create mode 100644 ui/neurovault/activities/mri_acquisition/items/MagneticFieldStrength.jsonld create mode 100644 ui/neurovault/activities/mri_acquisition/items/Manufacturer.jsonld create mode 100644 ui/neurovault/activities/mri_acquisition/items/ManufacturersModelName.jsonld create mode 100644 ui/neurovault/activities/mri_acquisition/items/PulseSequenceType.jsonld create mode 100644 ui/neurovault/activities/mri_acquisition/items/RepetitionTime.jsonld create mode 100644 ui/neurovault/activities/mri_acquisition/items/SliceTiming.jsonld create mode 100644 ui/neurovault/activities/mri_acquisition/items/acquisition_orientation.jsonld create mode 100644 ui/neurovault/activities/mri_acquisition/items/field_of_view.jsonld create mode 100644 ui/neurovault/activities/mri_acquisition/items/matrix_size.jsonld create mode 100644 ui/neurovault/activities/mri_acquisition/items/parallel_imaging.jsonld create mode 100644 ui/neurovault/activities/mri_acquisition/items/skip_factor.jsonld create mode 100644 ui/neurovault/activities/mri_acquisition/items/slice_thickness.jsonld create mode 100644 ui/neurovault/activities/mri_acquisition/mri_acquisition_schema.jsonld create mode 100644 ui/neurovault/activities/participants/items/group_comparison.jsonld create mode 100644 ui/neurovault/activities/participants/items/group_description.jsonld create mode 100644 ui/neurovault/activities/participants/items/handedness.jsonld create mode 100644 ui/neurovault/activities/participants/items/inclusion_exclusion_criteria.jsonld create mode 100644 ui/neurovault/activities/participants/items/number_of_rejected_subjects.jsonld create mode 100644 ui/neurovault/activities/participants/items/number_of_subjects.jsonld create mode 100644 ui/neurovault/activities/participants/items/proportion_male_subjects.jsonld create mode 100644 ui/neurovault/activities/participants/items/subject_age_max.jsonld create mode 100644 ui/neurovault/activities/participants/items/subject_age_mean.jsonld create mode 100644 ui/neurovault/activities/participants/items/subject_age_min.jsonld create mode 100644 ui/neurovault/activities/participants/participants_schema.jsonld create mode 100644 ui/neurovault/activities/preprocessing/items/SoftwareName.jsonld create mode 100644 ui/neurovault/activities/preprocessing/items/SoftwareVersion.jsonld create mode 100644 ui/neurovault/activities/preprocessing/items/b0_unwarping_software.jsonld create mode 100644 ui/neurovault/activities/preprocessing/items/motion_correction_interpolation.jsonld create mode 100644 ui/neurovault/activities/preprocessing/items/motion_correction_metric.jsonld create mode 100644 ui/neurovault/activities/preprocessing/items/motion_correction_reference.jsonld create mode 100644 ui/neurovault/activities/preprocessing/items/motion_correction_software.jsonld create mode 100644 ui/neurovault/activities/preprocessing/items/order_of_preprocessing_operations.jsonld create mode 100644 ui/neurovault/activities/preprocessing/items/quality_control.jsonld create mode 100644 ui/neurovault/activities/preprocessing/items/slice_timing_correction_software.jsonld create mode 100644 ui/neurovault/activities/preprocessing/items/used_b0_unwarping.jsonld create mode 100644 ui/neurovault/activities/preprocessing/items/used_motion_correction.jsonld create mode 100644 ui/neurovault/activities/preprocessing/items/used_motion_susceptibiity_correction.jsonld create mode 100644 ui/neurovault/activities/preprocessing/items/used_slice_timing_correction.jsonld create mode 100644 ui/neurovault/activities/preprocessing/preprocessing_schema.jsonld create mode 100644 ui/neurovault/protocols/neurovault_schema.jsonld create mode 100644 ui/requirements.txt create mode 100644 ui/templates/404.html create mode 100644 ui/templates/500.html create mode 100644 ui/templates/about.html create mode 100644 ui/templates/activity.html create mode 100644 ui/templates/base.html create mode 100644 ui/templates/index.html diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 47807bb2..5cc96985 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -76,6 +76,14 @@ repos: # additional_dependencies: [types-all, pandas-stubs] # args: [--config-file=pyproject.toml] +# Check formatting of CSS and HTML +# prettier: https://prettier.io/ +- repo: https://github.com/pre-commit/mirrors-prettier + rev: v4.0.0-alpha.8 + hooks: + - id: prettier + types_or: [css, html] + # Check that Python code complies with PEP8 guidelines # flake8 uses pydocstyle to check docstrings: https://flake8.pycqa.org/en/latest/ # flake8-docstrings: https://pypi.org/project/flake8-docstrings/ @@ -86,5 +94,5 @@ repos: rev: 7.0.0 hooks: - id: flake8 - args: [--config, .flake8, --verbose, ecobidas, tests, macros] + args: [--config, .flake8, --verbose, ecobidas, tests, macros, ui] additional_dependencies: [flake8-docstrings, flake8-use-fstring, flake8-functions, flake8-bugbear] diff --git a/ui/forms.py b/ui/forms.py new file mode 100644 index 00000000..15a228c7 --- /dev/null +++ b/ui/forms.py @@ -0,0 +1,235 @@ +from functools import lru_cache + +import requests +from flask import Flask, render_template +from flask_bootstrap import Bootstrap5 +from flask_wtf import CSRFProtect, FlaskForm +from markupsafe import Markup, escape +from modules import activity_url, get_activity, get_item +from rich import print +from wtforms import ( + DecimalField, + HiddenField, + IntegerField, + MultipleFileField, + RadioField, + SelectField, + StringField, + SubmitField, + TextAreaField, +) +from wtforms.validators import DataRequired + +LANG = "en" + +app = Flask(__name__) +app.secret_key = "tO$&!|0wkamvVia0?n$NqIRVWOG" + +# Bootstrap-Flask requires this line +bootstrap = Bootstrap5(app) + +# Flask-WTF requires this line +csrf = CSRFProtect(app) + + +class DyanmicForm(FlaskForm): + pass + + +@lru_cache +def query_choices(url): + try: + data = requests.get(url).json() + except Exception as exc: + print(exc) + data = None + return data + + +@app.route("/", methods=["GET", "POST"]) +def index(): + return render_template("index.html") + + +@app.route("/about") +def about(): + return render_template("about.html") + + +@app.route("//", methods=["GET", "POST"]) +def activity(protocol_name, activity_name): + protocol_name = escape(protocol_name) + activity_name = escape(activity_name) + + activity = get_activity(protocol_name, activity_name) + + items = get_items_for_activity(protocol_name, activity_name) + + form = generate_form(items) + + if form.validate_on_submit(): + for item, values in items.items(): + isVis = values["isVis"] + if isinstance(isVis, str): + isVis = isVis.replace(" ", "").split("==") + if len(isVis) == 2: + response = form[isVis[0]].data + value = items[isVis[0]]["choices"].get(response) + expected = int(isVis[1]) + items[item]["visibility"] = value == expected + + form = generate_form(items) + + return render_template( + "activity.html", + prefLabel=activity["prefLabel"][LANG], + preamble=Markup(activity["preamble"][LANG]), + form=form, + ) + + return render_template( + "activity.html", + prefLabel=activity["prefLabel"][LANG], + preamble=Markup(activity["preamble"][LANG]), + form=form, + ) + + +def generate_form(items): + for item_name, item in items.items(): + + validators = [] + if item["required"]: + validators.append(DataRequired()) + + question = f"{item['question']} {item['unit']}" + + if not item["visibility"]: + setattr( + DyanmicForm, + item_name, + HiddenField( + Markup(question), + validators=validators, + description=item["description"], + ), + ) + continue + + input_type = item["input_type"] + + if input_type not in ["select", "radio", "slider"]: + + FieldType = StringField + if input_type == "number": + FieldType = IntegerField + elif input_type in ["float", "slider"]: + FieldType = DecimalField + elif input_type == "textarea": + FieldType = TextAreaField + + setattr( + DyanmicForm, + item_name, + FieldType( + Markup(question), + validators=validators, + description=item["description"], + ), + ) + + else: + + is_multiple = item["is_multiple"] + + if is_multiple: + FieldType = MultipleFileField + if input_type == "select": + FieldType = SelectField + elif input_type == "radio": + FieldType = RadioField + + setattr( + DyanmicForm, + item_name, + FieldType( + Markup(question), + validators=validators, + description=item["description"], + choices=[key for key in item["choices"]], + ), + ) + + setattr(DyanmicForm, "submit", SubmitField("Submit")) # noqa B010 + + return DyanmicForm() + + +def get_items_for_activity(protocol_name, activity_name): + # TODO make sure items are presented in the right order + activity = get_activity(protocol_name, activity_name) + items = {} + for item in activity["ui"]["addProperties"]: + + item_name = item["variableName"] + + item_data = get_item(activity_url(protocol_name, activity_name).parent / item["isAbout"]) + + tmp = { + "visibility": False, + "required": False, + "isVis": item["isVis"], + "choices": get_choices(item_data), + } + + tmp["description"] = item_data.get("description") + tmp["question"] = item_data["question"][LANG] + tmp["input_type"] = item_data["ui"]["inputType"] + + if item["isVis"] == 1: + tmp["visibility"] = True + + if item["requiredValue"]: + tmp["required"] = True + + try: + unit = f"({item_data['responseOptions']['unitOptions'][0]['prefLabel'][LANG]})" + except KeyError: + unit = "" + tmp["unit"] = unit + + try: + is_multiple = item_data["responseOptions"].get("multipleChoice", False) + except KeyError: + is_multiple = False + tmp["is_multiple"] = is_multiple + + items[item_name] = tmp + + return items + + +def get_choices(item_data): + try: + choices = item_data["responseOptions"]["choices"] + if isinstance(choices, str): + choices = query_choices(choices)["choices"] + choices = {x["name"][LANG]: x["value"] for x in choices} + except KeyError: + choices = {} + return choices + + +@app.errorhandler(404) +def page_not_found(e): + return render_template("404.html"), 404 + + +@app.errorhandler(500) +def internal_server_error(e): + return render_template("500.html"), 500 + + +# keep this as is +if __name__ == "__main__": + app.run(debug=True) diff --git a/ui/modules.py b/ui/modules.py new file mode 100644 index 00000000..72b4053b --- /dev/null +++ b/ui/modules.py @@ -0,0 +1,28 @@ +# functions to be used by the routes +import json +from pathlib import Path + + +def activity_url(protocol_name, activity_name): + return ( + Path(__file__).parents[1] + / "cobidas_schema" + / "schemas" + / protocol_name + / "activities" + / activity_name + / f"{activity_name}_schema.jsonld" + ) + + +def get_activity(protocol_name, activity_name): + file = activity_url(protocol_name, activity_name) + with open(file) as f: + content = json.load(f) + return content + + +def get_item(file): + with open(file) as f: + content = json.load(f) + return content diff --git a/ui/neurovault/README_eCOBIDAS-en.html b/ui/neurovault/README_eCOBIDAS-en.html new file mode 100644 index 00000000..5d398bc2 --- /dev/null +++ b/ui/neurovault/README_eCOBIDAS-en.html @@ -0,0 +1,139 @@ +
+
+

COBIDAS Information Collection Protocol

+

+ The aim of this protocol is to help users collect information related to + the different components of the COBIDAS protocol. +

+

How to use it

+

+ You can navigate each section on the left and then answer the questions + corresponding to your fMRI analysis. This is meant to make sure that you + have not forgotten any of the essential information in the methods and + results parts of your article. +

+

+ At the end, you can click on Export (bottom left) to get a zip file + containing machine readable json files that captures information about + your method/results section: our next step is to use this to automate the + part of the methods writing and to submit the information alongside data + submission to Neurovault and other data archives. +

+

Have any questions? Something is missing? Let us know.

+ +

Why this project?

+

+ Poor methods and results description hinders the reproducibility and the + replicability of research. It also makes it hard to compare new and old + results and generally increases inefficiency in the research process. This + project is built on the hope that improving methods and results reporting + could improve our research. +

+

+ Follow the link if you want to know more about the + motivations behind this project. +

+

Background

+

+ This checklist is a project to make a user friendly checklist out the best + practices + report of + the Committee on Best Practices in Data Analysis and Sharing (COBIDAS) of the + Organization for Human Brain Mapping. +

+

+ This is very much of a work in progress but the next step is to expand the + list to cover all the items of the COBIDAS report for fMRI as well as for + the recent + extension to EEG and MEG. +

+

Want to help?

+

+ We are currently working on trying to expand the number of items used in + the checklist. All of this work is done in google spreadsheets: the + spreadsheet for each section is accessible by clicking on the + Source + at the top of each page. +

+

Want to know more?

+

+ Most of the information concerning this project can be found on this + github repository. +

+

+ If you want to be kept posted about the progress of the project, you can + join our + google group +

+

+ From more frequent updates and behind the scenes, come and join us on the + cobidas_checklist channel on the brainhack + + + channel. + +

+

+ There is also an [OSF project](https://osf.io/anvqy/) to centralize all + the information and repos. +

+

+ We have a + list + of short, middle, long term goals: if you are interested by any of those + get in touch. Many of them do not necessarily require super-advanced + technical skills (except maybe a certain love for working with spreadsheet + and wanting them to be super organized). +

+

Contributors

+

+ The list of the people involved in this project can be found + here. +

+

License

+

The protocol is licensed CC-BY-4.0

+

(c) 2020 COBIDAS Contributors

+
+
diff --git a/ui/neurovault/activities/experimental_design/experimental_design_schema.jsonld b/ui/neurovault/activities/experimental_design/experimental_design_schema.jsonld new file mode 100644 index 00000000..0b3bac44 --- /dev/null +++ b/ui/neurovault/activities/experimental_design/experimental_design_schema.jsonld @@ -0,0 +1,129 @@ +{ + "@context": "https://raw.githubusercontent.com/ReproNim/reproschema/1.0.0-rc4/contexts/generic", + "@type": "reproschema:Activity", + "@id": "experimental_design_schema.jsonld", + "schemaVersion": "1.0.0-rc4", + "version": "0.0.1", + "prefLabel": { + "en": "Experimental design" + }, + "description": "experimental design", + "preamble": { + "en": "

Source | Github repository | Reference

Describe your experimental design

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Source | Github repository | Reference

Describe your statistical inference

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details
This is the estimated smoothness used with Random Field Theory or a simulation-based inference method.
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details
Typically degrees of freedom (should be clear from the test statistic what these are).
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Source | Github repository | Reference

Describe the group level analysis

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details
For example, are variances assumed equal between groups.
" + } +} diff --git a/ui/neurovault/activities/group_modeling/items/group_model_type.jsonld b/ui/neurovault/activities/group_modeling/items/group_model_type.jsonld new file mode 100644 index 00000000..f1f3b7f6 --- /dev/null +++ b/ui/neurovault/activities/group_modeling/items/group_model_type.jsonld @@ -0,0 +1,30 @@ +{ + "@context": "https://raw.githubusercontent.com/ReproNim/reproschema/1.0.0-rc4/contexts/generic", + "@type": "reproschema:Field", + "@id": "group_model_type.jsonld", + "schemaVersion": "1.0.0-rc4", + "version": "0.0.1", + "prefLabel": { + "en": "group model type" + }, + "description": "group model type", + "ui": { + "inputType": "select" + }, + "question": { + "en": "7.1 - Type of group model used" + }, + "responseOptions": { + "valueType": "xsd:integer", + "choices": [ + { + "name": { + "en": "Regression" + }, + "value": 0 + } + ], + "minValue": 0, + "maxValue": 0 + } +} diff --git a/ui/neurovault/activities/group_modeling/items/group_modeling_software.jsonld b/ui/neurovault/activities/group_modeling/items/group_modeling_software.jsonld new file mode 100644 index 00000000..894ef68c --- /dev/null +++ b/ui/neurovault/activities/group_modeling/items/group_modeling_software.jsonld @@ -0,0 +1,23 @@ +{ + "@context": "https://raw.githubusercontent.com/ReproNim/reproschema/1.0.0-rc4/contexts/generic", + "@type": "reproschema:Field", + "@id": "group_modeling_software.jsonld", + "schemaVersion": "1.0.0-rc4", + "version": "0.0.1", + "prefLabel": { + "en": "group modeling software" + }, + "description": "group modeling software", + "ui": { + "inputType": "select" + }, + "question": { + "en": "7.3 - Software used for group modeling if different from overall package" + }, + "responseOptions": { + "valueType": "xsd:integer", + "choices": "https://raw.githubusercontent.com/ohbm/cobidas_schema/master/response_options/mri_softwares.jsonld", + "minValue": 0, + "maxValue": 0 + } +} diff --git a/ui/neurovault/activities/group_modeling/items/group_repeated_measures.jsonld b/ui/neurovault/activities/group_modeling/items/group_repeated_measures.jsonld new file mode 100644 index 00000000..73223aa8 --- /dev/null +++ b/ui/neurovault/activities/group_modeling/items/group_repeated_measures.jsonld @@ -0,0 +1,23 @@ +{ + "@context": "https://raw.githubusercontent.com/ReproNim/reproschema/1.0.0-rc4/contexts/generic", + "@type": "reproschema:Field", + "@id": "group_repeated_measures.jsonld", + "schemaVersion": "1.0.0-rc4", + "version": "0.0.1", + "prefLabel": { + "en": "group repeated measures" + }, + "description": "group repeated measures", + "ui": { + "inputType": "radio" + }, + "question": { + "en": "7.6 - Was this a repeated measures design at the group level?" + }, + "responseOptions": { + "valueType": "xsd:integer", + "choices": "https://raw.githubusercontent.com/ohbm/cobidas_schema/master/response_options/boolean.jsonld", + "minValue": 0, + "maxValue": 0 + } +} diff --git a/ui/neurovault/activities/group_modeling/items/group_repeated_measures_method.jsonld b/ui/neurovault/activities/group_modeling/items/group_repeated_measures_method.jsonld new file mode 100644 index 00000000..4bb0bd87 --- /dev/null +++ b/ui/neurovault/activities/group_modeling/items/group_repeated_measures_method.jsonld @@ -0,0 +1,17 @@ +{ + "@context": "https://raw.githubusercontent.com/ReproNim/reproschema/1.0.0-rc4/contexts/generic", + "@type": "reproschema:Field", + "@id": "group_repeated_measures_method.jsonld", + "schemaVersion": "1.0.0-rc4", + "version": "0.0.1", + "prefLabel": { + "en": "group repeated measures method" + }, + "description": "group repeated measures method", + "ui": { + "inputType": "textarea" + }, + "question": { + "en": "7.7 - If multiple measurements per subject, list method to account for within subject correlation, exact assumptions made about correlation/variance" + } +} diff --git a/ui/neurovault/activities/individual_subject_modeling/individual_subject_modeling_schema.jsonld b/ui/neurovault/activities/individual_subject_modeling/individual_subject_modeling_schema.jsonld new file mode 100644 index 00000000..bdcde850 --- /dev/null +++ b/ui/neurovault/activities/individual_subject_modeling/individual_subject_modeling_schema.jsonld @@ -0,0 +1,220 @@ +{ + "@context": "https://raw.githubusercontent.com/ReproNim/reproschema/1.0.0-rc4/contexts/generic", + "@type": "reproschema:Activity", + "@id": "individual_subject_modeling_schema.jsonld", + "schemaVersion": "1.0.0-rc4", + "version": "0.0.1", + "prefLabel": { + "en": "Individual subject modeling" + }, + "description": "individual subject modeling", + "preamble": { + "en": "

Source | Github repository | Reference

Describe your model specification at the subejct level

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b/ui/neurovault/activities/individual_subject_modeling/items/autocorrelation_model.jsonld @@ -0,0 +1,17 @@ +{ + "@context": "https://raw.githubusercontent.com/ReproNim/reproschema/1.0.0-rc4/contexts/generic", + "@type": "reproschema:Field", + "@id": "autocorrelation_model.jsonld", + "schemaVersion": "1.0.0-rc4", + "version": "0.0.1", + "prefLabel": { + "en": "autocorrelation model" + }, + "description": "autocorrelation model", + "ui": { + "inputType": "textarea" + }, + "question": { + "en": "6.13 - What autocorrelation model was used (or 'none' if none was used)" + } +} diff --git a/ui/neurovault/activities/individual_subject_modeling/items/contrast_definition.jsonld b/ui/neurovault/activities/individual_subject_modeling/items/contrast_definition.jsonld new file mode 100644 index 00000000..9fc7a54e --- /dev/null +++ b/ui/neurovault/activities/individual_subject_modeling/items/contrast_definition.jsonld @@ -0,0 +1,17 @@ +{ + "@context": "https://raw.githubusercontent.com/ReproNim/reproschema/1.0.0-rc4/contexts/generic", + "@type": "reproschema:Field", + "@id": "contrast_definition.jsonld", + "schemaVersion": "1.0.0-rc4", + "version": "0.0.1", + "prefLabel": { + "en": "contrast definition" + }, + "description": "contrast definition", + "ui": { + "inputType": "textarea" + }, + "question": { + "en": "6.14 - Exactly what terms are subtracted from what?" + } +} diff --git a/ui/neurovault/activities/individual_subject_modeling/items/contrast_definition_cogatlas.jsonld b/ui/neurovault/activities/individual_subject_modeling/items/contrast_definition_cogatlas.jsonld new file mode 100644 index 00000000..39df28c6 --- /dev/null +++ b/ui/neurovault/activities/individual_subject_modeling/items/contrast_definition_cogatlas.jsonld @@ -0,0 +1,17 @@ +{ + "@context": "https://raw.githubusercontent.com/ReproNim/reproschema/1.0.0-rc4/contexts/generic", + "@type": "reproschema:Field", + "@id": "contrast_definition_cogatlas.jsonld", + "schemaVersion": "1.0.0-rc4", + "version": "0.0.1", + "prefLabel": { + "en": "contrast definition cogatlas" + }, + "description": "contrast definition cogatlas", + "ui": { + "inputType": "textarea" + }, + "question": { + "en": "6.15 - Link to Cognitive Atlas definition of this contrast
details
Define these in terms of task or stimulus conditions (e.g., 'one-back task with objects versus zero-back task with objects') instead of underlying psychological concepts (e.g., 'working memory').
" + } +} diff --git a/ui/neurovault/activities/individual_subject_modeling/items/hemodynamic_response_function.jsonld b/ui/neurovault/activities/individual_subject_modeling/items/hemodynamic_response_function.jsonld new file mode 100644 index 00000000..e9f259fb --- /dev/null +++ b/ui/neurovault/activities/individual_subject_modeling/items/hemodynamic_response_function.jsonld @@ -0,0 +1,42 @@ +{ + "@context": "https://raw.githubusercontent.com/ReproNim/reproschema/1.0.0-rc4/contexts/generic", + "@type": "reproschema:Field", + "@id": "hemodynamic_response_function.jsonld", + "schemaVersion": "1.0.0-rc4", + "version": "0.0.1", + "prefLabel": { + "en": "hemodynamic response function" + }, + "description": "hemodynamic response function", + "ui": { + "inputType": "select" + }, + "question": { + "en": "6.4 - Nature of HRF model" + }, + "responseOptions": { + "valueType": "xsd:integer", + "choices": [ + { + "name": { + "en": "double gamma" + }, + "value": 0 + }, + { + "name": { + "en": "Fourrier set" + }, + "value": 1 + }, + { + "name": { + "en": "FIR" + }, + "value": 2 + } + ], + "minValue": 0, + "maxValue": 2 + } +} diff --git a/ui/neurovault/activities/individual_subject_modeling/items/high_pass_filter_method.jsonld b/ui/neurovault/activities/individual_subject_modeling/items/high_pass_filter_method.jsonld new file mode 100644 index 00000000..54cd4e2a --- /dev/null +++ b/ui/neurovault/activities/individual_subject_modeling/items/high_pass_filter_method.jsonld @@ -0,0 +1,17 @@ +{ + "@context": "https://raw.githubusercontent.com/ReproNim/reproschema/1.0.0-rc4/contexts/generic", + "@type": "reproschema:Field", + "@id": "high_pass_filter_method.jsonld", + "schemaVersion": "1.0.0-rc4", + "version": "0.0.1", + "prefLabel": { + "en": "high pass filter method" + }, + "description": "high pass filter method", + "ui": { + "inputType": "textarea" + }, + "question": { + "en": "6.12 - Describe method used for high pass filtering" + } +} diff --git a/ui/neurovault/activities/individual_subject_modeling/items/intrasubject_estimation_type.jsonld b/ui/neurovault/activities/individual_subject_modeling/items/intrasubject_estimation_type.jsonld new file mode 100644 index 00000000..92437f24 --- /dev/null +++ b/ui/neurovault/activities/individual_subject_modeling/items/intrasubject_estimation_type.jsonld @@ -0,0 +1,36 @@ +{ + "@context": "https://raw.githubusercontent.com/ReproNim/reproschema/1.0.0-rc4/contexts/generic", + "@type": "reproschema:Field", + "@id": "intrasubject_estimation_type.jsonld", + "schemaVersion": "1.0.0-rc4", + "version": "0.0.1", + "prefLabel": { + "en": "intrasubject estimation type" + }, + "description": "intrasubject estimation type", + "ui": { + "inputType": "select" + }, + "question": { + "en": "6.2 - Estimation method used for model" + }, + "responseOptions": { + "valueType": "xsd:integer", + "choices": [ + { + "name": { + "en": "ordinary least squares" + }, + "value": 0 + }, + { + "name": { + "en": "generalized least squares" + }, + "value": 1 + } + ], + "minValue": 0, + "maxValue": 1 + } +} diff --git a/ui/neurovault/activities/individual_subject_modeling/items/intrasubject_model_type.jsonld b/ui/neurovault/activities/individual_subject_modeling/items/intrasubject_model_type.jsonld new file mode 100644 index 00000000..2adbccf7 --- /dev/null +++ b/ui/neurovault/activities/individual_subject_modeling/items/intrasubject_model_type.jsonld @@ -0,0 +1,30 @@ +{ + "@context": "https://raw.githubusercontent.com/ReproNim/reproschema/1.0.0-rc4/contexts/generic", + "@type": "reproschema:Field", + "@id": "intrasubject_model_type.jsonld", + "schemaVersion": "1.0.0-rc4", + "version": "0.0.1", + "prefLabel": { + "en": "intrasubject model type" + }, + "description": "intrasubject model type", + "ui": { + "inputType": "radio" + }, + "question": { + "en": "6.1 - Type of group model used" + }, + "responseOptions": { + "valueType": "xsd:integer", + "choices": [ + { + "name": { + "en": "Regression" + }, + "value": 0 + } + ], + "minValue": 0, + "maxValue": 0 + } +} diff --git a/ui/neurovault/activities/individual_subject_modeling/items/intrasubject_modeling_software.jsonld b/ui/neurovault/activities/individual_subject_modeling/items/intrasubject_modeling_software.jsonld new file mode 100644 index 00000000..5bfcb659 --- /dev/null +++ b/ui/neurovault/activities/individual_subject_modeling/items/intrasubject_modeling_software.jsonld @@ -0,0 +1,23 @@ +{ + "@context": "https://raw.githubusercontent.com/ReproNim/reproschema/1.0.0-rc4/contexts/generic", + "@type": "reproschema:Field", + "@id": "intrasubject_modeling_software.jsonld", + "schemaVersion": "1.0.0-rc4", + "version": "0.0.1", + "prefLabel": { + "en": "intrasubject modeling software" + }, + "description": "intrasubject modeling software", + "ui": { + "inputType": "select" + }, + "question": { + "en": "6.3 - Software used for intrasubject modeling if different from overall package" + }, + "responseOptions": { + "valueType": "xsd:integer", + "choices": "https://raw.githubusercontent.com/ohbm/cobidas_schema/master/response_options/mri_softwares.jsonld", + "minValue": 0, + "maxValue": 0 + } +} diff --git a/ui/neurovault/activities/individual_subject_modeling/items/orthogonalization_description.jsonld b/ui/neurovault/activities/individual_subject_modeling/items/orthogonalization_description.jsonld new file mode 100644 index 00000000..b6cce576 --- /dev/null +++ b/ui/neurovault/activities/individual_subject_modeling/items/orthogonalization_description.jsonld @@ -0,0 +1,17 @@ +{ + "@context": "https://raw.githubusercontent.com/ReproNim/reproschema/1.0.0-rc4/contexts/generic", + "@type": "reproschema:Field", + "@id": "orthogonalization_description.jsonld", + "schemaVersion": "1.0.0-rc4", + "version": "0.0.1", + "prefLabel": { + "en": "orthogonalization description" + }, + "description": "orthogonalization description", + "ui": { + "inputType": "textarea" + }, + "question": { + "en": "6.10 - If orthogonalization was used, describe here" + } +} diff --git a/ui/neurovault/activities/individual_subject_modeling/items/used_dispersion_derivatives.jsonld b/ui/neurovault/activities/individual_subject_modeling/items/used_dispersion_derivatives.jsonld new file mode 100644 index 00000000..18f30f07 --- /dev/null +++ b/ui/neurovault/activities/individual_subject_modeling/items/used_dispersion_derivatives.jsonld @@ -0,0 +1,23 @@ +{ + "@context": "https://raw.githubusercontent.com/ReproNim/reproschema/1.0.0-rc4/contexts/generic", + "@type": "reproschema:Field", + "@id": "used_dispersion_derivatives.jsonld", + "schemaVersion": "1.0.0-rc4", + "version": "0.0.1", + "prefLabel": { + "en": "used dispersion derivatives" + }, + "description": "used dispersion derivatives", + "ui": { + "inputType": "radio" + }, + "question": { + "en": "6.6 - Were dispersion derivatives included?" + }, + "responseOptions": { + "valueType": "xsd:integer", + "choices": "https://raw.githubusercontent.com/ohbm/cobidas_schema/master/response_options/boolean.jsonld", + "minValue": 0, + "maxValue": 0 + } +} diff --git a/ui/neurovault/activities/individual_subject_modeling/items/used_high_pass_filter.jsonld b/ui/neurovault/activities/individual_subject_modeling/items/used_high_pass_filter.jsonld new file mode 100644 index 00000000..c2c8f014 --- /dev/null +++ b/ui/neurovault/activities/individual_subject_modeling/items/used_high_pass_filter.jsonld @@ -0,0 +1,23 @@ +{ + "@context": "https://raw.githubusercontent.com/ReproNim/reproschema/1.0.0-rc4/contexts/generic", + "@type": "reproschema:Field", + "@id": "used_high_pass_filter.jsonld", + "schemaVersion": "1.0.0-rc4", + "version": "0.0.1", + "prefLabel": { + "en": "used high pass filter" + }, + "description": "used high pass filter", + "ui": { + "inputType": "radio" + }, + "question": { + "en": "6.11 - 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Source | Github repository | Reference

Describe your spatial normalization

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Source | Github repository | Reference

Describe your acquisition parameters

" + }, + "ui": { + "shuffle": false, + "order": [ + "items/Manufacturer.jsonld", + "items/ManufacturersModelName.jsonld", + "items/MagneticFieldStrength.jsonld", + "items/PulseSequenceType.jsonld", + "items/parallel_imaging.jsonld", + "items/field_of_view.jsonld", + "items/matrix_size.jsonld", + "items/slice_thickness.jsonld", + "items/skip_factor.jsonld", + "items/acquisition_orientation.jsonld", + "items/SliceTiming.jsonld", + "items/RepetitionTime.jsonld", + "items/EchoTime.jsonld", + "items/FlipAngle.jsonld" + ], + "addProperties": [ + { + "variableName": "Manufacturer", + "isAbout": "items/Manufacturer.jsonld", + "prefLabel": { + "en": "scanner make" + }, + "isVis": true, + "requiredValue": false, + "allow": [ + "reproschema:Skipped" + ] + }, + { + "variableName": "ManufacturersModelName", + "isAbout": "items/ManufacturersModelName.jsonld", + "prefLabel": { + "en": "scanner model" + }, + "isVis": true, + "requiredValue": false, + "allow": [ + "reproschema:Skipped" + ] + }, + { + "variableName": "MagneticFieldStrength", + "isAbout": "items/MagneticFieldStrength.jsonld", + "prefLabel": { + "en": "field strength" + }, + "isVis": true, + "requiredValue": false, + "allow": [ + "reproschema:Skipped" + ] + }, + { + "variableName": "PulseSequenceType", + "isAbout": "items/PulseSequenceType.jsonld", + "prefLabel": { + "en": "pulse sequence" + }, + "isVis": true, + "requiredValue": false, + "allow": [ + "reproschema:Skipped" + ] + }, + { + "variableName": "parallel_imaging", + "isAbout": "items/parallel_imaging.jsonld", + "prefLabel": { + "en": "parallel imaging" + }, + "isVis": true, + "requiredValue": false, + "allow": [ + "reproschema:Skipped" + ] + }, + { + "variableName": "field_of_view", + "isAbout": "items/field_of_view.jsonld", + "prefLabel": { + "en": "field of view" + }, + "isVis": true, + "requiredValue": false, + "allow": [ + "reproschema:Skipped" + ] + }, + { + "variableName": "matrix_size", + "isAbout": "items/matrix_size.jsonld", + "prefLabel": { + "en": "matrix size" + }, + "isVis": true, + "requiredValue": false, + "allow": [ + "reproschema:Skipped" + ] + }, + { + "variableName": "slice_thickness", + "isAbout": "items/slice_thickness.jsonld", + "prefLabel": { + "en": "slice thickness" + }, + "isVis": true, + "requiredValue": false, + "allow": [ + "reproschema:Skipped" + ] + }, + { + "variableName": "skip_factor", + "isAbout": "items/skip_factor.jsonld", + "prefLabel": { + "en": "skip factor" + }, + "isVis": true, + "requiredValue": false, + "allow": [ + "reproschema:Skipped" + ] + }, + { + "variableName": "acquisition_orientation", + "isAbout": "items/acquisition_orientation.jsonld", + "prefLabel": { + "en": "acquisition orientation" + }, + "isVis": true, + "requiredValue": false, + "allow": [ + "reproschema:Skipped" + ] + }, + { + "variableName": "SliceTiming", + "isAbout": "items/SliceTiming.jsonld", + "prefLabel": { + "en": "order of acquisition" + }, + "isVis": true, + "requiredValue": false, + "allow": [ + "reproschema:Skipped" + ] + }, + { + "variableName": "RepetitionTime", + "isAbout": "items/RepetitionTime.jsonld", + "prefLabel": { + "en": "repetition time" + }, + "isVis": true, + "requiredValue": false, + "allow": [ + "reproschema:Skipped" + ] + }, + { + "variableName": "EchoTime", + "isAbout": "items/EchoTime.jsonld", + "prefLabel": { + "en": "echo time" + }, + "isVis": true, + "requiredValue": false, + "allow": [ + "reproschema:Skipped" + ] + }, + { + "variableName": "FlipAngle", + "isAbout": "items/FlipAngle.jsonld", + "prefLabel": { + "en": "flip angle" + }, + "isVis": true, + "requiredValue": false, + "allow": [ + "reproschema:Skipped" + ] + } + ], + "allow": [ + "reproschema:AutoAdvance", + "reproschema:AllowExport" + ] + } +} diff --git a/ui/neurovault/activities/participants/items/group_comparison.jsonld b/ui/neurovault/activities/participants/items/group_comparison.jsonld new file mode 100644 index 00000000..be14cf17 --- /dev/null +++ b/ui/neurovault/activities/participants/items/group_comparison.jsonld @@ -0,0 +1,23 @@ +{ + "@context": "https://raw.githubusercontent.com/ReproNim/reproschema/1.0.0-rc4/contexts/generic", + "@type": "reproschema:Field", + "@id": "group_comparison.jsonld", + "schemaVersion": "1.0.0-rc4", + "version": "0.0.1", + "prefLabel": { + "en": "group comparison" + }, + "description": "group comparison", + "ui": { + "inputType": "radio" + }, + "question": { + "en": "2.9 - Was this study a comparison between subject groups?" + }, + "responseOptions": { + "valueType": "xsd:integer", + "choices": "https://raw.githubusercontent.com/ohbm/cobidas_schema/master/response_options/boolean.jsonld", + "minValue": 0, + "maxValue": 0 + } +} diff --git a/ui/neurovault/activities/participants/items/group_description.jsonld b/ui/neurovault/activities/participants/items/group_description.jsonld new file mode 100644 index 00000000..c77f7219 --- /dev/null +++ b/ui/neurovault/activities/participants/items/group_description.jsonld @@ -0,0 +1,17 @@ +{ + "@context": "https://raw.githubusercontent.com/ReproNim/reproschema/1.0.0-rc4/contexts/generic", + "@type": "reproschema:Field", + "@id": "group_description.jsonld", + "schemaVersion": "1.0.0-rc4", + "version": "0.0.1", + "prefLabel": { + "en": "group description" + }, + "description": "group description", + "ui": { + "inputType": "textarea" + }, + "question": { + "en": "2.10 - A description of the groups being compared" + } +} diff --git a/ui/neurovault/activities/participants/items/handedness.jsonld b/ui/neurovault/activities/participants/items/handedness.jsonld new file mode 100644 index 00000000..7fd713cb --- /dev/null +++ b/ui/neurovault/activities/participants/items/handedness.jsonld @@ -0,0 +1,42 @@ +{ + "@context": "https://raw.githubusercontent.com/ReproNim/reproschema/1.0.0-rc4/contexts/generic", + "@type": "reproschema:Field", + "@id": "handedness.jsonld", + "schemaVersion": "1.0.0-rc4", + "version": "0.0.1", + "prefLabel": { + "en": "handedness" + }, + "description": "handedness", + "ui": { + "inputType": "radio" + }, + "question": { + "en": "2.5 - Handedness of subjects" + }, + "responseOptions": { + "valueType": "xsd:integer", + "choices": [ + { + "name": { + "en": "right" + }, + "value": 0 + }, + { + "name": { + "en": "left" + }, + "value": 1 + }, + { + "name": { + "en": "both" + }, + "value": 2 + } + ], + "minValue": 0, + "maxValue": 2 + } +} diff --git a/ui/neurovault/activities/participants/items/inclusion_exclusion_criteria.jsonld b/ui/neurovault/activities/participants/items/inclusion_exclusion_criteria.jsonld new file mode 100644 index 00000000..a9af6c13 --- /dev/null +++ b/ui/neurovault/activities/participants/items/inclusion_exclusion_criteria.jsonld @@ -0,0 +1,17 @@ +{ + "@context": "https://raw.githubusercontent.com/ReproNim/reproschema/1.0.0-rc4/contexts/generic", + "@type": "reproschema:Field", + "@id": "inclusion_exclusion_criteria.jsonld", + "schemaVersion": "1.0.0-rc4", + "version": "0.0.1", + "prefLabel": { + "en": "inclusion exclusion criteria" + }, + "description": "inclusion exclusion criteria", + "ui": { + "inputType": "textarea" + }, + "question": { + "en": "2.7 - Additional inclusion/exclusion criteria, if any.
details
Including specific sampling strategies that limit inclusion to a specific group, such as laboratory members.
" + } +} diff --git a/ui/neurovault/activities/participants/items/number_of_rejected_subjects.jsonld b/ui/neurovault/activities/participants/items/number_of_rejected_subjects.jsonld new file mode 100644 index 00000000..f2dca486 --- /dev/null +++ b/ui/neurovault/activities/participants/items/number_of_rejected_subjects.jsonld @@ -0,0 +1,20 @@ +{ + "@context": "https://raw.githubusercontent.com/ReproNim/reproschema/1.0.0-rc4/contexts/generic", + "@type": "reproschema:Field", + "@id": "number_of_rejected_subjects.jsonld", + "schemaVersion": "1.0.0-rc4", + "version": "0.0.1", + "prefLabel": { + "en": "number of rejected subjects" + }, + "description": "number of rejected subjects", + "ui": { + "inputType": "number" + }, + "question": { + "en": "2.8 - Number of subjects scanned but rejected from analysis" + }, + "responseOptions": { + "valueType": "xsd:integer" + } +} diff --git a/ui/neurovault/activities/participants/items/number_of_subjects.jsonld b/ui/neurovault/activities/participants/items/number_of_subjects.jsonld new file mode 100644 index 00000000..461a3768 --- /dev/null +++ b/ui/neurovault/activities/participants/items/number_of_subjects.jsonld @@ -0,0 +1,20 @@ +{ + "@context": "https://raw.githubusercontent.com/ReproNim/reproschema/1.0.0-rc4/contexts/generic", + "@type": "reproschema:Field", + "@id": "number_of_subjects.jsonld", + "schemaVersion": "1.0.0-rc4", + "version": "0.0.1", + "prefLabel": { + "en": "number of subjects" + }, + "description": "number of subjects", + "ui": { + "inputType": "number" + }, + "question": { + "en": "2.1 - Number of subjects entering into the analysis" + }, + "responseOptions": { + "valueType": "xsd:integer" + } +} diff --git a/ui/neurovault/activities/participants/items/proportion_male_subjects.jsonld b/ui/neurovault/activities/participants/items/proportion_male_subjects.jsonld new file mode 100644 index 00000000..89604b87 --- /dev/null +++ b/ui/neurovault/activities/participants/items/proportion_male_subjects.jsonld @@ -0,0 +1,145 @@ +{ + "@context": "https://raw.githubusercontent.com/ReproNim/reproschema/1.0.0-rc4/contexts/generic", + "@type": "reproschema:Field", + "@id": "proportion_male_subjects.jsonld", + "schemaVersion": "1.0.0-rc4", + "version": "0.0.1", + "prefLabel": { + "en": "proportion male subjects" + }, + "description": "proportion male subjects", + "ui": { + "inputType": "slider" + }, + "question": { + "en": "2.6 - The proportion of subjects who were male" + }, + "responseOptions": { + "valueType": "xsd:integer", + "choices": [ + { + "name": { + "en": "0.000" + }, + "value": 0 + }, + { + "name": { + "en": "5.263" + }, + "value": 1 + }, + { + "name": { + "en": "10.526" + }, + "value": 2 + }, + { + "name": { + "en": "15.789" + }, + "value": 3 + }, + { + "name": { + "en": "21.053" + }, + "value": 4 + }, + { + "name": { + "en": "26.316" + }, + "value": 5 + }, + { + "name": { + "en": "31.579" + }, + "value": 6 + }, + { + "name": { + "en": "36.842" + }, + "value": 7 + }, + { + "name": { + "en": "42.105" + }, + "value": 8 + }, + { + "name": { + "en": "47.368" + }, + "value": 9 + }, + { + "name": { + "en": "52.632" + }, + "value": 10 + }, + { + "name": { + "en": "57.895" + }, + "value": 11 + }, + { + "name": { + "en": "63.158" + }, + "value": 12 + }, + { + "name": { + "en": "68.421" + }, + "value": 13 + }, + { + "name": { + "en": "73.684" + }, + "value": 14 + }, + { + "name": { + "en": "78.947" + }, + "value": 15 + }, + { + "name": { + "en": "84.211" + }, + "value": 16 + }, + { + "name": { + "en": "89.474" + }, + "value": 17 + }, + { + "name": { + "en": "94.737" + }, + "value": 18 + }, + { + "name": { + "en": "100.000" + }, + "value": 19 + } + ], + "multipleChoice": false, + "minValue": 0, + "maxValue": 19 + } +} diff --git a/ui/neurovault/activities/participants/items/subject_age_max.jsonld b/ui/neurovault/activities/participants/items/subject_age_max.jsonld new file mode 100644 index 00000000..096b704f --- /dev/null +++ b/ui/neurovault/activities/participants/items/subject_age_max.jsonld @@ -0,0 +1,20 @@ +{ + "@context": "https://raw.githubusercontent.com/ReproNim/reproschema/1.0.0-rc4/contexts/generic", + "@type": "reproschema:Field", + "@id": "subject_age_max.jsonld", + "schemaVersion": "1.0.0-rc4", + "version": "0.0.1", + "prefLabel": { + "en": "subject age max" + }, + "description": "subject age max", + "ui": { + "inputType": "float" + }, + "question": { + "en": "2.4 - Maximum age of subjects" + }, + "responseOptions": { + "valueType": "xsd:float" + } +} diff --git a/ui/neurovault/activities/participants/items/subject_age_mean.jsonld b/ui/neurovault/activities/participants/items/subject_age_mean.jsonld new file mode 100644 index 00000000..72b91f13 --- /dev/null +++ b/ui/neurovault/activities/participants/items/subject_age_mean.jsonld @@ -0,0 +1,20 @@ +{ + "@context": "https://raw.githubusercontent.com/ReproNim/reproschema/1.0.0-rc4/contexts/generic", + "@type": "reproschema:Field", + "@id": "subject_age_mean.jsonld", + "schemaVersion": "1.0.0-rc4", + "version": "0.0.1", + "prefLabel": { + "en": "subject age mean" + }, + "description": "subject age mean", + "ui": { + "inputType": "float" + }, + "question": { + "en": "2.2 - Mean age of subjects" + }, + "responseOptions": { + "valueType": "xsd:float" + } +} diff --git a/ui/neurovault/activities/participants/items/subject_age_min.jsonld b/ui/neurovault/activities/participants/items/subject_age_min.jsonld new file mode 100644 index 00000000..11a58508 --- /dev/null +++ b/ui/neurovault/activities/participants/items/subject_age_min.jsonld @@ -0,0 +1,20 @@ +{ + "@context": "https://raw.githubusercontent.com/ReproNim/reproschema/1.0.0-rc4/contexts/generic", + "@type": "reproschema:Field", + "@id": "subject_age_min.jsonld", + "schemaVersion": "1.0.0-rc4", + "version": "0.0.1", + "prefLabel": { + "en": "subject age min" + }, + "description": "subject age min", + "ui": { + "inputType": "float" + }, + "question": { + "en": "2.3 - Minimum age of subjects" + }, + "responseOptions": { + "valueType": "xsd:float" + } +} diff --git a/ui/neurovault/activities/participants/participants_schema.jsonld b/ui/neurovault/activities/participants/participants_schema.jsonld new file mode 100644 index 00000000..8a7c4fe4 --- /dev/null +++ b/ui/neurovault/activities/participants/participants_schema.jsonld @@ -0,0 +1,155 @@ +{ + "@context": "https://raw.githubusercontent.com/ReproNim/reproschema/1.0.0-rc4/contexts/generic", + "@type": "reproschema:Activity", + "@id": "participants_schema.jsonld", + "schemaVersion": "1.0.0-rc4", + "version": "0.0.1", + "prefLabel": { + "en": "Participants" + }, + "description": "participants", + "preamble": { + "en": "

Source | Github repository | Reference

Describe your participant sample

" + }, + "ui": { + "shuffle": false, + "order": [ + "items/number_of_subjects.jsonld", + "items/subject_age_mean.jsonld", + "items/subject_age_min.jsonld", + "items/subject_age_max.jsonld", + "items/handedness.jsonld", + "items/proportion_male_subjects.jsonld", + "items/inclusion_exclusion_criteria.jsonld", + "items/number_of_rejected_subjects.jsonld", + "items/group_comparison.jsonld", + "items/group_description.jsonld" + ], + "addProperties": [ + { + "variableName": "number_of_subjects", + "isAbout": "items/number_of_subjects.jsonld", + "prefLabel": { + "en": "number of subjects" + }, + "isVis": true, + "requiredValue": false, + "allow": [ + "reproschema:Skipped" + ] + }, + { + "variableName": "subject_age_mean", + "isAbout": "items/subject_age_mean.jsonld", + "prefLabel": { + "en": "subject age mean" + }, + "isVis": true, + "requiredValue": false, + "allow": [ + "reproschema:Skipped" + ] + }, + { + "variableName": "subject_age_min", + "isAbout": "items/subject_age_min.jsonld", + "prefLabel": { + "en": "subject age min" + }, + "isVis": true, + "requiredValue": false, + "allow": [ + "reproschema:Skipped" + ] + }, + { + "variableName": "subject_age_max", + "isAbout": "items/subject_age_max.jsonld", + "prefLabel": { + "en": "subject age max" + }, + "isVis": true, + "requiredValue": false, + "allow": [ + "reproschema:Skipped" + ] + }, + { + "variableName": "handedness", + "isAbout": "items/handedness.jsonld", + "prefLabel": { + "en": "handedness" + }, + "isVis": true, + "requiredValue": false, + "allow": [ + "reproschema:Skipped" + ] + }, + { + "variableName": "proportion_male_subjects", + "isAbout": "items/proportion_male_subjects.jsonld", + "prefLabel": { + "en": "proportion male subjects" + }, + "isVis": true, + "requiredValue": false, + "allow": [ + "reproschema:Skipped" + ] + }, + { + "variableName": "inclusion_exclusion_criteria", + "isAbout": "items/inclusion_exclusion_criteria.jsonld", + "prefLabel": { + "en": "inclusion exclusion criteria" + }, + "isVis": true, + "requiredValue": false, + "allow": [ + "reproschema:Skipped" + ] + }, + { + "variableName": "number_of_rejected_subjects", + "isAbout": "items/number_of_rejected_subjects.jsonld", + "prefLabel": { + "en": "number of rejected subjects" + }, + "isVis": true, + "requiredValue": false, + "allow": [ + "reproschema:Skipped" + ] + }, + { + "variableName": "group_comparison", + "isAbout": "items/group_comparison.jsonld", + "prefLabel": { + "en": "group comparison" + }, + "isVis": true, + "requiredValue": false, + "allow": [ + "reproschema:Skipped" + ] + }, + { + "variableName": "group_description", + "isAbout": "items/group_description.jsonld", + "prefLabel": { + "en": "group description" + }, + "isVis": "group_comparison == 1", + "requiredValue": false, + "allow": [ + "reproschema:Skipped" + ] + } + ], + "allow": [ + "reproschema:AutoAdvance", + "reproschema:AllowExport" + ] + } +} diff --git a/ui/neurovault/activities/preprocessing/items/SoftwareName.jsonld b/ui/neurovault/activities/preprocessing/items/SoftwareName.jsonld new file mode 100644 index 00000000..e1a109b1 --- /dev/null +++ b/ui/neurovault/activities/preprocessing/items/SoftwareName.jsonld @@ -0,0 +1,23 @@ +{ + "@context": "https://raw.githubusercontent.com/ReproNim/reproschema/1.0.0-rc4/contexts/generic", + "@type": "reproschema:Field", + "@id": "SoftwareName.jsonld", + "schemaVersion": "1.0.0-rc4", + "version": "0.0.1", + "prefLabel": { + "en": "software package" + }, + "description": "software package", + "ui": { + "inputType": "select" + }, + "question": { + "en": "4.1 - If a single software package was used for all analyses, specify that here" + }, + "responseOptions": { + "valueType": "xsd:integer", + "choices": "https://raw.githubusercontent.com/ohbm/cobidas_schema/master/response_options/mri_softwares.jsonld", + "minValue": 0, + "maxValue": 0 + } +} diff --git a/ui/neurovault/activities/preprocessing/items/SoftwareVersion.jsonld b/ui/neurovault/activities/preprocessing/items/SoftwareVersion.jsonld new file mode 100644 index 00000000..fd70d3ea --- /dev/null +++ b/ui/neurovault/activities/preprocessing/items/SoftwareVersion.jsonld @@ -0,0 +1,17 @@ +{ + "@context": "https://raw.githubusercontent.com/ReproNim/reproschema/1.0.0-rc4/contexts/generic", + "@type": "reproschema:Field", + "@id": "SoftwareVersion.jsonld", + "schemaVersion": "1.0.0-rc4", + "version": "0.0.1", + "prefLabel": { + "en": "software version" + }, + "description": "software version", + "ui": { + "inputType": "textarea" + }, + "question": { + "en": "4.2 - Version of software package used" + } +} diff --git a/ui/neurovault/activities/preprocessing/items/b0_unwarping_software.jsonld b/ui/neurovault/activities/preprocessing/items/b0_unwarping_software.jsonld new file mode 100644 index 00000000..b69bf97f --- /dev/null +++ b/ui/neurovault/activities/preprocessing/items/b0_unwarping_software.jsonld @@ -0,0 +1,23 @@ +{ + "@context": "https://raw.githubusercontent.com/ReproNim/reproschema/1.0.0-rc4/contexts/generic", + "@type": "reproschema:Field", + "@id": "b0_unwarping_software.jsonld", + "schemaVersion": "1.0.0-rc4", + "version": "0.0.1", + "prefLabel": { + "en": "b0 unwarping software" + }, + "description": "b0 unwarping software", + "ui": { + "inputType": "select" + }, + "question": { + "en": "4.6 - Specify software used for distortion correction if different from the main package" + }, + "responseOptions": { + "valueType": "xsd:integer", + "choices": "https://raw.githubusercontent.com/ohbm/cobidas_schema/master/response_options/mri_softwares.jsonld", + "minValue": 0, + "maxValue": 0 + } +} diff --git a/ui/neurovault/activities/preprocessing/items/motion_correction_interpolation.jsonld b/ui/neurovault/activities/preprocessing/items/motion_correction_interpolation.jsonld new file mode 100644 index 00000000..5ae21815 --- /dev/null +++ b/ui/neurovault/activities/preprocessing/items/motion_correction_interpolation.jsonld @@ -0,0 +1,23 @@ +{ + "@context": "https://raw.githubusercontent.com/ReproNim/reproschema/1.0.0-rc4/contexts/generic", + "@type": "reproschema:Field", + "@id": "motion_correction_interpolation.jsonld", + "schemaVersion": "1.0.0-rc4", + "version": "0.0.1", + "prefLabel": { + "en": "motion correction interpolation" + }, + "description": "motion correction interpolation", + "ui": { + "inputType": "select" + }, + "question": { + "en": "4.13 - Interpolation method used for motion correction" + }, + "responseOptions": { + "valueType": "xsd:integer", + "choices": "https://raw.githubusercontent.com/ohbm/cobidas_schema/master/response_options/interpolations.jsonld", + "minValue": 0, + "maxValue": 0 + } +} diff --git a/ui/neurovault/activities/preprocessing/items/motion_correction_metric.jsonld b/ui/neurovault/activities/preprocessing/items/motion_correction_metric.jsonld new file mode 100644 index 00000000..98ab1c42 --- /dev/null +++ b/ui/neurovault/activities/preprocessing/items/motion_correction_metric.jsonld @@ -0,0 +1,23 @@ +{ + "@context": "https://raw.githubusercontent.com/ReproNim/reproschema/1.0.0-rc4/contexts/generic", + "@type": "reproschema:Field", + "@id": "motion_correction_metric.jsonld", + "schemaVersion": "1.0.0-rc4", + "version": "0.0.1", + "prefLabel": { + "en": "motion correction metric" + }, + "description": "motion correction metric", + "ui": { + "inputType": "select" + }, + "question": { + "en": "4.12 - Similarity metric used for motion correction" + }, + "responseOptions": { + "valueType": "xsd:integer", + "choices": "https://raw.githubusercontent.com/ohbm/cobidas_schema/master/response_options/cost_functions.jsonld", + "minValue": 0, + "maxValue": 0 + } +} diff --git a/ui/neurovault/activities/preprocessing/items/motion_correction_reference.jsonld b/ui/neurovault/activities/preprocessing/items/motion_correction_reference.jsonld new file mode 100644 index 00000000..9514078b --- /dev/null +++ b/ui/neurovault/activities/preprocessing/items/motion_correction_reference.jsonld @@ -0,0 +1,17 @@ +{ + "@context": "https://raw.githubusercontent.com/ReproNim/reproschema/1.0.0-rc4/contexts/generic", + "@type": "reproschema:Field", + "@id": "motion_correction_reference.jsonld", + "schemaVersion": "1.0.0-rc4", + "version": "0.0.1", + "prefLabel": { + "en": "motion correction reference" + }, + "description": "motion correction reference", + "ui": { + "inputType": "textarea" + }, + "question": { + "en": "4.11 - Reference scan used for motion correction" + } +} diff --git a/ui/neurovault/activities/preprocessing/items/motion_correction_software.jsonld b/ui/neurovault/activities/preprocessing/items/motion_correction_software.jsonld new file mode 100644 index 00000000..2b07c45c --- /dev/null +++ b/ui/neurovault/activities/preprocessing/items/motion_correction_software.jsonld @@ -0,0 +1,23 @@ +{ + "@context": "https://raw.githubusercontent.com/ReproNim/reproschema/1.0.0-rc4/contexts/generic", + "@type": "reproschema:Field", + "@id": "motion_correction_software.jsonld", + "schemaVersion": "1.0.0-rc4", + "version": "0.0.1", + "prefLabel": { + "en": "motion correction software" + }, + "description": "motion correction software", + "ui": { + "inputType": "select" + }, + "question": { + "en": "4.10 - Specify software used for motion correction if different from the main package" + }, + "responseOptions": { + "valueType": "xsd:integer", + "choices": "https://raw.githubusercontent.com/ohbm/cobidas_schema/master/response_options/mri_softwares.jsonld", + "minValue": 0, + "maxValue": 0 + } +} diff --git a/ui/neurovault/activities/preprocessing/items/order_of_preprocessing_operations.jsonld b/ui/neurovault/activities/preprocessing/items/order_of_preprocessing_operations.jsonld new file mode 100644 index 00000000..b7f6a098 --- /dev/null +++ b/ui/neurovault/activities/preprocessing/items/order_of_preprocessing_operations.jsonld @@ -0,0 +1,17 @@ +{ + "@context": "https://raw.githubusercontent.com/ReproNim/reproschema/1.0.0-rc4/contexts/generic", + "@type": "reproschema:Field", + "@id": "order_of_preprocessing_operations.jsonld", + "schemaVersion": "1.0.0-rc4", + "version": "0.0.1", + "prefLabel": { + "en": "order of preprocessing operations" + }, + "description": "order of preprocessing operations", + "ui": { + "inputType": "textarea" + }, + "question": { + "en": "4.3 - Specify order of preprocessing operations" + } +} diff --git a/ui/neurovault/activities/preprocessing/items/quality_control.jsonld b/ui/neurovault/activities/preprocessing/items/quality_control.jsonld new file mode 100644 index 00000000..db0ab0e2 --- /dev/null +++ b/ui/neurovault/activities/preprocessing/items/quality_control.jsonld @@ -0,0 +1,17 @@ +{ + "@context": "https://raw.githubusercontent.com/ReproNim/reproschema/1.0.0-rc4/contexts/generic", + "@type": "reproschema:Field", + "@id": "quality_control.jsonld", + "schemaVersion": "1.0.0-rc4", + "version": "0.0.1", + "prefLabel": { + "en": "quality control" + }, + "description": "quality control", + "ui": { + "inputType": "textarea" + }, + "question": { + "en": "4.4 - Describe quality control measures" + } +} diff --git a/ui/neurovault/activities/preprocessing/items/slice_timing_correction_software.jsonld b/ui/neurovault/activities/preprocessing/items/slice_timing_correction_software.jsonld new file mode 100644 index 00000000..525a1439 --- /dev/null +++ b/ui/neurovault/activities/preprocessing/items/slice_timing_correction_software.jsonld @@ -0,0 +1,17 @@ +{ + "@context": "https://raw.githubusercontent.com/ReproNim/reproschema/1.0.0-rc4/contexts/generic", + "@type": "reproschema:Field", + "@id": "slice_timing_correction_software.jsonld", + "schemaVersion": "1.0.0-rc4", + "version": "0.0.1", + "prefLabel": { + "en": "slice timing correction software" + }, + "description": "slice timing correction software", + "ui": { + "inputType": "textarea" + }, + "question": { + "en": "4.8 - Specify software used for slice timing correction if different from the main package" + } +} diff --git a/ui/neurovault/activities/preprocessing/items/used_b0_unwarping.jsonld b/ui/neurovault/activities/preprocessing/items/used_b0_unwarping.jsonld new file mode 100644 index 00000000..edaf5c97 --- /dev/null +++ b/ui/neurovault/activities/preprocessing/items/used_b0_unwarping.jsonld @@ -0,0 +1,23 @@ +{ + "@context": "https://raw.githubusercontent.com/ReproNim/reproschema/1.0.0-rc4/contexts/generic", + "@type": "reproschema:Field", + "@id": "used_b0_unwarping.jsonld", + "schemaVersion": "1.0.0-rc4", + "version": "0.0.1", + "prefLabel": { + "en": "used b0 unwarping" + }, + "description": "used b0 unwarping", + "ui": { + "inputType": "radio" + }, + "question": { + "en": "4.5 - Was B0 distortion correction used?" + }, + "responseOptions": { + "valueType": "xsd:integer", + "choices": "https://raw.githubusercontent.com/ohbm/cobidas_schema/master/response_options/boolean.jsonld", + "minValue": 0, + "maxValue": 0 + } +} diff --git a/ui/neurovault/activities/preprocessing/items/used_motion_correction.jsonld b/ui/neurovault/activities/preprocessing/items/used_motion_correction.jsonld new file mode 100644 index 00000000..42942532 --- /dev/null +++ b/ui/neurovault/activities/preprocessing/items/used_motion_correction.jsonld @@ -0,0 +1,23 @@ +{ + "@context": "https://raw.githubusercontent.com/ReproNim/reproschema/1.0.0-rc4/contexts/generic", + "@type": "reproschema:Field", + "@id": "used_motion_correction.jsonld", + "schemaVersion": "1.0.0-rc4", + "version": "0.0.1", + "prefLabel": { + "en": "used motion correction" + }, + "description": "used motion correction", + "ui": { + "inputType": "radio" + }, + "question": { + "en": "4.9 - Was motion correction used?" + }, + "responseOptions": { + "valueType": "xsd:integer", + "choices": "https://raw.githubusercontent.com/ohbm/cobidas_schema/master/response_options/boolean.jsonld", + "minValue": 0, + "maxValue": 0 + } +} diff --git a/ui/neurovault/activities/preprocessing/items/used_motion_susceptibiity_correction.jsonld b/ui/neurovault/activities/preprocessing/items/used_motion_susceptibiity_correction.jsonld new file mode 100644 index 00000000..00c086b5 --- /dev/null +++ b/ui/neurovault/activities/preprocessing/items/used_motion_susceptibiity_correction.jsonld @@ -0,0 +1,23 @@ +{ + "@context": "https://raw.githubusercontent.com/ReproNim/reproschema/1.0.0-rc4/contexts/generic", + "@type": "reproschema:Field", + "@id": "used_motion_susceptibiity_correction.jsonld", + "schemaVersion": "1.0.0-rc4", + "version": "0.0.1", + "prefLabel": { + "en": "used motion susceptibiity correction" + }, + "description": "used motion susceptibiity correction", + "ui": { + "inputType": "radio" + }, + "question": { + "en": "4.14 - Was motion-susceptibility correction used?" + }, + "responseOptions": { + "valueType": "xsd:integer", + "choices": "https://raw.githubusercontent.com/ohbm/cobidas_schema/master/response_options/boolean.jsonld", + "minValue": 0, + "maxValue": 0 + } +} diff --git a/ui/neurovault/activities/preprocessing/items/used_slice_timing_correction.jsonld b/ui/neurovault/activities/preprocessing/items/used_slice_timing_correction.jsonld new file mode 100644 index 00000000..a5d8c55e --- /dev/null +++ b/ui/neurovault/activities/preprocessing/items/used_slice_timing_correction.jsonld @@ -0,0 +1,23 @@ +{ + "@context": "https://raw.githubusercontent.com/ReproNim/reproschema/1.0.0-rc4/contexts/generic", + "@type": "reproschema:Field", + "@id": "used_slice_timing_correction.jsonld", + "schemaVersion": "1.0.0-rc4", + "version": "0.0.1", + "prefLabel": { + "en": "used slice timing correction" + }, + "description": "used slice timing correction", + "ui": { + "inputType": "radio" + }, + "question": { + "en": "4.7 - Was slice timing correction used?" + }, + "responseOptions": { + "valueType": "xsd:integer", + "choices": "https://raw.githubusercontent.com/ohbm/cobidas_schema/master/response_options/boolean.jsonld", + "minValue": 0, + "maxValue": 0 + } +} diff --git a/ui/neurovault/activities/preprocessing/preprocessing_schema.jsonld b/ui/neurovault/activities/preprocessing/preprocessing_schema.jsonld new file mode 100644 index 00000000..81b02fa5 --- /dev/null +++ b/ui/neurovault/activities/preprocessing/preprocessing_schema.jsonld @@ -0,0 +1,207 @@ +{ + "@context": "https://raw.githubusercontent.com/ReproNim/reproschema/1.0.0-rc4/contexts/generic", + "@type": "reproschema:Activity", + "@id": "preprocessing_schema.jsonld", + "schemaVersion": "1.0.0-rc4", + "version": "0.0.1", + "prefLabel": { + "en": "Preprocessing" + }, + "description": "preprocessing", + "preamble": { + "en": "

Source | Github repository | Reference

Describe your preprocessing

" + }, + "ui": { + "shuffle": false, + "order": [ + "items/SoftwareName.jsonld", + "items/SoftwareVersion.jsonld", + "items/order_of_preprocessing_operations.jsonld", + "items/quality_control.jsonld", + "items/used_b0_unwarping.jsonld", + "items/b0_unwarping_software.jsonld", + "items/used_slice_timing_correction.jsonld", + "items/slice_timing_correction_software.jsonld", + "items/used_motion_correction.jsonld", + "items/motion_correction_software.jsonld", + "items/motion_correction_reference.jsonld", + "items/motion_correction_metric.jsonld", + "items/motion_correction_interpolation.jsonld", + "items/used_motion_susceptibiity_correction.jsonld" + ], + "addProperties": [ + { + "variableName": "SoftwareName", + "isAbout": "items/SoftwareName.jsonld", + "prefLabel": { + "en": "software package" + }, + "isVis": true, + "requiredValue": false, + "allow": [ + "reproschema:Skipped" + ] + }, + { + "variableName": "SoftwareVersion", + "isAbout": "items/SoftwareVersion.jsonld", + "prefLabel": { + "en": "software version" + }, + "isVis": true, + "requiredValue": false, + "allow": [ + "reproschema:Skipped" + ] + }, + { + "variableName": "order_of_preprocessing_operations", + "isAbout": "items/order_of_preprocessing_operations.jsonld", + "prefLabel": { + "en": "order of preprocessing operations" + }, + "isVis": true, + "requiredValue": false, + "allow": [ + "reproschema:Skipped" + ] + }, + { + "variableName": "quality_control", + "isAbout": "items/quality_control.jsonld", + "prefLabel": { + "en": "quality control" + }, + "isVis": true, + "requiredValue": false, + "allow": [ + "reproschema:Skipped" + ] + }, + { + "variableName": "used_b0_unwarping", + "isAbout": "items/used_b0_unwarping.jsonld", + "prefLabel": { + "en": "used b0 unwarping" + }, + "isVis": true, + "requiredValue": false, + "allow": [ + "reproschema:Skipped" + ] + }, + { + "variableName": "b0_unwarping_software", + "isAbout": "items/b0_unwarping_software.jsonld", + "prefLabel": { + "en": "b0 unwarping software" + }, + "isVis": "used_b0_unwarping == 1", + "requiredValue": false, + "allow": [ + "reproschema:Skipped" + ] + }, + { + "variableName": "used_slice_timing_correction", + "isAbout": "items/used_slice_timing_correction.jsonld", + "prefLabel": { + "en": "used slice timing correction" + }, + "isVis": true, + "requiredValue": false, + "allow": [ + "reproschema:Skipped" + ] + }, + { + "variableName": "slice_timing_correction_software", + "isAbout": "items/slice_timing_correction_software.jsonld", + "prefLabel": { + "en": "slice timing correction software" + }, + "isVis": "used_slice_timing_correction == 1", + "requiredValue": false, + "allow": [ + "reproschema:Skipped" + ] + }, + { + "variableName": "used_motion_correction", + "isAbout": "items/used_motion_correction.jsonld", + "prefLabel": { + "en": "used motion correction" + }, + "isVis": true, + "requiredValue": false, + "allow": [ + "reproschema:Skipped" + ] + }, + { + "variableName": "motion_correction_software", + "isAbout": "items/motion_correction_software.jsonld", + "prefLabel": { + "en": "motion correction software" + }, + "isVis": "used_motion_correction == 1", + "requiredValue": false, + "allow": [ + "reproschema:Skipped" + ] + }, + { + "variableName": "motion_correction_reference", + "isAbout": "items/motion_correction_reference.jsonld", + "prefLabel": { + "en": "motion correction reference" + }, + "isVis": "used_motion_correction == 1", + "requiredValue": false, + "allow": [ + "reproschema:Skipped" + ] + }, + { + "variableName": "motion_correction_metric", + "isAbout": "items/motion_correction_metric.jsonld", + "prefLabel": { + "en": "motion correction metric" + }, + "isVis": "used_motion_correction == 1", + "requiredValue": false, + "allow": [ + "reproschema:Skipped" + ] + }, + { + "variableName": "motion_correction_interpolation", + "isAbout": "items/motion_correction_interpolation.jsonld", + "prefLabel": { + "en": "motion correction interpolation" + }, + "isVis": "used_motion_correction == 1", + "requiredValue": false, + "allow": [ + "reproschema:Skipped" + ] + }, + { + "variableName": "used_motion_susceptibiity_correction", + "isAbout": "items/used_motion_susceptibiity_correction.jsonld", + "prefLabel": { + "en": "used motion susceptibiity correction" + }, + "isVis": true, + "requiredValue": false, + "allow": [ + "reproschema:Skipped" + ] + } + ], + "allow": [ + "reproschema:AutoAdvance", + "reproschema:AllowExport" + ] + } +} diff --git a/ui/neurovault/protocols/neurovault_schema.jsonld b/ui/neurovault/protocols/neurovault_schema.jsonld new file mode 100644 index 00000000..af243448 --- /dev/null +++ b/ui/neurovault/protocols/neurovault_schema.jsonld @@ -0,0 +1,133 @@ +{ + "@context": "https://raw.githubusercontent.com/ReproNim/reproschema/1.0.0-rc4/contexts/generic", + "@type": "reproschema:Protocol", + "@id": "neurovault_schema.jsonld", + "schemaVersion": "1.0.0-rc4", + "version": "0.0.1", + "prefLabel": { + "en": "neurovault" + }, + "description": "neurovault", + "preamble": { + "en": "" + }, + "ui": { + "shuffle": false, + "order": [ + "../activities/experimental_design/experimental_design_schema.jsonld", + "../activities/participants/participants_schema.jsonld", + "../activities/mri_acquisition/mri_acquisition_schema.jsonld", + "../activities/preprocessing/preprocessing_schema.jsonld", + "../activities/intersubject_registration/intersubject_registration_schema.jsonld", + "../activities/individual_subject_modeling/individual_subject_modeling_schema.jsonld", + "../activities/group_modeling/group_modeling_schema.jsonld", + "../activities/group_inference/group_inference_schema.jsonld" + ], + "addProperties": [ + { + "variableName": "experimental_design", + "isAbout": "../activities/experimental_design/experimental_design_schema.jsonld", + "prefLabel": { + "en": "Experimental design" + }, + "isVis": true, + "requiredValue": false, + "allow": [ + "reproschema:Skipped" + ] + }, + { + "variableName": "participants", + "isAbout": "../activities/participants/participants_schema.jsonld", + "prefLabel": { + "en": "Participants" + }, + "isVis": true, + "requiredValue": false, + "allow": [ + "reproschema:Skipped" + ] + }, + { + "variableName": "mri_acquisition", + "isAbout": "../activities/mri_acquisition/mri_acquisition_schema.jsonld", + "prefLabel": { + "en": "MRI acquisition" + }, + "isVis": true, + "requiredValue": false, + "allow": [ + "reproschema:Skipped" + ] + }, + { + "variableName": "preprocessing", + "isAbout": "../activities/preprocessing/preprocessing_schema.jsonld", + "prefLabel": { + "en": "Preprocessing" + }, + "isVis": true, + "requiredValue": false, + "allow": [ + "reproschema:Skipped" + ] + }, + { + "variableName": "intersubject_registration", + "isAbout": "../activities/intersubject_registration/intersubject_registration_schema.jsonld", + "prefLabel": { + "en": "Intersubject registration" + }, + "isVis": true, + "requiredValue": false, + "allow": [ + "reproschema:Skipped" + ] + }, + { + "variableName": "individual_subject_modeling", + "isAbout": "../activities/individual_subject_modeling/individual_subject_modeling_schema.jsonld", + "prefLabel": { + "en": "Individual subject modeling" + }, + "isVis": true, + "requiredValue": false, + "allow": [ + "reproschema:Skipped" + ] + }, + { + "variableName": "group_modeling", + "isAbout": "../activities/group_modeling/group_modeling_schema.jsonld", + "prefLabel": { + "en": "Group modeling" + }, + "isVis": true, + "requiredValue": false, + "allow": [ + "reproschema:Skipped" + ] + }, + { + "variableName": "group_inference", + "isAbout": "../activities/group_inference/group_inference_schema.jsonld", + "prefLabel": { + "en": "Group inference" + }, + "isVis": true, + "requiredValue": false, + "allow": [ + "reproschema:Skipped" + ] + } + ], + "allow": [ + "reproschema:AutoAdvance", + "reproschema:AllowExport" + ] + }, + "landingPage": { + "@id": "../README_eCOBIDAS-en.html", + "inLanguage": "en" + } +} diff --git a/ui/requirements.txt b/ui/requirements.txt new file mode 100644 index 00000000..1698b1f4 --- /dev/null +++ b/ui/requirements.txt @@ -0,0 +1,3 @@ +flask +Flask-WTF +bootstrap-flask diff --git a/ui/templates/404.html b/ui/templates/404.html new file mode 100644 index 00000000..a822154d --- /dev/null +++ b/ui/templates/404.html @@ -0,0 +1,14 @@ +{% extends 'base.html' %} {% block title %} 404 Error - Page Not Found {% +endblock %} {% block content %} + +
+
+
+

Page not found (Error 404)

+ +

Go to search page

+
+
+
+ +{% endblock %} diff --git a/ui/templates/500.html b/ui/templates/500.html new file mode 100644 index 00000000..c308186c --- /dev/null +++ b/ui/templates/500.html @@ -0,0 +1,14 @@ +{% extends 'base.html' %} {% block title %} 500 Error - Internal Server Error {% +endblock %} {% block content %} + +
+
+
+

Internal server error (500)

+ +

Go to search page

+
+
+
+ +{% endblock %} diff --git a/ui/templates/about.html b/ui/templates/about.html new file mode 100644 index 00000000..21f5da26 --- /dev/null +++ b/ui/templates/about.html @@ -0,0 +1 @@ +{% extends 'base.html' %} diff --git a/ui/templates/activity.html b/ui/templates/activity.html new file mode 100644 index 00000000..0e43cc54 --- /dev/null +++ b/ui/templates/activity.html @@ -0,0 +1,14 @@ +{% extends 'base.html' %} {% from 'bootstrap5/form.html' import render_form %} +{% block content %} + +
+
+
+

{{ prefLabel }}

+ + {{ preamble }} {{ render_form(form) }} +
+
+ + {% endblock %} +
diff --git a/ui/templates/base.html b/ui/templates/base.html new file mode 100644 index 00000000..883623a5 --- /dev/null +++ b/ui/templates/base.html @@ -0,0 +1,52 @@ +{% from 'bootstrap4/nav.html' import render_nav_item %} + + + + + + + + {% block title %} {% endblock %} + + {{ bootstrap.load_css() }} + + + + + + + +
+
+
+

eCOBIDAS

+
+
+ + + + {% block content %} {% endblock %} + + + {{ bootstrap.load_js() }} +
+ + +
+
+
+
eCOBIDAS
+
+
+
+ diff --git a/ui/templates/index.html b/ui/templates/index.html new file mode 100644 index 00000000..fd220352 --- /dev/null +++ b/ui/templates/index.html @@ -0,0 +1,18 @@ +{% extends 'base.html' %} {% block title %} TBD {% endblock %} {% block content +%} + + + +
+
+
+

TBD

+
+
+
+ +{% endblock %} From 69a273a001c17951d47498ba4099ef44ca0fa21b Mon Sep 17 00:00:00 2001 From: Remi Gau Date: Tue, 21 May 2024 09:02:18 -0400 Subject: [PATCH 02/31] add protocol page --- ui/{forms.py => app.py} | 84 ++++++++++++++++++++++++++++----- ui/modules.py | 18 +++++++ ui/templates/activity.html | 2 +- ui/templates/base.html | 30 +++++++----- ui/templates/new_checklist.html | 1 + ui/templates/protocol.html | 26 ++++++++++ 6 files changed, 138 insertions(+), 23 deletions(-) rename ui/{forms.py => app.py} (71%) create mode 100644 ui/templates/new_checklist.html create mode 100644 ui/templates/protocol.html diff --git a/ui/forms.py b/ui/app.py similarity index 71% rename from ui/forms.py rename to ui/app.py index 15a228c7..debce858 100644 --- a/ui/forms.py +++ b/ui/app.py @@ -1,11 +1,12 @@ from functools import lru_cache +from pathlib import Path import requests from flask import Flask, render_template from flask_bootstrap import Bootstrap5 from flask_wtf import CSRFProtect, FlaskForm from markupsafe import Markup, escape -from modules import activity_url, get_activity, get_item +from modules import activity_url, get_activity, get_item, get_protocol, protocol_url from rich import print from wtforms import ( DecimalField, @@ -46,6 +47,20 @@ def query_choices(url): return data +@lru_cache +def get_landing_page(url: Path): + try: + if str(url).startswith("https:"): + data = requests.get(url) + else: + with open(url) as f: + data = f.read() + except Exception as exc: + print(exc) + data = None + return data + + @app.route("/", methods=["GET", "POST"]) def index(): return render_template("index.html") @@ -56,7 +71,39 @@ def about(): return render_template("about.html") -@app.route("//", methods=["GET", "POST"]) +@app.route("/new") +def new(): + return render_template("new_checklist.html") + + +@app.route("/protocol/", methods=["GET", "POST"]) +def protocol(protocol_name): + + protocol_content = get_protocol(protocol_name) + + landing_page_url = protocol_url(protocol_name).parent / protocol_content["landingPage"]["@id"] + landing_page = get_landing_page(landing_page_url) + + activities = [ + {"name": "Start", "link": f"/protocol/{protocol_name}"}, + ] + activities.extend( + { + "name": activity["prefLabel"][LANG], + "link": f"/protocol/{protocol_name}/{activity['variableName']}", + } + for activity in protocol_content["ui"]["addProperties"] + ) + return render_template( + "protocol.html", + prefLabel=protocol_name, + preamble=protocol_content["preamble"][LANG], + activities=activities, + landing_page=Markup(landing_page), + ) + + +@app.route("/protocol//", methods=["GET", "POST"]) def activity(protocol_name, activity_name): protocol_name = escape(protocol_name) activity_name = escape(activity_name) @@ -68,15 +115,8 @@ def activity(protocol_name, activity_name): form = generate_form(items) if form.validate_on_submit(): - for item, values in items.items(): - isVis = values["isVis"] - if isinstance(isVis, str): - isVis = isVis.replace(" ", "").split("==") - if len(isVis) == 2: - response = form[isVis[0]].data - value = items[isVis[0]]["choices"].get(response) - expected = int(isVis[1]) - items[item]["visibility"] = value == expected + + items = update_visbility(items, form) form = generate_form(items) @@ -95,6 +135,23 @@ def activity(protocol_name, activity_name): ) +def update_visbility(items, form): + for item, values in items.items(): + isVis = values["isVis"] + if isinstance(isVis, str): + isVis = isVis.replace(" ", "").split("==") + if len(isVis) > 2: + app.logger.warning("More than 1 '=='") + if len(isVis) < 2: + app.logger.warning(f"Unsupported JavaScript expression: {isVis}") + if len(isVis) == 2: + response = form[isVis[0]].data + value = items[isVis[0]]["choices"].get(response) + expected = int(isVis[1]) + items[item]["visibility"] = value == expected + return items + + def generate_form(items): for item_name, item in items.items(): @@ -118,13 +175,17 @@ def generate_form(items): input_type = item["input_type"] + default = None + if input_type not in ["select", "radio", "slider"]: FieldType = StringField if input_type == "number": FieldType = IntegerField + default = 0 elif input_type in ["float", "slider"]: FieldType = DecimalField + default = 0 elif input_type == "textarea": FieldType = TextAreaField @@ -135,6 +196,7 @@ def generate_form(items): Markup(question), validators=validators, description=item["description"], + default=default, ), ) diff --git a/ui/modules.py b/ui/modules.py index 72b4053b..8657eeb7 100644 --- a/ui/modules.py +++ b/ui/modules.py @@ -15,6 +15,24 @@ def activity_url(protocol_name, activity_name): ) +def protocol_url(protocol_name): + return ( + Path(__file__).parents[1] + / "cobidas_schema" + / "schemas" + / protocol_name + / "protocols" + / f"{protocol_name}_schema.jsonld" + ) + + +def get_protocol(protocol_name): + file = protocol_url(protocol_name) + with open(file) as f: + content = json.load(f) + return content + + def get_activity(protocol_name, activity_name): file = activity_url(protocol_name, activity_name) with open(file) as f: diff --git a/ui/templates/activity.html b/ui/templates/activity.html index 0e43cc54..8c40abd2 100644 --- a/ui/templates/activity.html +++ b/ui/templates/activity.html @@ -3,7 +3,7 @@
-
+

{{ prefLabel }}

{{ preamble }} {{ render_form(form) }} diff --git a/ui/templates/base.html b/ui/templates/base.html index 883623a5..97a25bf5 100644 --- a/ui/templates/base.html +++ b/ui/templates/base.html @@ -23,19 +23,25 @@
-
+

eCOBIDAS

- - - {% block content %} {% endblock %} +
{{ bootstrap.load_js() }} @@ -43,9 +49,11 @@

eCOBIDAS

-
-
-
eCOBIDAS
+
+
+
+
eCOBIDAS
+
diff --git a/ui/templates/new_checklist.html b/ui/templates/new_checklist.html new file mode 100644 index 00000000..21f5da26 --- /dev/null +++ b/ui/templates/new_checklist.html @@ -0,0 +1 @@ +{% extends 'base.html' %} diff --git a/ui/templates/protocol.html b/ui/templates/protocol.html new file mode 100644 index 00000000..993301ef --- /dev/null +++ b/ui/templates/protocol.html @@ -0,0 +1,26 @@ +{% extends 'base.html' %} {% from 'bootstrap5/form.html' import render_form %} +{% block content %} + +
+
+

{{ prefLabel }}

+ {{ preamble }} +
+ +
+
{{ landing_page }}
+
+
+ +{% endblock %} From c6920d289a6837118bef215d1f2722961d44badb Mon Sep 17 00:00:00 2001 From: Remi Gau Date: Tue, 21 May 2024 09:43:41 -0400 Subject: [PATCH 03/31] display activity in protocol page --- ui/app.py | 53 ++++++++++++++++++++++++++------------ ui/templates/activity.html | 14 ---------- ui/templates/protocol.html | 12 +++++---- 3 files changed, 44 insertions(+), 35 deletions(-) delete mode 100644 ui/templates/activity.html diff --git a/ui/app.py b/ui/app.py index debce858..1a72ae09 100644 --- a/ui/app.py +++ b/ui/app.py @@ -84,8 +84,21 @@ def protocol(protocol_name): landing_page_url = protocol_url(protocol_name).parent / protocol_content["landingPage"]["@id"] landing_page = get_landing_page(landing_page_url) + activities = get_nav_bar_content(protocol_name) + + return render_template( + "protocol.html", + protocol_pref_label=protocol_name, + protocol_preamble=protocol_content["preamble"][LANG], + activities=activities, + landing_page=Markup(landing_page), + ) + + +def get_nav_bar_content(protocol_name, activity_name=None): + protocol_content = get_protocol(protocol_name) activities = [ - {"name": "Start", "link": f"/protocol/{protocol_name}"}, + {"name": "Start", "link": "#"}, ] activities.extend( { @@ -94,13 +107,12 @@ def protocol(protocol_name): } for activity in protocol_content["ui"]["addProperties"] ) - return render_template( - "protocol.html", - prefLabel=protocol_name, - preamble=protocol_content["preamble"][LANG], - activities=activities, - landing_page=Markup(landing_page), - ) + if activity_name: + activities[0]["link"] = f"/protocol/{protocol_name}" + for activity in activities: + if activity["name"] == activity_name: + activity["link"] = "#" + return activities @app.route("/protocol//", methods=["GET", "POST"]) @@ -110,9 +122,11 @@ def activity(protocol_name, activity_name): activity = get_activity(protocol_name, activity_name) + activities = get_nav_bar_content(protocol_name, activity["prefLabel"][LANG]) + items = get_items_for_activity(protocol_name, activity_name) - form = generate_form(items) + form = generate_form(items, prefix=activity_name) if form.validate_on_submit(): @@ -121,16 +135,20 @@ def activity(protocol_name, activity_name): form = generate_form(items) return render_template( - "activity.html", - prefLabel=activity["prefLabel"][LANG], - preamble=Markup(activity["preamble"][LANG]), + "protocol.html", + protocol_pref_label=protocol_name, + activity_pref_label=activity["prefLabel"][LANG], + activity_preamble=Markup(activity["preamble"][LANG]), + activities=activities, form=form, ) return render_template( - "activity.html", - prefLabel=activity["prefLabel"][LANG], - preamble=Markup(activity["preamble"][LANG]), + "protocol.html", + protocol_pref_label=protocol_name, + activity_pref_label=activity["prefLabel"][LANG], + activity_preamble=Markup(activity["preamble"][LANG]), + activities=activities, form=form, ) @@ -152,7 +170,7 @@ def update_visbility(items, form): return items -def generate_form(items): +def generate_form(items, prefix): for item_name, item in items.items(): validators = [] @@ -169,6 +187,7 @@ def generate_form(items): Markup(question), validators=validators, description=item["description"], + _prefix=prefix, ), ) continue @@ -197,6 +216,7 @@ def generate_form(items): validators=validators, description=item["description"], default=default, + _prefix=prefix, ), ) @@ -219,6 +239,7 @@ def generate_form(items): validators=validators, description=item["description"], choices=[key for key in item["choices"]], + _prefix=prefix, ), ) diff --git a/ui/templates/activity.html b/ui/templates/activity.html deleted file mode 100644 index 8c40abd2..00000000 --- a/ui/templates/activity.html +++ /dev/null @@ -1,14 +0,0 @@ -{% extends 'base.html' %} {% from 'bootstrap5/form.html' import render_form %} -{% block content %} - -
-
-
-

{{ prefLabel }}

- - {{ preamble }} {{ render_form(form) }} -
-
- - {% endblock %} -
diff --git a/ui/templates/protocol.html b/ui/templates/protocol.html index 993301ef..2b50fce6 100644 --- a/ui/templates/protocol.html +++ b/ui/templates/protocol.html @@ -1,10 +1,9 @@ {% extends 'base.html' %} {% from 'bootstrap5/form.html' import render_form %} {% block content %} -
-

{{ prefLabel }}

- {{ preamble }} +

{{ protocol_pref_label }}

+ {% if landing_page %} {{ protocol_preamble }} {% endif %}
    {% for act in activities %} @@ -19,8 +18,11 @@

    {{ prefLabel }}

    {% endfor %}
-
{{ landing_page }}
+
+ {% if landing_page %} {{ landing_page }} {% else %} +

{{ activity_pref_label }}

+ {{ activity_preamble }} {{ render_form(form) }} {% endif %} +
- {% endblock %} From db86e449b98f47a8934476052c688a23a7c045c7 Mon Sep 17 00:00:00 2001 From: Remi Gau Date: Tue, 21 May 2024 10:03:09 -0400 Subject: [PATCH 04/31] fix issue new instance form --- ui/app.py | 54 +++++++++++++++++++++++++++++++----------------------- 1 file changed, 31 insertions(+), 23 deletions(-) diff --git a/ui/app.py b/ui/app.py index 1a72ae09..e112f363 100644 --- a/ui/app.py +++ b/ui/app.py @@ -2,7 +2,7 @@ from pathlib import Path import requests -from flask import Flask, render_template +from flask import Flask, render_template, request from flask_bootstrap import Bootstrap5 from flask_wtf import CSRFProtect, FlaskForm from markupsafe import Markup, escape @@ -33,10 +33,6 @@ csrf = CSRFProtect(app) -class DyanmicForm(FlaskForm): - pass - - @lru_cache def query_choices(url): try: @@ -117,6 +113,7 @@ def get_nav_bar_content(protocol_name, activity_name=None): @app.route("/protocol//", methods=["GET", "POST"]) def activity(protocol_name, activity_name): + protocol_name = escape(protocol_name) activity_name = escape(activity_name) @@ -126,22 +123,26 @@ def activity(protocol_name, activity_name): items = get_items_for_activity(protocol_name, activity_name) - form = generate_form(items, prefix=activity_name) + if request.method == "POST": - if form.validate_on_submit(): + form = generate_form(form=None, items=items, prefix=activity_name) - items = update_visbility(items, form) + if form.validate_on_submit(): - form = generate_form(items) + items = update_visbility(items, form) - return render_template( - "protocol.html", - protocol_pref_label=protocol_name, - activity_pref_label=activity["prefLabel"][LANG], - activity_preamble=Markup(activity["preamble"][LANG]), - activities=activities, - form=form, - ) + form = generate_form(items) + + return render_template( + "protocol.html", + protocol_pref_label=protocol_name, + activity_pref_label=activity["prefLabel"][LANG], + activity_preamble=Markup(activity["preamble"][LANG]), + activities=activities, + form=form, + ) + + form = generate_form(form=None, items=items, prefix=activity_name) return render_template( "protocol.html", @@ -170,7 +171,14 @@ def update_visbility(items, form): return items -def generate_form(items, prefix): +def generate_form(form=None, items=None, prefix=None): + + class DyanmicForm(FlaskForm): + pass + + if form is None: + form = DyanmicForm + for item_name, item in items.items(): validators = [] @@ -181,7 +189,7 @@ def generate_form(items, prefix): if not item["visibility"]: setattr( - DyanmicForm, + form, item_name, HiddenField( Markup(question), @@ -209,7 +217,7 @@ def generate_form(items, prefix): FieldType = TextAreaField setattr( - DyanmicForm, + form, item_name, FieldType( Markup(question), @@ -232,7 +240,7 @@ def generate_form(items, prefix): FieldType = RadioField setattr( - DyanmicForm, + form, item_name, FieldType( Markup(question), @@ -243,9 +251,9 @@ def generate_form(items, prefix): ), ) - setattr(DyanmicForm, "submit", SubmitField("Submit")) # noqa B010 + setattr(form, "submit", SubmitField("Submit")) # noqa B010 - return DyanmicForm() + return form() def get_items_for_activity(protocol_name, activity_name): From 1371a632c85f4ace1e3b4b6d9b46e2b5f774383e Mon Sep 17 00:00:00 2001 From: Remi Gau Date: Tue, 21 May 2024 17:50:14 -0400 Subject: [PATCH 05/31] fix path activity --- ui/app.py | 147 +++++++++++++++++++++++++------------ ui/modules.py | 28 ++----- ui/templates/base.html | 47 +++++++++--- ui/templates/protocol.html | 4 +- 4 files changed, 144 insertions(+), 82 deletions(-) diff --git a/ui/app.py b/ui/app.py index e112f363..7db1a105 100644 --- a/ui/app.py +++ b/ui/app.py @@ -1,29 +1,32 @@ +import json from functools import lru_cache from pathlib import Path +from typing import Any import requests from flask import Flask, render_template, request from flask_bootstrap import Bootstrap5 from flask_wtf import CSRFProtect, FlaskForm from markupsafe import Markup, escape -from modules import activity_url, get_activity, get_item, get_protocol, protocol_url +from modules import get_item, get_protocol, protocol_url from rich import print from wtforms import ( + DateField, DecimalField, HiddenField, IntegerField, - MultipleFileField, RadioField, SelectField, + SelectMultipleField, StringField, SubmitField, TextAreaField, ) from wtforms.validators import DataRequired -LANG = "en" +LANG: str = "en" -app = Flask(__name__) +app: Flask = Flask(__name__) app.secret_key = "tO$&!|0wkamvVia0?n$NqIRVWOG" # Bootstrap-Flask requires this line @@ -34,7 +37,7 @@ @lru_cache -def query_choices(url): +def query_choices(url: str) -> None | dict[str, Any]: try: data = requests.get(url).json() except Exception as exc: @@ -44,13 +47,12 @@ def query_choices(url): @lru_cache -def get_landing_page(url: Path): +def get_landing_page(url: Path) -> None | dict[str, Any]: try: if str(url).startswith("https:"): data = requests.get(url) else: - with open(url) as f: - data = f.read() + data = Path(url).read_text() except Exception as exc: print(exc) data = None @@ -58,22 +60,22 @@ def get_landing_page(url: Path): @app.route("/", methods=["GET", "POST"]) -def index(): +def index() -> str: return render_template("index.html") @app.route("/about") -def about(): +def about() -> str: return render_template("about.html") @app.route("/new") -def new(): +def new() -> str: return render_template("new_checklist.html") @app.route("/protocol/", methods=["GET", "POST"]) -def protocol(protocol_name): +def protocol(protocol_name: str) -> str: protocol_content = get_protocol(protocol_name) @@ -91,58 +93,84 @@ def protocol(protocol_name): ) -def get_nav_bar_content(protocol_name, activity_name=None): +def sort_ui_properties(properties: list[dict[str, Any]], order: list[str]) -> list[dict[str, Any]]: + tmp = [] + for i in order: + for prop in properties: + if prop["isAbout"] == i: + tmp.append(prop) + break + return tmp + + +def get_nav_bar_content( + protocol_name: str, activity_name: str | None = None +) -> list[dict[str, str]]: protocol_content = get_protocol(protocol_name) + + order = protocol_content["ui"]["order"] + properties = protocol_content["ui"]["addProperties"] + properties = sort_ui_properties(properties=properties, order=order) + activities = [ - {"name": "Start", "link": "#"}, + {"name": "Start", "link": "#", "class": "nav-link active"}, ] activities.extend( { "name": activity["prefLabel"][LANG], "link": f"/protocol/{protocol_name}/{activity['variableName']}", + "class": "nav-link", } - for activity in protocol_content["ui"]["addProperties"] + for activity in properties ) + if activity_name: activities[0]["link"] = f"/protocol/{protocol_name}" + activities[0]["class"] = "nav-link" for activity in activities: if activity["name"] == activity_name: activity["link"] = "#" + activity["class"] = "nav-link active" + return activities @app.route("/protocol//", methods=["GET", "POST"]) -def activity(protocol_name, activity_name): +def activity(protocol_name, activity_name) -> str: protocol_name = escape(protocol_name) activity_name = escape(activity_name) - activity = get_activity(protocol_name, activity_name) - - activities = get_nav_bar_content(protocol_name, activity["prefLabel"][LANG]) - - items = get_items_for_activity(protocol_name, activity_name) + protocol_content = get_protocol(protocol_name) + properties = protocol_content["ui"]["addProperties"] + for activity in properties: + if activity["variableName"] == activity_name: + is_about_activity = activity["isAbout"] + break + activity_file = protocol_url(protocol_name).parent / is_about_activity - if request.method == "POST": + with open(activity_file) as f: + activity = json.load(f) - form = generate_form(form=None, items=items, prefix=activity_name) + activities = get_nav_bar_content(protocol_name, activity["prefLabel"][LANG]) - if form.validate_on_submit(): + items = get_items_for_activity(activity_file) - items = update_visbility(items, form) + form = generate_form(items=items, prefix=activity_name) - form = generate_form(items) + if request.method == "POST" and form.validate_on_submit(): + items = update_visibility(items, form) - return render_template( - "protocol.html", - protocol_pref_label=protocol_name, - activity_pref_label=activity["prefLabel"][LANG], - activity_preamble=Markup(activity["preamble"][LANG]), - activities=activities, - form=form, - ) + form = generate_form(items, prefix=activity_name) - form = generate_form(form=None, items=items, prefix=activity_name) + return render_template( + "protocol.html", + protocol_pref_label=protocol_name, + activity_pref_label=activity["prefLabel"][LANG], + activity_preamble=Markup(activity["preamble"][LANG]), + activities=activities, + form=form, + ) return render_template( "protocol.html", @@ -154,7 +182,7 @@ def activity(protocol_name, activity_name): ) -def update_visbility(items, form): +def update_visibility(items: dict[str, Any], form): for item, values in items.items(): isVis = values["isVis"] if isinstance(isVis, str): @@ -171,13 +199,12 @@ def update_visbility(items, form): return items -def generate_form(form=None, items=None, prefix=None): +def generate_form(items=None, prefix=None): class DyanmicForm(FlaskForm): pass - if form is None: - form = DyanmicForm + form = DyanmicForm for item_name, item in items.items(): @@ -204,13 +231,32 @@ class DyanmicForm(FlaskForm): default = None - if input_type not in ["select", "radio", "slider"]: + if input_type == "date": + + print(item_name) + + FieldType = DateField + + setattr( + form, + item_name, + FieldType( + Markup(question), + validators=validators, + description=item["description"], + default=default, + _prefix=prefix, + format="%Y-%m-%d", + ), + ) + + elif input_type not in ["select", "radio", "slider"]: FieldType = StringField if input_type == "number": FieldType = IntegerField default = 0 - elif input_type in ["float", "slider"]: + elif input_type in ["float"]: FieldType = DecimalField default = 0 elif input_type == "textarea": @@ -233,10 +279,10 @@ class DyanmicForm(FlaskForm): is_multiple = item["is_multiple"] if is_multiple: - FieldType = MultipleFileField + FieldType = SelectMultipleField if input_type == "select": FieldType = SelectField - elif input_type == "radio": + elif input_type in ["radio", "slider"]: FieldType = RadioField setattr( @@ -256,15 +302,20 @@ class DyanmicForm(FlaskForm): return form() -def get_items_for_activity(protocol_name, activity_name): - # TODO make sure items are presented in the right order - activity = get_activity(protocol_name, activity_name) +def get_items_for_activity(activity_file): + with open(activity_file) as f: + activity = json.load(f) + + order = activity["ui"]["order"] + properties = activity["ui"]["addProperties"] + properties = sort_ui_properties(properties=properties, order=order) + items = {} - for item in activity["ui"]["addProperties"]: + for item in properties: item_name = item["variableName"] - item_data = get_item(activity_url(protocol_name, activity_name).parent / item["isAbout"]) + item_data = get_item(activity_file.parent / item["isAbout"]) tmp = { "visibility": False, diff --git a/ui/modules.py b/ui/modules.py index 8657eeb7..d59e66ed 100644 --- a/ui/modules.py +++ b/ui/modules.py @@ -1,21 +1,11 @@ # functions to be used by the routes import json +from functools import lru_cache from pathlib import Path +from typing import Any -def activity_url(protocol_name, activity_name): - return ( - Path(__file__).parents[1] - / "cobidas_schema" - / "schemas" - / protocol_name - / "activities" - / activity_name - / f"{activity_name}_schema.jsonld" - ) - - -def protocol_url(protocol_name): +def protocol_url(protocol_name: Path) -> Path: return ( Path(__file__).parents[1] / "cobidas_schema" @@ -26,21 +16,15 @@ def protocol_url(protocol_name): ) -def get_protocol(protocol_name): +@lru_cache +def get_protocol(protocol_name: str) -> dict[str, Any]: file = protocol_url(protocol_name) with open(file) as f: content = json.load(f) return content -def get_activity(protocol_name, activity_name): - file = activity_url(protocol_name, activity_name) - with open(file) as f: - content = json.load(f) - return content - - -def get_item(file): +def get_item(file: Path) -> dict[str, Any]: with open(file) as f: content = json.load(f) return content diff --git a/ui/templates/base.html b/ui/templates/base.html index 97a25bf5..bee7f598 100644 --- a/ui/templates/base.html +++ b/ui/templates/base.html @@ -1,5 +1,3 @@ -{% from 'bootstrap4/nav.html' import render_nav_item %} - @@ -30,14 +28,43 @@

eCOBIDAS

- + {% block content %} {% endblock %}
diff --git a/ui/templates/protocol.html b/ui/templates/protocol.html index 2b50fce6..7d6d6492 100644 --- a/ui/templates/protocol.html +++ b/ui/templates/protocol.html @@ -5,11 +5,11 @@

{{ protocol_pref_label }}

{% if landing_page %} {{ protocol_preamble }} {% endif %}
-
    +
      {% for act in activities %}
    • {{ act['name'] }} Date: Wed, 22 May 2024 11:56:38 -0400 Subject: [PATCH 06/31] style items and deal with sliders items --- ui/app.py | 282 +++++++++++------- ui/neurovault/README_eCOBIDAS-en.html | 139 --------- .../experimental_design_schema.jsonld | 129 -------- .../items/length_of_blocks.jsonld | 28 -- .../items/length_of_runs.jsonld | 28 -- .../items/length_of_trials.jsonld | 28 -- .../items/number_of_experimental_units.jsonld | 20 -- .../items/number_of_imaging_runs.jsonld | 20 -- .../items/optimization.jsonld | 23 -- .../items/optimization_method.jsonld | 17 -- .../items/type_of_design.jsonld | 42 --- .../group_inference_schema.jsonld | 64 ---- .../items/group_smoothness_fwhm.jsonld | 20 -- .../items/group_statistic_parameters.jsonld | 20 -- .../items/group_statistic_type.jsonld | 66 ---- .../group_modeling_schema.jsonld | 116 ------- .../items/group_estimation_type.jsonld | 36 --- .../items/group_inference_type.jsonld | 42 --- .../items/group_model_multilevel.jsonld | 17 -- .../items/group_model_type.jsonld | 30 -- .../items/group_modeling_software.jsonld | 23 -- .../items/group_repeated_measures.jsonld | 23 -- .../group_repeated_measures_method.jsonld | 17 -- .../individual_subject_modeling_schema.jsonld | 220 -------------- .../items/autocorrelation_model.jsonld | 17 -- .../items/contrast_definition.jsonld | 17 -- .../items/contrast_definition_cogatlas.jsonld | 17 -- .../hemodynamic_response_function.jsonld | 42 --- .../items/high_pass_filter_method.jsonld | 17 -- .../items/intrasubject_estimation_type.jsonld | 36 --- .../items/intrasubject_model_type.jsonld | 30 -- .../intrasubject_modeling_software.jsonld | 23 -- .../orthogonalization_description.jsonld | 17 -- .../items/used_dispersion_derivatives.jsonld | 23 -- .../items/used_high_pass_filter.jsonld | 23 -- .../items/used_motion_regressors.jsonld | 23 -- .../items/used_orthogonalization.jsonld | 23 -- .../items/used_reaction_time_regressor.jsonld | 23 -- .../items/used_temporal_derivatives.jsonld | 23 -- .../intersubject_registration_schema.jsonld | 233 --------------- .../items/coordinate_space.jsonld | 42 --- ...nctional_coregistered_to_structural.jsonld | 23 -- .../functional_coregistration_method.jsonld | 17 -- .../items/interpolation_method.jsonld | 23 -- .../intersubject_registration_software.jsonld | 23 -- .../intersubject_transformation_type.jsonld | 36 --- .../items/nonlinear_transform_type.jsonld | 17 -- .../items/object_image_type.jsonld | 17 -- .../items/resampled_voxel_size.jsonld | 20 -- .../items/smoothing_fwhm.jsonld | 28 -- .../items/smoothing_type.jsonld | 21 -- .../items/target_resolution.jsonld | 28 -- .../items/target_template_image.jsonld | 17 -- .../items/transform_similarity_metric.jsonld | 17 -- .../used_intersubject_registration.jsonld | 23 -- .../items/used_smoothing.jsonld | 23 -- .../mri_acquisition/items/EchoTime.jsonld | 28 -- .../mri_acquisition/items/FlipAngle.jsonld | 28 -- .../items/MagneticFieldStrength.jsonld | 28 -- .../mri_acquisition/items/Manufacturer.jsonld | 42 --- .../items/ManufacturersModelName.jsonld | 17 -- .../items/PulseSequenceType.jsonld | 60 ---- .../items/RepetitionTime.jsonld | 28 -- .../mri_acquisition/items/SliceTiming.jsonld | 42 --- .../items/acquisition_orientation.jsonld | 42 --- .../items/field_of_view.jsonld | 28 -- .../mri_acquisition/items/matrix_size.jsonld | 20 -- .../items/parallel_imaging.jsonld | 17 -- .../mri_acquisition/items/skip_factor.jsonld | 28 -- .../items/slice_thickness.jsonld | 28 -- .../mri_acquisition_schema.jsonld | 207 ------------- .../items/group_comparison.jsonld | 23 -- .../items/group_description.jsonld | 17 -- .../participants/items/handedness.jsonld | 42 --- .../items/inclusion_exclusion_criteria.jsonld | 17 -- .../items/number_of_rejected_subjects.jsonld | 20 -- .../items/number_of_subjects.jsonld | 20 -- .../items/proportion_male_subjects.jsonld | 145 --------- .../participants/items/subject_age_max.jsonld | 20 -- .../items/subject_age_mean.jsonld | 20 -- .../participants/items/subject_age_min.jsonld | 20 -- .../participants/participants_schema.jsonld | 155 ---------- .../preprocessing/items/SoftwareName.jsonld | 23 -- .../items/SoftwareVersion.jsonld | 17 -- .../items/b0_unwarping_software.jsonld | 23 -- .../motion_correction_interpolation.jsonld | 23 -- .../items/motion_correction_metric.jsonld | 23 -- .../items/motion_correction_reference.jsonld | 17 -- .../items/motion_correction_software.jsonld | 23 -- .../order_of_preprocessing_operations.jsonld | 17 -- .../items/quality_control.jsonld | 17 -- .../slice_timing_correction_software.jsonld | 17 -- .../items/used_b0_unwarping.jsonld | 23 -- .../items/used_motion_correction.jsonld | 23 -- ...sed_motion_susceptibiity_correction.jsonld | 23 -- .../items/used_slice_timing_correction.jsonld | 23 -- .../preprocessing/preprocessing_schema.jsonld | 207 ------------- .../protocols/neurovault_schema.jsonld | 133 --------- ui/static/style.css | 3 + ui/templates/base.html | 87 +++--- 100 files changed, 218 insertions(+), 4058 deletions(-) delete mode 100644 ui/neurovault/README_eCOBIDAS-en.html delete mode 100644 ui/neurovault/activities/experimental_design/experimental_design_schema.jsonld delete mode 100644 ui/neurovault/activities/experimental_design/items/length_of_blocks.jsonld delete mode 100644 ui/neurovault/activities/experimental_design/items/length_of_runs.jsonld delete mode 100644 ui/neurovault/activities/experimental_design/items/length_of_trials.jsonld delete mode 100644 ui/neurovault/activities/experimental_design/items/number_of_experimental_units.jsonld delete mode 100644 ui/neurovault/activities/experimental_design/items/number_of_imaging_runs.jsonld delete mode 100644 ui/neurovault/activities/experimental_design/items/optimization.jsonld delete mode 100644 ui/neurovault/activities/experimental_design/items/optimization_method.jsonld delete mode 100644 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TextAreaField, ) -from wtforms.validators import DataRequired +from wtforms.validators import DataRequired, NumberRange LANG: str = "en" -app: Flask = Flask(__name__) -app.secret_key = "tO$&!|0wkamvVia0?n$NqIRVWOG" - -# Bootstrap-Flask requires this line -bootstrap = Bootstrap5(app) - -# Flask-WTF requires this line -csrf = CSRFProtect(app) - @lru_cache def query_choices(url: str) -> None | dict[str, Any]: @@ -59,50 +50,6 @@ def get_landing_page(url: Path) -> None | dict[str, Any]: return data -@app.route("/", methods=["GET", "POST"]) -def index() -> str: - return render_template("index.html") - - -@app.route("/about") -def about() -> str: - return render_template("about.html") - - -@app.route("/new") -def new() -> str: - return render_template("new_checklist.html") - - -@app.route("/protocol/", methods=["GET", "POST"]) -def protocol(protocol_name: str) -> str: - - protocol_content = get_protocol(protocol_name) - - landing_page_url = protocol_url(protocol_name).parent / protocol_content["landingPage"]["@id"] - landing_page = get_landing_page(landing_page_url) - - activities = get_nav_bar_content(protocol_name) - - return render_template( - "protocol.html", - protocol_pref_label=protocol_name, - protocol_preamble=protocol_content["preamble"][LANG], - activities=activities, - landing_page=Markup(landing_page), - ) - - -def sort_ui_properties(properties: list[dict[str, Any]], order: list[str]) -> list[dict[str, Any]]: - tmp = [] - for i in order: - for prop in properties: - if prop["isAbout"] == i: - tmp.append(prop) - break - return tmp - - def get_nav_bar_content( protocol_name: str, activity_name: str | None = None ) -> list[dict[str, str]]: @@ -135,53 +82,6 @@ def get_nav_bar_content( return activities -@app.route("/protocol//", methods=["GET", "POST"]) -def activity(protocol_name, activity_name) -> str: - - protocol_name = escape(protocol_name) - activity_name = escape(activity_name) - - protocol_content = get_protocol(protocol_name) - properties = protocol_content["ui"]["addProperties"] - for activity in properties: - if activity["variableName"] == activity_name: - is_about_activity = activity["isAbout"] - break - activity_file = protocol_url(protocol_name).parent / is_about_activity - - with open(activity_file) as f: - activity = json.load(f) - - activities = get_nav_bar_content(protocol_name, activity["prefLabel"][LANG]) - - items = get_items_for_activity(activity_file) - - form = generate_form(items=items, prefix=activity_name) - - if request.method == "POST" and form.validate_on_submit(): - items = update_visibility(items, form) - - form = generate_form(items, prefix=activity_name) - - return render_template( - "protocol.html", - protocol_pref_label=protocol_name, - activity_pref_label=activity["prefLabel"][LANG], - activity_preamble=Markup(activity["preamble"][LANG]), - activities=activities, - form=form, - ) - - return render_template( - "protocol.html", - protocol_pref_label=protocol_name, - activity_pref_label=activity["prefLabel"][LANG], - activity_preamble=Markup(activity["preamble"][LANG]), - activities=activities, - form=form, - ) - - def update_visibility(items: dict[str, Any], form): for item, values in items.items(): isVis = values["isVis"] @@ -191,11 +91,17 @@ def update_visibility(items: dict[str, Any], form): app.logger.warning("More than 1 '=='") if len(isVis) < 2: app.logger.warning(f"Unsupported JavaScript expression: {isVis}") - if len(isVis) == 2: - response = form[isVis[0]].data - value = items[isVis[0]]["choices"].get(response) + if len(isVis) == 2 and form[isVis[0]].data: + response = int(form[isVis[0]].data) expected = int(isVis[1]) - items[item]["visibility"] = value == expected + items[item]["visibility"] = response == expected + return items + + +def update_format(items: dict[str, Any], form): + for i in items: + if form[i].data: + items[i]["is_answered"] = True return items @@ -208,6 +114,10 @@ class DyanmicForm(FlaskForm): for item_name, item in items.items(): + render_kw = {"style": "border-color: red; border-width: 2px;"} + if item["is_answered"]: + render_kw = {"style": "border-color: green; border-width: 2px;"} + validators = [] if item["required"]: validators.append(DataRequired()) @@ -247,6 +157,7 @@ class DyanmicForm(FlaskForm): default=default, _prefix=prefix, format="%Y-%m-%d", + render_kw=render_kw, ), ) @@ -255,10 +166,8 @@ class DyanmicForm(FlaskForm): FieldType = StringField if input_type == "number": FieldType = IntegerField - default = 0 elif input_type in ["float"]: FieldType = DecimalField - default = 0 elif input_type == "textarea": FieldType = TextAreaField @@ -271,6 +180,35 @@ class DyanmicForm(FlaskForm): description=item["description"], default=default, _prefix=prefix, + render_kw=render_kw, + ), + ) + + elif input_type == "slider": + + # FieldType = DecimalRangeField + # render_kw["value"]= "50.0" + # render_kw["min"]= "0.0" + # render_kw["max"]= "100.0" + # render_kw["step"]= "0.5" + + min_label = float(item["choices"][0][1]) + max_label = float(item["choices"][-1][1]) + + question += f" (min={min_label}, max={max_label})" + + FieldType = DecimalField + validators.append(NumberRange(min=min_label, max=max_label)) + + setattr( + form, + item_name, + FieldType( + Markup(question), + validators=validators, + description=item["description"], + _prefix=prefix, + render_kw=render_kw, ), ) @@ -280,9 +218,9 @@ class DyanmicForm(FlaskForm): if is_multiple: FieldType = SelectMultipleField - if input_type == "select": + elif input_type == "select": FieldType = SelectField - elif input_type in ["radio", "slider"]: + elif input_type == "radio": FieldType = RadioField setattr( @@ -292,16 +230,18 @@ class DyanmicForm(FlaskForm): Markup(question), validators=validators, description=item["description"], - choices=[key for key in item["choices"]], + choices=item["choices"], _prefix=prefix, + render_kw=render_kw, ), ) - setattr(form, "submit", SubmitField("Submit")) # noqa B010 + setattr(form, "submit", SubmitField("Save")) # noqa B010 return form() +@lru_cache def get_items_for_activity(activity_file): with open(activity_file) as f: activity = json.load(f) @@ -322,6 +262,7 @@ def get_items_for_activity(activity_file): "required": False, "isVis": item["isVis"], "choices": get_choices(item_data), + "is_answered": False, } tmp["description"] = item_data.get("description") @@ -351,17 +292,119 @@ def get_items_for_activity(activity_file): return items +def sort_ui_properties(properties: list[dict[str, Any]], order: list[str]) -> list[dict[str, Any]]: + tmp = [] + for i in order: + for prop in properties: + if prop["isAbout"] == i: + tmp.append(prop) + break + return tmp + + def get_choices(item_data): try: choices = item_data["responseOptions"]["choices"] if isinstance(choices, str): choices = query_choices(choices)["choices"] - choices = {x["name"][LANG]: x["value"] for x in choices} + choices = [(x["value"], x["name"][LANG]) for x in choices] except KeyError: choices = {} return choices +test_config = None + +# create and configure the app +app = Flask(__name__, instance_relative_config=True) +app.config.from_mapping( + SECRET_KEY="tO$&!|0wkamvVia0?n$NqIRVWOG", + DATABASE=Path(app.instance_path) / "flaskr.sqlite", +) + +if test_config is None: + # load the instance config, if it exists, when not testing + app.config.from_pyfile("config.py", silent=True) +else: + # load the test config if passed in + app.config.from_mapping(test_config) + +# ensure the instance folder exists +Path(app.instance_path).mkdir(parents=True, exist_ok=True) + +# Bootstrap-Flask requires this line +bootstrap = Bootstrap5(app) + +# Flask-WTF requires this line +csrf = CSRFProtect(app) + + +@app.route("/protocol/", methods=["GET", "POST"]) +def protocol(protocol_name: str) -> str: + + protocol_content = get_protocol(protocol_name) + + landing_page_url = protocol_url(protocol_name).parent / protocol_content["landingPage"]["@id"] + landing_page = get_landing_page(landing_page_url) + + activities = get_nav_bar_content(protocol_name) + + return render_template( + "protocol.html", + protocol_pref_label=protocol_name, + protocol_preamble=protocol_content["preamble"][LANG], + activities=activities, + landing_page=Markup(landing_page), + ) + + +@app.route("/protocol//", methods=["GET", "POST"]) +def activity(protocol_name, activity_name) -> str: + + protocol_name = escape(protocol_name) + activity_name = escape(activity_name) + + protocol_content = get_protocol(protocol_name) + properties = protocol_content["ui"]["addProperties"] + for activity in properties: + if activity["variableName"] == activity_name: + is_about_activity = activity["isAbout"] + break + activity_file = protocol_url(protocol_name).parent / is_about_activity + + with open(activity_file) as f: + activity = json.load(f) + + activities = get_nav_bar_content(protocol_name, activity["prefLabel"][LANG]) + + items = get_items_for_activity(activity_file) + + form = generate_form(items=items, prefix=activity_name) + + if request.method == "POST" and form.is_submitted(): + items = update_visibility(items, form) + items = update_format(items, form) + form = generate_form(items, prefix=activity_name) + + return render_template( + "protocol.html", + protocol_pref_label=protocol_name, + activity_pref_label=activity["prefLabel"][LANG], + activity_preamble=Markup(activity["preamble"][LANG]), + activities=activities, + form=form, + ) + + return render_template( + "protocol.html", + protocol_pref_label=protocol_name, + activity_pref_label=activity["prefLabel"][LANG], + activity_preamble=Markup(activity["preamble"][LANG]), + activities=activities, + form=form, + ) + + @app.errorhandler(404) def page_not_found(e): return render_template("404.html"), 404 @@ -372,6 +415,21 @@ def internal_server_error(e): return render_template("500.html"), 500 +@app.route("/", methods=["GET", "POST"]) +def index() -> str: + return render_template("index.html") + + +@app.route("/about") +def about() -> str: + return render_template("about.html") + + +@app.route("/new") +def new() -> str: + return render_template("new_checklist.html") + + # keep this as is if __name__ == "__main__": app.run(debug=True) diff --git a/ui/neurovault/README_eCOBIDAS-en.html b/ui/neurovault/README_eCOBIDAS-en.html deleted file mode 100644 index 5d398bc2..00000000 --- a/ui/neurovault/README_eCOBIDAS-en.html +++ /dev/null @@ -1,139 +0,0 @@ -
      -
      -

      COBIDAS Information Collection Protocol

      -

      - The aim of this protocol is to help users collect information related to - the different components of the COBIDAS protocol. -

      -

      How to use it

      -

      - You can navigate each section on the left and then answer the questions - corresponding to your fMRI analysis. This is meant to make sure that you - have not forgotten any of the essential information in the methods and - results parts of your article. -

      -

      - At the end, you can click on Export (bottom left) to get a zip file - containing machine readable json files that captures information about - your method/results section: our next step is to use this to automate the - part of the methods writing and to submit the information alongside data - submission to Neurovault and other data archives. -

      -

      Have any questions? Something is missing? Let us know.

      - -

      Why this project?

      -

      - Poor methods and results description hinders the reproducibility and the - replicability of research. It also makes it hard to compare new and old - results and generally increases inefficiency in the research process. This - project is built on the hope that improving methods and results reporting - could improve our research. -

      -

      - Follow the link if you want to know more about the - motivations behind this project. -

      -

      Background

      -

      - This checklist is a project to make a user friendly checklist out the best - practices - report of - the Committee on Best Practices in Data Analysis and Sharing (COBIDAS) of the - Organization for Human Brain Mapping. -

      -

      - This is very much of a work in progress but the next step is to expand the - list to cover all the items of the COBIDAS report for fMRI as well as for - the recent - extension to EEG and MEG. -

      -

      Want to help?

      -

      - We are currently working on trying to expand the number of items used in - the checklist. All of this work is done in google spreadsheets: the - spreadsheet for each section is accessible by clicking on the - Source - at the top of each page. -

      -

      Want to know more?

      -

      - Most of the information concerning this project can be found on this - github repository. -

      -

      - If you want to be kept posted about the progress of the project, you can - join our - google group -

      -

      - From more frequent updates and behind the scenes, come and join us on the - cobidas_checklist channel on the brainhack - - - channel. - -

      -

      - There is also an [OSF project](https://osf.io/anvqy/) to centralize all - the information and repos. -

      -

      - We have a - list - of short, middle, long term goals: if you are interested by any of those - get in touch. Many of them do not necessarily require super-advanced - technical skills (except maybe a certain love for working with spreadsheet - and wanting them to be super organized). -

      -

      Contributors

      -

      - The list of the people involved in this project can be found - here. -

      -

      License

      -

      The protocol is licensed CC-BY-4.0

      -

      (c) 2020 COBIDAS Contributors

      -
      -
      diff --git a/ui/neurovault/activities/experimental_design/experimental_design_schema.jsonld b/ui/neurovault/activities/experimental_design/experimental_design_schema.jsonld deleted file mode 100644 index 0b3bac44..00000000 --- a/ui/neurovault/activities/experimental_design/experimental_design_schema.jsonld +++ /dev/null @@ -1,129 +0,0 @@ -{ - "@context": "https://raw.githubusercontent.com/ReproNim/reproschema/1.0.0-rc4/contexts/generic", - "@type": "reproschema:Activity", - "@id": "experimental_design_schema.jsonld", - "schemaVersion": "1.0.0-rc4", - "version": "0.0.1", - "prefLabel": { - "en": "Experimental design" - }, - "description": "experimental design", - "preamble": { - "en": "

      Source | Github repository | Reference

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}, - "responseOptions": { - "valueType": "xsd:float", - "unitOptions": [ - { - "prefLabel": { - "en": "seconds" - }, - "value": "seconds" - } - ] - } -} diff --git a/ui/neurovault/activities/experimental_design/items/length_of_runs.jsonld b/ui/neurovault/activities/experimental_design/items/length_of_runs.jsonld deleted file mode 100644 index 95a04ab0..00000000 --- a/ui/neurovault/activities/experimental_design/items/length_of_runs.jsonld +++ /dev/null @@ -1,28 +0,0 @@ -{ - "@context": "https://raw.githubusercontent.com/ReproNim/reproschema/1.0.0-rc4/contexts/generic", - "@type": "reproschema:Field", - "@id": "length_of_runs.jsonld", - "schemaVersion": "1.0.0-rc4", - "version": "0.0.1", - "prefLabel": { - "en": "length of runs" - }, - "description": "length of runs", - "ui": { - "inputType": "float" - }, - "question": { - "en": "1.4 - Length of each imaging run" - }, - "responseOptions": { - "valueType": "xsd:float", - "unitOptions": [ - { - "prefLabel": { - "en": "seconds" - }, - "value": "seconds" - } - ] - } -} diff --git a/ui/neurovault/activities/experimental_design/items/length_of_trials.jsonld b/ui/neurovault/activities/experimental_design/items/length_of_trials.jsonld deleted file mode 100644 index 27e04f68..00000000 --- a/ui/neurovault/activities/experimental_design/items/length_of_trials.jsonld +++ /dev/null @@ -1,28 +0,0 @@ -{ - "@context": "https://raw.githubusercontent.com/ReproNim/reproschema/1.0.0-rc4/contexts/generic", - "@type": "reproschema:Field", - "@id": "length_of_trials.jsonld", - "schemaVersion": "1.0.0-rc4", - "version": "0.0.1", - "prefLabel": { - "en": "length of trials" - }, - "description": "length of trials", - "ui": { - "inputType": "float" - }, - "question": { - "en": "1.6 - Length of individual trials" - }, - "responseOptions": { - "valueType": "xsd:float", - "unitOptions": [ - { - "prefLabel": { - "en": "seconds" - }, - "value": "seconds" - } - ] - } -} diff --git a/ui/neurovault/activities/experimental_design/items/number_of_experimental_units.jsonld b/ui/neurovault/activities/experimental_design/items/number_of_experimental_units.jsonld deleted file mode 100644 index e1e4230f..00000000 --- a/ui/neurovault/activities/experimental_design/items/number_of_experimental_units.jsonld +++ /dev/null @@ -1,20 +0,0 @@ -{ - 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      Source | Github repository | Reference

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      " - } -} diff --git a/ui/neurovault/activities/group_modeling/items/group_model_type.jsonld b/ui/neurovault/activities/group_modeling/items/group_model_type.jsonld deleted file mode 100644 index f1f3b7f6..00000000 --- a/ui/neurovault/activities/group_modeling/items/group_model_type.jsonld +++ /dev/null @@ -1,30 +0,0 @@ -{ - "@context": "https://raw.githubusercontent.com/ReproNim/reproschema/1.0.0-rc4/contexts/generic", - "@type": "reproschema:Field", - "@id": "group_model_type.jsonld", - "schemaVersion": "1.0.0-rc4", - "version": "0.0.1", - "prefLabel": { - "en": "group model type" - }, - "description": "group model type", - "ui": { - "inputType": "select" - }, - "question": { - "en": "7.1 - Type of group model used" - }, - "responseOptions": { - "valueType": "xsd:integer", - "choices": [ - { - "name": { - "en": "Regression" - }, - "value": 0 - } - ], - "minValue": 0, - "maxValue": 0 - } -} diff --git a/ui/neurovault/activities/group_modeling/items/group_modeling_software.jsonld b/ui/neurovault/activities/group_modeling/items/group_modeling_software.jsonld deleted file mode 100644 index 894ef68c..00000000 --- a/ui/neurovault/activities/group_modeling/items/group_modeling_software.jsonld +++ /dev/null @@ -1,23 +0,0 @@ -{ - "@context": "https://raw.githubusercontent.com/ReproNim/reproschema/1.0.0-rc4/contexts/generic", - "@type": "reproschema:Field", - "@id": "group_modeling_software.jsonld", - "schemaVersion": "1.0.0-rc4", - "version": "0.0.1", - "prefLabel": { - "en": "group modeling software" - }, - "description": "group modeling software", - "ui": { - "inputType": "select" - }, - "question": { - "en": "7.3 - Software used for group modeling if different from overall package" - }, - "responseOptions": { - "valueType": "xsd:integer", - "choices": "https://raw.githubusercontent.com/ohbm/cobidas_schema/master/response_options/mri_softwares.jsonld", - "minValue": 0, - "maxValue": 0 - } -} diff --git a/ui/neurovault/activities/group_modeling/items/group_repeated_measures.jsonld b/ui/neurovault/activities/group_modeling/items/group_repeated_measures.jsonld deleted file mode 100644 index 73223aa8..00000000 --- a/ui/neurovault/activities/group_modeling/items/group_repeated_measures.jsonld +++ /dev/null @@ -1,23 +0,0 @@ -{ - "@context": "https://raw.githubusercontent.com/ReproNim/reproschema/1.0.0-rc4/contexts/generic", - "@type": "reproschema:Field", - "@id": "group_repeated_measures.jsonld", - "schemaVersion": "1.0.0-rc4", - "version": "0.0.1", - "prefLabel": { - "en": "group repeated measures" - }, - "description": "group repeated measures", - "ui": { - "inputType": "radio" - }, - "question": { - "en": "7.6 - Was this a repeated measures design at the group level?" - }, - "responseOptions": { - "valueType": "xsd:integer", - "choices": "https://raw.githubusercontent.com/ohbm/cobidas_schema/master/response_options/boolean.jsonld", - "minValue": 0, - "maxValue": 0 - } -} diff --git a/ui/neurovault/activities/group_modeling/items/group_repeated_measures_method.jsonld b/ui/neurovault/activities/group_modeling/items/group_repeated_measures_method.jsonld deleted file mode 100644 index 4bb0bd87..00000000 --- a/ui/neurovault/activities/group_modeling/items/group_repeated_measures_method.jsonld +++ /dev/null @@ -1,17 +0,0 @@ -{ - "@context": "https://raw.githubusercontent.com/ReproNim/reproschema/1.0.0-rc4/contexts/generic", - "@type": "reproschema:Field", - "@id": "group_repeated_measures_method.jsonld", - "schemaVersion": "1.0.0-rc4", - "version": "0.0.1", - "prefLabel": { - "en": "group repeated measures method" - }, - "description": "group repeated measures method", - "ui": { - "inputType": "textarea" - }, - "question": { - "en": "7.7 - If multiple measurements per subject, list method to account for within subject correlation, exact assumptions made about correlation/variance" - } -} diff --git a/ui/neurovault/activities/individual_subject_modeling/individual_subject_modeling_schema.jsonld b/ui/neurovault/activities/individual_subject_modeling/individual_subject_modeling_schema.jsonld deleted file mode 100644 index bdcde850..00000000 --- a/ui/neurovault/activities/individual_subject_modeling/individual_subject_modeling_schema.jsonld +++ /dev/null @@ -1,220 +0,0 @@ -{ - "@context": "https://raw.githubusercontent.com/ReproNim/reproschema/1.0.0-rc4/contexts/generic", - "@type": "reproschema:Activity", - "@id": "individual_subject_modeling_schema.jsonld", - "schemaVersion": "1.0.0-rc4", - "version": "0.0.1", - "prefLabel": { - "en": "Individual subject modeling" - }, - "description": "individual subject modeling", - "preamble": { - "en": "

      Source | Github repository | Reference

      Describe your model specification at the subejct level

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      details
      Define these in terms of task or stimulus conditions (e.g., 'one-back task with objects versus zero-back task with objects') instead of underlying psychological concepts (e.g., 'working memory').
      " - } -} diff --git a/ui/neurovault/activities/individual_subject_modeling/items/hemodynamic_response_function.jsonld b/ui/neurovault/activities/individual_subject_modeling/items/hemodynamic_response_function.jsonld deleted file mode 100644 index e9f259fb..00000000 --- a/ui/neurovault/activities/individual_subject_modeling/items/hemodynamic_response_function.jsonld +++ /dev/null @@ -1,42 +0,0 @@ -{ - "@context": "https://raw.githubusercontent.com/ReproNim/reproschema/1.0.0-rc4/contexts/generic", - "@type": "reproschema:Field", - "@id": "hemodynamic_response_function.jsonld", - "schemaVersion": "1.0.0-rc4", - "version": "0.0.1", - "prefLabel": { - "en": "hemodynamic response function" - }, - "description": "hemodynamic response function", - "ui": { - "inputType": "select" - }, - "question": { - "en": "6.4 - Nature of HRF model" - }, - "responseOptions": { - "valueType": "xsd:integer", - "choices": [ - { - "name": { - "en": "double gamma" - }, - "value": 0 - }, - { - "name": { - "en": "Fourrier set" - 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      Source | Github repository | Reference

      Describe your spatial normalization

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"choices": "https://raw.githubusercontent.com/ohbm/cobidas_schema/master/response_options/mri_softwares.jsonld", - "minValue": 0, - "maxValue": 0 - } -} diff --git a/ui/neurovault/activities/intersubject_registration/items/intersubject_transformation_type.jsonld b/ui/neurovault/activities/intersubject_registration/items/intersubject_transformation_type.jsonld deleted file mode 100644 index c0b5f3f6..00000000 --- a/ui/neurovault/activities/intersubject_registration/items/intersubject_transformation_type.jsonld +++ /dev/null @@ -1,36 +0,0 @@ -{ - "@context": "https://raw.githubusercontent.com/ReproNim/reproschema/1.0.0-rc4/contexts/generic", - "@type": "reproschema:Field", - "@id": "intersubject_transformation_type.jsonld", - "schemaVersion": "1.0.0-rc4", - "version": "0.0.1", - "prefLabel": { - "en": "intersubject transformation type" - }, - "description": "intersubject transformation type", - "ui": { - "inputType": "select" - }, - "question": { - "en": "5.3 - Was linear or nonlinear registration used?" - 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      Source | Github repository | Reference

      Describe your acquisition parameters

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}, - "responseOptions": { - "valueType": "xsd:float" - } -} diff --git a/ui/neurovault/activities/participants/items/subject_age_min.jsonld b/ui/neurovault/activities/participants/items/subject_age_min.jsonld deleted file mode 100644 index 11a58508..00000000 --- a/ui/neurovault/activities/participants/items/subject_age_min.jsonld +++ /dev/null @@ -1,20 +0,0 @@ -{ - "@context": "https://raw.githubusercontent.com/ReproNim/reproschema/1.0.0-rc4/contexts/generic", - "@type": "reproschema:Field", - "@id": "subject_age_min.jsonld", - "schemaVersion": "1.0.0-rc4", - "version": "0.0.1", - "prefLabel": { - "en": "subject age min" - }, - "description": "subject age min", - "ui": { - "inputType": "float" - }, - "question": { - "en": "2.3 - Minimum age of subjects" - }, - "responseOptions": { - "valueType": "xsd:float" - } -} diff --git a/ui/neurovault/activities/participants/participants_schema.jsonld b/ui/neurovault/activities/participants/participants_schema.jsonld deleted file mode 100644 index 8a7c4fe4..00000000 --- a/ui/neurovault/activities/participants/participants_schema.jsonld +++ /dev/null @@ -1,155 +0,0 @@ -{ - 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      Source | Github repository | Reference

      Describe your participant sample

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"@type": "reproschema:Field", - "@id": "SoftwareVersion.jsonld", - "schemaVersion": "1.0.0-rc4", - "version": "0.0.1", - "prefLabel": { - "en": "software version" - }, - "description": "software version", - "ui": { - "inputType": "textarea" - }, - "question": { - "en": "4.2 - Version of software package used" - } -} diff --git a/ui/neurovault/activities/preprocessing/items/b0_unwarping_software.jsonld b/ui/neurovault/activities/preprocessing/items/b0_unwarping_software.jsonld deleted file mode 100644 index b69bf97f..00000000 --- a/ui/neurovault/activities/preprocessing/items/b0_unwarping_software.jsonld +++ /dev/null @@ -1,23 +0,0 @@ -{ - "@context": "https://raw.githubusercontent.com/ReproNim/reproschema/1.0.0-rc4/contexts/generic", - "@type": "reproschema:Field", - "@id": "b0_unwarping_software.jsonld", - "schemaVersion": "1.0.0-rc4", - "version": "0.0.1", - "prefLabel": { - "en": "b0 unwarping software" - }, - "description": "b0 unwarping software", - "ui": { - "inputType": "select" - }, - "question": { - "en": "4.6 - Specify software used for distortion correction if different from the main package" - }, - "responseOptions": { - "valueType": "xsd:integer", - "choices": "https://raw.githubusercontent.com/ohbm/cobidas_schema/master/response_options/mri_softwares.jsonld", - "minValue": 0, - "maxValue": 0 - } -} diff --git a/ui/neurovault/activities/preprocessing/items/motion_correction_interpolation.jsonld b/ui/neurovault/activities/preprocessing/items/motion_correction_interpolation.jsonld deleted file mode 100644 index 5ae21815..00000000 --- a/ui/neurovault/activities/preprocessing/items/motion_correction_interpolation.jsonld +++ /dev/null @@ -1,23 +0,0 @@ -{ - "@context": "https://raw.githubusercontent.com/ReproNim/reproschema/1.0.0-rc4/contexts/generic", - "@type": "reproschema:Field", - "@id": "motion_correction_interpolation.jsonld", - "schemaVersion": "1.0.0-rc4", - "version": "0.0.1", - "prefLabel": { - "en": "motion correction interpolation" - }, - "description": "motion correction interpolation", - "ui": { - "inputType": "select" - }, - "question": { - "en": "4.13 - Interpolation method used for motion correction" - }, - "responseOptions": { - "valueType": "xsd:integer", - "choices": "https://raw.githubusercontent.com/ohbm/cobidas_schema/master/response_options/interpolations.jsonld", - "minValue": 0, - "maxValue": 0 - } -} diff --git a/ui/neurovault/activities/preprocessing/items/motion_correction_metric.jsonld b/ui/neurovault/activities/preprocessing/items/motion_correction_metric.jsonld deleted file mode 100644 index 98ab1c42..00000000 --- a/ui/neurovault/activities/preprocessing/items/motion_correction_metric.jsonld +++ /dev/null @@ -1,23 +0,0 @@ -{ - "@context": "https://raw.githubusercontent.com/ReproNim/reproschema/1.0.0-rc4/contexts/generic", - "@type": "reproschema:Field", - "@id": "motion_correction_metric.jsonld", - "schemaVersion": "1.0.0-rc4", - "version": "0.0.1", - "prefLabel": { - "en": "motion correction metric" - }, - "description": "motion correction metric", - "ui": { - "inputType": "select" - }, - "question": { - "en": "4.12 - Similarity metric used for motion correction" - }, - "responseOptions": { - "valueType": "xsd:integer", - "choices": "https://raw.githubusercontent.com/ohbm/cobidas_schema/master/response_options/cost_functions.jsonld", - "minValue": 0, - "maxValue": 0 - } -} diff --git a/ui/neurovault/activities/preprocessing/items/motion_correction_reference.jsonld b/ui/neurovault/activities/preprocessing/items/motion_correction_reference.jsonld deleted file mode 100644 index 9514078b..00000000 --- a/ui/neurovault/activities/preprocessing/items/motion_correction_reference.jsonld +++ /dev/null @@ -1,17 +0,0 @@ -{ - "@context": "https://raw.githubusercontent.com/ReproNim/reproschema/1.0.0-rc4/contexts/generic", - "@type": "reproschema:Field", - "@id": "motion_correction_reference.jsonld", - "schemaVersion": "1.0.0-rc4", - "version": "0.0.1", - "prefLabel": { - "en": "motion correction reference" - }, - "description": "motion correction reference", - "ui": { - "inputType": "textarea" - }, - "question": { - "en": "4.11 - Reference scan used for motion correction" - } -} diff --git a/ui/neurovault/activities/preprocessing/items/motion_correction_software.jsonld b/ui/neurovault/activities/preprocessing/items/motion_correction_software.jsonld deleted file mode 100644 index 2b07c45c..00000000 --- a/ui/neurovault/activities/preprocessing/items/motion_correction_software.jsonld +++ /dev/null @@ -1,23 +0,0 @@ -{ - "@context": "https://raw.githubusercontent.com/ReproNim/reproschema/1.0.0-rc4/contexts/generic", - "@type": "reproschema:Field", - "@id": "motion_correction_software.jsonld", - "schemaVersion": "1.0.0-rc4", - "version": "0.0.1", - "prefLabel": { - "en": "motion correction software" - }, - "description": "motion correction software", - "ui": { - "inputType": "select" - }, - "question": { - "en": "4.10 - Specify software used for motion correction if different from the main package" - }, - "responseOptions": { - "valueType": "xsd:integer", - "choices": "https://raw.githubusercontent.com/ohbm/cobidas_schema/master/response_options/mri_softwares.jsonld", - "minValue": 0, - "maxValue": 0 - } -} diff --git a/ui/neurovault/activities/preprocessing/items/order_of_preprocessing_operations.jsonld b/ui/neurovault/activities/preprocessing/items/order_of_preprocessing_operations.jsonld deleted file mode 100644 index b7f6a098..00000000 --- a/ui/neurovault/activities/preprocessing/items/order_of_preprocessing_operations.jsonld +++ /dev/null @@ -1,17 +0,0 @@ -{ - "@context": "https://raw.githubusercontent.com/ReproNim/reproschema/1.0.0-rc4/contexts/generic", - "@type": "reproschema:Field", - "@id": "order_of_preprocessing_operations.jsonld", - "schemaVersion": "1.0.0-rc4", - "version": "0.0.1", - "prefLabel": { - "en": "order of preprocessing operations" - }, - "description": "order of preprocessing operations", - "ui": { - "inputType": "textarea" - }, - "question": { - "en": "4.3 - Specify order of preprocessing operations" - } -} diff --git a/ui/neurovault/activities/preprocessing/items/quality_control.jsonld b/ui/neurovault/activities/preprocessing/items/quality_control.jsonld deleted file mode 100644 index db0ab0e2..00000000 --- a/ui/neurovault/activities/preprocessing/items/quality_control.jsonld +++ /dev/null @@ -1,17 +0,0 @@ -{ - "@context": "https://raw.githubusercontent.com/ReproNim/reproschema/1.0.0-rc4/contexts/generic", - "@type": "reproschema:Field", - "@id": "quality_control.jsonld", - "schemaVersion": "1.0.0-rc4", - "version": "0.0.1", - "prefLabel": { - "en": "quality control" - }, - "description": "quality control", - "ui": { - "inputType": "textarea" - }, - "question": { - "en": "4.4 - Describe quality control measures" - } -} diff --git a/ui/neurovault/activities/preprocessing/items/slice_timing_correction_software.jsonld b/ui/neurovault/activities/preprocessing/items/slice_timing_correction_software.jsonld deleted file mode 100644 index 525a1439..00000000 --- a/ui/neurovault/activities/preprocessing/items/slice_timing_correction_software.jsonld +++ /dev/null @@ -1,17 +0,0 @@ -{ - "@context": "https://raw.githubusercontent.com/ReproNim/reproschema/1.0.0-rc4/contexts/generic", - "@type": "reproschema:Field", - "@id": "slice_timing_correction_software.jsonld", - "schemaVersion": "1.0.0-rc4", - "version": "0.0.1", - "prefLabel": { - "en": "slice timing correction software" - }, - "description": "slice timing correction software", - "ui": { - "inputType": "textarea" - }, - "question": { - "en": "4.8 - Specify software used for slice timing correction if different from the main package" - } -} diff --git a/ui/neurovault/activities/preprocessing/items/used_b0_unwarping.jsonld b/ui/neurovault/activities/preprocessing/items/used_b0_unwarping.jsonld deleted file mode 100644 index edaf5c97..00000000 --- a/ui/neurovault/activities/preprocessing/items/used_b0_unwarping.jsonld +++ /dev/null @@ -1,23 +0,0 @@ -{ - "@context": "https://raw.githubusercontent.com/ReproNim/reproschema/1.0.0-rc4/contexts/generic", - "@type": "reproschema:Field", - "@id": "used_b0_unwarping.jsonld", - "schemaVersion": "1.0.0-rc4", - "version": "0.0.1", - "prefLabel": { - "en": "used b0 unwarping" - }, - "description": "used b0 unwarping", - "ui": { - "inputType": "radio" - }, - "question": { - "en": "4.5 - Was B0 distortion correction used?" - }, - "responseOptions": { - "valueType": "xsd:integer", - "choices": "https://raw.githubusercontent.com/ohbm/cobidas_schema/master/response_options/boolean.jsonld", - "minValue": 0, - "maxValue": 0 - } -} diff --git a/ui/neurovault/activities/preprocessing/items/used_motion_correction.jsonld b/ui/neurovault/activities/preprocessing/items/used_motion_correction.jsonld deleted file mode 100644 index 42942532..00000000 --- a/ui/neurovault/activities/preprocessing/items/used_motion_correction.jsonld +++ /dev/null @@ -1,23 +0,0 @@ -{ - "@context": "https://raw.githubusercontent.com/ReproNim/reproschema/1.0.0-rc4/contexts/generic", - "@type": "reproschema:Field", - "@id": "used_motion_correction.jsonld", - "schemaVersion": "1.0.0-rc4", - "version": "0.0.1", - "prefLabel": { - "en": "used motion correction" - }, - "description": "used motion correction", - "ui": { - "inputType": "radio" - }, - "question": { - "en": "4.9 - Was motion correction used?" - }, - "responseOptions": { - "valueType": "xsd:integer", - "choices": "https://raw.githubusercontent.com/ohbm/cobidas_schema/master/response_options/boolean.jsonld", - "minValue": 0, - "maxValue": 0 - } -} diff --git a/ui/neurovault/activities/preprocessing/items/used_motion_susceptibiity_correction.jsonld b/ui/neurovault/activities/preprocessing/items/used_motion_susceptibiity_correction.jsonld deleted file mode 100644 index 00c086b5..00000000 --- a/ui/neurovault/activities/preprocessing/items/used_motion_susceptibiity_correction.jsonld +++ /dev/null @@ -1,23 +0,0 @@ -{ - "@context": "https://raw.githubusercontent.com/ReproNim/reproschema/1.0.0-rc4/contexts/generic", - "@type": "reproschema:Field", - "@id": "used_motion_susceptibiity_correction.jsonld", - "schemaVersion": "1.0.0-rc4", - "version": "0.0.1", - "prefLabel": { - "en": "used motion susceptibiity correction" - }, - "description": "used motion susceptibiity correction", - "ui": { - "inputType": "radio" - }, - "question": { - "en": "4.14 - Was motion-susceptibility correction used?" - }, - "responseOptions": { - "valueType": "xsd:integer", - "choices": "https://raw.githubusercontent.com/ohbm/cobidas_schema/master/response_options/boolean.jsonld", - "minValue": 0, - "maxValue": 0 - } -} diff --git a/ui/neurovault/activities/preprocessing/items/used_slice_timing_correction.jsonld b/ui/neurovault/activities/preprocessing/items/used_slice_timing_correction.jsonld deleted file mode 100644 index a5d8c55e..00000000 --- a/ui/neurovault/activities/preprocessing/items/used_slice_timing_correction.jsonld +++ /dev/null @@ -1,23 +0,0 @@ -{ - "@context": "https://raw.githubusercontent.com/ReproNim/reproschema/1.0.0-rc4/contexts/generic", - "@type": "reproschema:Field", - "@id": "used_slice_timing_correction.jsonld", - "schemaVersion": "1.0.0-rc4", - "version": "0.0.1", - "prefLabel": { - "en": "used slice timing correction" - }, - "description": "used slice timing correction", - "ui": { - "inputType": "radio" - }, - "question": { - "en": "4.7 - Was slice timing correction used?" - }, - "responseOptions": { - "valueType": "xsd:integer", - "choices": "https://raw.githubusercontent.com/ohbm/cobidas_schema/master/response_options/boolean.jsonld", - "minValue": 0, - "maxValue": 0 - } -} diff --git a/ui/neurovault/activities/preprocessing/preprocessing_schema.jsonld b/ui/neurovault/activities/preprocessing/preprocessing_schema.jsonld deleted file mode 100644 index 81b02fa5..00000000 --- a/ui/neurovault/activities/preprocessing/preprocessing_schema.jsonld +++ /dev/null @@ -1,207 +0,0 @@ -{ - "@context": "https://raw.githubusercontent.com/ReproNim/reproschema/1.0.0-rc4/contexts/generic", - "@type": "reproschema:Activity", - "@id": "preprocessing_schema.jsonld", - "schemaVersion": "1.0.0-rc4", - "version": "0.0.1", - "prefLabel": { - "en": "Preprocessing" - }, - "description": "preprocessing", - "preamble": { - "en": "

      Source | Github repository | Reference

      Describe your preprocessing

      " - }, - "ui": { - "shuffle": false, - "order": [ - "items/SoftwareName.jsonld", - "items/SoftwareVersion.jsonld", - "items/order_of_preprocessing_operations.jsonld", - "items/quality_control.jsonld", - "items/used_b0_unwarping.jsonld", - "items/b0_unwarping_software.jsonld", - "items/used_slice_timing_correction.jsonld", - "items/slice_timing_correction_software.jsonld", - "items/used_motion_correction.jsonld", - "items/motion_correction_software.jsonld", - "items/motion_correction_reference.jsonld", - "items/motion_correction_metric.jsonld", - "items/motion_correction_interpolation.jsonld", - "items/used_motion_susceptibiity_correction.jsonld" - ], - "addProperties": [ - { - "variableName": "SoftwareName", - "isAbout": "items/SoftwareName.jsonld", - "prefLabel": { - "en": "software package" - }, - "isVis": true, - "requiredValue": false, - "allow": [ - "reproschema:Skipped" - ] - }, - { - "variableName": "SoftwareVersion", - "isAbout": "items/SoftwareVersion.jsonld", - "prefLabel": { - "en": "software version" - }, - "isVis": true, - "requiredValue": false, - "allow": [ - "reproschema:Skipped" - ] - }, - { - "variableName": "order_of_preprocessing_operations", - "isAbout": "items/order_of_preprocessing_operations.jsonld", - "prefLabel": { - "en": "order of preprocessing operations" - }, - "isVis": true, - "requiredValue": false, - "allow": [ - "reproschema:Skipped" - ] - }, - { - "variableName": "quality_control", - "isAbout": "items/quality_control.jsonld", - "prefLabel": { - "en": "quality control" - }, - "isVis": true, - "requiredValue": false, - "allow": [ - "reproschema:Skipped" - ] - }, - { - "variableName": "used_b0_unwarping", - "isAbout": "items/used_b0_unwarping.jsonld", - "prefLabel": { - "en": "used b0 unwarping" - }, - "isVis": true, - "requiredValue": false, - "allow": [ - "reproschema:Skipped" - ] - }, - { - "variableName": "b0_unwarping_software", - "isAbout": "items/b0_unwarping_software.jsonld", - "prefLabel": { - "en": "b0 unwarping software" - }, - "isVis": "used_b0_unwarping == 1", - "requiredValue": false, - "allow": [ - "reproschema:Skipped" - ] - }, - { - "variableName": "used_slice_timing_correction", - "isAbout": "items/used_slice_timing_correction.jsonld", - "prefLabel": { - "en": "used slice timing correction" - }, - "isVis": true, - "requiredValue": false, - "allow": [ - "reproschema:Skipped" - ] - }, - { - "variableName": "slice_timing_correction_software", - "isAbout": "items/slice_timing_correction_software.jsonld", - "prefLabel": { - "en": "slice timing correction software" - }, - "isVis": "used_slice_timing_correction == 1", - "requiredValue": false, - "allow": [ - "reproschema:Skipped" - ] - }, - { - "variableName": "used_motion_correction", - "isAbout": "items/used_motion_correction.jsonld", - "prefLabel": { - "en": "used motion correction" - }, - "isVis": true, - "requiredValue": false, - "allow": [ - "reproschema:Skipped" - ] - }, - { - "variableName": "motion_correction_software", - "isAbout": "items/motion_correction_software.jsonld", - "prefLabel": { - "en": "motion correction software" - }, - "isVis": "used_motion_correction == 1", - "requiredValue": false, - "allow": [ - "reproschema:Skipped" - ] - }, - { - "variableName": "motion_correction_reference", - "isAbout": "items/motion_correction_reference.jsonld", - "prefLabel": { - "en": "motion correction reference" - }, - "isVis": "used_motion_correction == 1", - "requiredValue": false, - "allow": [ - "reproschema:Skipped" - ] - }, - { - "variableName": "motion_correction_metric", - "isAbout": "items/motion_correction_metric.jsonld", - "prefLabel": { - "en": "motion correction metric" - }, - "isVis": "used_motion_correction == 1", - "requiredValue": false, - "allow": [ - "reproschema:Skipped" - ] - }, - { - "variableName": "motion_correction_interpolation", - "isAbout": "items/motion_correction_interpolation.jsonld", - "prefLabel": { - "en": "motion correction interpolation" - }, - "isVis": "used_motion_correction == 1", - "requiredValue": false, - "allow": [ - "reproschema:Skipped" - ] - }, - { - "variableName": "used_motion_susceptibiity_correction", - "isAbout": "items/used_motion_susceptibiity_correction.jsonld", - "prefLabel": { - "en": "used motion susceptibiity correction" - }, - "isVis": true, - "requiredValue": false, - "allow": [ - "reproschema:Skipped" - ] - } - ], - "allow": [ - "reproschema:AutoAdvance", - "reproschema:AllowExport" - ] - } -} diff --git a/ui/neurovault/protocols/neurovault_schema.jsonld b/ui/neurovault/protocols/neurovault_schema.jsonld deleted file mode 100644 index af243448..00000000 --- a/ui/neurovault/protocols/neurovault_schema.jsonld +++ /dev/null @@ -1,133 +0,0 @@ -{ - "@context": "https://raw.githubusercontent.com/ReproNim/reproschema/1.0.0-rc4/contexts/generic", - "@type": "reproschema:Protocol", - "@id": "neurovault_schema.jsonld", - "schemaVersion": "1.0.0-rc4", - "version": "0.0.1", - "prefLabel": { - "en": "neurovault" - }, - "description": "neurovault", - "preamble": { - "en": "" - }, - "ui": { - "shuffle": false, - "order": [ - "../activities/experimental_design/experimental_design_schema.jsonld", - "../activities/participants/participants_schema.jsonld", - "../activities/mri_acquisition/mri_acquisition_schema.jsonld", - "../activities/preprocessing/preprocessing_schema.jsonld", - "../activities/intersubject_registration/intersubject_registration_schema.jsonld", - "../activities/individual_subject_modeling/individual_subject_modeling_schema.jsonld", - "../activities/group_modeling/group_modeling_schema.jsonld", - "../activities/group_inference/group_inference_schema.jsonld" - ], - "addProperties": [ - { - "variableName": "experimental_design", - "isAbout": "../activities/experimental_design/experimental_design_schema.jsonld", - "prefLabel": { - "en": "Experimental design" - }, - "isVis": true, - "requiredValue": false, - "allow": [ - "reproschema:Skipped" - ] - }, - { - "variableName": "participants", - "isAbout": "../activities/participants/participants_schema.jsonld", - "prefLabel": { - "en": "Participants" - }, - "isVis": true, - "requiredValue": false, - "allow": [ - "reproschema:Skipped" - ] - }, - { - "variableName": "mri_acquisition", - "isAbout": "../activities/mri_acquisition/mri_acquisition_schema.jsonld", - "prefLabel": { - "en": "MRI acquisition" - }, - "isVis": true, - "requiredValue": false, - "allow": [ - "reproschema:Skipped" - ] - }, - { - "variableName": "preprocessing", - "isAbout": "../activities/preprocessing/preprocessing_schema.jsonld", - "prefLabel": { - "en": "Preprocessing" - }, - "isVis": true, - "requiredValue": false, - "allow": [ - "reproschema:Skipped" - ] - }, - { - "variableName": "intersubject_registration", - "isAbout": "../activities/intersubject_registration/intersubject_registration_schema.jsonld", - "prefLabel": { - "en": "Intersubject registration" - }, - "isVis": true, - "requiredValue": false, - "allow": [ - "reproschema:Skipped" - ] - }, - { - "variableName": "individual_subject_modeling", - "isAbout": "../activities/individual_subject_modeling/individual_subject_modeling_schema.jsonld", - "prefLabel": { - "en": "Individual subject modeling" - }, - "isVis": true, - "requiredValue": false, - "allow": [ - "reproschema:Skipped" - ] - }, - { - "variableName": "group_modeling", - "isAbout": "../activities/group_modeling/group_modeling_schema.jsonld", - "prefLabel": { - "en": "Group modeling" - }, - "isVis": true, - "requiredValue": false, - "allow": [ - "reproschema:Skipped" - ] - }, - { - "variableName": "group_inference", - "isAbout": "../activities/group_inference/group_inference_schema.jsonld", - "prefLabel": { - "en": "Group inference" - }, - "isVis": true, - "requiredValue": false, - "allow": [ - "reproschema:Skipped" - ] - } - ], - "allow": [ - "reproschema:AutoAdvance", - "reproschema:AllowExport" - ] - }, - "landingPage": { - "@id": "../README_eCOBIDAS-en.html", - "inLanguage": "en" - } -} diff --git a/ui/static/style.css b/ui/static/style.css new file mode 100644 index 00000000..f218de1e --- /dev/null +++ b/ui/static/style.css @@ -0,0 +1,3 @@ +body { + background: #e8f1f9; +} diff --git a/ui/templates/base.html b/ui/templates/base.html index bee7f598..b61cd454 100644 --- a/ui/templates/base.html +++ b/ui/templates/base.html @@ -8,17 +8,18 @@ {{ bootstrap.load_css() }} - + +
      {% block header %}{% endblock %}
      +
      @@ -28,43 +29,45 @@

      eCOBIDAS

      - +
      + +
      {% block content %} {% endblock %}
      From a87de833f26c3ba9c500f66fca573e7369314cfd Mon Sep 17 00:00:00 2001 From: Remi Gau Date: Wed, 22 May 2024 15:04:52 -0400 Subject: [PATCH 07/31] add min and max value for int and float --- ecobidas/create_schema.py | 1 + ecobidas/inputs/data-dictionary.json | 2 +- ecobidas/inputs/neurovault/neurovault.tsv | 42 +++++++++++------------ ecobidas/item.py | 21 ++++++++++++ ui/app.py | 11 ++++++ ui/templates/protocol.html | 13 +++++++ 6 files changed, 68 insertions(+), 22 deletions(-) diff --git a/ecobidas/create_schema.py b/ecobidas/create_schema.py index ad0ddedd..d113b782 100644 --- a/ecobidas/create_schema.py +++ b/ecobidas/create_schema.py @@ -90,6 +90,7 @@ def create_schema( print_item_info(activity_idx, item_idx, item_info) item = define_new_item(item_info) + item.write(os.path.join(activity_path, "items")) activity.append_item(item) diff --git a/ecobidas/inputs/data-dictionary.json b/ecobidas/inputs/data-dictionary.json index faaf664a..121dd087 100644 --- a/ecobidas/inputs/data-dictionary.json +++ b/ecobidas/inputs/data-dictionary.json @@ -80,7 +80,7 @@ }, "choices": { "VariableName": "choices", - "Description": "list of possible responses", + "Description": "List of possible responses. Options are separated by a pipe '|'. For integers, floats, and sliders, the values represent min | max | step. If they are not provided, it should be assumed that they ar None or null.", "RequirementLevel": "required" }, "mandatory": { diff --git a/ecobidas/inputs/neurovault/neurovault.tsv b/ecobidas/inputs/neurovault/neurovault.tsv index 5e72b5ab..c9f12a45 100644 --- a/ecobidas/inputs/neurovault/neurovault.tsv +++ b/ecobidas/inputs/neurovault/neurovault.tsv @@ -1,36 +1,36 @@ activity_pref_label activity_order item_order question unit details field_type choices item item_pref_label visibility item_description include mandatory preamble bids_status bids_file bids_key bids_key_for_unit -Experimental design 1 1 Type of design select blocked | event_related | hybrid block/event type of design 1 type of design 1 1 Describe your experimental design -Experimental design 1 2 Number of imaging runs acquired integer number of imaging runs 1 number of imaging runs 1 2 -Experimental design 1 3 Number of blocks, trials or experimental units per imaging run integer number of experimental units 1 number of experimental units 1 2 -Experimental design 1 4 Length of each imaging run seconds float length of runs 1 length of runs 1 2 -Experimental design 1 5 For blocked designs, length of blocks seconds float length of blocks 1 length of blocks 1 2 -Experimental design 1 6 Length of individual trials seconds float length of trials 1 length of trials 1 2 +Experimental design 1 1 Type of design select blocked | event_related | hybrid block/event type_of_design type of design 1 type of design 1 1 Describe your experimental design +Experimental design 1 2 Number of imaging runs acquired integer 0 number of imaging runs 1 number of imaging runs 1 2 +Experimental design 1 3 Number of blocks, trials or experimental units per imaging run integer 0 number of experimental units 1 number of experimental units 1 2 +Experimental design 1 4 Length of each imaging run seconds float 0 length of runs 1 length of runs 1 2 +Experimental design 1 5 For blocked designs, length of blocks seconds float 0 length of blocks type_of_design in [0, 2] length of blocks 1 2 +Experimental design 1 6 Length of individual trials seconds float 0 length of trials 1 length of trials 1 2 Experimental design 1 7 Was the design optimized for efficiency? radio preset:boolean optimization 1 optimization 1 2 Experimental design 1 8 What method was used for optimization? textarea optimization method optimization == 1 optimization method 1 3 -Participants 2 1 Number of subjects entering into the analysis integer number of subjects 1 number of subjects 1 1 Describe your participant sample -Participants 2 2 Mean age of subjects float subject age mean 1 subject age mean 1 1 -Participants 2 3 Minimum age of subjects float subject age min 1 subject age min 1 2 -Participants 2 4 Maximum age of subjects float subject age max 1 subject age max 1 2 +Participants 2 1 Number of subjects entering into the analysis integer 0 number of subjects 1 number of subjects 1 1 Describe your participant sample +Participants 2 2 Mean age of subjects float 0 subject age mean 1 subject age mean 1 1 +Participants 2 3 Minimum age of subjects float 0 subject age min 1 subject age min 1 2 +Participants 2 4 Maximum age of subjects float 0 subject age max 1 subject age max 1 2 Participants 2 5 Handedness of subjects radio right | left | both handedness 1 handedness 1 2 -Participants 2 6 The proportion of subjects who were male slider 0 | 100 | 20 proportion male subjects 1 proportion male subjects 1 2 +Participants 2 6 The proportion of subjects who were male float 0 | 1 proportion male subjects 1 proportion male subjects 1 2 Participants 2 7 Additional inclusion/exclusion criteria, if any. Including specific sampling strategies that limit inclusion to a specific group, such as laboratory members. textarea inclusion exclusion criteria 1 inclusion exclusion criteria 1 3 -Participants 2 8 Number of subjects scanned but rejected from analysis integer number of rejected subjects 1 number of rejected subjects 1 2 +Participants 2 8 Number of subjects scanned but rejected from analysis integer 0 number of rejected subjects 1 number of rejected subjects 1 2 Participants 2 9 Was this study a comparison between subject groups? radio preset:boolean group comparison 1 group comparison 1 1 Participants 2 10 A description of the groups being compared textarea group description group_comparison == 1 group description 1 2 MRI acquisition 3 1 Manufacturer of MRI scanner select Siemens | Philips | General Electric Manufacturer scanner make 1 scanner make 1 1 Describe your acquisition parameters MRI acquisition 3 2 Model of MRI scanner textarea ManufacturersModelName scanner model 1 scanner model 1 1 -MRI acquisition 3 3 Field strength of MRI scanner Tesla float MagneticFieldStrength field strength 1 field strength 1 1 +MRI acquisition 3 3 Field strength of MRI scanner Tesla float 0 MagneticFieldStrength field strength 1 field strength 1 1 MRI acquisition 3 4 Description of pulse sequence used for fMRI select Gradient echo | Spin echo | Mutliband gradient echo | MPRAGE | MP2RAGE | FLASH PulseSequenceType pulse sequence 1 pulse sequence 1 1 MRI acquisition 3 5 Description of parallel imaging method and parameters textarea parallel imaging 1 parallel imaging 1 3 MRI acquisition 3 6 Imaging field of view Millimeters float field of view 1 field of view 1 2 MRI acquisition 3 7 Matrix size for MRI acquisition integer matrix size 1 matrix size 1 2 -MRI acquisition 3 8 Distance between slices (includes skip or distance factor). Millimeters float slice thickness 1 slice thickness 1 1 -MRI acquisition 3 9 The size of the skipped area between slices. Millimeters float skip factor 1 skip factor 1 2 +MRI acquisition 3 8 Distance between slices (includes skip or distance factor). Millimeters float 0 slice thickness 1 slice thickness 1 1 +MRI acquisition 3 9 The size of the skipped area between slices. Millimeters float 0 skip factor 1 skip factor 1 2 MRI acquisition 3 10 The orientation of slices radio axial | sagittal | frontal acquisition orientation 1 acquisition orientation 1 2 MRI acquisition 3 11 Order of acquisition of slices select ascending | descending | interleaved SliceTiming order of acquisition 1 order of acquisition 1 3 -MRI acquisition 3 12 Repetition time (TR) Milliseconds float RepetitionTime repetition time 1 repetition time 1 1 -MRI acquisition 3 13 Echo time (TE) Milliseconds float EchoTime echo time 1 echo time 1 1 -MRI acquisition 3 14 Flip angle Degrees float FlipAngle flip angle 1 flip angle 1 2 +MRI acquisition 3 12 Repetition time (TR) Milliseconds float 0 RepetitionTime repetition time 1 repetition time 1 1 +MRI acquisition 3 13 Echo time (TE) Milliseconds float 0 EchoTime echo time 1 echo time 1 1 +MRI acquisition 3 14 Flip angle Degrees float 0 FlipAngle flip angle 1 flip angle 1 2 Preprocessing 4 1 If a single software package was used for all analyses, specify that here select preset:mri_softwares SoftwareName software package 1 software package 1 1 Describe your preprocessing Preprocessing 4 2 Version of software package used textarea SoftwareVersion software version 1 software version 1 1 Preprocessing 4 3 Specify order of preprocessing operations textarea order of preprocessing operations 1 order of preprocessing operations 1 2 @@ -56,11 +56,11 @@ Intersubject registration 5 8 Were the functional images coregistered to the sub Intersubject registration 5 9 Method used to coregister functional to structural images textarea functional coregistration method functional_coregistered_to_structural == 1 functional coregistration method 1 3 Intersubject registration 5 10 Name of coordinate space for registration target select MNI | Talairach | MNI2Tal coordinate space 1 coordinate space 1 1 Intersubject registration 5 11 Name of target template image textarea target template image 1 target template image 1 2 -Intersubject registration 5 12 Voxel size of target template Millimeters float target resolution 1 target resolution 1 1 +Intersubject registration 5 12 Voxel size of target template Millimeters float 0 target resolution 1 target resolution 1 1 Intersubject registration 5 13 Was spatial smoothing applied? radio preset:boolean used smoothing 1 used smoothing 1 1 Intersubject registration 5 14 Describe the type of smoothing applied text smoothing type used_smoothing == 1 smoothing type 1 1 Intersubject registration 5 15 The full-width at half-maximum of the smoothing kernel Millimeters float smoothing fwhm used_smoothing == 1 smoothing fwhm 1 1 -Intersubject registration 5 16 Voxel size in mm of the resampled, atlas-space images float resampled voxel size 1 resampled voxel size 1 1 +Intersubject registration 5 16 Voxel size in mm of the resampled, atlas-space images float 0 resampled voxel size 1 resampled voxel size 1 1 Individual subject modeling 6 1 Type of group model used radio Regression intrasubject model type 1 intrasubject model type 1 1 Describe your model specification at the subejct level Individual subject modeling 6 2 Estimation method used for model select ordinary least squares | generalized least squares intrasubject estimation type 1 intrasubject estimation type 1 1 Individual subject modeling 6 3 Software used for intrasubject modeling if different from overall package select preset:mri_softwares intrasubject modeling software 1 intrasubject modeling software 1 2 @@ -85,4 +85,4 @@ Group modeling 7 6 Was this a repeated measures design at the group level? rad Group modeling 7 7 If multiple measurements per subject, list method to account for within subject correlation, exact assumptions made about correlation/variance textarea group repeated measures method group_repeated_measures == 1 group repeated measures method 1 3 Group inference 8 1 Type of statistic that is the basis of the inference select Z | T | F | X2 | PostProb | NonparametricP | MonteCarloP group statistic type 1 group statistic type 1 2 Describe your statistical inference Group inference 8 2 Parameters of the null distribution of the test statisic. Typically degrees of freedom (should be clear from the test statistic what these are). float group statistic parameters 1 group statistic parameters 1 1 -Group inference 8 3 Noise smoothness for statistical inference This is the estimated smoothness used with Random Field Theory or a simulation-based inference method. float group smoothness fwhm 1 group smoothness fwhm 1 1 +Group inference 8 3 Noise smoothness for statistical inference This is the estimated smoothness used with Random Field Theory or a simulation-based inference method. float 0 group smoothness fwhm 1 group smoothness fwhm 1 1 diff --git a/ecobidas/item.py b/ecobidas/item.py index 603f5f37..abbe7505 100644 --- a/ecobidas/item.py +++ b/ecobidas/item.py @@ -1,5 +1,6 @@ import re +from loguru import logger from numpy import isnan, linspace from reproschema.models.item import Item, ResponseOption @@ -174,6 +175,26 @@ def define_choices(item: Item, field_type: str, choices: list) -> Item: if field_type in {"multitext", "text"}: return item + if field_type in {"int", "float"}: + if field_type == "int": + field_type = "integer" + + response_options = ResponseOption() + response_options.set_valueType(field_type) + + if choices and isinstance(choices, list): + min_value = int(choices[0]) + response_options.set_min(min_value) + if len(choices) > 1: + max_value = int(choices[1]) + response_options.set_max(max_value) + else: + logger.warning(f"No min or max value defined for {field_type} item.") + + item.set_input_type(response_options) + + return item + elif field_type == "slider": response_options = slider_response(choices) item.set_input_type(response_options) diff --git a/ui/app.py b/ui/app.py index ae4077e1..ec5305ec 100644 --- a/ui/app.py +++ b/ui/app.py @@ -382,10 +382,14 @@ def activity(protocol_name, activity_name) -> str: form = generate_form(items=items, prefix=activity_name) if request.method == "POST" and form.is_submitted(): + items = update_visibility(items, form) items = update_format(items, form) form = generate_form(items, prefix=activity_name) + completed_items = sum(bool(i["is_answered"]) for i in items.values()) + nb_items = sum(bool(i["visibility"]) for i in items.values()) + return render_template( "protocol.html", protocol_pref_label=protocol_name, @@ -393,8 +397,13 @@ def activity(protocol_name, activity_name) -> str: activity_preamble=Markup(activity["preamble"][LANG]), activities=activities, form=form, + nb_items=nb_items, + completed_items=completed_items, ) + completed_items = sum(bool(i["is_answered"]) for i in items.values()) + nb_items = sum(bool(i["visibility"]) for i in items.values()) + return render_template( "protocol.html", protocol_pref_label=protocol_name, @@ -402,6 +411,8 @@ def activity(protocol_name, activity_name) -> str: activity_preamble=Markup(activity["preamble"][LANG]), activities=activities, form=form, + nb_items=nb_items, + completed_items=completed_items, ) diff --git a/ui/templates/protocol.html b/ui/templates/protocol.html index 7d6d6492..8db0f8f5 100644 --- a/ui/templates/protocol.html +++ b/ui/templates/protocol.html @@ -21,6 +21,19 @@

      {{ protocol_pref_label }}

      {% if landing_page %} {{ landing_page }} {% else %}

      {{ activity_pref_label }}

      +

      + +
      + +

      + {{ activity_preamble }} {{ render_form(form) }} {% endif %}
      From 4337accfa8ec416774decb22db6859b11e15b20c Mon Sep 17 00:00:00 2001 From: Remi Gau Date: Wed, 22 May 2024 18:06:53 -0400 Subject: [PATCH 08/31] add min max to float and refactor ui --- ecobidas/inputs/pet/pet.tsv | 6 +- ecobidas/item.py | 2 - ui/app.py | 116 ++++++++++++++++++++++++------------ ui/static/style.css | 2 +- ui/templates/base.html | 103 ++++++++++++++++++-------------- ui/templates/protocol.html | 47 +++++++++------ 6 files changed, 169 insertions(+), 107 deletions(-) diff --git a/ecobidas/inputs/pet/pet.tsv b/ecobidas/inputs/pet/pet.tsv index 773c0f74..32f8fc6d 100644 --- a/ecobidas/inputs/pet/pet.tsv +++ b/ecobidas/inputs/pet/pet.tsv @@ -57,10 +57,10 @@ activity_order question details field_type choices unit item item_order visibili 5 Reconstruction data labels select sampleStartTime | sampleDuration | activity | activitySD reconstruction_data_labels 18 1 reconstruction data labels reconstruction data labels 1 1 Data Acquisition Reconstruction Reconstruction 0 5 Reference paper for the attenuation correction method used. textarea AttenuationCorrectionMethodReference 19 1 AttenuationCorrectionMethodReference AttenuationCorrectionMethodReference 1 2 Data Acquisition Reconstruction Reconstruction 1 _pet.json AttenuationCorrectionMethodReference 6 Boolean that specifies if continuous blood measurements are available. radio preset:boolean ContinuousBloodAvail 1 1 ContinuousBloodAvail ContinuousBloodAvail 1 1 Radioligand Continuous blood Continuous blood 1 _pet.json ContinuousBloodAvail -6 The rate at which the blood was withdrawn from the subject. float ml/s ContinuousBloodWithdrawalRate 2 ContinuousBloodAvail == 1 ContinuousBloodWithdrawalRate ContinuousBloodWithdrawalRate 1 2 Radioligand Continuous blood Continuous blood 1 _pet.json ContinuousBloodWithdrawalRate +6 The rate at which the blood was withdrawn from the subject. float ml/s ContinuousBloodWithdrawalRate 2 ContinuousBloodAvail == 1 ContinuousBloodWithdrawalRate ContinuousBloodWithdrawalRate 1 2 Radioligand Continuous blood Continuous blood 1 _pet.json ContinuousBloodWithdrawalRate 6 Description of the type of tubing used, ideally including the material and (internal) diameter. textarea ContinuousBloodTubingType 3 ContinuousBloodAvail == 1 ContinuousBloodTubingType ContinuousBloodTubingType 1 2 Radioligand Continuous blood Continuous blood 1 _pet.json ContinuousBloodTubingType -6 The length of the blood tubing, from the subject to the detector. float cm ContinuousBloodTubingLength 4 ContinuousBloodAvail == 1 ContinuousBloodTubingLength ContinuousBloodTubingLength 1 2 Radioligand Continuous blood Continuous blood 1 _pet.json ContinuousBloodTubingLength -6 External dispersion time constant resulting from tubing. float s ContinuousBloodDispersionConstant 5 ContinuousBloodAvail == 1 ContinuousBloodDispersionConstant ContinuousBloodDispersionConstant 1 2 Radioligand Continuous blood Continuous blood 1 _pet.json ContinuousBloodDispersionConstant +6 The length of the blood tubing, from the subject to the detector. float cm ContinuousBloodTubingLength 4 ContinuousBloodAvail == 1 ContinuousBloodTubingLength ContinuousBloodTubingLength 1 2 Radioligand Continuous blood Continuous blood 1 _pet.json ContinuousBloodTubingLength +6 External dispersion time constant resulting from tubing. float s ContinuousBloodDispersionConstant 5 ContinuousBloodAvail == 1 ContinuousBloodDispersionConstant ContinuousBloodDispersionConstant 1 2 Radioligand Continuous blood Continuous blood 1 _pet.json ContinuousBloodDispersionConstant 6 Dispersion correction Boolean flag specifying whether the continuous blood radio preset:boolean ContinuousBloodDispersionCorrected 6 ContinuousBloodAvail == 1 ContinuousBloodDispersionCorrected ContinuousBloodDispersionCorrected 1 1 Radioligand Continuous blood Continuous blood 1 _pet.json ContinuousBloodDispersionCorrected 6 Boolean that specifies if discrete blood measurements are available. Boolean that specifies if discrete blood measurements are available. radio preset:boolean DiscreteBloodAvail 7 1 DiscreteBloodAvail DiscreteBloodAvail 1 1 Radioligand Discrete blood Discrete blood 1 _pet.json DiscreteBloodAvail 6 Measured haematocrit, i.e. the volume of erythrocytes divided by the volume of whole blood. slider 0 | 1 DiscreteBloodHaematocrit 8 DiscreteBloodAvail == 1 DiscreteBloodHaematocrit DiscreteBloodHaematocrit 1 2 Radioligand Discrete blood Discrete blood 1 _pet.json DiscreteBloodHaematocrit diff --git a/ecobidas/item.py b/ecobidas/item.py index abbe7505..2cc00bad 100644 --- a/ecobidas/item.py +++ b/ecobidas/item.py @@ -235,8 +235,6 @@ def slider_response(choices: list) -> ResponseOption: response_options.set_max(1) response_options.set_max(steps - 1) - linspace(min, max, steps) - # TODO update after render off slide item has been improved for i, opt in enumerate(linspace(min, max, steps)): response_options.add_choice(f"{opt:.3f}", i) diff --git a/ui/app.py b/ui/app.py index ec5305ec..942d3a63 100644 --- a/ui/app.py +++ b/ui/app.py @@ -114,9 +114,11 @@ class DyanmicForm(FlaskForm): for item_name, item in items.items(): - render_kw = {"style": "border-color: red; border-width: 2px;"} - if item["is_answered"]: - render_kw = {"style": "border-color: green; border-width: 2px;"} + render_kw = ( + {"style": "border-color: green; border-width: 2px;"} + if item["is_answered"] + else {"style": "border-color: red; border-width: 2px;"} + ) validators = [] if item["required"]: @@ -143,8 +145,6 @@ class DyanmicForm(FlaskForm): if input_type == "date": - print(item_name) - FieldType = DateField setattr( @@ -166,11 +166,20 @@ class DyanmicForm(FlaskForm): FieldType = StringField if input_type == "number": FieldType = IntegerField - elif input_type in ["float"]: + elif input_type == "float": FieldType = DecimalField elif input_type == "textarea": FieldType = TextAreaField + if input_type in ["number", "float"]: + minimum = item["min"] + maximum = item["max"] + validators.append(NumberRange(min=minimum, max=maximum)) + if minimum is not None and maximum is not None: + question += f" ({minimum=}, {maximum=})" + elif minimum is not None: + question += f" ({minimum=})" + setattr( form, item_name, @@ -214,33 +223,54 @@ class DyanmicForm(FlaskForm): else: - is_multiple = item["is_multiple"] - - if is_multiple: - FieldType = SelectMultipleField - elif input_type == "select": - FieldType = SelectField - elif input_type == "radio": - FieldType = RadioField - - setattr( - form, - item_name, - FieldType( - Markup(question), - validators=validators, - description=item["description"], - choices=item["choices"], - _prefix=prefix, - render_kw=render_kw, - ), - ) + form = add_choice_based_items(form, prefix, item_name, item) setattr(form, "submit", SubmitField("Save")) # noqa B010 return form() +def add_choice_based_items(form, prefix, item_name, item): + + question = f"{item['question']} {item['unit']}" + + input_type = item["input_type"] + + render_kw = ( + {"style": "border-color: green; border-width: 2px;"} + if item["is_answered"] + else {"style": "border-color: red; border-width: 2px;"} + ) + + validators = [] + if item["required"]: + validators.append(DataRequired()) + + is_multiple = item["is_multiple"] + + if is_multiple: + FieldType = SelectMultipleField + elif input_type == "select": + FieldType = SelectField + elif input_type == "radio": + FieldType = RadioField + + setattr( + form, + item_name, + FieldType( + Markup(question), + validators=validators, + description=item["description"], + choices=item["choices"], + _prefix=prefix, + render_kw=render_kw, + ), + ) + + return form + + @lru_cache def get_items_for_activity(activity_file): with open(activity_file) as f: @@ -275,17 +305,27 @@ def get_items_for_activity(activity_file): if item["requiredValue"]: tmp["required"] = True - try: - unit = f"({item_data['responseOptions']['unitOptions'][0]['prefLabel'][LANG]})" - except KeyError: - unit = "" - tmp["unit"] = unit - - try: - is_multiple = item_data["responseOptions"].get("multipleChoice", False) - except KeyError: - is_multiple = False - tmp["is_multiple"] = is_multiple + if response_options := item_data.get("responseOptions"): + try: + unit = f"({response_options['unitOptions'][0]['prefLabel'][LANG]})" + except KeyError: + unit = "" + tmp["unit"] = unit + + tmp["min"] = response_options.get("minValue") + tmp["max"] = response_options.get("maxValue") + + try: + is_multiple = response_options.get("multipleChoice", False) + except KeyError: + is_multiple = False + tmp["is_multiple"] = is_multiple + + else: + tmp["unit"] = "" + tmp["min"] = None + tmp["max"] = None + tmp["is_multiple"] = None items[item_name] = tmp diff --git a/ui/static/style.css b/ui/static/style.css index f218de1e..b0a2694d 100644 --- a/ui/static/style.css +++ b/ui/static/style.css @@ -1,3 +1,3 @@ body { - background: #e8f1f9; + background: #edf1f5; } diff --git a/ui/templates/base.html b/ui/templates/base.html index b61cd454..20b2a123 100644 --- a/ui/templates/base.html +++ b/ui/templates/base.html @@ -21,54 +21,67 @@
      {% block header %}{% endblock %}
      -
      -
      -

      eCOBIDAS

      -
      +
      +
      -
      -
      - -
      - +
      {% block content %} {% endblock %}
      diff --git a/ui/templates/protocol.html b/ui/templates/protocol.html index 8db0f8f5..b205ae4b 100644 --- a/ui/templates/protocol.html +++ b/ui/templates/protocol.html @@ -1,30 +1,32 @@ {% extends 'base.html' %} {% from 'bootstrap5/form.html' import render_form %} {% block content %}
      -
      -

      {{ protocol_pref_label }}

      - {% if landing_page %} {{ protocol_preamble }} {% endif %} +
      - +

      {{ protocol_pref_label }}

      +
      + +
      - {% if landing_page %} {{ landing_page }} {% else %} + {% if landing_page %} {{ protocol_preamble }} {{ landing_page }} {% else + %}

      {{ activity_pref_label }}

      @@ -34,7 +36,16 @@

      {{ activity_pref_label }}

      >

      - {{ activity_preamble }} {{ render_form(form) }} {% endif %} + {{ activity_preamble }} + +
      +
      {{ render_form(form) }}
      +
      + + {% endif %}
      From cf5c94c832f011065af8796d441f88edf80e472f Mon Sep 17 00:00:00 2001 From: Remi Gau Date: Wed, 22 May 2024 19:41:09 -0400 Subject: [PATCH 09/31] refactor --- ui/app.py | 374 ++++---------------------------------------------- ui/modules.py | 330 ++++++++++++++++++++++++++++++++++++++++++++ 2 files changed, 358 insertions(+), 346 deletions(-) diff --git a/ui/app.py b/ui/app.py index 942d3a63..93d8cc0d 100644 --- a/ui/app.py +++ b/ui/app.py @@ -1,357 +1,21 @@ import json -from functools import lru_cache from pathlib import Path from typing import Any -import requests from flask import Flask, render_template, request from flask_bootstrap import Bootstrap5 -from flask_wtf import CSRFProtect, FlaskForm +from flask_wtf import CSRFProtect from markupsafe import Markup, escape -from modules import get_item, get_protocol, protocol_url -from rich import print -from wtforms import ( - DateField, - DecimalField, - HiddenField, - IntegerField, - RadioField, - SelectField, - SelectMultipleField, - StringField, - SubmitField, - TextAreaField, +from modules import ( + LANG, + generate_form, + get_items_for_activity, + get_landing_page, + get_nav_bar_content, + get_protocol, + protocol_url, + update_format, ) -from wtforms.validators import DataRequired, NumberRange - -LANG: str = "en" - - -@lru_cache -def query_choices(url: str) -> None | dict[str, Any]: - try: - data = requests.get(url).json() - except Exception as exc: - print(exc) - data = None - return data - - -@lru_cache -def get_landing_page(url: Path) -> None | dict[str, Any]: - try: - if str(url).startswith("https:"): - data = requests.get(url) - else: - data = Path(url).read_text() - except Exception as exc: - print(exc) - data = None - return data - - -def get_nav_bar_content( - protocol_name: str, activity_name: str | None = None -) -> list[dict[str, str]]: - protocol_content = get_protocol(protocol_name) - - order = protocol_content["ui"]["order"] - properties = protocol_content["ui"]["addProperties"] - properties = sort_ui_properties(properties=properties, order=order) - - activities = [ - {"name": "Start", "link": "#", "class": "nav-link active"}, - ] - activities.extend( - { - "name": activity["prefLabel"][LANG], - "link": f"/protocol/{protocol_name}/{activity['variableName']}", - "class": "nav-link", - } - for activity in properties - ) - - if activity_name: - activities[0]["link"] = f"/protocol/{protocol_name}" - activities[0]["class"] = "nav-link" - for activity in activities: - if activity["name"] == activity_name: - activity["link"] = "#" - activity["class"] = "nav-link active" - - return activities - - -def update_visibility(items: dict[str, Any], form): - for item, values in items.items(): - isVis = values["isVis"] - if isinstance(isVis, str): - isVis = isVis.replace(" ", "").split("==") - if len(isVis) > 2: - app.logger.warning("More than 1 '=='") - if len(isVis) < 2: - app.logger.warning(f"Unsupported JavaScript expression: {isVis}") - if len(isVis) == 2 and form[isVis[0]].data: - response = int(form[isVis[0]].data) - expected = int(isVis[1]) - items[item]["visibility"] = response == expected - return items - - -def update_format(items: dict[str, Any], form): - for i in items: - if form[i].data: - items[i]["is_answered"] = True - return items - - -def generate_form(items=None, prefix=None): - - class DyanmicForm(FlaskForm): - pass - - form = DyanmicForm - - for item_name, item in items.items(): - - render_kw = ( - {"style": "border-color: green; border-width: 2px;"} - if item["is_answered"] - else {"style": "border-color: red; border-width: 2px;"} - ) - - validators = [] - if item["required"]: - validators.append(DataRequired()) - - question = f"{item['question']} {item['unit']}" - - if not item["visibility"]: - setattr( - form, - item_name, - HiddenField( - Markup(question), - validators=validators, - description=item["description"], - _prefix=prefix, - ), - ) - continue - - input_type = item["input_type"] - - default = None - - if input_type == "date": - - FieldType = DateField - - setattr( - form, - item_name, - FieldType( - Markup(question), - validators=validators, - description=item["description"], - default=default, - _prefix=prefix, - format="%Y-%m-%d", - render_kw=render_kw, - ), - ) - - elif input_type not in ["select", "radio", "slider"]: - - FieldType = StringField - if input_type == "number": - FieldType = IntegerField - elif input_type == "float": - FieldType = DecimalField - elif input_type == "textarea": - FieldType = TextAreaField - - if input_type in ["number", "float"]: - minimum = item["min"] - maximum = item["max"] - validators.append(NumberRange(min=minimum, max=maximum)) - if minimum is not None and maximum is not None: - question += f" ({minimum=}, {maximum=})" - elif minimum is not None: - question += f" ({minimum=})" - - setattr( - form, - item_name, - FieldType( - Markup(question), - validators=validators, - description=item["description"], - default=default, - _prefix=prefix, - render_kw=render_kw, - ), - ) - - elif input_type == "slider": - - # FieldType = DecimalRangeField - # render_kw["value"]= "50.0" - # render_kw["min"]= "0.0" - # render_kw["max"]= "100.0" - # render_kw["step"]= "0.5" - - min_label = float(item["choices"][0][1]) - max_label = float(item["choices"][-1][1]) - - question += f" (min={min_label}, max={max_label})" - - FieldType = DecimalField - validators.append(NumberRange(min=min_label, max=max_label)) - - setattr( - form, - item_name, - FieldType( - Markup(question), - validators=validators, - description=item["description"], - _prefix=prefix, - render_kw=render_kw, - ), - ) - - else: - - form = add_choice_based_items(form, prefix, item_name, item) - - setattr(form, "submit", SubmitField("Save")) # noqa B010 - - return form() - - -def add_choice_based_items(form, prefix, item_name, item): - - question = f"{item['question']} {item['unit']}" - - input_type = item["input_type"] - - render_kw = ( - {"style": "border-color: green; border-width: 2px;"} - if item["is_answered"] - else {"style": "border-color: red; border-width: 2px;"} - ) - - validators = [] - if item["required"]: - validators.append(DataRequired()) - - is_multiple = item["is_multiple"] - - if is_multiple: - FieldType = SelectMultipleField - elif input_type == "select": - FieldType = SelectField - elif input_type == "radio": - FieldType = RadioField - - setattr( - form, - item_name, - FieldType( - Markup(question), - validators=validators, - description=item["description"], - choices=item["choices"], - _prefix=prefix, - render_kw=render_kw, - ), - ) - - return form - - -@lru_cache -def get_items_for_activity(activity_file): - with open(activity_file) as f: - activity = json.load(f) - - order = activity["ui"]["order"] - properties = activity["ui"]["addProperties"] - properties = sort_ui_properties(properties=properties, order=order) - - items = {} - for item in properties: - - item_name = item["variableName"] - - item_data = get_item(activity_file.parent / item["isAbout"]) - - tmp = { - "visibility": False, - "required": False, - "isVis": item["isVis"], - "choices": get_choices(item_data), - "is_answered": False, - } - - tmp["description"] = item_data.get("description") - tmp["question"] = item_data["question"][LANG] - tmp["input_type"] = item_data["ui"]["inputType"] - - if item["isVis"] == 1: - tmp["visibility"] = True - - if item["requiredValue"]: - tmp["required"] = True - - if response_options := item_data.get("responseOptions"): - try: - unit = f"({response_options['unitOptions'][0]['prefLabel'][LANG]})" - except KeyError: - unit = "" - tmp["unit"] = unit - - tmp["min"] = response_options.get("minValue") - tmp["max"] = response_options.get("maxValue") - - try: - is_multiple = response_options.get("multipleChoice", False) - except KeyError: - is_multiple = False - tmp["is_multiple"] = is_multiple - - else: - tmp["unit"] = "" - tmp["min"] = None - tmp["max"] = None - tmp["is_multiple"] = None - - items[item_name] = tmp - - return items - - -def sort_ui_properties(properties: list[dict[str, Any]], order: list[str]) -> list[dict[str, Any]]: - tmp = [] - for i in order: - for prop in properties: - if prop["isAbout"] == i: - tmp.append(prop) - break - return tmp - - -def get_choices(item_data): - try: - choices = item_data["responseOptions"]["choices"] - if isinstance(choices, str): - choices = query_choices(choices)["choices"] - choices = [(x["value"], x["name"][LANG]) for x in choices] - except KeyError: - choices = {} - return choices - test_config = None @@ -379,6 +43,22 @@ def get_choices(item_data): csrf = CSRFProtect(app) +def update_visibility(items: dict[str, Any], form): + for item, values in items.items(): + isVis = values["isVis"] + if isinstance(isVis, str): + isVis = isVis.replace(" ", "").split("==") + if len(isVis) > 2: + app.logger.warning("More than 1 '=='") + if len(isVis) < 2: + app.logger.warning(f"Unsupported JavaScript expression: {isVis}") + if len(isVis) == 2 and form[isVis[0]].data: + response = int(form[isVis[0]].data) + expected = int(isVis[1]) + items[item]["visibility"] = response == expected + return items + + @app.route("/protocol/", methods=["GET", "POST"]) def protocol(protocol_name: str) -> str: @@ -424,7 +104,9 @@ def activity(protocol_name, activity_name) -> str: if request.method == "POST" and form.is_submitted(): items = update_visibility(items, form) + items = update_format(items, form) + form = generate_form(items, prefix=activity_name) completed_items = sum(bool(i["is_answered"]) for i in items.values()) diff --git a/ui/modules.py b/ui/modules.py index d59e66ed..f8d85bfd 100644 --- a/ui/modules.py +++ b/ui/modules.py @@ -4,6 +4,26 @@ from pathlib import Path from typing import Any +import requests +from flask_wtf import FlaskForm +from markupsafe import Markup +from rich import print +from wtforms import ( + DateField, + DecimalField, + HiddenField, + IntegerField, + RadioField, + SelectField, + SelectMultipleField, + StringField, + SubmitField, + TextAreaField, +) +from wtforms.validators import DataRequired, NumberRange + +LANG: str = "en" + def protocol_url(protocol_name: Path) -> Path: return ( @@ -28,3 +48,313 @@ def get_item(file: Path) -> dict[str, Any]: with open(file) as f: content = json.load(f) return content + + +@lru_cache +def query_choices(url: str) -> None | dict[str, Any]: + try: + data = requests.get(url).json() + except Exception as exc: + print(exc) + data = None + return data + + +@lru_cache +def get_landing_page(url: Path) -> None | dict[str, Any]: + try: + if str(url).startswith("https:"): + data = requests.get(url) + else: + data = Path(url).read_text() + except Exception as exc: + print(exc) + data = None + return data + + +def get_nav_bar_content( + protocol_name: str, activity_name: str | None = None +) -> list[dict[str, str]]: + protocol_content = get_protocol(protocol_name) + + order = protocol_content["ui"]["order"] + properties = protocol_content["ui"]["addProperties"] + properties = sort_ui_properties(properties=properties, order=order) + + activities = [ + {"name": "Start", "link": "#", "class": "nav-link active"}, + ] + activities.extend( + { + "name": activity["prefLabel"][LANG], + "link": f"/protocol/{protocol_name}/{activity['variableName']}", + "class": "nav-link", + } + for activity in properties + ) + + if activity_name: + activities[0]["link"] = f"/protocol/{protocol_name}" + activities[0]["class"] = "nav-link" + for activity in activities: + if activity["name"] == activity_name: + activity["link"] = "#" + activity["class"] = "nav-link active" + + return activities + + +def update_format(items: dict[str, Any], form): + for i in items: + if form[i].data: + items[i]["is_answered"] = True + return items + + +def generate_form(items=None, prefix=None): + + class DyanmicForm(FlaskForm): + pass + + form = DyanmicForm + + for item_name, item in items.items(): + + render_kw = ( + {"style": "border-color: green; border-width: 2px;"} + if item["is_answered"] + else {"style": "border-color: red; border-width: 2px;"} + ) + + validators = [] + if item["required"]: + validators.append(DataRequired()) + + question = f"{item['question']} {item['unit']}" + + if not item["visibility"]: + setattr( + form, + item_name, + HiddenField( + Markup(question), + validators=validators, + description=item["description"], + _prefix=prefix, + ), + ) + continue + + input_type = item["input_type"] + + default = None + + if input_type == "date": + + FieldType = DateField + + setattr( + form, + item_name, + FieldType( + Markup(question), + validators=validators, + description=item["description"], + default=default, + _prefix=prefix, + format="%Y-%m-%d", + render_kw=render_kw, + ), + ) + + elif input_type not in ["select", "radio", "slider"]: + + FieldType = StringField + if input_type == "number": + FieldType = IntegerField + elif input_type == "float": + FieldType = DecimalField + elif input_type == "textarea": + FieldType = TextAreaField + + if input_type in ["number", "float"]: + minimum = item["min"] + maximum = item["max"] + validators.append(NumberRange(min=minimum, max=maximum)) + if minimum is not None and maximum is not None: + question += f" ({minimum=}, {maximum=})" + elif minimum is not None: + question += f" ({minimum=})" + + setattr( + form, + item_name, + FieldType( + Markup(question), + validators=validators, + description=item["description"], + default=default, + _prefix=prefix, + render_kw=render_kw, + ), + ) + + elif input_type == "slider": + + # FieldType = DecimalRangeField + # render_kw["value"]= "50.0" + # render_kw["min"]= "0.0" + # render_kw["max"]= "100.0" + # render_kw["step"]= "0.5" + + min_label = float(item["choices"][0][1]) + max_label = float(item["choices"][-1][1]) + + question += f" (min={min_label}, max={max_label})" + + FieldType = DecimalField + validators.append(NumberRange(min=min_label, max=max_label)) + + setattr( + form, + item_name, + FieldType( + Markup(question), + validators=validators, + description=item["description"], + _prefix=prefix, + render_kw=render_kw, + ), + ) + + else: + + form = add_choice_based_items(form, prefix, item_name, item) + + setattr(form, "submit", SubmitField("Save")) # noqa B010 + + return form() + + +def add_choice_based_items(form, prefix, item_name, item): + + question = f"{item['question']} {item['unit']}" + + input_type = item["input_type"] + + render_kw = ( + {"style": "border-color: green; border-width: 2px;"} + if item["is_answered"] + else {"style": "border-color: red; border-width: 2px;"} + ) + + validators = [] + if item["required"]: + validators.append(DataRequired()) + + is_multiple = item["is_multiple"] + + if is_multiple: + FieldType = SelectMultipleField + elif input_type == "select": + FieldType = SelectField + elif input_type == "radio": + FieldType = RadioField + + setattr( + form, + item_name, + FieldType( + Markup(question), + validators=validators, + description=item["description"], + choices=item["choices"], + _prefix=prefix, + render_kw=render_kw, + ), + ) + + return form + + +@lru_cache +def get_items_for_activity(activity_file): + with open(activity_file) as f: + activity = json.load(f) + + order = activity["ui"]["order"] + properties = activity["ui"]["addProperties"] + properties = sort_ui_properties(properties=properties, order=order) + + items = {} + for item in properties: + + item_name = item["variableName"] + + item_data = get_item(activity_file.parent / item["isAbout"]) + + tmp = { + "visibility": False, + "required": False, + "isVis": item["isVis"], + "choices": get_choices(item_data), + "is_answered": False, + } + + tmp["description"] = item_data.get("description") + tmp["question"] = item_data["question"][LANG] + tmp["input_type"] = item_data["ui"]["inputType"] + + if item["isVis"] == 1: + tmp["visibility"] = True + + if item["requiredValue"]: + tmp["required"] = True + + if response_options := item_data.get("responseOptions"): + try: + unit = f"({response_options['unitOptions'][0]['prefLabel'][LANG]})" + except KeyError: + unit = "" + tmp["unit"] = unit + + tmp["min"] = response_options.get("minValue") + tmp["max"] = response_options.get("maxValue") + + try: + is_multiple = response_options.get("multipleChoice", False) + except KeyError: + is_multiple = False + tmp["is_multiple"] = is_multiple + + else: + tmp["unit"] = "" + tmp["min"] = None + tmp["max"] = None + tmp["is_multiple"] = None + + items[item_name] = tmp + + return items + + +def sort_ui_properties(properties: list[dict[str, Any]], order: list[str]) -> list[dict[str, Any]]: + tmp = [] + for i in order: + for prop in properties: + if prop["isAbout"] == i: + tmp.append(prop) + break + return tmp + + +def get_choices(item_data): + try: + choices = item_data["responseOptions"]["choices"] + if isinstance(choices, str): + choices = query_choices(choices)["choices"] + choices = [(x["value"], x["name"][LANG]) for x in choices] + except KeyError: + choices = {} + return choices From 1c980070dc0fc0cadaf908b7b6538145477572bb Mon Sep 17 00:00:00 2001 From: Remi Gau Date: Wed, 22 May 2024 23:34:45 -0400 Subject: [PATCH 10/31] basic upload --- ui/app.py | 54 +++++++++++++++++++++++++++++++++++++--- ui/templates/about.html | 10 +++++++- ui/tmp/participants.json | 15 +++++++++++ ui/tmp/participants.tsv | 11 ++++++++ 4 files changed, 85 insertions(+), 5 deletions(-) create mode 100644 ui/tmp/participants.json create mode 100644 ui/tmp/participants.tsv diff --git a/ui/app.py b/ui/app.py index 93d8cc0d..8bb64393 100644 --- a/ui/app.py +++ b/ui/app.py @@ -2,9 +2,10 @@ from pathlib import Path from typing import Any -from flask import Flask, render_template, request +import pandas as pd +from flask import Flask, flash, redirect, render_template, request from flask_bootstrap import Bootstrap5 -from flask_wtf import CSRFProtect +from flask_wtf import CSRFProtect, FlaskForm from markupsafe import Markup, escape from modules import ( LANG, @@ -16,14 +17,23 @@ protocol_url, update_format, ) +from rich import print +from werkzeug.utils import secure_filename +from wtforms import MultipleFileField, SubmitField test_config = None +UPLOAD_FOLDER = Path(__file__).parent / "tmp" +UPLOAD_FOLDER.mkdir(parents=True, exist_ok=True) +ALLOWED_EXTENSIONS = {"tsv", "json"} + # create and configure the app app = Flask(__name__, instance_relative_config=True) app.config.from_mapping( SECRET_KEY="tO$&!|0wkamvVia0?n$NqIRVWOG", DATABASE=Path(app.instance_path) / "flaskr.sqlite", + UPLOAD_FOLDER=UPLOAD_FOLDER, + MAX_CONTENT_LENGTH=16 * 1000 * 1000, ) if test_config is None: @@ -153,9 +163,45 @@ def index() -> str: return render_template("index.html") -@app.route("/about") +def allowed_file(filename): + return "." in filename and filename.rsplit(".", 1)[1].lower() in ALLOWED_EXTENSIONS + + +class UploadForm(FlaskForm): + participants = MultipleFileField("Upload participants.tsv and participants.json") + submit = SubmitField("Upload") + + +@app.route("/about", methods=["GET", "POST"]) def about() -> str: - return render_template("about.html") + form = UploadForm() + if request.method == "POST" and form.is_submitted(): + print(f"{form.participants.data=}") + print(f"{form.participants.name=}") + if len(form.participants.data) != 2: + flash("2 files must be uploaded.", "error") + return redirect(request.url) + if all(file.filename != "participants.json" for file in form.participants.data): + flash("No 'participants.json' was uploaded.", "error") + return redirect(request.url) + if all(file.filename != "participants.tsv" for file in form.participants.data): + flash("No 'participants.tsv' was uploaded.", "error") + return redirect(request.url) + for file in form.participants.data: + if allowed_file(file.filename): + filename = secure_filename(file.filename) + file.save(Path(app.config["UPLOAD_FOLDER"]) / filename) + + participants_tsv = pd.read_csv( + Path(app.config["UPLOAD_FOLDER"]) / "participants.tsv", sep="\t" + ) + with open(Path(app.config["UPLOAD_FOLDER"]) / "participants.json") as f: + participants_json = json.load(f) + + print(participants_tsv) + print(participants_json) + + return render_template("about.html", form=form) @app.route("/new") diff --git a/ui/templates/about.html b/ui/templates/about.html index 21f5da26..fbf4157d 100644 --- a/ui/templates/about.html +++ b/ui/templates/about.html @@ -1 +1,9 @@ -{% extends 'base.html' %} +{% extends 'base.html' %} {% from 'bootstrap5/form.html' import render_form %} +{% block content %} {% with messages = +get_flashed_messages(with_categories=true) %} {% if messages %} +
        + {% for message in messages %} +
      • {{ message }}
        • + {% endfor %} +
      +{% endif %} {% endwith %} {{ render_form(form) }} {% endblock %} diff --git a/ui/tmp/participants.json b/ui/tmp/participants.json new file mode 100644 index 00000000..f6c22a1b --- /dev/null +++ b/ui/tmp/participants.json @@ -0,0 +1,15 @@ +{ + "dominant_hand": { + "LongName": "dominant_hand", + "Levels": { + "left": { + "Description": "left", + "TermURL": "http://purl.bioontology.org/ontology/SNOMEDCT/87683000" + }, + "right": { + "Description": "right", + "TermURL": "http://purl.bioontology.org/ontology/SNOMEDCT/46669005" + } + } + } +} diff --git a/ui/tmp/participants.tsv b/ui/tmp/participants.tsv new file mode 100644 index 00000000..20272906 --- /dev/null +++ b/ui/tmp/participants.tsv @@ -0,0 +1,11 @@ +participant_id dominant_hand +sub-01 left +sub-02 right +sub-03 right +sub-04 right +sub-05 right +sub-06 left +sub-07 right +sub-08 right +sub-09 right +sub-10 left From 569c7105f3d8ec1b5b651cd90e17f1786cdcb2ba Mon Sep 17 00:00:00 2001 From: Remi Gau Date: Thu, 23 May 2024 11:37:38 -0400 Subject: [PATCH 11/31] enable upload --- cobidas_schema | 2 +- inputs/bids_template/participants.json | 66 +++++++++----- inputs/bids_template/participants.tsv | 19 +++- reproschema-py | 2 +- ui/app.py | 119 ++++++++++++++----------- ui/templates/about.html | 9 +- ui/templates/protocol.html | 45 ++++++++++ ui/tmp/participants.json | 23 +++-- ui/tmp/participants.tsv | 46 +++++++--- 9 files changed, 229 insertions(+), 102 deletions(-) diff --git a/cobidas_schema b/cobidas_schema index 780e4dbb..1705ce2f 160000 --- a/cobidas_schema +++ b/cobidas_schema @@ -1 +1 @@ -Subproject commit 780e4dbb53bb8892cba08cc25e380dcb507a0a6d +Subproject commit 1705ce2f92b859a6b4f3c898e345caee174e6e7c diff --git a/inputs/bids_template/participants.json b/inputs/bids_template/participants.json index ea635cc6..c6791aad 100644 --- a/inputs/bids_template/participants.json +++ b/inputs/bids_template/participants.json @@ -1,29 +1,53 @@ { "age": { - "LongName": "", - "Description": "age of the participant", - "Levels": [], - "Units": "years", - "TermURL": "" + "Annotations": { + "IsAbout": { + "TermURL": "nb:Age", + "Label": "" + }, + "Transformation": { + "TermURL": "nb:FromInt", + "Label": "integer data" + }, + "MissingValues": [ + "", + "n/a", + " " + ] + }, + "Description": "There should have been a description here, but there wasn't. :(" }, - "sex": { - "LongName": "", - "Description": "sex of the participant as reported by the participant", - "Levels": { - "m": "male", - "f": "female" + "participant_id": { + "Annottations": { + "IsAbout": { + "TermURL": "nb:ParticipantID", + "Label": "" + }, + "Identifies": "participant" }, - "Units": "", - "TermURL": "" + "Description": "There should have been a description here, but there wasn't. :(" }, - "handedness": { - "LongName": "", - "Description": "handedness of the participant as reported by the participant", - "Levels": { - "l": "left", - "r": "right" + "sex": { + "Annotations": { + "IsAbout": { + "TermURL": "nb:Sex", + "Label": "" + }, + "Levels": { + "F": { + "TermURL": "snomed:248152002", + "Label": "" + }, + "M": { + "TermURL": "snomed:248153007", + "Label": "" + }, + "M,": { + "TermURL": "snomed:248153007", + "Label": "" + } + } }, - "Units": "", - "TermURL": "" + "Description": "There should have been a description here, but there wasn't. :(" } } diff --git a/inputs/bids_template/participants.tsv b/inputs/bids_template/participants.tsv index de75fec9..43679380 100644 --- a/inputs/bids_template/participants.tsv +++ b/inputs/bids_template/participants.tsv @@ -1,2 +1,17 @@ -participant_id age sex -sub-01 0 m +participant_id sex age +sub-01 F 26 +sub-02 M 24 +sub-03 F 27 +sub-04 F 20 +sub-05 M, 22 +sub-06 F 26 +sub-07 M 24 +sub-08 M 21 +sub-09 M 26 +sub-10 F 21 +sub-11 F 24 +sub-12 F 22 +sub-13 F 21 +sub-14 F 30 +sub-15 F 24 +sub-16 M 19 diff --git a/reproschema-py b/reproschema-py index 68996c17..f61cf2f8 160000 --- a/reproschema-py +++ b/reproschema-py @@ -1 +1 @@ -Subproject commit 68996c17155489cb8019ff50cec1fb52d8698f11 +Subproject commit f61cf2f80ff86faa2dffc1ddf4e6b7a4dce76f3c diff --git a/ui/app.py b/ui/app.py index 8bb64393..2f7a556a 100644 --- a/ui/app.py +++ b/ui/app.py @@ -102,6 +102,10 @@ def activity(protocol_name, activity_name) -> str: break activity_file = protocol_url(protocol_name).parent / is_about_activity + upload_form = None + if protocol_name == "neurovault" and activity_name == "participants": + upload_form = UploadForm() + with open(activity_file) as f: activity = json.load(f) @@ -111,27 +115,68 @@ def activity(protocol_name, activity_name) -> str: form = generate_form(items=items, prefix=activity_name) - if request.method == "POST" and form.is_submitted(): - - items = update_visibility(items, form) - - items = update_format(items, form) - - form = generate_form(items, prefix=activity_name) - - completed_items = sum(bool(i["is_answered"]) for i in items.values()) - nb_items = sum(bool(i["visibility"]) for i in items.values()) - - return render_template( - "protocol.html", - protocol_pref_label=protocol_name, - activity_pref_label=activity["prefLabel"][LANG], - activity_preamble=Markup(activity["preamble"][LANG]), - activities=activities, - form=form, - nb_items=nb_items, - completed_items=completed_items, - ) + if request.method == "POST": + + if upload_form.is_submitted(): + + if len(upload_form.participants.data) != 2: + flash("2 files must be uploaded.") + return redirect(request.url) + if all(file.filename != "participants.json" for file in upload_form.participants.data): + flash("No 'participants.json' was uploaded.") + return redirect(request.url) + if all(file.filename != "participants.tsv" for file in upload_form.participants.data): + flash("No 'participants.tsv' was uploaded.") + return redirect(request.url) + + for file in upload_form.participants.data: + if allowed_file(file.filename): + filename = secure_filename(file.filename) + file.save(Path(app.config["UPLOAD_FOLDER"]) / filename) + + participants_tsv = pd.read_csv( + Path(app.config["UPLOAD_FOLDER"]) / "participants.tsv", sep="\t" + ) + with open(Path(app.config["UPLOAD_FOLDER"]) / "participants.json") as f: + participants_json = json.load(f) + + if not participants_json.get("participant_id") or not participants_json[ + "participant_id" + ].get("Annotations"): + flash( + Markup( + "The 'participants.json' was not annotated. " + "Annotate your data with " + "the neurobagel online annotation tool" + ) + ) + return redirect(request.url) + + print(participants_tsv) + print(participants_json) + + elif form.is_submitted(): + + items = update_visibility(items, form) + + items = update_format(items, form) + + form = generate_form(items, prefix=activity_name) + + completed_items = sum(bool(i["is_answered"]) for i in items.values()) + nb_items = sum(bool(i["visibility"]) for i in items.values()) + + return render_template( + "protocol.html", + protocol_pref_label=protocol_name, + activity_pref_label=activity["prefLabel"][LANG], + activity_preamble=Markup(activity["preamble"][LANG]), + activities=activities, + form=form, + nb_items=nb_items, + completed_items=completed_items, + upload_form=upload_form, + ) completed_items = sum(bool(i["is_answered"]) for i in items.values()) nb_items = sum(bool(i["visibility"]) for i in items.values()) @@ -145,6 +190,7 @@ def activity(protocol_name, activity_name) -> str: form=form, nb_items=nb_items, completed_items=completed_items, + upload_form=upload_form, ) @@ -172,36 +218,9 @@ class UploadForm(FlaskForm): submit = SubmitField("Upload") -@app.route("/about", methods=["GET", "POST"]) +@app.route("/about") def about() -> str: - form = UploadForm() - if request.method == "POST" and form.is_submitted(): - print(f"{form.participants.data=}") - print(f"{form.participants.name=}") - if len(form.participants.data) != 2: - flash("2 files must be uploaded.", "error") - return redirect(request.url) - if all(file.filename != "participants.json" for file in form.participants.data): - flash("No 'participants.json' was uploaded.", "error") - return redirect(request.url) - if all(file.filename != "participants.tsv" for file in form.participants.data): - flash("No 'participants.tsv' was uploaded.", "error") - return redirect(request.url) - for file in form.participants.data: - if allowed_file(file.filename): - filename = secure_filename(file.filename) - file.save(Path(app.config["UPLOAD_FOLDER"]) / filename) - - participants_tsv = pd.read_csv( - Path(app.config["UPLOAD_FOLDER"]) / "participants.tsv", sep="\t" - ) - with open(Path(app.config["UPLOAD_FOLDER"]) / "participants.json") as f: - participants_json = json.load(f) - - print(participants_tsv) - print(participants_json) - - return render_template("about.html", form=form) + return render_template("about.html") @app.route("/new") diff --git a/ui/templates/about.html b/ui/templates/about.html index fbf4157d..16afcfca 100644 --- a/ui/templates/about.html +++ b/ui/templates/about.html @@ -1,9 +1,2 @@ {% extends 'base.html' %} {% from 'bootstrap5/form.html' import render_form %} -{% block content %} {% with messages = -get_flashed_messages(with_categories=true) %} {% if messages %} -
        - {% for message in messages %} -
      • {{ message }}
        • - {% endfor %} -
      -{% endif %} {% endwith %} {{ render_form(form) }} {% endblock %} +{% block content %} {% endblock %} diff --git a/ui/templates/protocol.html b/ui/templates/protocol.html index b205ae4b..cb8da6e9 100644 --- a/ui/templates/protocol.html +++ b/ui/templates/protocol.html @@ -38,6 +38,51 @@

      {{ activity_pref_label }}

      {{ activity_preamble }} + + + + + + + + + + + + + {% if upload_form %} +
      + {% with messages = get_flashed_messages() %} {% if messages %} {% for + message in messages %} + + {% endfor %} {% endif %} {% endwith %} {{ render_form(upload_form) }} +
      + {% endif %} +
      Date: Thu, 23 May 2024 15:04:24 -0400 Subject: [PATCH 12/31] refactor --- .pre-commit-config.yaml | 2 +- .vscode/extensions.json | 13 +- .vscode/settings.json | 2 +- ecobidas/inputs/data-dictionary.json | 407 ++++++++------- inputs/bids_template/dataset_description.json | 34 +- inputs/bids_template/participants.json | 92 ++-- .../phenotype/EpilepsyClassification2017.json | 493 +++++++++--------- ...-01_ses-01_acq-FullExample_run-01_T1w.json | 76 +-- ...01_ses-01_acq-ShortExample_run-01_T1w.json | 10 +- .../sub-01_ses-01_task-FilterExample_eeg.json | 14 +- .../sub-01_ses-01_task-FullExample_eeg.json | 60 +-- ...sub-01_ses-01_task-MinimalExample_eeg.json | 16 +- ...b-01_ses-01_task-ReferenceExample_eeg.json | 8 +- ...01_ses-01_task-Case1_run-01_phasediff.json | 6 +- ...ub-01_ses-01_task-Case2_run-01_phase1.json | 4 +- ...ub-01_ses-01_task-Case2_run-01_phase2.json | 4 +- ...-01_ses-01_task-Case3_run-01_fieldmap.json | 4 +- ...1_ses-01_task-Case4_dir-LR_run-01_epi.json | 6 +- ...1_ses-01_task-FullExample_run-01_bold.json | 102 ++-- ...ses-01_task-FullExample_run-01_events.json | 40 +- ..._ses-01_task-ShortExample_run-01_bold.json | 4 +- .../ieeg/sub-01_ses-01_coordsystem.json | 12 +- ...1_ses-01_task-LongExample_run-01_ieeg.json | 84 +-- ...ullExample_acq-CTF_run-1_proc-sss_meg.json | 76 +-- ...ortExample_acq-CTF_run-1_proc-sss_meg.json | 52 +- mlc_config.json | 34 +- ui/__init__.py | 0 ui/app.py | 192 +++---- ui/forms.py | 187 +++++++ ui/modules.py | 190 +------ 30 files changed, 1110 insertions(+), 1114 deletions(-) create mode 100644 ui/__init__.py create mode 100644 ui/forms.py diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 5cc96985..8e71e605 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -82,7 +82,7 @@ repos: rev: v4.0.0-alpha.8 hooks: - id: prettier - types_or: [css, html] + types_or: [css, html, json] # Check that Python code complies with PEP8 guidelines # flake8 uses pydocstyle to check docstrings: https://flake8.pycqa.org/en/latest/ diff --git a/.vscode/extensions.json b/.vscode/extensions.json index 94acca4c..ecf4b70a 100644 --- a/.vscode/extensions.json +++ b/.vscode/extensions.json @@ -1,9 +1,8 @@ { - "recommendations": [ - "ms-python.python", - "sourcery.sourcery", - "ms-python.vscode-pylance" - ], - "unwantedRecommendations": [ - ] + "recommendations": [ + "ms-python.python", + "sourcery.sourcery", + "ms-python.vscode-pylance" + ], + "unwantedRecommendations": [] } diff --git a/.vscode/settings.json b/.vscode/settings.json index 24ed099a..d166cb12 100644 --- a/.vscode/settings.json +++ b/.vscode/settings.json @@ -1,3 +1,3 @@ { - "restructuredtext.pythonRecommendation.disabled": true + "restructuredtext.pythonRecommendation.disabled": true } diff --git a/ecobidas/inputs/data-dictionary.json b/ecobidas/inputs/data-dictionary.json index 121dd087..b7774bfd 100644 --- a/ecobidas/inputs/data-dictionary.json +++ b/ecobidas/inputs/data-dictionary.json @@ -1,207 +1,206 @@ { - "include": { - "VariableName": "include", - "Description": "Whether the item should be generated and included in the activity.", - "RequirementLevel": "required" - }, - "activity_pref_label": { - "VariableName": "activity_pref_label", - "Description": "preferred label of the activity", - "RequirementLevel": "required" - }, - "preamble": { - "VariableName": "preamble", - "Description": "introductory text to the activity", - "RequirementLevel": "recommended" - }, - "activity_order": { - "VariableName": "activity_order", - "Description": "position in which the activity is supposed to be presented in a protocol" - }, - "item": { - "VariableName": "item", - "Description": "name of the item", - "RequirementLevel": "required" - }, - "item_pref_label": { - "VariableName": "item_pref_label", - "Description": "preferred label of the item", - "RequirementLevel": "recommended" - }, - "item_description": { - "VariableName": "item_description", - "Description": "description of the item", - "RequirementLevel": "recommended" - }, - "item_order": { - "VariableName": "item_order", - "Description": "Position in which the item is supposed to be presented in the activity.", - "RequirementLevel": "required" - }, - "duplicate": { - "VariableName": "duplicate", - "Description": "reports the number of items that have the same name in this spreadsheet" - }, - "question": { - "VariableName": "question", - "Description": "question corresponding to the item", - "RequirementLevel": "required" - }, - "field_type": { - "VariableName": "field_type", - "Description": "type of response expected", - "RequirementLevel": "required", - "Levels": [ - { - "Name": "integer", - "Description": "" - }, - { - "Name": "text", - "Description": "a text answer is expected" - }, - { - "Name": "float", - "Description": "" - }, - { - "Name": "radio", - "Description": "" - }, - { - "Name": "select", - "Description": "" - }, - { - "Name": "slider", - "Description": "" - } - ] - }, - "choices": { - "VariableName": "choices", - "Description": "List of possible responses. Options are separated by a pipe '|'. For integers, floats, and sliders, the values represent min | max | step. If they are not provided, it should be assumed that they ar None or null.", - "RequirementLevel": "required" - }, - "mandatory": { - "VariableName": "mandatory", - "Description": "whether an answer to the item is required", - "Default": 1, - "Levels": [ - { - "Name": 1, - "Description": "a response to this item is required" - }, - { - "Name": 0, - "Description": "a response to this item is not required" - } - ], - "RequirementLevel": "recommended" - }, - "visibility": { - "VariableName": "visibility", - "Description": "Lists the conditions that have to be fulfilled for each item to be displayed to the user. By default, an item will be displayed. Other it will only be shown if a specific answer has been given to a previous item: in this case the expression in this cell must be a valid javascript expression like: 'previousItem === 1' ", - "RequirementLevel": "required" - }, - "details": { - "VariableName": "details", - "Description": "Some questions might require some additional information to be understandable by all users, so any extra information to be displayed to the users should be put the detail column.", - "RequirementLevel": "recommended" - }, - "bids_status": { - "VariableName": "bids_status", - "Description": "list if the item can be found in a BIDS (Brain Imaging Data Structure) dataset", - "Levels": [ - { - "Name": 0, - "Description": "does not exist in BIDS" - }, - { - "Name": 1, - "Description": "exist in BIDS and can be extracted" - }, - { - "Name": 2, - "Description": "could be included in BIDS" - }, - { - "Name": 3, - "Description": "unknown" - } - ] - }, - "bids_file": { - "VariableName": "bids_file", - "Description": "list the bids file in which the item can be found" - }, - "bids_key": { - "VariableName": "bids_key", - "Description": "list the json key corresponding to this item in the bids json file" - }, - "bids_key_for_unit": { - "VariableName": "bids_key_for_unit", + "include": { + "VariableName": "include", + "Description": "Whether the item should be generated and included in the activity.", + "RequirementLevel": "required" + }, + "activity_pref_label": { + "VariableName": "activity_pref_label", + "Description": "preferred label of the activity", + "RequirementLevel": "required" + }, + "preamble": { + "VariableName": "preamble", + "Description": "introductory text to the activity", + "RequirementLevel": "recommended" + }, + "activity_order": { + "VariableName": "activity_order", + "Description": "position in which the activity is supposed to be presented in a protocol" + }, + "item": { + "VariableName": "item", + "Description": "name of the item", + "RequirementLevel": "required" + }, + "item_pref_label": { + "VariableName": "item_pref_label", + "Description": "preferred label of the item", + "RequirementLevel": "recommended" + }, + "item_description": { + "VariableName": "item_description", + "Description": "description of the item", + "RequirementLevel": "recommended" + }, + "item_order": { + "VariableName": "item_order", + "Description": "Position in which the item is supposed to be presented in the activity.", + "RequirementLevel": "required" + }, + "duplicate": { + "VariableName": "duplicate", + "Description": "reports the number of items that have the same name in this spreadsheet" + }, + "question": { + "VariableName": "question", + "Description": "question corresponding to the item", + "RequirementLevel": "required" + }, + "field_type": { + "VariableName": "field_type", + "Description": "type of response expected", + "RequirementLevel": "required", + "Levels": [ + { + "Name": "integer", "Description": "" - }, - "unit": { - "VariableName": "unit", - "Description": "unit of the item", - "RequirementLevel": "optional" - }, - "in_Carp_2012": { - "VariableName": "in_Carp_2012", - "Description": "name of the item in the literature review of [Carp, 2012](https://drive.google.com/file/d/1TBSxC52kXVERl9JmfbBPC7uCas4QN_vg/view?usp=sharing)", - "RequirementLevel": "optional" - }, - "neurovault": { - "VariableName": "neurovault", - "Description": "refers to the name of this item in a Neurovault collection", - "RequirementLevel": "optional" - }, - "fsl_default": { - "VariableName": "fsl_default", - "Description": "default value for FSL", - "RequirementLevel": "optional" - }, - "spm_default": { - "VariableName": "spm_default", - "Description": "default value for SPM", - "RequirementLevel": "optional" - }, - "percent_of_studies": { - "VariableName": "percent_of_studies", - "Description": "Percent of studies reporting the item in [Carp, 2012](https://drive.google.com/file/d/1TBSxC52kXVERl9JmfbBPC7uCas4QN_vg/view?usp=sharing). If the number is in **bold**, it was approximately extracted from one of the figures of the paper (because it was not reported in the text of the article).", - "RequirementLevel": "optional" - }, - "percent_of_studies_anat": { - "VariableName": "percent_of_studies_anat", - "Description": "Percent of studies reporting this item in for the anatomical data in the papers reviewed by [Carp, 2012](https://drive.google.com/file/d/1TBSxC52kXVERl9JmfbBPC7uCas4QN_vg/view?usp=sharing). If the number is in **bold**, it was approximately extracted from one of the figures of the paper (because it was not reported in the text of the article).", - "RequirementLevel": "optional" - }, - "percent_reported": { - "VariableName": "percent_reported", - "Description": "Frequency at which items are present in the eyetracking literature (see the [preprint](https://psyarxiv.com/f6qcy/))", - "RequirementLevel": "optional" - }, - "use_case_meta-analysis": { - "VariableName": "use_case_meta-analysis", - "Description": "Whether the item could be important to evaluate studies for a meta-analysis.", - "RequirementLevel": "optional" - }, - "meta-analysis_comment": { - "VariableName": "meta-analysis_comment", - "Description": "Comment for inclusion in a meta-analysis.", - "RequirementLevel": "optional" - }, - "nidm_results": { - "VariableName": "nidm_results", - "Description": "Mention where information this item can be found in an NIDM results package.", - "RequirementLevel": "optional" - }, - "mri_type": { - "VariableName": "mri_type", - "Description": "Mention the type of MRI this item is applicable to.", - "RequirementLevel": "optional" - } - + }, + { + "Name": "text", + "Description": "a text answer is expected" + }, + { + "Name": "float", + "Description": "" + }, + { + "Name": "radio", + "Description": "" + }, + { + "Name": "select", + "Description": "" + }, + { + "Name": "slider", + "Description": "" + } + ] + }, + "choices": { + "VariableName": "choices", + "Description": "List of possible responses. Options are separated by a pipe '|'. For integers, floats, and sliders, the values represent min | max | step. If they are not provided, it should be assumed that they ar None or null.", + "RequirementLevel": "required" + }, + "mandatory": { + "VariableName": "mandatory", + "Description": "whether an answer to the item is required", + "Default": 1, + "Levels": [ + { + "Name": 1, + "Description": "a response to this item is required" + }, + { + "Name": 0, + "Description": "a response to this item is not required" + } + ], + "RequirementLevel": "recommended" + }, + "visibility": { + "VariableName": "visibility", + "Description": "Lists the conditions that have to be fulfilled for each item to be displayed to the user. By default, an item will be displayed. Other it will only be shown if a specific answer has been given to a previous item: in this case the expression in this cell must be a valid javascript expression like: 'previousItem === 1' ", + "RequirementLevel": "required" + }, + "details": { + "VariableName": "details", + "Description": "Some questions might require some additional information to be understandable by all users, so any extra information to be displayed to the users should be put the detail column.", + "RequirementLevel": "recommended" + }, + "bids_status": { + "VariableName": "bids_status", + "Description": "list if the item can be found in a BIDS (Brain Imaging Data Structure) dataset", + "Levels": [ + { + "Name": 0, + "Description": "does not exist in BIDS" + }, + { + "Name": 1, + "Description": "exist in BIDS and can be extracted" + }, + { + "Name": 2, + "Description": "could be included in BIDS" + }, + { + "Name": 3, + "Description": "unknown" + } + ] + }, + "bids_file": { + "VariableName": "bids_file", + "Description": "list the bids file in which the item can be found" + }, + "bids_key": { + "VariableName": "bids_key", + "Description": "list the json key corresponding to this item in the bids json file" + }, + "bids_key_for_unit": { + "VariableName": "bids_key_for_unit", + "Description": "" + }, + "unit": { + "VariableName": "unit", + "Description": "unit of the item", + "RequirementLevel": "optional" + }, + "in_Carp_2012": { + "VariableName": "in_Carp_2012", + "Description": "name of the item in the literature review of [Carp, 2012](https://drive.google.com/file/d/1TBSxC52kXVERl9JmfbBPC7uCas4QN_vg/view?usp=sharing)", + "RequirementLevel": "optional" + }, + "neurovault": { + "VariableName": "neurovault", + "Description": "refers to the name of this item in a Neurovault collection", + "RequirementLevel": "optional" + }, + "fsl_default": { + "VariableName": "fsl_default", + "Description": "default value for FSL", + "RequirementLevel": "optional" + }, + "spm_default": { + "VariableName": "spm_default", + "Description": "default value for SPM", + "RequirementLevel": "optional" + }, + "percent_of_studies": { + "VariableName": "percent_of_studies", + "Description": "Percent of studies reporting the item in [Carp, 2012](https://drive.google.com/file/d/1TBSxC52kXVERl9JmfbBPC7uCas4QN_vg/view?usp=sharing). If the number is in **bold**, it was approximately extracted from one of the figures of the paper (because it was not reported in the text of the article).", + "RequirementLevel": "optional" + }, + "percent_of_studies_anat": { + "VariableName": "percent_of_studies_anat", + "Description": "Percent of studies reporting this item in for the anatomical data in the papers reviewed by [Carp, 2012](https://drive.google.com/file/d/1TBSxC52kXVERl9JmfbBPC7uCas4QN_vg/view?usp=sharing). If the number is in **bold**, it was approximately extracted from one of the figures of the paper (because it was not reported in the text of the article).", + "RequirementLevel": "optional" + }, + "percent_reported": { + "VariableName": "percent_reported", + "Description": "Frequency at which items are present in the eyetracking literature (see the [preprint](https://psyarxiv.com/f6qcy/))", + "RequirementLevel": "optional" + }, + "use_case_meta-analysis": { + "VariableName": "use_case_meta-analysis", + "Description": "Whether the item could be important to evaluate studies for a meta-analysis.", + "RequirementLevel": "optional" + }, + "meta-analysis_comment": { + "VariableName": "meta-analysis_comment", + "Description": "Comment for inclusion in a meta-analysis.", + "RequirementLevel": "optional" + }, + "nidm_results": { + "VariableName": "nidm_results", + "Description": "Mention where information this item can be found in an NIDM results package.", + "RequirementLevel": "optional" + }, + "mri_type": { + "VariableName": "mri_type", + "Description": "Mention the type of MRI this item is applicable to.", + "RequirementLevel": "optional" + } } diff --git a/inputs/bids_template/dataset_description.json b/inputs/bids_template/dataset_description.json index ff7497be..a526671c 100644 --- a/inputs/bids_template/dataset_description.json +++ b/inputs/bids_template/dataset_description.json @@ -1,25 +1,13 @@ { - "Name": "", - "BIDSVersion": "1.0.2", - "DatasetType": "", - "License": "", - "Authors": [ - "", - "", - "" - ], - "Acknowledgements": "", - "HowToAcknowledge": "", - "Funding": [ - "", - "", - "" - ], - "EthicsApprovals": "", - "ReferencesAndLinks": [ - "", - "", - "" - ], - "DatasetDOI": "" + "Name": "", + "BIDSVersion": "1.0.2", + "DatasetType": "", + "License": "", + "Authors": ["", "", ""], + "Acknowledgements": "", + "HowToAcknowledge": "", + "Funding": ["", "", ""], + "EthicsApprovals": "", + "ReferencesAndLinks": ["", "", ""], + "DatasetDOI": "" } diff --git a/inputs/bids_template/participants.json b/inputs/bids_template/participants.json index c6791aad..4f6f9ff0 100644 --- a/inputs/bids_template/participants.json +++ b/inputs/bids_template/participants.json @@ -1,53 +1,49 @@ { - "age": { - "Annotations": { - "IsAbout": { - "TermURL": "nb:Age", - "Label": "" - }, - "Transformation": { - "TermURL": "nb:FromInt", - "Label": "integer data" - }, - "MissingValues": [ - "", - "n/a", - " " - ] - }, - "Description": "There should have been a description here, but there wasn't. :(" + "age": { + "Annotations": { + "IsAbout": { + "TermURL": "nb:Age", + "Label": "" + }, + "Transformation": { + "TermURL": "nb:FromInt", + "Label": "integer data" + }, + "MissingValues": ["", "n/a", " "] }, - "participant_id": { - "Annottations": { - "IsAbout": { - "TermURL": "nb:ParticipantID", - "Label": "" - }, - "Identifies": "participant" - }, - "Description": "There should have been a description here, but there wasn't. :(" + "Description": "There should have been a description here, but there wasn't. :(" + }, + "participant_id": { + "Annottations": { + "IsAbout": { + "TermURL": "nb:ParticipantID", + "Label": "" + }, + "Identifies": "participant" }, - "sex": { - "Annotations": { - "IsAbout": { - "TermURL": "nb:Sex", - "Label": "" - }, - "Levels": { - "F": { - "TermURL": "snomed:248152002", - "Label": "" - }, - "M": { - "TermURL": "snomed:248153007", - "Label": "" - }, - "M,": { - "TermURL": "snomed:248153007", - "Label": "" - } - } + "Description": "There should have been a description here, but there wasn't. :(" + }, + "sex": { + "Annotations": { + "IsAbout": { + "TermURL": "nb:Sex", + "Label": "" + }, + "Levels": { + "F": { + "TermURL": "snomed:248152002", + "Label": "" }, - "Description": "There should have been a description here, but there wasn't. :(" - } + "M": { + "TermURL": "snomed:248153007", + "Label": "" + }, + "M,": { + "TermURL": "snomed:248153007", + "Label": "" + } + } + }, + "Description": "There should have been a description here, but there wasn't. :(" + } } diff --git a/inputs/bids_template/phenotype/EpilepsyClassification2017.json b/inputs/bids_template/phenotype/EpilepsyClassification2017.json index 6c819138..e6d2778a 100644 --- a/inputs/bids_template/phenotype/EpilepsyClassification2017.json +++ b/inputs/bids_template/phenotype/EpilepsyClassification2017.json @@ -1,263 +1,246 @@ { - "epilepsy_classification": { - "LongName": "Epilepsy Classification", - "Description": "ILAE classification of the epilepsies", - "TermURL": "", - "Citation": "Scheffer, I. E., Berkovic, S., Capovilla, G., Connolly, M. B., French, J., Guilhoto, L., ... & Nordli, D. R. (2017). ILAE classification of the epilepsies: position paper of the ILAE Commission for Classification and Terminology. Epilepsia, 58(4), 512-521.", + "epilepsy_classification": { + "LongName": "Epilepsy Classification", + "Description": "ILAE classification of the epilepsies", + "TermURL": "", + "Citation": "Scheffer, I. E., Berkovic, S., Capovilla, G., Connolly, M. B., French, J., Guilhoto, L., ... & Nordli, D. R. (2017). ILAE classification of the epilepsies: position paper of the ILAE Commission for Classification and Terminology. Epilepsia, 58(4), 512-521.", + "Levels": { + "seizure_type": { + "LongName": "Seizure type", + "Description": "Seizures are classified by onset: Generalised, Focal and Unknown", "Levels": { - "seizure_type": { - "LongName": "Seizure type", - "Description": "Seizures are classified by onset: Generalised, Focal and Unknown", - "Levels": { - "Generalised": { - "Levels": { - "Motor": [ - "GeneralizedTonicClonicAndVariants", - "GeneralizedTonic", - "GeneralizedAtonic", - "Myoclonic", - "MyoclonicAtonic", - "EpilepticSpasms" - ], - "NonMotor": [ - "TypicalAbsence", - "AtypicalAbsence", - "MyoclonicAbsence", - "AbsenceWithEyelidMyoclonia" - ] - } - }, - "Focal": { - "Levels": { - "Awareness": [ - "Aware", - "ImpairedAwareness" - ], - "Motor": [ - "FocalClonicSeizure", - "FocalTonicSeizure", - "FocalMotorSeizureWithDystonia", - "FocalMyoclonicSeizure", - "FocalAtonicSeizure", - "FocalMotorSeizureWithParesisOrParalysis", - "FocalEpilepticSpasms", - "FocalHyperkineticSeizure", - "FocalAutomatismSeizure", - "FocalMotorSeizureWithDysarthriaOrAnarthria", - "FocalMotorSeizureWithNegativeMyoclonus", - "FocalMotorSeizureWithVersion", - "FocalBilateralMotorSeizure" - ], - "NonMotor": { - "Levels": { - "FocalSensorySeizure": [ - "FocalSomatosensorySeizure", - "FocalSensoryVisualSeizure", - "FocalSensoryAuditorySeizure", - "FocalSensoryOlfactorySeizure", - "FocalSensoryGustatorySeizure", - "FocalSensoryVestibularSeizure", - "FocalSensorySeizureWithHotOrColdSensations", - "FocalSensorySeizureWithCephalicSensation" - ], - "FocalCognitiveSeizure": [ - "FocalCognitiveSeizureWithExpressiveDysphasiaOrAphasia", - "FocalCognitiveSeizureWithAnomia", - "FocalCognitiveSeizureWithReceptiveDysphasiaOrAphasia", - "FocalCognitiveSeizureWithAuditoryAgnosia", - "FocalCognitiveSeizureWithConductionDysphasiaOrAphasia", - "FocalCognitiveSeizureWithDyslexiaOrAlexia", - "FocalCognitiveSeizureWithMemoryIpairment", - "FocalCognitiveSeizureWithDejaVuOrJamaisVu", - "FocalCognitiveSeizureWithHallucination", - "FocalCognitiveSeizureWithIllusion", - "FocalCognitiveSeizureWithDissociation", - "FocalCognitiveSeizureWithForcedThinking", - "FocalCognitiveSeizureWithDyscalculiaOrAcalculia", - "FocalCognitiveSeizureWithDysgraphiaOrAgraphia", - "FocalCognitiveSeizureWithLeftRightConfusion", - "FocalCognitiveSeizureWithNeglect" - ], - "FocalEmotionalSeizure": [ - "FocalEmotionalSeizureWithFearOrAnxietyOrPanic", - "FocalEmotionalSeizureWithLaughingGelastic", - "FocalEmotionalSeizureWithCryingDacrystic", - "FocalEmotionalSeizureWithPleasure", - "FocalEmotionalSeizureWithAnger" - ], - "FocalAutonomicSeizure": [ - "FocalAutonomicSeizureWithPalpitationsOrTachycardiaOrBradycardiaOrAsystole", - "FocalAutonomicSeizureWithEpigastricSensation", - "FocalAutonomicSeizureWithPallorOrFlushing", - "FocalAutonomicSeizureWithHypoventilationOrHyperventilationOrAlteredRespiration", - "FocalAutonomicSeizureWithPiloerection", - "FocalAutonomicSeizureWithErection", - "FocalAutonomicSeizureWithUrgeToUrinateOrDefecate", - "FocalAutonomicSeizureWithLacrimation", - "FocalAutonomicSeizureWithPupillaryDilationOrConstriction" - ], - "FocalBehaviouralArrestSeizure": [ - "FocalBehaviouralArrestSeizure" - ] - } - }, - "FocalToBilateralTonicClonicSeizure": [ - "FocalToBilateralTonicClonicSeizure" - ] - } - }, - "Unknown": { - "Levels": { - "Motor": [ - "TonicClonic", - "EpilepticSpasms" - ], - "NonMotor": [ - "BehaviourArrest", - "Unclassified" - ] - } - } - } - }, - "epilepsy_type": { - "LongName": "Epilepsy type", - "Description": "Epilepsy types are divided into four categories: Generalised Epilepsy, Focal Epilepsy, Combined generalised and focal Epilepsy and Unknown Epilepsy", - "Levels": { - "Generalised": { - "LongName": "Generalised Epilepsy", - "Description": "Patients with generalized epilepsy have generalized seizure types, and may have typical interictal and/or ictal EEG findings that accompany generalized seizure types (for example generalized spike and wave)." - }, - "Focal": { - "LongName": "Focal Epilepsy", - "Description": "Patients with focal epilepsy have focal seizure types, and may have typical interictal and/or ictal EEG findings that accompany focal seizure types (such as focal sharp waves or focal interictal slowing)." - }, - "Combined": { - "LongName": "Combined generalised and focal Epilepsy", - "Description": "Patients may have both generalized and focal seizure types, with interictal and/or ictal EEG findings that accompany both seizure types." - }, - "Unknown": { - "LongName": "Unknown Epilepsy", - "Description": "The term 'unknown' is used to denote where it is understood that the patient has epilepsy, but it is not possible to denote whether it is focal, generalized, or combined focal and generalized. This may occur due to insufficient information to classify the epilepsy, for example if the EEG is normal/uninformative." - } - } - }, - "epilepsy_syndrome": { - "LongName": "Epilepsy Syndrome", - "Description": "Epilepsies are organized by reliably identifying common clinical and electrical characteristics into epilepsy syndromes. Such syndromes have a typical age of seizure onset, specific seizure types and EEG characteristics and often other features which when taken together allow the specific epilepsy syndrome diagnosis.", - "Levels": { - "NeonatalInfantile": [ - "SelfLimitedNeonatalSeizuresAndSelfLimitedFamilialNeonatalEpilepsy", - "SelfLimitedFamilialAndNonFamilialInfantileEpilepsy", - "EarlyMyoclonicEncephalopathy", - "OhtaharaSyndrome", - "WestSyndrome", - "DravetSyndrome", - "MyoclonicEpilepsyInInfancy", - "EpilepsyOfInfancyWithMigratingFocalSeizures", - "MyoclonicEncephalopathyInNonProgressiveDisorders", - "FebrileSeizuresPlusGeneticEpilepsyWithFebrileSeizuresPlus" - ], - "Childhood": [ - "EpilepsyWithMyoclonicAtonicSeizures", - "EpilepsyWithEyelidMyoclonias", - "LennoxGastautSyndrome", - "ChildhoodAbsenceEpilepsy", - "EpilepsyWithMyoclonicAbsences", - "PanayiotopoulosSyndrome", - "ChildhoodOccipitalEpilepsyGastautType", - "PhotosensitiveOccipitalLobeEpilepsy", - "ChildhoodEpilepsyWithCentrotemporalSpikes", - "AtypicalChildhoodEpilepsyWithCentrotemporalSpikes", - "EpilepticEncephalopathyWithContinuousSpikeAndWaveDuringSleep", - "LandauKleffnerSyndrome", - "AutosomalDominantNocturnalFrontalLobeEpilepsy" - ], - "AdolescentAdult": [ - "JuvenileAbsenceEpilepsy", - "JuvenileMyoclonicEpilepsy", - "EpilepsyWithGeneralizedTonicClonicSeizuresAlone", - "AutosomalDominantEpilepsyWithAuditoryFeatures", - "OtherFamilialTemporalLobeEpilepsies" - ], - "AnyAge": [ - "FamilialFocalEpilepsyWithVariableFoci", - "ReflexEpilepsies", - "ProgressiveMyoclonusEpilepsies" - ] - } - }, - "etiology": { - "LongName": "Epilepsy etiology", - "Description": "At each stage, etiology (cause and comorbidities) should be identified. These are divided into six categories.", + "Generalised": { + "Levels": { + "Motor": [ + "GeneralizedTonicClonicAndVariants", + "GeneralizedTonic", + "GeneralizedAtonic", + "Myoclonic", + "MyoclonicAtonic", + "EpilepticSpasms" + ], + "NonMotor": [ + "TypicalAbsence", + "AtypicalAbsence", + "MyoclonicAbsence", + "AbsenceWithEyelidMyoclonia" + ] + } + }, + "Focal": { + "Levels": { + "Awareness": ["Aware", "ImpairedAwareness"], + "Motor": [ + "FocalClonicSeizure", + "FocalTonicSeizure", + "FocalMotorSeizureWithDystonia", + "FocalMyoclonicSeizure", + "FocalAtonicSeizure", + "FocalMotorSeizureWithParesisOrParalysis", + "FocalEpilepticSpasms", + "FocalHyperkineticSeizure", + "FocalAutomatismSeizure", + "FocalMotorSeizureWithDysarthriaOrAnarthria", + "FocalMotorSeizureWithNegativeMyoclonus", + "FocalMotorSeizureWithVersion", + "FocalBilateralMotorSeizure" + ], + "NonMotor": { "Levels": { - "Genetic": { - "LongName": "Genetic Etiology", - "Description": "The concept of genetic epilepsy is that the epilepsy is, as best we understand, the direct result of a known or presumed genetic defect(s) in which seizures are the core symptom of the disorder.", - "Levels": [ - "ChromosomalAbnormalities", - "GeneAbnormalities" - ] - }, - "Structural": { - "LongName": "Structural Etiology", - "Description": "Structural epilepsies are conceptualized as having a distinct structural brain abnormality that has been demonstrated to be associated with a substantially increased risk of epilepsy in appropriately designed studies.", - "Levels": [ - "MalformationsOfCorticalDevelopment", - "VascularMalformations", - "HippocampalSclerosis", - "HypoxicIschemicStructuralAbnormalities", - "TraumaticBrainInjury", - "Tumors", - "PorencephalicCyst" - ] - }, - "Metabolic": { - "LongName": "Metabolic Etiology", - "Description": "Metabolic epilepsies are conceptualized as having a distinct metabolic abnormality that has been demonstrated to be associated with a substantially increased risk of developing epilepsy in appropriately designed studies.", - "Levels": [ - "BiotinidaseAndHolocarboxylaseSynthaseDeficiency", - "CerebralFolateDeficiency", - "CreatineDisorders", - "FolinicAcidResponsiveSeizures", - "GlucoseTransporter1Deficiency", - "MitochondrialDisorders", - "PeroxisomalDisorders", - "PyridoxineDependentEpilepsy" - ] - }, - "Immune": { - "LongName": "Immune Etiology", - "Description": "Immune epilepsies are conceptualized as having a distinct immune-mediated etiology with evidence of central nervous system inflammation, that has been demonstrated to be associated with a substantially increased risk of developing epilepsy.", - "Levels": [ - "RasmussenSyndrome", - "AntibodyMediatedEtiologies" - ] - }, - "Infectious": { - "LongName": "Infectious Etiology", - "Description": "The commonest etiology for epilepsy worldwide is infectious, especially in developing countries. Infections in the central nervous system can cause both acute symptomatic seizures (which occur closely related to the timing of the initial infection) and epilepsy.", - "Levels": [ - "BacterialMeningitis", - "CerebralMalaria", - "CerebralToxoplasmosis", - "CMV", - "HIV", - "Neurocysticercosis", - "Tuberculosis", - "ViralEncephalitis", - "OtherInfections" - ] - }, - "Unknown": { - "LongName": "Unknown Etiology", - "Description": "'Unknown' is meant to be viewed neutrally and to designate that the nature of the underlying cause of the epilepsy is as yet unknown; it may have a fundamental genetic defect at its core or there may be a separate as yet unrecognized disorder.", - "Levels": [ - "FebrileInfectionRelatedEpilepsySyndrome" - ] - } + "FocalSensorySeizure": [ + "FocalSomatosensorySeizure", + "FocalSensoryVisualSeizure", + "FocalSensoryAuditorySeizure", + "FocalSensoryOlfactorySeizure", + "FocalSensoryGustatorySeizure", + "FocalSensoryVestibularSeizure", + "FocalSensorySeizureWithHotOrColdSensations", + "FocalSensorySeizureWithCephalicSensation" + ], + "FocalCognitiveSeizure": [ + "FocalCognitiveSeizureWithExpressiveDysphasiaOrAphasia", + "FocalCognitiveSeizureWithAnomia", + "FocalCognitiveSeizureWithReceptiveDysphasiaOrAphasia", + "FocalCognitiveSeizureWithAuditoryAgnosia", + "FocalCognitiveSeizureWithConductionDysphasiaOrAphasia", + "FocalCognitiveSeizureWithDyslexiaOrAlexia", + "FocalCognitiveSeizureWithMemoryIpairment", + "FocalCognitiveSeizureWithDejaVuOrJamaisVu", + "FocalCognitiveSeizureWithHallucination", + "FocalCognitiveSeizureWithIllusion", + "FocalCognitiveSeizureWithDissociation", + "FocalCognitiveSeizureWithForcedThinking", + "FocalCognitiveSeizureWithDyscalculiaOrAcalculia", + "FocalCognitiveSeizureWithDysgraphiaOrAgraphia", + "FocalCognitiveSeizureWithLeftRightConfusion", + "FocalCognitiveSeizureWithNeglect" + ], + "FocalEmotionalSeizure": [ + "FocalEmotionalSeizureWithFearOrAnxietyOrPanic", + "FocalEmotionalSeizureWithLaughingGelastic", + "FocalEmotionalSeizureWithCryingDacrystic", + "FocalEmotionalSeizureWithPleasure", + "FocalEmotionalSeizureWithAnger" + ], + "FocalAutonomicSeizure": [ + "FocalAutonomicSeizureWithPalpitationsOrTachycardiaOrBradycardiaOrAsystole", + "FocalAutonomicSeizureWithEpigastricSensation", + "FocalAutonomicSeizureWithPallorOrFlushing", + "FocalAutonomicSeizureWithHypoventilationOrHyperventilationOrAlteredRespiration", + "FocalAutonomicSeizureWithPiloerection", + "FocalAutonomicSeizureWithErection", + "FocalAutonomicSeizureWithUrgeToUrinateOrDefecate", + "FocalAutonomicSeizureWithLacrimation", + "FocalAutonomicSeizureWithPupillaryDilationOrConstriction" + ], + "FocalBehaviouralArrestSeizure": [ + "FocalBehaviouralArrestSeizure" + ] } + }, + "FocalToBilateralTonicClonicSeizure": [ + "FocalToBilateralTonicClonicSeizure" + ] } + }, + "Unknown": { + "Levels": { + "Motor": ["TonicClonic", "EpilepticSpasms"], + "NonMotor": ["BehaviourArrest", "Unclassified"] + } + } + } + }, + "epilepsy_type": { + "LongName": "Epilepsy type", + "Description": "Epilepsy types are divided into four categories: Generalised Epilepsy, Focal Epilepsy, Combined generalised and focal Epilepsy and Unknown Epilepsy", + "Levels": { + "Generalised": { + "LongName": "Generalised Epilepsy", + "Description": "Patients with generalized epilepsy have generalized seizure types, and may have typical interictal and/or ictal EEG findings that accompany generalized seizure types (for example generalized spike and wave)." + }, + "Focal": { + "LongName": "Focal Epilepsy", + "Description": "Patients with focal epilepsy have focal seizure types, and may have typical interictal and/or ictal EEG findings that accompany focal seizure types (such as focal sharp waves or focal interictal slowing)." + }, + "Combined": { + "LongName": "Combined generalised and focal Epilepsy", + "Description": "Patients may have both generalized and focal seizure types, with interictal and/or ictal EEG findings that accompany both seizure types." + }, + "Unknown": { + "LongName": "Unknown Epilepsy", + "Description": "The term 'unknown' is used to denote where it is understood that the patient has epilepsy, but it is not possible to denote whether it is focal, generalized, or combined focal and generalized. This may occur due to insufficient information to classify the epilepsy, for example if the EEG is normal/uninformative." + } + } + }, + "epilepsy_syndrome": { + "LongName": "Epilepsy Syndrome", + "Description": "Epilepsies are organized by reliably identifying common clinical and electrical characteristics into epilepsy syndromes. Such syndromes have a typical age of seizure onset, specific seizure types and EEG characteristics and often other features which when taken together allow the specific epilepsy syndrome diagnosis.", + "Levels": { + "NeonatalInfantile": [ + "SelfLimitedNeonatalSeizuresAndSelfLimitedFamilialNeonatalEpilepsy", + "SelfLimitedFamilialAndNonFamilialInfantileEpilepsy", + "EarlyMyoclonicEncephalopathy", + "OhtaharaSyndrome", + "WestSyndrome", + "DravetSyndrome", + "MyoclonicEpilepsyInInfancy", + "EpilepsyOfInfancyWithMigratingFocalSeizures", + "MyoclonicEncephalopathyInNonProgressiveDisorders", + "FebrileSeizuresPlusGeneticEpilepsyWithFebrileSeizuresPlus" + ], + "Childhood": [ + "EpilepsyWithMyoclonicAtonicSeizures", + "EpilepsyWithEyelidMyoclonias", + "LennoxGastautSyndrome", + "ChildhoodAbsenceEpilepsy", + "EpilepsyWithMyoclonicAbsences", + "PanayiotopoulosSyndrome", + "ChildhoodOccipitalEpilepsyGastautType", + "PhotosensitiveOccipitalLobeEpilepsy", + "ChildhoodEpilepsyWithCentrotemporalSpikes", + "AtypicalChildhoodEpilepsyWithCentrotemporalSpikes", + "EpilepticEncephalopathyWithContinuousSpikeAndWaveDuringSleep", + "LandauKleffnerSyndrome", + "AutosomalDominantNocturnalFrontalLobeEpilepsy" + ], + "AdolescentAdult": [ + "JuvenileAbsenceEpilepsy", + "JuvenileMyoclonicEpilepsy", + "EpilepsyWithGeneralizedTonicClonicSeizuresAlone", + "AutosomalDominantEpilepsyWithAuditoryFeatures", + "OtherFamilialTemporalLobeEpilepsies" + ], + "AnyAge": [ + "FamilialFocalEpilepsyWithVariableFoci", + "ReflexEpilepsies", + "ProgressiveMyoclonusEpilepsies" + ] + } + }, + "etiology": { + "LongName": "Epilepsy etiology", + "Description": "At each stage, etiology (cause and comorbidities) should be identified. These are divided into six categories.", + "Levels": { + "Genetic": { + "LongName": "Genetic Etiology", + "Description": "The concept of genetic epilepsy is that the epilepsy is, as best we understand, the direct result of a known or presumed genetic defect(s) in which seizures are the core symptom of the disorder.", + "Levels": ["ChromosomalAbnormalities", "GeneAbnormalities"] + }, + "Structural": { + "LongName": "Structural Etiology", + "Description": "Structural epilepsies are conceptualized as having a distinct structural brain abnormality that has been demonstrated to be associated with a substantially increased risk of epilepsy in appropriately designed studies.", + "Levels": [ + "MalformationsOfCorticalDevelopment", + "VascularMalformations", + "HippocampalSclerosis", + "HypoxicIschemicStructuralAbnormalities", + "TraumaticBrainInjury", + "Tumors", + "PorencephalicCyst" + ] + }, + "Metabolic": { + "LongName": "Metabolic Etiology", + "Description": "Metabolic epilepsies are conceptualized as having a distinct metabolic abnormality that has been demonstrated to be associated with a substantially increased risk of developing epilepsy in appropriately designed studies.", + "Levels": [ + "BiotinidaseAndHolocarboxylaseSynthaseDeficiency", + "CerebralFolateDeficiency", + "CreatineDisorders", + "FolinicAcidResponsiveSeizures", + "GlucoseTransporter1Deficiency", + "MitochondrialDisorders", + "PeroxisomalDisorders", + "PyridoxineDependentEpilepsy" + ] + }, + "Immune": { + "LongName": "Immune Etiology", + "Description": "Immune epilepsies are conceptualized as having a distinct immune-mediated etiology with evidence of central nervous system inflammation, that has been demonstrated to be associated with a substantially increased risk of developing epilepsy.", + "Levels": ["RasmussenSyndrome", "AntibodyMediatedEtiologies"] + }, + "Infectious": { + "LongName": "Infectious Etiology", + "Description": "The commonest etiology for epilepsy worldwide is infectious, especially in developing countries. Infections in the central nervous system can cause both acute symptomatic seizures (which occur closely related to the timing of the initial infection) and epilepsy.", + "Levels": [ + "BacterialMeningitis", + "CerebralMalaria", + "CerebralToxoplasmosis", + "CMV", + "HIV", + "Neurocysticercosis", + "Tuberculosis", + "ViralEncephalitis", + "OtherInfections" + ] + }, + "Unknown": { + "LongName": "Unknown Etiology", + "Description": "'Unknown' is meant to be viewed neutrally and to designate that the nature of the underlying cause of the epilepsy is as yet unknown; it may have a fundamental genetic defect at its core or there may be a separate as yet unrecognized disorder.", + "Levels": ["FebrileInfectionRelatedEpilepsySyndrome"] + } } + } } + } } diff --git a/inputs/bids_template/sub-01/ses-01/anat/sub-01_ses-01_acq-FullExample_run-01_T1w.json b/inputs/bids_template/sub-01/ses-01/anat/sub-01_ses-01_acq-FullExample_run-01_T1w.json index f9e6edc3..9369d099 100644 --- a/inputs/bids_template/sub-01/ses-01/anat/sub-01_ses-01_acq-FullExample_run-01_T1w.json +++ b/inputs/bids_template/sub-01/ses-01/anat/sub-01_ses-01_acq-FullExample_run-01_T1w.json @@ -1,40 +1,40 @@ { - "Manufacturer": "Sielips / Phimens", - "ManufacturersModelName": "Terra", - "MagneticFieldStrength": 7, - "DeviceSerialNumber": 1234, - "StationName": "International space station", - "SoftwareVersions": " ", - "ReceiveCoilName": " ", - "ReceiveCoilActiveElements": " ", - "GradientSetType": " ", - "MRTransmitCoilSequence": " ", - "MatrixCoilMode": " ", - "CoilCombinationMethod": " ", - "PulseSequenceType": "MPRAGE", - "ScanningSequence": " ", - "SequenceVariant": " ", - "ScanOptions": " ", - "SequenceName": " ", - "PulseSequenceDetails": " ", - "NonlinearGradientCorrection": " ", - "NumberShots": 2, - "ParallelReductionFactorInPlane": 2, - "ParallelAcquisitionTechnique": "GRAPPA", - "PartialFourier": " ", - "PartialFourierDirection": " ", - "PhaseEncodingDirection": "i", - "WaterFatShift": " ", - "EchoTrainLength": " ", - "EchoTime": 2, - "InversionTime": " ", - "SliceEncodingDirection": " ", - "DwellTime": " ", - "FlipAngle": 90, - "MultibandAccelerationFactor": " ", - "AnatomicalLandmarkCoordinates": " ", - "InstitutionName": "BCBL", - "InstitutionAddress": "Zoomlandia", - "InstitutionalDepartmentName": " ", - "ContrastBolusIngredient": " " + "Manufacturer": "Sielips / Phimens", + "ManufacturersModelName": "Terra", + "MagneticFieldStrength": 7, + "DeviceSerialNumber": 1234, + "StationName": "International space station", + "SoftwareVersions": " ", + "ReceiveCoilName": " ", + "ReceiveCoilActiveElements": " ", + "GradientSetType": " ", + "MRTransmitCoilSequence": " ", + "MatrixCoilMode": " ", + "CoilCombinationMethod": " ", + "PulseSequenceType": "MPRAGE", + "ScanningSequence": " ", + "SequenceVariant": " ", + "ScanOptions": " ", + "SequenceName": " ", + "PulseSequenceDetails": " ", + "NonlinearGradientCorrection": " ", + "NumberShots": 2, + "ParallelReductionFactorInPlane": 2, + "ParallelAcquisitionTechnique": "GRAPPA", + "PartialFourier": " ", + "PartialFourierDirection": " ", + "PhaseEncodingDirection": "i", + "WaterFatShift": " ", + "EchoTrainLength": " ", + "EchoTime": 2, + "InversionTime": " ", + "SliceEncodingDirection": " ", + "DwellTime": " ", + "FlipAngle": 90, + "MultibandAccelerationFactor": " ", + "AnatomicalLandmarkCoordinates": " ", + "InstitutionName": "BCBL", + "InstitutionAddress": "Zoomlandia", + "InstitutionalDepartmentName": " ", + "ContrastBolusIngredient": " " } diff --git a/inputs/bids_template/sub-01/ses-01/anat/sub-01_ses-01_acq-ShortExample_run-01_T1w.json b/inputs/bids_template/sub-01/ses-01/anat/sub-01_ses-01_acq-ShortExample_run-01_T1w.json index 7c84958b..d4783dd1 100644 --- a/inputs/bids_template/sub-01/ses-01/anat/sub-01_ses-01_acq-ShortExample_run-01_T1w.json +++ b/inputs/bids_template/sub-01/ses-01/anat/sub-01_ses-01_acq-ShortExample_run-01_T1w.json @@ -1,7 +1,7 @@ { - "PhaseEncodingDirection": " ", - "EffectiveEchoSpacing": " ", - "TotalReadoutTime": " ", - "EchoTime": " ", - "SliceTiming": " " + "PhaseEncodingDirection": " ", + "EffectiveEchoSpacing": " ", + "TotalReadoutTime": " ", + "EchoTime": " ", + "SliceTiming": " " } diff --git a/inputs/bids_template/sub-01/ses-01/eeg/sub-01_ses-01_task-FilterExample_eeg.json b/inputs/bids_template/sub-01/ses-01/eeg/sub-01_ses-01_task-FilterExample_eeg.json index bdd6c031..7cb3ef2d 100644 --- a/inputs/bids_template/sub-01/ses-01/eeg/sub-01_ses-01_task-FilterExample_eeg.json +++ b/inputs/bids_template/sub-01/ses-01/eeg/sub-01_ses-01_task-FilterExample_eeg.json @@ -1,9 +1,9 @@ { - "HardwareFilters": { - "Highpass RC filter": { - "Half amplitude cutoff (Hz)": 0.0159, - "Roll-off": "6dB/Octave" - } - }, - "SoftwareFilters": "n/a" + "HardwareFilters": { + "Highpass RC filter": { + "Half amplitude cutoff (Hz)": 0.0159, + "Roll-off": "6dB/Octave" + } + }, + "SoftwareFilters": "n/a" } diff --git a/inputs/bids_template/sub-01/ses-01/eeg/sub-01_ses-01_task-FullExample_eeg.json b/inputs/bids_template/sub-01/ses-01/eeg/sub-01_ses-01_task-FullExample_eeg.json index 094f659e..72f6a07d 100644 --- a/inputs/bids_template/sub-01/ses-01/eeg/sub-01_ses-01_task-FullExample_eeg.json +++ b/inputs/bids_template/sub-01/ses-01/eeg/sub-01_ses-01_task-FullExample_eeg.json @@ -1,32 +1,32 @@ { - "TaskName": "Testdata", - "TaskDescription": "resting state", - "Instructions": "", - "CogAtlasID": "", - "CogPOID": "", - "InstitutionName": "University of Open Science", - "InstitutionalDepartmentName": "", - "InstitutionAddress": " Third rock from the sun", - "Manufacturer": "Biosemi", - "ManufacturersModelName": "ActiveTwo", - "DeviceSerialNumber": "BHD2020", - "SoftwareVersions": "13.11", - "PowerLineFrequency": 50, - "SamplingFrequency": 512, - "EEGChannelCount": 64, - "EOGChannelCount": 2, - "ECGChannelCount": 2, - "EMGChannelCount": 3, - "MiscChannelCount": [], - "TriggerChannelCount": [], - "EEGPlacementScheme": "10-20 international system", - "EEGReference": "right and left earlobes", - "EEGGround": "CMS-DRL", - "CapManufacturer": "", - "CapManufacturersModelName": "", - "HardwareFilters": "", - "SoftwareFilters": "", - "RecordingDuration": 5, - "RecordingType": "continuous", - "SubjectArtefactDescription": "" + "TaskName": "Testdata", + "TaskDescription": "resting state", + "Instructions": "", + "CogAtlasID": "", + "CogPOID": "", + "InstitutionName": "University of Open Science", + "InstitutionalDepartmentName": "", + "InstitutionAddress": " Third rock from the sun", + "Manufacturer": "Biosemi", + "ManufacturersModelName": "ActiveTwo", + "DeviceSerialNumber": "BHD2020", + "SoftwareVersions": "13.11", + "PowerLineFrequency": 50, + "SamplingFrequency": 512, + "EEGChannelCount": 64, + "EOGChannelCount": 2, + "ECGChannelCount": 2, + "EMGChannelCount": 3, + "MiscChannelCount": [], + "TriggerChannelCount": [], + "EEGPlacementScheme": "10-20 international system", + "EEGReference": "right and left earlobes", + "EEGGround": "CMS-DRL", + "CapManufacturer": "", + "CapManufacturersModelName": "", + "HardwareFilters": "", + "SoftwareFilters": "", + "RecordingDuration": 5, + "RecordingType": "continuous", + "SubjectArtefactDescription": "" } diff --git a/inputs/bids_template/sub-01/ses-01/eeg/sub-01_ses-01_task-MinimalExample_eeg.json b/inputs/bids_template/sub-01/ses-01/eeg/sub-01_ses-01_task-MinimalExample_eeg.json index 8e906e13..df0a0394 100644 --- a/inputs/bids_template/sub-01/ses-01/eeg/sub-01_ses-01_task-MinimalExample_eeg.json +++ b/inputs/bids_template/sub-01/ses-01/eeg/sub-01_ses-01_task-MinimalExample_eeg.json @@ -1,10 +1,10 @@ { - "TaskName": "", - "SamplingFrequency": [], - "EEGChannelCount": [], - "EOGChannelCount": [], - "ECGChannelCount": [], - "EMGChannelCount": [], - "EEGReference": "", - "PowerLineFrequency": [] + "TaskName": "", + "SamplingFrequency": [], + "EEGChannelCount": [], + "EOGChannelCount": [], + "ECGChannelCount": [], + "EMGChannelCount": [], + "EEGReference": "", + "PowerLineFrequency": [] } diff --git a/inputs/bids_template/sub-01/ses-01/eeg/sub-01_ses-01_task-ReferenceExample_eeg.json b/inputs/bids_template/sub-01/ses-01/eeg/sub-01_ses-01_task-ReferenceExample_eeg.json index 84685231..069171de 100644 --- a/inputs/bids_template/sub-01/ses-01/eeg/sub-01_ses-01_task-ReferenceExample_eeg.json +++ b/inputs/bids_template/sub-01/ses-01/eeg/sub-01_ses-01_task-ReferenceExample_eeg.json @@ -1,6 +1,6 @@ { - "Manufacturer": "Biosemi", - "ManufacturersModelName": "ActiveTwo", - "EEGReference": "CMS, placed on Cz", - "EEGGround": "DRL, placed on Fz" + "Manufacturer": "Biosemi", + "ManufacturersModelName": "ActiveTwo", + "EEGReference": "CMS, placed on Cz", + "EEGGround": "DRL, placed on Fz" } diff --git a/inputs/bids_template/sub-01/ses-01/fmap/sub-01_ses-01_task-Case1_run-01_phasediff.json b/inputs/bids_template/sub-01/ses-01/fmap/sub-01_ses-01_task-Case1_run-01_phasediff.json index 3b526d76..177c54a2 100644 --- a/inputs/bids_template/sub-01/ses-01/fmap/sub-01_ses-01_task-Case1_run-01_phasediff.json +++ b/inputs/bids_template/sub-01/ses-01/fmap/sub-01_ses-01_task-Case1_run-01_phasediff.json @@ -1,5 +1,5 @@ { - "EchoTime1": "", - "EchoTime2": "", - "IntendedFor": "" + "EchoTime1": "", + "EchoTime2": "", + "IntendedFor": "" } diff --git a/inputs/bids_template/sub-01/ses-01/fmap/sub-01_ses-01_task-Case2_run-01_phase1.json b/inputs/bids_template/sub-01/ses-01/fmap/sub-01_ses-01_task-Case2_run-01_phase1.json index 78edee63..008125cb 100644 --- a/inputs/bids_template/sub-01/ses-01/fmap/sub-01_ses-01_task-Case2_run-01_phase1.json +++ b/inputs/bids_template/sub-01/ses-01/fmap/sub-01_ses-01_task-Case2_run-01_phase1.json @@ -1,4 +1,4 @@ { - "EchoTime": "", - "IntendedFor": "" + "EchoTime": "", + "IntendedFor": "" } diff --git a/inputs/bids_template/sub-01/ses-01/fmap/sub-01_ses-01_task-Case2_run-01_phase2.json b/inputs/bids_template/sub-01/ses-01/fmap/sub-01_ses-01_task-Case2_run-01_phase2.json index 78edee63..008125cb 100644 --- a/inputs/bids_template/sub-01/ses-01/fmap/sub-01_ses-01_task-Case2_run-01_phase2.json +++ b/inputs/bids_template/sub-01/ses-01/fmap/sub-01_ses-01_task-Case2_run-01_phase2.json @@ -1,4 +1,4 @@ { - "EchoTime": "", - "IntendedFor": "" + "EchoTime": "", + "IntendedFor": "" } diff --git a/inputs/bids_template/sub-01/ses-01/fmap/sub-01_ses-01_task-Case3_run-01_fieldmap.json b/inputs/bids_template/sub-01/ses-01/fmap/sub-01_ses-01_task-Case3_run-01_fieldmap.json index 701be5b5..b7c47944 100644 --- a/inputs/bids_template/sub-01/ses-01/fmap/sub-01_ses-01_task-Case3_run-01_fieldmap.json +++ b/inputs/bids_template/sub-01/ses-01/fmap/sub-01_ses-01_task-Case3_run-01_fieldmap.json @@ -1,4 +1,4 @@ { - "Units": "", - "IntendedFor": "" + "Units": "", + "IntendedFor": "" } diff --git a/inputs/bids_template/sub-01/ses-01/fmap/sub-01_ses-01_task-Case4_dir-LR_run-01_epi.json b/inputs/bids_template/sub-01/ses-01/fmap/sub-01_ses-01_task-Case4_dir-LR_run-01_epi.json index f895c797..aaf2fac0 100644 --- a/inputs/bids_template/sub-01/ses-01/fmap/sub-01_ses-01_task-Case4_dir-LR_run-01_epi.json +++ b/inputs/bids_template/sub-01/ses-01/fmap/sub-01_ses-01_task-Case4_dir-LR_run-01_epi.json @@ -1,5 +1,5 @@ { - "PhaseEncodingDirection": "", - "TotalReadoutTime": "", - "IntendedFor": "" + "PhaseEncodingDirection": "", + "TotalReadoutTime": "", + "IntendedFor": "" } diff --git a/inputs/bids_template/sub-01/ses-01/func/sub-01_ses-01_task-FullExample_run-01_bold.json b/inputs/bids_template/sub-01/ses-01/func/sub-01_ses-01_task-FullExample_run-01_bold.json index dd0196e1..f0d9071e 100644 --- a/inputs/bids_template/sub-01/ses-01/func/sub-01_ses-01_task-FullExample_run-01_bold.json +++ b/inputs/bids_template/sub-01/ses-01/func/sub-01_ses-01_task-FullExample_run-01_bold.json @@ -1,53 +1,53 @@ { - "TaskName": "", - "RepetitionTime": [], - "VolumeTiming": [], - "DelayTime": [], - "SliceTiming": "", - "AcquisitionDuration": [], - "PhaseEncodingDirection": "", - "EffectiveEchoSpacing": "", - "EchoTime": "", - "Manufacturer": "", - "ManufacturersModelName": "", - "MagneticFieldStrength": "", - "DeviceSerialNumber": "", - "StationName": " ", - "SoftwareVersions": " ", - "HardcopyDeviceSoftwareVersion": "", - "ReceiveCoilName": " ", - "GradientSetType": "", - "MRTransmitCoilSequence": "", - "MatrixCoilMode": "", - "CoilCombinationMethod": "", - "PulseSequenceType": "", - "ScanningSequence": "", - "SequenceVariant": "", - "ScanOptions": "", - "SequenceName": "", - "PulseSequenceDetails": "", - "NonlinearGradientCorrection": "", - "NumberShots": "", - "ParallelReductionFactorInPlane": "", - "ParallelAcquisitionTechnique": "", - "PartialFourier": "", - "PartialFourierDirection": "", - "WaterFatShift": "", - "EchoTrainLength": "", - "InversionTime": "", - "SliceEncodingDirection": "", - "DwellTime": "", - "TotalReadoutTime": "", - "DelayAfterTrigger": [], - "NumberOfVolumesDiscardedByScanner": "", - "NumberOfVolumesDiscardedByUser": "", - "FlipAngle": "", - "MultibandAccelerationFactor": "", - "Instructions": "", - "TaskDescription": "", - "CogAtlasID": "", - "CogPOID": "", - "InstitutionName": "", - "InstitutionAddress": "", - "InstitutionalDepartmentName": "" + "TaskName": "", + "RepetitionTime": [], + "VolumeTiming": [], + "DelayTime": [], + "SliceTiming": "", + "AcquisitionDuration": [], + "PhaseEncodingDirection": "", + "EffectiveEchoSpacing": "", + "EchoTime": "", + "Manufacturer": "", + "ManufacturersModelName": "", + "MagneticFieldStrength": "", + "DeviceSerialNumber": "", + "StationName": " ", + "SoftwareVersions": " ", + "HardcopyDeviceSoftwareVersion": "", + "ReceiveCoilName": " ", + "GradientSetType": "", + "MRTransmitCoilSequence": "", + "MatrixCoilMode": "", + "CoilCombinationMethod": "", + "PulseSequenceType": "", + "ScanningSequence": "", + "SequenceVariant": "", + "ScanOptions": "", + "SequenceName": "", + "PulseSequenceDetails": "", + "NonlinearGradientCorrection": "", + "NumberShots": "", + "ParallelReductionFactorInPlane": "", + "ParallelAcquisitionTechnique": "", + "PartialFourier": "", + "PartialFourierDirection": "", + "WaterFatShift": "", + "EchoTrainLength": "", + "InversionTime": "", + "SliceEncodingDirection": "", + "DwellTime": "", + "TotalReadoutTime": "", + "DelayAfterTrigger": [], + "NumberOfVolumesDiscardedByScanner": "", + "NumberOfVolumesDiscardedByUser": "", + "FlipAngle": "", + "MultibandAccelerationFactor": "", + "Instructions": "", + "TaskDescription": "", + "CogAtlasID": "", + "CogPOID": "", + "InstitutionName": "", + "InstitutionAddress": "", + "InstitutionalDepartmentName": "" } diff --git a/inputs/bids_template/sub-01/ses-01/func/sub-01_ses-01_task-FullExample_run-01_events.json b/inputs/bids_template/sub-01/ses-01/func/sub-01_ses-01_task-FullExample_run-01_events.json index ef826855..ecc5cb70 100644 --- a/inputs/bids_template/sub-01/ses-01/func/sub-01_ses-01_task-FullExample_run-01_events.json +++ b/inputs/bids_template/sub-01/ses-01/func/sub-01_ses-01_task-FullExample_run-01_events.json @@ -1,23 +1,23 @@ { - "trial_type": { - "LongName": "", - "Description": "Emotion image type", - "Levels": { - "afraid": "A face showing fear is displayed", - "angry": "A face showing anger is displayed" - }, - "Units": "", - "TermURL": "" + "trial_type": { + "LongName": "", + "Description": "Emotion image type", + "Levels": { + "afraid": "A face showing fear is displayed", + "angry": "A face showing anger is displayed" }, - "identifier": { - "LongName": "Unique identifier from Karolinska (KDEF) database", - "Description": "ID from KDEF database used to identify the displayed image" - }, - "StimulusPresentation": { - "OperatingSystem": "Linux Ubuntu 18.04.5", - "SoftwareName": "Psychtoolbox", - "SoftwareRRID": "SCR_002881", - "SoftwareVersion": "3.0.14", - "Code": "doi:10.5281/zenodo.3361717" - } + "Units": "", + "TermURL": "" + }, + "identifier": { + "LongName": "Unique identifier from Karolinska (KDEF) database", + "Description": "ID from KDEF database used to identify the displayed image" + }, + "StimulusPresentation": { + "OperatingSystem": "Linux Ubuntu 18.04.5", + "SoftwareName": "Psychtoolbox", + "SoftwareRRID": "SCR_002881", + "SoftwareVersion": "3.0.14", + "Code": "doi:10.5281/zenodo.3361717" + } } diff --git a/inputs/bids_template/sub-01/ses-01/func/sub-01_ses-01_task-ShortExample_run-01_bold.json b/inputs/bids_template/sub-01/ses-01/func/sub-01_ses-01_task-ShortExample_run-01_bold.json index c174d522..d22eef01 100644 --- a/inputs/bids_template/sub-01/ses-01/func/sub-01_ses-01_task-ShortExample_run-01_bold.json +++ b/inputs/bids_template/sub-01/ses-01/func/sub-01_ses-01_task-ShortExample_run-01_bold.json @@ -1,4 +1,4 @@ { - "TaskName": "", - "RepetitionTime": "" + "TaskName": "", + "RepetitionTime": "" } diff --git a/inputs/bids_template/sub-01/ses-01/ieeg/sub-01_ses-01_coordsystem.json b/inputs/bids_template/sub-01/ses-01/ieeg/sub-01_ses-01_coordsystem.json index 584414b7..445eb6ab 100644 --- a/inputs/bids_template/sub-01/ses-01/ieeg/sub-01_ses-01_coordsystem.json +++ b/inputs/bids_template/sub-01/ses-01/ieeg/sub-01_ses-01_coordsystem.json @@ -1,8 +1,8 @@ { - "iEEGCoordinateSystem": "", - "iEEGCoordinateUnits": "", - "iEEGCoordinateProcessingDescripton": "", - "IndendedFor": "", - "iEEGCoordinateProcessingDescription": "", - "iEEGCoordinateProcessingReference": "" + "iEEGCoordinateSystem": "", + "iEEGCoordinateUnits": "", + "iEEGCoordinateProcessingDescripton": "", + "IndendedFor": "", + "iEEGCoordinateProcessingDescription": "", + "iEEGCoordinateProcessingReference": "" } diff --git a/inputs/bids_template/sub-01/ses-01/ieeg/sub-01_ses-01_task-LongExample_run-01_ieeg.json b/inputs/bids_template/sub-01/ses-01/ieeg/sub-01_ses-01_task-LongExample_run-01_ieeg.json index 3eaab252..43df8494 100644 --- a/inputs/bids_template/sub-01/ses-01/ieeg/sub-01_ses-01_task-LongExample_run-01_ieeg.json +++ b/inputs/bids_template/sub-01/ses-01/ieeg/sub-01_ses-01_task-LongExample_run-01_ieeg.json @@ -1,45 +1,45 @@ { - "TaskName": "", - "SamplingFrequency": "", - "PowerLineFrequency": "", - "SoftwareFilters": "", - "DCOffsetCorrection": "", - "HardwareFilters": { - "HighpassFilter": { - "CutoffFrequency": [] - }, - "LowpassFilter": { - "CutoffFrequency": [] - } + "TaskName": "", + "SamplingFrequency": "", + "PowerLineFrequency": "", + "SoftwareFilters": "", + "DCOffsetCorrection": "", + "HardwareFilters": { + "HighpassFilter": { + "CutoffFrequency": [] }, - "Manufacturer": "", - "ManufacturersModelName": "", - "TaskDescription": "", - "Instructions": "", - "CogAtlasID": "", - "CogPOID": "", - "InstitutionName": "", - "InstitutionAddress": "", - "DeviceSerialNumber": "", - "ECOGChannelCount": "", - "SEEGChannelCount": "", - "EEGChannelCount": "", - "EOGChannelCount": "", - "ECGChannelCount": "", - "EMGChannelCount": "", - "MiscChannelCount": "", - "TriggerChannelCount": "", - "RecordingDuration": "", - "RecordingType": "", - "EpochLength": "", - "SubjectArtefactDescription": "", - "SoftwareVersions": "", - "iEEGReference": "", - "ElectrodeManufacturer": "", - "ElectrodeManufacturersModelName": "", - "iEEGGround": "", - "iEEGPlacementScheme": "", - "iEEGElectrodeGroups": "", - "ElectricalStimulation": "", - "ElectricalStimulationParameters": "" + "LowpassFilter": { + "CutoffFrequency": [] + } + }, + "Manufacturer": "", + "ManufacturersModelName": "", + "TaskDescription": "", + "Instructions": "", + "CogAtlasID": "", + "CogPOID": "", + "InstitutionName": "", + "InstitutionAddress": "", + "DeviceSerialNumber": "", + "ECOGChannelCount": "", + "SEEGChannelCount": "", + "EEGChannelCount": "", + "EOGChannelCount": "", + "ECGChannelCount": "", + "EMGChannelCount": "", + "MiscChannelCount": "", + "TriggerChannelCount": "", + "RecordingDuration": "", + "RecordingType": "", + "EpochLength": "", + "SubjectArtefactDescription": "", + "SoftwareVersions": "", + "iEEGReference": "", + "ElectrodeManufacturer": "", + "ElectrodeManufacturersModelName": "", + "iEEGGround": "", + "iEEGPlacementScheme": "", + "iEEGElectrodeGroups": "", + "ElectricalStimulation": "", + "ElectricalStimulationParameters": "" } diff --git a/inputs/bids_template/sub-01/ses-01/meg/sub-01_task-FullExample_acq-CTF_run-1_proc-sss_meg.json b/inputs/bids_template/sub-01/ses-01/meg/sub-01_task-FullExample_acq-CTF_run-1_proc-sss_meg.json index 8c1b41f6..08c6708b 100644 --- a/inputs/bids_template/sub-01/ses-01/meg/sub-01_task-FullExample_acq-CTF_run-1_proc-sss_meg.json +++ b/inputs/bids_template/sub-01/ses-01/meg/sub-01_task-FullExample_acq-CTF_run-1_proc-sss_meg.json @@ -1,40 +1,40 @@ { - "TaskName": "resting", - "InstitutionName": "University of open science", - "InstitutionAddress": "3rd planet from the sun", - "Manufacturer": "", - "ManufacturersModelName": "", - "SoftwareVersions": "", - "TaskDescription": "", - "Instructions": "Close your eyes and enjoy the ride.", - "CogPOID": "", - "DeviceSerialNumber": "", - "SamplingFrequency": "", - "PowerLineFrequency": 50, - "DewarPosition": "", - "SoftwareFilters": "", - "DigitizedLandmarks": "", - "DigitizedHeadPoints": "", - "MEGChannelCount": 42, - "MEGREFChannelCount": 42, - "EEGChannelCount": 42, - "ECOGChannelCount": 42, - "SEEGChannelCount": 42, - "EOGChannelCount": 42, - "ECGChannelCount": 42, - "EMGChannelCount": 42, - "MiscChannelCount": "", - "TriggerChannelCount": "", - "RecordingDuration": 600, - "RecordingType": "continuous", - "EpochLength": 2, - "ContinuousHeadLocalization": "", - "HeadCoilFrequency": [1470], - "MaxMovement": "", - "SubjectArtefactDescription": "", - "AssociatedEmptyRoom": "", - "EEGSamplingFrequency": "", - "EEGPlacementScheme": "", - "ManufacturersAmplifierModelName": "", - "EEGReference": "" + "TaskName": "resting", + "InstitutionName": "University of open science", + "InstitutionAddress": "3rd planet from the sun", + "Manufacturer": "", + "ManufacturersModelName": "", + "SoftwareVersions": "", + "TaskDescription": "", + "Instructions": "Close your eyes and enjoy the ride.", + "CogPOID": "", + "DeviceSerialNumber": "", + "SamplingFrequency": "", + "PowerLineFrequency": 50, + "DewarPosition": "", + "SoftwareFilters": "", + "DigitizedLandmarks": "", + "DigitizedHeadPoints": "", + "MEGChannelCount": 42, + "MEGREFChannelCount": 42, + "EEGChannelCount": 42, + "ECOGChannelCount": 42, + "SEEGChannelCount": 42, + "EOGChannelCount": 42, + "ECGChannelCount": 42, + "EMGChannelCount": 42, + "MiscChannelCount": "", + "TriggerChannelCount": "", + "RecordingDuration": 600, + "RecordingType": "continuous", + "EpochLength": 2, + "ContinuousHeadLocalization": "", + "HeadCoilFrequency": [1470], + "MaxMovement": "", + "SubjectArtefactDescription": "", + "AssociatedEmptyRoom": "", + "EEGSamplingFrequency": "", + "EEGPlacementScheme": "", + "ManufacturersAmplifierModelName": "", + "EEGReference": "" } diff --git a/inputs/bids_template/sub-01/ses-01/meg/sub-01_task-ShortExample_acq-CTF_run-1_proc-sss_meg.json b/inputs/bids_template/sub-01/ses-01/meg/sub-01_task-ShortExample_acq-CTF_run-1_proc-sss_meg.json index 3c6e1852..fdeca9e5 100644 --- a/inputs/bids_template/sub-01/ses-01/meg/sub-01_task-ShortExample_acq-CTF_run-1_proc-sss_meg.json +++ b/inputs/bids_template/sub-01/ses-01/meg/sub-01_task-ShortExample_acq-CTF_run-1_proc-sss_meg.json @@ -1,28 +1,28 @@ { - "InstitutionName": "Stanford University", - "InstitutionAddress": "450 Serra Mall, Stanford, CA 94305-2004, USA", - "Manufacturer": "CTF", - "ManufacturersModelName": "CTF-275", - "DeviceSerialNumber": "11035", - "SoftwareVersions": "Acq 5.4.2-linux-20070507", - "PowerLineFrequency": 60, - "SamplingFrequency": 2400, - "MEGChannelCount": 270, - "MEGREFChannelCount": 26, - "EEGChannelCount": 0, - "EOGChannelCount": 2, - "ECGChannelCount": 1, - "EMGChannelCount": 0, - "DewarPosition": "upright", - "SoftwareFilters": { - "SpatialCompensation": {"GradientOrder": "3rd"} - }, - "RecordingDuration": 600, - "RecordingType": "continuous", - "EpochLength": 0, - "TaskName": "rest", - "ContinuousHeadLocalization": true, - "HeadCoilFrequency": [1470,1530,1590], - "DigitizedLandmarks": true, - "DigitizedHeadPoints": true + "InstitutionName": "Stanford University", + "InstitutionAddress": "450 Serra Mall, Stanford, CA 94305-2004, USA", + "Manufacturer": "CTF", + "ManufacturersModelName": "CTF-275", + "DeviceSerialNumber": "11035", + "SoftwareVersions": "Acq 5.4.2-linux-20070507", + "PowerLineFrequency": 60, + "SamplingFrequency": 2400, + "MEGChannelCount": 270, + "MEGREFChannelCount": 26, + "EEGChannelCount": 0, + "EOGChannelCount": 2, + "ECGChannelCount": 1, + "EMGChannelCount": 0, + "DewarPosition": "upright", + "SoftwareFilters": { + "SpatialCompensation": { "GradientOrder": "3rd" } + }, + "RecordingDuration": 600, + "RecordingType": "continuous", + "EpochLength": 0, + "TaskName": "rest", + "ContinuousHeadLocalization": true, + "HeadCoilFrequency": [1470, 1530, 1590], + "DigitizedLandmarks": true, + "DigitizedHeadPoints": true } diff --git a/mlc_config.json b/mlc_config.json index 234eb33a..b9fb1b2e 100644 --- a/mlc_config.json +++ b/mlc_config.json @@ -1,19 +1,19 @@ { - "ignorePatterns": [ - { - "pattern": "^https://doi.org/.*" - }, - { - "pattern": "^.*shinyapps.*" - }, - { - "pattern": "^https://static-content.springer.com" - }, - { - "pattern": "^https://twitter.com/.*$" - }, - { - "pattern": "^https://neurovault.org/.*$" - } - ] + "ignorePatterns": [ + { + "pattern": "^https://doi.org/.*" + }, + { + "pattern": "^.*shinyapps.*" + }, + { + "pattern": "^https://static-content.springer.com" + }, + { + "pattern": "^https://twitter.com/.*$" + }, + { + "pattern": "^https://neurovault.org/.*$" + } + ] } diff --git a/ui/__init__.py b/ui/__init__.py new file mode 100644 index 00000000..e69de29b diff --git a/ui/app.py b/ui/app.py index 2f7a556a..6e98b6b6 100644 --- a/ui/app.py +++ b/ui/app.py @@ -5,21 +5,21 @@ import pandas as pd from flask import Flask, flash, redirect, render_template, request from flask_bootstrap import Bootstrap5 -from flask_wtf import CSRFProtect, FlaskForm -from markupsafe import Markup, escape -from modules import ( +from flask_wtf import CSRFProtect +from markupsafe import Markup +from rich import print +from werkzeug.utils import secure_filename + +from .forms import UploadForm, generate_form +from .modules import ( LANG, - generate_form, - get_items_for_activity, get_landing_page, get_nav_bar_content, get_protocol, + prep_activity_page, protocol_url, update_format, ) -from rich import print -from werkzeug.utils import secure_filename -from wtforms import MultipleFileField, SubmitField test_config = None @@ -88,96 +88,17 @@ def protocol(protocol_name: str) -> str: ) -@app.route("/protocol//", methods=["GET", "POST"]) -def activity(protocol_name, activity_name) -> str: - - protocol_name = escape(protocol_name) - activity_name = escape(activity_name) +@app.get("/protocol//") +def activity_get(protocol_name, activity_name) -> str: - protocol_content = get_protocol(protocol_name) - properties = protocol_content["ui"]["addProperties"] - for activity in properties: - if activity["variableName"] == activity_name: - is_about_activity = activity["isAbout"] - break - activity_file = protocol_url(protocol_name).parent / is_about_activity + activities, activity, items = prep_activity_page(protocol_name, activity_name) upload_form = None if protocol_name == "neurovault" and activity_name == "participants": upload_form = UploadForm() - with open(activity_file) as f: - activity = json.load(f) - - activities = get_nav_bar_content(protocol_name, activity["prefLabel"][LANG]) - - items = get_items_for_activity(activity_file) - form = generate_form(items=items, prefix=activity_name) - if request.method == "POST": - - if upload_form.is_submitted(): - - if len(upload_form.participants.data) != 2: - flash("2 files must be uploaded.") - return redirect(request.url) - if all(file.filename != "participants.json" for file in upload_form.participants.data): - flash("No 'participants.json' was uploaded.") - return redirect(request.url) - if all(file.filename != "participants.tsv" for file in upload_form.participants.data): - flash("No 'participants.tsv' was uploaded.") - return redirect(request.url) - - for file in upload_form.participants.data: - if allowed_file(file.filename): - filename = secure_filename(file.filename) - file.save(Path(app.config["UPLOAD_FOLDER"]) / filename) - - participants_tsv = pd.read_csv( - Path(app.config["UPLOAD_FOLDER"]) / "participants.tsv", sep="\t" - ) - with open(Path(app.config["UPLOAD_FOLDER"]) / "participants.json") as f: - participants_json = json.load(f) - - if not participants_json.get("participant_id") or not participants_json[ - "participant_id" - ].get("Annotations"): - flash( - Markup( - "The 'participants.json' was not annotated. " - "Annotate your data with " - "the neurobagel online annotation tool" - ) - ) - return redirect(request.url) - - print(participants_tsv) - print(participants_json) - - elif form.is_submitted(): - - items = update_visibility(items, form) - - items = update_format(items, form) - - form = generate_form(items, prefix=activity_name) - - completed_items = sum(bool(i["is_answered"]) for i in items.values()) - nb_items = sum(bool(i["visibility"]) for i in items.values()) - - return render_template( - "protocol.html", - protocol_pref_label=protocol_name, - activity_pref_label=activity["prefLabel"][LANG], - activity_preamble=Markup(activity["preamble"][LANG]), - activities=activities, - form=form, - nb_items=nb_items, - completed_items=completed_items, - upload_form=upload_form, - ) - completed_items = sum(bool(i["is_answered"]) for i in items.values()) nb_items = sum(bool(i["visibility"]) for i in items.values()) @@ -194,6 +115,92 @@ def activity(protocol_name, activity_name) -> str: ) +@app.post("/protocol//") +def activity_post(protocol_name, activity_name) -> str: + + activities, activity, items = prep_activity_page(protocol_name, activity_name) + + upload_form = None + if protocol_name == "neurovault" and activity_name == "participants": + upload_form = UploadForm() + + form = generate_form(items=items, prefix=activity_name) + + if upload_form.is_submitted(): + + nb_files_uploaded = len(upload_form.participants.data) + participants_json_uploaded = any( + file.filename == "participants.json" for file in upload_form.participants.data + ) + participants_tsv_uploaded = any( + file.filename == "participants.tsv" for file in upload_form.participants.data + ) + + if nb_files_uploaded != 2: + message = "2 files must be uploaded." + if not participants_json_uploaded: + message = "No 'participants.json' was uploaded." + if not participants_tsv_uploaded: + message = "No 'participants.tsv' was uploaded." + + if ( + nb_files_uploaded != 2 + or not participants_json_uploaded + or not participants_tsv_uploaded + ): + flash(message) + return redirect(request.url) + + for file in upload_form.participants.data: + if allowed_file(file.filename): + filename = secure_filename(file.filename) + file.save(Path(app.config["UPLOAD_FOLDER"]) / filename) + + participants_tsv = pd.read_csv( + Path(app.config["UPLOAD_FOLDER"]) / "participants.tsv", sep="\t" + ) + with open(Path(app.config["UPLOAD_FOLDER"]) / "participants.json") as f: + participants_json = json.load(f) + + if not participants_json.get("participant_id") or not participants_json[ + "participant_id" + ].get("Annotations"): + flash( + Markup( + "The 'participants.json' was not annotated. " + "Annotate your data with " + "the neurobagel online annotation tool" + ) + ) + return redirect(request.url) + + print(participants_tsv) + print(participants_json) + + elif form.is_submitted(): + + items = update_visibility(items, form) + + items = update_format(items, form) + + form = generate_form(items, prefix=activity_name) + + completed_items = sum(bool(i["is_answered"]) for i in items.values()) + nb_items = sum(bool(i["visibility"]) for i in items.values()) + + return render_template( + "protocol.html", + protocol_pref_label=protocol_name, + activity_pref_label=activity["prefLabel"][LANG], + activity_preamble=Markup(activity["preamble"][LANG]), + activities=activities, + form=form, + nb_items=nb_items, + completed_items=completed_items, + upload_form=upload_form, + ) + + @app.errorhandler(404) def page_not_found(e): return render_template("404.html"), 404 @@ -213,11 +220,6 @@ def allowed_file(filename): return "." in filename and filename.rsplit(".", 1)[1].lower() in ALLOWED_EXTENSIONS -class UploadForm(FlaskForm): - participants = MultipleFileField("Upload participants.tsv and participants.json") - submit = SubmitField("Upload") - - @app.route("/about") def about() -> str: return render_template("about.html") diff --git a/ui/forms.py b/ui/forms.py new file mode 100644 index 00000000..dcd3d383 --- /dev/null +++ b/ui/forms.py @@ -0,0 +1,187 @@ +from flask_wtf import FlaskForm +from markupsafe import Markup +from wtforms import ( + DateField, + DecimalField, + HiddenField, + IntegerField, + MultipleFileField, + RadioField, + SelectField, + SelectMultipleField, + StringField, + SubmitField, + TextAreaField, +) +from wtforms.validators import DataRequired, NumberRange + + +class UploadForm(FlaskForm): + participants = MultipleFileField("Upload participants.tsv and participants.json") + submit = SubmitField("Upload") + + +def generate_form(items=None, prefix=None): + + class DyanmicForm(FlaskForm): + pass + + form = DyanmicForm + + for item_name, item in items.items(): + + render_kw = ( + {"style": "border-color: green; border-width: 2px;"} + if item["is_answered"] + else {"style": "border-color: red; border-width: 2px;"} + ) + + validators = [] + if item["required"]: + validators.append(DataRequired()) + + question = f"{item['question']} {item['unit']}" + + if not item["visibility"]: + setattr( + form, + item_name, + HiddenField( + Markup(question), + validators=validators, + description=item["description"], + _prefix=prefix, + ), + ) + continue + + input_type = item["input_type"] + + default = None + + if input_type == "date": + + FieldType = DateField + + setattr( + form, + item_name, + FieldType( + Markup(question), + validators=validators, + description=item["description"], + default=default, + _prefix=prefix, + format="%Y-%m-%d", + render_kw=render_kw, + ), + ) + + elif input_type not in ["select", "radio", "slider"]: + + FieldType = StringField + if input_type == "number": + FieldType = IntegerField + elif input_type == "float": + FieldType = DecimalField + elif input_type == "textarea": + FieldType = TextAreaField + + if input_type in ["number", "float"]: + minimum = item["min"] + maximum = item["max"] + validators.append(NumberRange(min=minimum, max=maximum)) + if minimum is not None and maximum is not None: + question += f" ({minimum=}, {maximum=})" + elif minimum is not None: + question += f" ({minimum=})" + + setattr( + form, + item_name, + FieldType( + Markup(question), + validators=validators, + description=item["description"], + default=default, + _prefix=prefix, + render_kw=render_kw, + ), + ) + + elif input_type == "slider": + + # FieldType = DecimalRangeField + # render_kw["value"]= "50.0" + # render_kw["min"]= "0.0" + # render_kw["max"]= "100.0" + # render_kw["step"]= "0.5" + + min_label = float(item["choices"][0][1]) + max_label = float(item["choices"][-1][1]) + + question += f" (min={min_label}, max={max_label})" + + FieldType = DecimalField + validators.append(NumberRange(min=min_label, max=max_label)) + + setattr( + form, + item_name, + FieldType( + Markup(question), + validators=validators, + description=item["description"], + _prefix=prefix, + render_kw=render_kw, + ), + ) + + else: + + form = add_choice_based_items(form, prefix, item_name, item) + + setattr(form, "submit", SubmitField("Save")) # noqa B010 + + return form() + + +def add_choice_based_items(form, prefix, item_name, item): + + question = f"{item['question']} {item['unit']}" + + input_type = item["input_type"] + + render_kw = ( + {"style": "border-color: green; border-width: 2px;"} + if item["is_answered"] + else {"style": "border-color: red; border-width: 2px;"} + ) + + validators = [] + if item["required"]: + validators.append(DataRequired()) + + is_multiple = item["is_multiple"] + + if is_multiple: + FieldType = SelectMultipleField + elif input_type == "select": + FieldType = SelectField + elif input_type == "radio": + FieldType = RadioField + + setattr( + form, + item_name, + FieldType( + Markup(question), + validators=validators, + description=item["description"], + choices=item["choices"], + _prefix=prefix, + render_kw=render_kw, + ), + ) + + return form diff --git a/ui/modules.py b/ui/modules.py index f8d85bfd..4f13a026 100644 --- a/ui/modules.py +++ b/ui/modules.py @@ -5,22 +5,8 @@ from typing import Any import requests -from flask_wtf import FlaskForm -from markupsafe import Markup +from markupsafe import escape from rich import print -from wtforms import ( - DateField, - DecimalField, - HiddenField, - IntegerField, - RadioField, - SelectField, - SelectMultipleField, - StringField, - SubmitField, - TextAreaField, -) -from wtforms.validators import DataRequired, NumberRange LANG: str = "en" @@ -112,170 +98,26 @@ def update_format(items: dict[str, Any], form): return items -def generate_form(items=None, prefix=None): - - class DyanmicForm(FlaskForm): - pass - - form = DyanmicForm - - for item_name, item in items.items(): - - render_kw = ( - {"style": "border-color: green; border-width: 2px;"} - if item["is_answered"] - else {"style": "border-color: red; border-width: 2px;"} - ) - - validators = [] - if item["required"]: - validators.append(DataRequired()) - - question = f"{item['question']} {item['unit']}" - - if not item["visibility"]: - setattr( - form, - item_name, - HiddenField( - Markup(question), - validators=validators, - description=item["description"], - _prefix=prefix, - ), - ) - continue - - input_type = item["input_type"] - - default = None - - if input_type == "date": - - FieldType = DateField - - setattr( - form, - item_name, - FieldType( - Markup(question), - validators=validators, - description=item["description"], - default=default, - _prefix=prefix, - format="%Y-%m-%d", - render_kw=render_kw, - ), - ) - - elif input_type not in ["select", "radio", "slider"]: - - FieldType = StringField - if input_type == "number": - FieldType = IntegerField - elif input_type == "float": - FieldType = DecimalField - elif input_type == "textarea": - FieldType = TextAreaField - - if input_type in ["number", "float"]: - minimum = item["min"] - maximum = item["max"] - validators.append(NumberRange(min=minimum, max=maximum)) - if minimum is not None and maximum is not None: - question += f" ({minimum=}, {maximum=})" - elif minimum is not None: - question += f" ({minimum=})" - - setattr( - form, - item_name, - FieldType( - Markup(question), - validators=validators, - description=item["description"], - default=default, - _prefix=prefix, - render_kw=render_kw, - ), - ) - - elif input_type == "slider": - - # FieldType = DecimalRangeField - # render_kw["value"]= "50.0" - # render_kw["min"]= "0.0" - # render_kw["max"]= "100.0" - # render_kw["step"]= "0.5" - - min_label = float(item["choices"][0][1]) - max_label = float(item["choices"][-1][1]) - - question += f" (min={min_label}, max={max_label})" - - FieldType = DecimalField - validators.append(NumberRange(min=min_label, max=max_label)) - - setattr( - form, - item_name, - FieldType( - Markup(question), - validators=validators, - description=item["description"], - _prefix=prefix, - render_kw=render_kw, - ), - ) +def prep_activity_page(protocol_name, activity_name): + protocol_name = escape(protocol_name) + activity_name = escape(activity_name) - else: - - form = add_choice_based_items(form, prefix, item_name, item) - - setattr(form, "submit", SubmitField("Save")) # noqa B010 - - return form() - - -def add_choice_based_items(form, prefix, item_name, item): - - question = f"{item['question']} {item['unit']}" + protocol_content = get_protocol(protocol_name) + properties = protocol_content["ui"]["addProperties"] + for activity in properties: + if activity["variableName"] == activity_name: + is_about_activity = activity["isAbout"] + break + activity_file = protocol_url(protocol_name).parent / is_about_activity - input_type = item["input_type"] + with open(activity_file) as f: + activity = json.load(f) - render_kw = ( - {"style": "border-color: green; border-width: 2px;"} - if item["is_answered"] - else {"style": "border-color: red; border-width: 2px;"} - ) + activities = get_nav_bar_content(protocol_name, activity["prefLabel"][LANG]) - validators = [] - if item["required"]: - validators.append(DataRequired()) - - is_multiple = item["is_multiple"] - - if is_multiple: - FieldType = SelectMultipleField - elif input_type == "select": - FieldType = SelectField - elif input_type == "radio": - FieldType = RadioField - - setattr( - form, - item_name, - FieldType( - Markup(question), - validators=validators, - description=item["description"], - choices=item["choices"], - _prefix=prefix, - render_kw=render_kw, - ), - ) + items = get_items_for_activity(activity_file) - return form + return activities, activity, items @lru_cache From 79af006f34c55b9690e84f53a7bedf12e71fb9e0 Mon Sep 17 00:00:00 2001 From: Remi Gau Date: Thu, 23 May 2024 23:11:16 -0400 Subject: [PATCH 13/31] package --- .flake8 | 2 + .pre-commit-config.yaml | 2 +- ui/.gitignore | 182 ++++++++++++++++++++ ui/.pre-commit-config.yaml | 88 ++++++++++ ui/README.md | 13 ++ ui/__init__.py | 0 ui/ecobidas_ui/__init__.py | 79 +++++++++ ui/ecobidas_ui/about.py | 8 + ui/ecobidas_ui/auth.py | 88 ++++++++++ ui/ecobidas_ui/db.py | 38 ++++ ui/{ => ecobidas_ui}/forms.py | 2 - ui/{ => ecobidas_ui}/modules.py | 2 +- ui/{app.py => ecobidas_ui/protocol.py} | 105 +++-------- ui/ecobidas_ui/schema.sql | 17 ++ ui/{ => ecobidas_ui}/static/style.css | 0 ui/{ => ecobidas_ui}/templates/404.html | 10 +- ui/{ => ecobidas_ui}/templates/500.html | 10 +- ui/ecobidas_ui/templates/about.html | 1 + ui/ecobidas_ui/templates/auth/login.html | 11 ++ ui/ecobidas_ui/templates/auth/register.html | 11 ++ ui/{ => ecobidas_ui}/templates/base.html | 54 +++++- ui/{ => ecobidas_ui}/templates/index.html | 0 ui/ecobidas_ui/templates/protocol.html | 54 ++++++ ui/pyproject.toml | 84 +++++++++ ui/requirements.txt | 59 ++++++- ui/templates/about.html | 2 - ui/templates/new_checklist.html | 1 - ui/templates/protocol.html | 97 ----------- ui/tests/conftest.py | 41 +++++ ui/tests/data.sql | 8 + ui/tox.ini | 33 ++++ 31 files changed, 900 insertions(+), 202 deletions(-) create mode 100644 ui/.gitignore create mode 100644 ui/.pre-commit-config.yaml create mode 100644 ui/README.md delete mode 100644 ui/__init__.py create mode 100644 ui/ecobidas_ui/__init__.py create mode 100644 ui/ecobidas_ui/about.py create mode 100644 ui/ecobidas_ui/auth.py create mode 100644 ui/ecobidas_ui/db.py rename ui/{ => ecobidas_ui}/forms.py (99%) rename ui/{ => ecobidas_ui}/modules.py (99%) rename ui/{app.py => ecobidas_ui/protocol.py} (66%) create mode 100644 ui/ecobidas_ui/schema.sql rename ui/{ => ecobidas_ui}/static/style.css (100%) rename ui/{ => ecobidas_ui}/templates/404.html (68%) rename ui/{ => ecobidas_ui}/templates/500.html (67%) create mode 100644 ui/ecobidas_ui/templates/about.html create mode 100644 ui/ecobidas_ui/templates/auth/login.html create mode 100644 ui/ecobidas_ui/templates/auth/register.html rename ui/{ => ecobidas_ui}/templates/base.html (60%) rename ui/{ => ecobidas_ui}/templates/index.html (100%) create mode 100644 ui/ecobidas_ui/templates/protocol.html create mode 100644 ui/pyproject.toml delete mode 100644 ui/templates/about.html delete mode 100644 ui/templates/new_checklist.html delete mode 100644 ui/templates/protocol.html create mode 100644 ui/tests/conftest.py create mode 100644 ui/tests/data.sql create mode 100644 ui/tox.ini diff --git a/.flake8 b/.flake8 index 05feb7c7..9bc1cf29 100644 --- a/.flake8 +++ b/.flake8 @@ -1,6 +1,8 @@ [flake8] exclude = .git, + ./env + **/env docstring-convention = numpy max-line-length = 150 diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 8e71e605..2e5f250b 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -94,5 +94,5 @@ repos: rev: 7.0.0 hooks: - id: flake8 - args: [--config, .flake8, --verbose, ecobidas, tests, macros, ui] + args: [--config, .flake8, --verbose, ecobidas, tests, macros] additional_dependencies: [flake8-docstrings, flake8-use-fstring, flake8-functions, flake8-bugbear] diff --git a/ui/.gitignore b/ui/.gitignore new file mode 100644 index 00000000..df574294 --- /dev/null +++ b/ui/.gitignore @@ -0,0 +1,182 @@ +*.DS_Store +*.DS_Store + +.vscode/*.log + +.~lock* + +ecobidas_ui/_version.py + +tmp + +.~lock* + +# pytest +.pytest_cache/ + +# jupyter notebook +.ipynb_checkpoints/ +Untitled.ipynb + + +Pipfile + +## Byte-compiled / optimized / DLL files +__pycache__/ +*.py[cod] +*$py.class + +# C extensions +*.so + +# Distribution / packaging +.Python +build/ +develop-eggs/ +dist/ +downloads/ +eggs/ +.eggs/ +lib64/ +parts/ +sdist/ +var/ +wheels/ +share/python-wheels/ +*.egg-info/ +.installed.cfg +*.egg +MANIFEST + +# PyInstaller +# Usually these files are written by a python script from a template +# before PyInstaller builds the exe, so as to inject date/other infos into it. +*.manifest +*.spec + +# Installer logs +pip-log.txt +pip-delete-this-directory.txt + +# Unit test / coverage reports +htmlcov/ +.tox/ +.nox/ +.coverage +.coverage.* +.cache +nosetests.xml +coverage.xml +*.cover +*.py,cover +.hypothesis/ +.pytest_cache/ +cover/ + +# Translations +*.mo +*.pot + +# Django stuff: +*.log +local_settings.py +db.sqlite3 +db.sqlite3-journal + +# Flask stuff: +instance/ +.webassets-cache + +# Scrapy stuff: +.scrapy + +# Sphinx documentation +docs/_build/ + +# PyBuilder +.pybuilder/ +target/ + +# Jupyter Notebook +.ipynb_checkpoints + +# IPython +profile_default/ +ipython_config.py + +# pyenv +# For a library or package, you might want to ignore these files since the code is +# intended to run in multiple environments; otherwise, check them in: +# .python-version + +# pipenv +# According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control. +# However, in case of collaboration, if having platform-specific dependencies or dependencies +# having no cross-platform support, pipenv may install dependencies that don't work, or not +# install all needed dependencies. +#Pipfile.lock + +# poetry +# Similar to Pipfile.lock, it is generally recommended to include poetry.lock in version control. +# This is especially recommended for binary packages to ensure reproducibility, and is more +# commonly ignored for libraries. +# https://python-poetry.org/docs/basic-usage/#commit-your-poetrylock-file-to-version-control +#poetry.lock + +# pdm +# Similar to Pipfile.lock, it is generally recommended to include pdm.lock in version control. +#pdm.lock +# pdm stores project-wide configurations in .pdm.toml, but it is recommended to not include it +# in version control. +# https://pdm.fming.dev/#use-with-ide +.pdm.toml + +# PEP 582; used by e.g. github.com/David-OConnor/pyflow and github.com/pdm-project/pdm +__pypackages__/ + +# Celery stuff +celerybeat-schedule +celerybeat.pid + +# SageMath parsed files +*.sage.py + +# Environments +.env +.venv +env/ +venv/ +ENV/ +env.bak/ +venv.bak/ + +# Spyder project settings +.spyderproject +.spyproject + +# Rope project settings +.ropeproject + +# mkdocs documentation +/site + +# mypy +.mypy_cache/ +.dmypy.json +dmypy.json + +# Pyre type checker +.pyre/ + +# pytype static type analyzer +.pytype/ + +# Cython debug symbols +cython_debug/ + +# PyCharm +# JetBrains specific template is maintained in a separate JetBrains.gitignore that can +# be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore +# and can be added to the global gitignore or merged into this file. For a more nuclear +# option (not recommended) you can uncomment the following to ignore the entire idea folder. +#.idea/ diff --git a/ui/.pre-commit-config.yaml b/ui/.pre-commit-config.yaml new file mode 100644 index 00000000..b62ac004 --- /dev/null +++ b/ui/.pre-commit-config.yaml @@ -0,0 +1,88 @@ +--- +# See https://pre-commit.com for more information +# See https://pre-commit.com/hooks.html for more hooks +repos: +- repo: https://github.com/pre-commit/pre-commit-hooks + rev: v4.6.0 + hooks: + - id: check-ast + - id: check-case-conflict + - id: check-json + - id: check-merge-conflict + - id: check-toml + - id: check-yaml + - id: end-of-file-fixer + - id: mixed-line-ending + - id: trailing-whitespace + +# Sorts Python imports alphabetically and by section with `isort`. +- repo: https://github.com/pycqa/isort + rev: 5.13.2 + hooks: + - id: isort + args: [--profile, black, --settings-path, pyproject.toml] + +# Automatically upgrade syntax for newer versions of the language. +- repo: https://github.com/asottile/pyupgrade + rev: v3.15.2 + hooks: + - id: pyupgrade + args: [--py311-plus] + +# Aplly black formatting to python code +# https://github.com/psf/black +- repo: https://github.com/psf/black-pre-commit-mirror + rev: 24.4.2 + hooks: + - id: black + args: [--config, pyproject.toml] + +# Checks for spelling errors +- repo: https://github.com/codespell-project/codespell + rev: v2.2.6 + hooks: + - id: codespell + args: [--toml, pyproject.toml] + additional_dependencies: [tomli] + +# Format YAML files +- repo: https://github.com/jumanjihouse/pre-commit-hook-yamlfmt + rev: 0.2.3 + hooks: + - id: yamlfmt + args: [--mapping, '4', --sequence, '4', --offset, '0'] + +# Format TOML files +- repo: https://github.com/macisamuele/language-formatters-pre-commit-hooks + rev: v2.13.0 + hooks: + - id: pretty-format-toml + args: [--autofix, --indent, '4'] + +# - repo: https://github.com/pre-commit/mirrors-mypy +# rev: v1.8.0 +# hooks: +# - id: mypy +# additional_dependencies: [types-all, pandas-stubs] +# args: [--config-file=pyproject.toml] + +# Check formatting of CSS and HTML +# prettier: https://prettier.io/ +- repo: https://github.com/pre-commit/mirrors-prettier + rev: v4.0.0-alpha.8 + hooks: + - id: prettier + types_or: [css, html, json] + +# Check that Python code complies with PEP8 guidelines +# flake8 uses pydocstyle to check docstrings: https://flake8.pycqa.org/en/latest/ +# flake8-docstrings: https://pypi.org/project/flake8-docstrings/ +# flake8-use-fstring forces to use fstrings: https://pypi.org/project/flake8-use-fstring/ +# flake8-functions checks functions quality: https://pypi.org/project/flake8-functions/ +# flake8-bugbear detects some common bugs: https://github.com/PyCQA/flake8-bugbear +- repo: https://github.com/pyCQA/flake8 + rev: 7.0.0 + hooks: + - id: flake8 + args: [--config, .flake8, --verbose, ecobidas_ui, tests] + additional_dependencies: [flake8-docstrings, flake8-use-fstring, flake8-functions, flake8-bugbear] diff --git a/ui/README.md b/ui/README.md new file mode 100644 index 00000000..2cbb4114 --- /dev/null +++ b/ui/README.md @@ -0,0 +1,13 @@ +# README + + +``` +flask --app ecobidas_ui init-db +``` + +```bash +flask --app ecobidas_ui --debug run +``` + + diff --git a/ui/__init__.py b/ui/__init__.py deleted file mode 100644 index e69de29b..00000000 diff --git a/ui/ecobidas_ui/__init__.py b/ui/ecobidas_ui/__init__.py new file mode 100644 index 00000000..94ec69f0 --- /dev/null +++ b/ui/ecobidas_ui/__init__.py @@ -0,0 +1,79 @@ +from logging.config import dictConfig +from pathlib import Path + +from flask import Flask, render_template +from flask_bootstrap import Bootstrap5 +from flask_wtf import CSRFProtect + + +def create_app(test_config=None): + from ecobidas_ui import about, auth, db, protocol + + dictConfig( + { + "version": 1, + "formatters": { + "default": { + "format": "[%(asctime)s] %(levelname)s in %(module)s: %(message)s", + } + }, + "handlers": { + "wsgi": { + "class": "logging.StreamHandler", + "stream": "ext://flask.logging.wsgi_errors_stream", + "formatter": "default", + } + }, + "root": {"level": "INFO", "handlers": ["wsgi"]}, + } + ) + + # create and configure the app + UPLOAD_FOLDER = Path(__file__).parent / "tmp" + UPLOAD_FOLDER.mkdir(parents=True, exist_ok=True) + + # create and configure the app + app = Flask(__name__, instance_relative_config=True) + app.config.from_mapping( + SECRET_KEY="tO$&!|0wkamvVia0?n$NqIRVWOG", + DATABASE=Path(app.instance_path) / "flaskr.sqlite", + UPLOAD_FOLDER=UPLOAD_FOLDER, + MAX_CONTENT_LENGTH=16 * 1000 * 1000, + ) + + if test_config is None: + # load the instance config, if it exists, when not testing + app.config.from_pyfile("config.py", silent=True) + else: + # load the test config if passed in + app.config.from_mapping(test_config) + + # ensure the instance folder exists + Path(app.instance_path).mkdir(parents=True, exist_ok=True) + + # Bootstrap-Flask requires this line + bootstrap = Bootstrap5(app) # noqa + + # Flask-WTF requires this line + csrf = CSRFProtect(app) # noqa + + db.init_app(app) + + app.register_blueprint(auth.bp) + app.register_blueprint(about.bp) + app.register_blueprint(protocol.bp) + app.add_url_rule("/about", endpoint="about") + + @app.route("/", methods=["GET", "POST"]) + def index() -> str: + return render_template("index.html") + + @app.errorhandler(404) + def page_not_found(e): + return render_template("404.html"), 404 + + @app.errorhandler(500) + def internal_server_error(e): + return render_template("500.html"), 500 + + return app diff --git a/ui/ecobidas_ui/about.py b/ui/ecobidas_ui/about.py new file mode 100644 index 00000000..dce45834 --- /dev/null +++ b/ui/ecobidas_ui/about.py @@ -0,0 +1,8 @@ +from flask import Blueprint, render_template + +bp = Blueprint("about", __name__) + + +@bp.route("/about") +def about() -> str: + return render_template("about.html") diff --git a/ui/ecobidas_ui/auth.py b/ui/ecobidas_ui/auth.py new file mode 100644 index 00000000..571eebac --- /dev/null +++ b/ui/ecobidas_ui/auth.py @@ -0,0 +1,88 @@ +import functools + +from ecobidas_ui.db import get_db +from flask import Blueprint, flash, g, redirect, render_template, request, session, url_for +from werkzeug.security import check_password_hash, generate_password_hash + +bp = Blueprint("auth", __name__, url_prefix="/auth") + + +@bp.route("/register", methods=("GET", "POST")) +def register(): + if request.method == "POST": + username = request.form["username"] + password = request.form["password"] + db = get_db() + error = None + + if not username: + error = "Username is required." + elif not password: + error = "Password is required." + + if error is None: + try: + db.execute( + "INSERT INTO user (username, password) VALUES (?, ?)", + (username, generate_password_hash(password)), + ) + db.commit() + except db.IntegrityError: + error = f"User {username} is already registered." + else: + return redirect(url_for("auth.login")) + + flash(error) + + return render_template("auth/register.html") + + +@bp.route("/login", methods=("GET", "POST")) +def login(): + if request.method == "POST": + username = request.form["username"] + password = request.form["password"] + db = get_db() + error = None + user = db.execute("SELECT * FROM user WHERE username = ?", (username,)).fetchone() + + if user is None: + error = "Incorrect username." + elif not check_password_hash(user["password"], password): + error = "Incorrect password." + + if error is None: + session.clear() + session["user_id"] = user["id"] + return redirect(url_for("index")) + + flash(error) + + return render_template("auth/login.html") + + +@bp.before_app_request +def load_logged_in_user(): + user_id = session.get("user_id") + + if user_id is None: + g.user = None + else: + g.user = get_db().execute("SELECT * FROM user WHERE id = ?", (user_id,)).fetchone() + + +@bp.route("/logout") +def logout(): + session.clear() + return redirect(url_for("index")) + + +def login_required(view): + @functools.wraps(view) + def wrapped_view(**kwargs): + if g.user is None: + return redirect(url_for("auth.login")) + + return view(**kwargs) + + return wrapped_view diff --git a/ui/ecobidas_ui/db.py b/ui/ecobidas_ui/db.py new file mode 100644 index 00000000..922c9a2e --- /dev/null +++ b/ui/ecobidas_ui/db.py @@ -0,0 +1,38 @@ +import sqlite3 + +import click +from flask import current_app, g + + +def get_db(): + if "db" not in g: + g.db = sqlite3.connect(current_app.config["DATABASE"], detect_types=sqlite3.PARSE_DECLTYPES) + g.db.row_factory = sqlite3.Row + + return g.db + + +def close_db(e=None): + db = g.pop("db", None) + + if db is not None: + db.close() + + +def init_db(): + db = get_db() + + with current_app.open_resource("schema.sql") as f: + db.executescript(f.read().decode("utf8")) + + +@click.command("init-db") +def init_db_command(): + """Clear the existing data and create new tables.""" + init_db() + click.echo("Initialized the database.") + + +def init_app(app): + app.teardown_appcontext(close_db) + app.cli.add_command(init_db_command) diff --git a/ui/forms.py b/ui/ecobidas_ui/forms.py similarity index 99% rename from ui/forms.py rename to ui/ecobidas_ui/forms.py index dcd3d383..c0d5dcfc 100644 --- a/ui/forms.py +++ b/ui/ecobidas_ui/forms.py @@ -60,9 +60,7 @@ class DyanmicForm(FlaskForm): default = None if input_type == "date": - FieldType = DateField - setattr( form, item_name, diff --git a/ui/modules.py b/ui/ecobidas_ui/modules.py similarity index 99% rename from ui/modules.py rename to ui/ecobidas_ui/modules.py index 4f13a026..79a54ee4 100644 --- a/ui/modules.py +++ b/ui/ecobidas_ui/modules.py @@ -13,7 +13,7 @@ def protocol_url(protocol_name: Path) -> Path: return ( - Path(__file__).parents[1] + Path(__file__).parents[2] / "cobidas_schema" / "schemas" / protocol_name diff --git a/ui/app.py b/ui/ecobidas_ui/protocol.py similarity index 66% rename from ui/app.py rename to ui/ecobidas_ui/protocol.py index 6e98b6b6..9f1ff37a 100644 --- a/ui/app.py +++ b/ui/ecobidas_ui/protocol.py @@ -3,15 +3,8 @@ from typing import Any import pandas as pd -from flask import Flask, flash, redirect, render_template, request -from flask_bootstrap import Bootstrap5 -from flask_wtf import CSRFProtect -from markupsafe import Markup -from rich import print -from werkzeug.utils import secure_filename - -from .forms import UploadForm, generate_form -from .modules import ( +from ecobidas_ui.forms import UploadForm, generate_form +from ecobidas_ui.modules import ( LANG, get_landing_page, get_nav_bar_content, @@ -20,48 +13,25 @@ protocol_url, update_format, ) +from flask import Blueprint, current_app, flash, redirect, render_template, request +from markupsafe import Markup +from rich import print +from werkzeug.utils import secure_filename -test_config = None +bp = Blueprint("protocol", __name__, url_prefix="/protocol") -UPLOAD_FOLDER = Path(__file__).parent / "tmp" -UPLOAD_FOLDER.mkdir(parents=True, exist_ok=True) ALLOWED_EXTENSIONS = {"tsv", "json"} -# create and configure the app -app = Flask(__name__, instance_relative_config=True) -app.config.from_mapping( - SECRET_KEY="tO$&!|0wkamvVia0?n$NqIRVWOG", - DATABASE=Path(app.instance_path) / "flaskr.sqlite", - UPLOAD_FOLDER=UPLOAD_FOLDER, - MAX_CONTENT_LENGTH=16 * 1000 * 1000, -) - -if test_config is None: - # load the instance config, if it exists, when not testing - app.config.from_pyfile("config.py", silent=True) -else: - # load the test config if passed in - app.config.from_mapping(test_config) - -# ensure the instance folder exists -Path(app.instance_path).mkdir(parents=True, exist_ok=True) - -# Bootstrap-Flask requires this line -bootstrap = Bootstrap5(app) - -# Flask-WTF requires this line -csrf = CSRFProtect(app) - def update_visibility(items: dict[str, Any], form): for item, values in items.items(): isVis = values["isVis"] if isinstance(isVis, str): isVis = isVis.replace(" ", "").split("==") - if len(isVis) > 2: - app.logger.warning("More than 1 '=='") - if len(isVis) < 2: - app.logger.warning(f"Unsupported JavaScript expression: {isVis}") + # if len(isVis) > 2: + # app.logger.warning("More than 1 '=='") + # if len(isVis) < 2: + # app.logger.warning(f"Unsupported JavaScript expression: {isVis}") if len(isVis) == 2 and form[isVis[0]].data: response = int(form[isVis[0]].data) expected = int(isVis[1]) @@ -69,7 +39,7 @@ def update_visibility(items: dict[str, Any], form): return items -@app.route("/protocol/", methods=["GET", "POST"]) +@bp.route("/protocol/", methods=["GET", "POST"]) def protocol(protocol_name: str) -> str: protocol_content = get_protocol(protocol_name) @@ -88,14 +58,14 @@ def protocol(protocol_name: str) -> str: ) -@app.get("/protocol//") +@bp.get("/protocol//") def activity_get(protocol_name, activity_name) -> str: activities, activity, items = prep_activity_page(protocol_name, activity_name) upload_form = None if protocol_name == "neurovault" and activity_name == "participants": - upload_form = UploadForm() + upload_form = UploadForm(prefix="upload-") form = generate_form(items=items, prefix=activity_name) @@ -115,18 +85,18 @@ def activity_get(protocol_name, activity_name) -> str: ) -@app.post("/protocol//") +@bp.post("/protocol//") def activity_post(protocol_name, activity_name) -> str: activities, activity, items = prep_activity_page(protocol_name, activity_name) upload_form = None if protocol_name == "neurovault" and activity_name == "participants": - upload_form = UploadForm() + upload_form = UploadForm(prefix="upload-") form = generate_form(items=items, prefix=activity_name) - if upload_form.is_submitted(): + if upload_form and upload_form.participants.data: nb_files_uploaded = len(upload_form.participants.data) participants_json_uploaded = any( @@ -154,12 +124,12 @@ def activity_post(protocol_name, activity_name) -> str: for file in upload_form.participants.data: if allowed_file(file.filename): filename = secure_filename(file.filename) - file.save(Path(app.config["UPLOAD_FOLDER"]) / filename) + file.save(Path(current_app.config["UPLOAD_FOLDER"]) / filename) participants_tsv = pd.read_csv( - Path(app.config["UPLOAD_FOLDER"]) / "participants.tsv", sep="\t" + Path(current_app.config["UPLOAD_FOLDER"]) / "participants.tsv", sep="\t" ) - with open(Path(app.config["UPLOAD_FOLDER"]) / "participants.json") as f: + with open(Path(current_app.config["UPLOAD_FOLDER"]) / "participants.json") as f: participants_json = json.load(f) if not participants_json.get("participant_id") or not participants_json[ @@ -167,9 +137,10 @@ def activity_post(protocol_name, activity_name) -> str: ].get("Annotations"): flash( Markup( - "The 'participants.json' was not annotated. " + "

      The 'participants.json' was not annotated. " "Annotate your data with " - "the neurobagel online annotation tool" + "the neurobagel online annotation tool

      " ) ) return redirect(request.url) @@ -201,35 +172,5 @@ def activity_post(protocol_name, activity_name) -> str: ) -@app.errorhandler(404) -def page_not_found(e): - return render_template("404.html"), 404 - - -@app.errorhandler(500) -def internal_server_error(e): - return render_template("500.html"), 500 - - -@app.route("/", methods=["GET", "POST"]) -def index() -> str: - return render_template("index.html") - - def allowed_file(filename): return "." in filename and filename.rsplit(".", 1)[1].lower() in ALLOWED_EXTENSIONS - - -@app.route("/about") -def about() -> str: - return render_template("about.html") - - -@app.route("/new") -def new() -> str: - return render_template("new_checklist.html") - - -# keep this as is -if __name__ == "__main__": - app.run(debug=True) diff --git a/ui/ecobidas_ui/schema.sql b/ui/ecobidas_ui/schema.sql new file mode 100644 index 00000000..be76d7e0 --- /dev/null +++ b/ui/ecobidas_ui/schema.sql @@ -0,0 +1,17 @@ +DROP TABLE IF EXISTS user; +DROP TABLE IF EXISTS post; + +CREATE TABLE user ( + id INTEGER PRIMARY KEY AUTOINCREMENT, + username TEXT UNIQUE NOT NULL, + password TEXT NOT NULL +); + +CREATE TABLE post ( + id INTEGER PRIMARY KEY AUTOINCREMENT, + author_id INTEGER NOT NULL, + created TIMESTAMP NOT NULL DEFAULT CURRENT_TIMESTAMP, + title TEXT NOT NULL, + body TEXT NOT NULL, + FOREIGN KEY (author_id) REFERENCES user (id) +); diff --git a/ui/static/style.css b/ui/ecobidas_ui/static/style.css similarity index 100% rename from ui/static/style.css rename to ui/ecobidas_ui/static/style.css diff --git a/ui/templates/404.html b/ui/ecobidas_ui/templates/404.html similarity index 68% rename from ui/templates/404.html rename to ui/ecobidas_ui/templates/404.html index a822154d..2b792a20 100644 --- a/ui/templates/404.html +++ b/ui/ecobidas_ui/templates/404.html @@ -1,14 +1,14 @@ -{% extends 'base.html' %} {% block title %} 404 Error - Page Not Found {% -endblock %} {% block content %} - +{% extends 'base.html' %} + +{% block title %} 404 Error - Page Not Found {% endblock %} + +{% block content %}

      Page not found (Error 404)

      -

      Go to search page

      - {% endblock %} diff --git a/ui/templates/500.html b/ui/ecobidas_ui/templates/500.html similarity index 67% rename from ui/templates/500.html rename to ui/ecobidas_ui/templates/500.html index c308186c..fa47eb51 100644 --- a/ui/templates/500.html +++ b/ui/ecobidas_ui/templates/500.html @@ -1,14 +1,14 @@ -{% extends 'base.html' %} {% block title %} 500 Error - Internal Server Error {% -endblock %} {% block content %} - +{% extends 'base.html' %} + +{% block title %} 500 Error - Internal Server Error {% endblock %} + +{% block content %}

      Internal server error (500)

      -

      Go to search page

      - {% endblock %} diff --git a/ui/ecobidas_ui/templates/about.html b/ui/ecobidas_ui/templates/about.html new file mode 100644 index 00000000..f65fd260 --- /dev/null +++ b/ui/ecobidas_ui/templates/about.html @@ -0,0 +1 @@ +{% extends 'base.html' %} {% block content %} {% endblock %} diff --git a/ui/ecobidas_ui/templates/auth/login.html b/ui/ecobidas_ui/templates/auth/login.html new file mode 100644 index 00000000..fdd4b28e --- /dev/null +++ b/ui/ecobidas_ui/templates/auth/login.html @@ -0,0 +1,11 @@ +{% extends 'base.html' %} {% block header %} +

      {% block title %}Log In{% endblock %}

      +{% endblock %} {% block content %} +
      + + + + + +
      +{% endblock %} diff --git a/ui/ecobidas_ui/templates/auth/register.html b/ui/ecobidas_ui/templates/auth/register.html new file mode 100644 index 00000000..e13922dd --- /dev/null +++ b/ui/ecobidas_ui/templates/auth/register.html @@ -0,0 +1,11 @@ +{% extends 'base.html' %} {% block header %} +

      {% block title %}Register{% endblock %}

      +{% endblock %} {% block content %} +
      + + + + + +
      +{% endblock %} diff --git a/ui/templates/base.html b/ui/ecobidas_ui/templates/base.html similarity index 60% rename from ui/templates/base.html rename to ui/ecobidas_ui/templates/base.html index 20b2a123..138bae4b 100644 --- a/ui/templates/base.html +++ b/ui/ecobidas_ui/templates/base.html @@ -15,10 +15,58 @@ - + + + + + + + + + + + -
      {% block header %}{% endblock %}
      +
      +
      {% block header %}{% endblock %}
      + + {% with messages = get_flashed_messages() %} {% if messages %} {% for + message in messages %} + + {% endfor %} {% endif %} {% endwith %} +
      diff --git a/ui/templates/index.html b/ui/ecobidas_ui/templates/index.html similarity index 100% rename from ui/templates/index.html rename to ui/ecobidas_ui/templates/index.html diff --git a/ui/ecobidas_ui/templates/protocol.html b/ui/ecobidas_ui/templates/protocol.html new file mode 100644 index 00000000..09831912 --- /dev/null +++ b/ui/ecobidas_ui/templates/protocol.html @@ -0,0 +1,54 @@ +{% extends 'base.html' %} {% from 'bootstrap5/form.html' import render_form %} +{% block content %} +
      +
      +
      +

      {{ protocol_pref_label }}

      +
      + +
      +
      +
      + {% if landing_page %} {{ protocol_preamble }} {{ landing_page }} {% else + %} +

      {{ activity_pref_label }}

      +

      + +
      + +

      + + {{ activity_preamble }} {% if upload_form %} +
      {{ render_form(upload_form) }}
      + {% endif %} + +
      +
      {{ render_form(form) }}
      +
      + + {% endif %} +
      +
      +
      +{% endblock %} diff --git a/ui/pyproject.toml b/ui/pyproject.toml new file mode 100644 index 00000000..cc39cf21 --- /dev/null +++ b/ui/pyproject.toml @@ -0,0 +1,84 @@ +[build-system] +build-backend = "hatchling.build" +requires = ["hatchling", "hatch-vcs"] + +[project] +authors = [{name = "Remi Gau"}] +dependencies = [ + "flask", + "Flask-WTF", + "bootstrap-flask", + "pandas", + "rich" +] +description = "UI for eCOBIDAS" +license = {text = "GPL 3.0"} +maintainers = [{name = "Remi Gau", email = "remi.gau2@mcgill.ca"}] +name = "ecobidas_ui" +readme = "README.md" +requires-python = ">=3.11" +# Version from setuptools_scm +# dynamic = ["version"] +version = "0.1.0" + +[project.optional-dependencies] +dev = [ + 'tox' +] +test = [ + "coverage", + "pytest>=6.0.0", + "pytest-cov" +] + +[tool.black] +line-length = 100 + +[tool.codespell] +# ignore-words-list = "" +skip = "./.git,*.svg,env," + +[tool.hatch.build.hooks.vcs] +version-file = "ecobidas_ui/_version.py" + +[tool.hatch.build.targets.wheel] +packages = ["ecobidas_ui"] + +[tool.hatch.version] +source = "vcs" + +[tool.isort] +combine_as_imports = true +line_length = 100 +profile = "black" +skip_gitignore = true + +[tool.mypy] +check_untyped_defs = true +disallow_any_generics = true +disallow_incomplete_defs = true +disallow_untyped_defs = true +enable_error_code = ["ignore-without-code", "redundant-expr"] # "truthy-bool" +no_implicit_optional = true +show_error_codes = true +# strict = true +warn_redundant_casts = true +warn_unreachable = true +warn_unused_ignores = true + +[[tool.mypy.overrides]] +ignore_missing_imports = true +module = [ + "rich" +] + +[[tool.mypy.overrides]] +ignore_errors = true +module = ['tests.*'] + +[tool.pytest.ini_options] +addopts = "-ra --strict-config --strict-markers --doctest-modules --showlocals -s -v" +doctest_optionflags = "NORMALIZE_WHITESPACE ELLIPSIS" +junit_family = "xunit2" +minversion = "6.0" +xfail_strict = true diff --git a/ui/requirements.txt b/ui/requirements.txt index 1698b1f4..90798301 100644 --- a/ui/requirements.txt +++ b/ui/requirements.txt @@ -1,3 +1,56 @@ -flask -Flask-WTF -bootstrap-flask +# +# This file is autogenerated by pip-compile with Python 3.11 +# by the following command: +# +# pip-compile --output-file=requirements.txt --strip-extras pyproject.toml +# +blinker==1.8.2 + # via flask +bootstrap-flask==2.4.0 + # via ecobidas_ui (pyproject.toml) +click==8.1.7 + # via flask +flask==3.0.3 + # via + # bootstrap-flask + # ecobidas_ui (pyproject.toml) + # flask-wtf +flask-wtf==1.2.1 + # via ecobidas_ui (pyproject.toml) +itsdangerous==2.2.0 + # via + # flask + # flask-wtf +jinja2==3.1.4 + # via flask +markdown-it-py==3.0.0 + # via rich +markupsafe==2.1.5 + # via + # jinja2 + # werkzeug + # wtforms +mdurl==0.1.2 + # via markdown-it-py +numpy==1.26.4 + # via pandas +pandas==2.2.2 + # via ecobidas_ui (pyproject.toml) +pygments==2.18.0 + # via rich +python-dateutil==2.9.0.post0 + # via pandas +pytz==2024.1 + # via pandas +rich==13.7.1 + # via ecobidas_ui (pyproject.toml) +six==1.16.0 + # via python-dateutil +tzdata==2024.1 + # via pandas +werkzeug==3.0.3 + # via flask +wtforms==3.1.2 + # via + # bootstrap-flask + # flask-wtf diff --git a/ui/templates/about.html b/ui/templates/about.html deleted file mode 100644 index 16afcfca..00000000 --- a/ui/templates/about.html +++ /dev/null @@ -1,2 +0,0 @@ -{% extends 'base.html' %} {% from 'bootstrap5/form.html' import render_form %} -{% block content %} {% endblock %} diff --git a/ui/templates/new_checklist.html b/ui/templates/new_checklist.html deleted file mode 100644 index 21f5da26..00000000 --- a/ui/templates/new_checklist.html +++ /dev/null @@ -1 +0,0 @@ -{% extends 'base.html' %} diff --git a/ui/templates/protocol.html b/ui/templates/protocol.html deleted file mode 100644 index cb8da6e9..00000000 --- a/ui/templates/protocol.html +++ /dev/null @@ -1,97 +0,0 @@ -{% extends 'base.html' %} {% from 'bootstrap5/form.html' import render_form %} -{% block content %} -
      -
      -
      -

      {{ protocol_pref_label }}

      -
      - -
      -
      -
      - {% if landing_page %} {{ protocol_preamble }} {{ landing_page }} {% else - %} -

      {{ activity_pref_label }}

      -

      - -
      - -

      - - {{ activity_preamble }} - - - - - - - - - - - - - - {% if upload_form %} -
      - {% with messages = get_flashed_messages() %} {% if messages %} {% for - message in messages %} - - {% endfor %} {% endif %} {% endwith %} {{ render_form(upload_form) }} -
      - {% endif %} - -
      -
      {{ render_form(form) }}
      -
      - - {% endif %} -
      -
      -
      -{% endblock %} diff --git a/ui/tests/conftest.py b/ui/tests/conftest.py new file mode 100644 index 00000000..94bece32 --- /dev/null +++ b/ui/tests/conftest.py @@ -0,0 +1,41 @@ +import os +import tempfile +from pathlib import Path + +import pytest +from ecobidas_ui import create_app +from ecobidas_ui.db import get_db, init_db + +with open(Path(__file__).parent / "data.sql", "rb") as f: + _data_sql = f.read().decode("utf8") + + +@pytest.fixture +def app(): + db_fd, db_path = tempfile.mkstemp() + + app = create_app( + { + "TESTING": True, + "DATABASE": db_path, + } + ) + + with app.app_context(): + init_db() + get_db().executescript(_data_sql) + + yield app + + os.close(db_fd) + os.unlink(db_path) + + +@pytest.fixture +def client(app): + return app.test_client() + + +@pytest.fixture +def runner(app): + return app.test_cli_runner() diff --git a/ui/tests/data.sql b/ui/tests/data.sql new file mode 100644 index 00000000..9b680065 --- /dev/null +++ b/ui/tests/data.sql @@ -0,0 +1,8 @@ +INSERT INTO user (username, password) +VALUES + ('test', 'pbkdf2:sha256:50000$TCI4GzcX$0de171a4f4dac32e3364c7ddc7c14f3e2fa61f2d17574483f7ffbb431b4acb2f'), + ('other', 'pbkdf2:sha256:50000$kJPKsz6N$d2d4784f1b030a9761f5ccaeeaca413f27f2ecb76d6168407af962ddce849f79'); + +INSERT INTO post (title, body, author_id, created) +VALUES + ('test title', 'test' || x'0a' || 'body', 1, '2018-01-01 00:00:00'); diff --git a/ui/tox.ini b/ui/tox.ini new file mode 100644 index 00000000..4ff19c02 --- /dev/null +++ b/ui/tox.ini @@ -0,0 +1,33 @@ +; See https://tox.wiki/en +[tox] +requires = + tox>=4 +; run lint by default when just calling "tox" +env_list = lint + +; ENVIRONMENTS +; ------------ +[style] +description = common environment for style checkers (rely on pre-commit hooks) +skip_install = true +deps = + pre-commit + +; COMMANDS +; -------- +[testenv:lint] +description = install pre-commit hooks and run all linters and formatters +skip_install = true +deps = + {[style]deps} +commands = + pre-commit install + pre-commit run --all-files --show-diff-on-failure {posargs:} + +[testenv:update_dependencies] +description = update requirements.txt +skip_install = true +deps = + pip-tools +commands = + pip-compile --strip-extras -o requirements.txt pyproject.toml {posargs:} From f273fa47995f682704c1a57bd3d310fcea087018 Mon Sep 17 00:00:00 2001 From: Remi Gau Date: Fri, 24 May 2024 10:14:52 -0400 Subject: [PATCH 14/31] reorganize items description and details --- ecobidas/create_schema.py | 2 - ecobidas/inputs/neurovault/neurovault.tsv | 176 ++--- ecobidas/item.py | 15 +- .../items/number_of_subjects.jsonld | 2 +- .../activity_3/items/integer_item.jsonld | 2 +- .../activity_3/items/slider_item.jsonld | 2 +- .../activities/activity_4/items/TEXT.jsonld | 2 +- .../activity_4/items/float_item.jsonld | 2 +- .../activity_4/items/multitext_item.jsonld | 2 +- .../items/mri_softwares.jsonld | 2 +- .../select_activity/items/radio_item.jsonld | 2 +- .../items/radio_item_multiple_choice.jsonld | 2 +- .../select_activity/items/select_item.jsonld | 2 +- .../items/select_item_multiple_choice.jsonld | 2 +- .../items/yes_no_do_not_know.jsonld | 2 +- .../activities/visibility/items/base.jsonld | 2 +- .../activities/visibility/items/base0.jsonld | 2 +- .../activities/visibility/items/base1.jsonld | 2 +- .../visibility/items/multi_2_or_5.jsonld | 2 +- .../visibility/items/multi_gt_5.jsonld | 2 +- .../visibility/items/multi_lt_2.jsonld | 2 +- .../visibility/items/radio_vis.jsonld | 2 +- .../visibility/items/select_boolean.jsonld | 2 +- .../visibility/items/select_boolean0.jsonld | 2 +- .../visibility/items/select_boolean1.jsonld | 2 +- tests/data/protocols/test_schema.jsonld | 12 +- tests/test_convert_to_schema.py | 11 +- ui/LICENSE | 674 ++++++++++++++++++ ui/README.md | 7 + ui/ecobidas_ui/protocol.py | 15 +- ui/ecobidas_ui/templates/about.html | 128 +++- ui/ecobidas_ui/templates/auth/login.html | 6 +- ui/ecobidas_ui/templates/auth/register.html | 6 +- ui/ecobidas_ui/templates/base.html | 96 ++- ui/ecobidas_ui/templates/index.html | 15 +- ui/ecobidas_ui/templates/protocol.html | 11 +- ui/ecobidas_ui/{modules.py => utils.py} | 23 +- ui/pyproject.toml | 3 +- ui/requirements.txt | 10 + 39 files changed, 1054 insertions(+), 200 deletions(-) create mode 100644 ui/LICENSE rename ui/ecobidas_ui/{modules.py => utils.py} (88%) diff --git a/ecobidas/create_schema.py b/ecobidas/create_schema.py index d113b782..c7dd37d7 100644 --- a/ecobidas/create_schema.py +++ b/ecobidas/create_schema.py @@ -85,8 +85,6 @@ def create_schema( item_info = get_item_info(this_item) - item_info["id"] = f"{activity_idx:.0f}.{item_idx:.0f}" - print_item_info(activity_idx, item_idx, item_info) item = define_new_item(item_info) diff --git a/ecobidas/inputs/neurovault/neurovault.tsv b/ecobidas/inputs/neurovault/neurovault.tsv index c9f12a45..2226b696 100644 --- a/ecobidas/inputs/neurovault/neurovault.tsv +++ b/ecobidas/inputs/neurovault/neurovault.tsv @@ -1,88 +1,88 @@ -activity_pref_label activity_order item_order question unit details field_type choices item item_pref_label visibility item_description include mandatory preamble bids_status bids_file bids_key bids_key_for_unit -Experimental design 1 1 Type of design select blocked | event_related | hybrid block/event type_of_design type of design 1 type of design 1 1 Describe your experimental design -Experimental design 1 2 Number of imaging runs acquired integer 0 number of imaging runs 1 number of imaging runs 1 2 -Experimental design 1 3 Number of blocks, trials or experimental units per imaging run integer 0 number of experimental units 1 number of experimental units 1 2 -Experimental design 1 4 Length of each imaging run seconds float 0 length of runs 1 length of runs 1 2 -Experimental design 1 5 For blocked designs, length of blocks seconds float 0 length of blocks type_of_design in [0, 2] length of blocks 1 2 -Experimental design 1 6 Length of individual trials seconds float 0 length of trials 1 length of trials 1 2 -Experimental design 1 7 Was the design optimized for efficiency? radio preset:boolean optimization 1 optimization 1 2 -Experimental design 1 8 What method was used for optimization? textarea optimization method optimization == 1 optimization method 1 3 -Participants 2 1 Number of subjects entering into the analysis integer 0 number of subjects 1 number of subjects 1 1 Describe your participant sample -Participants 2 2 Mean age of subjects float 0 subject age mean 1 subject age mean 1 1 -Participants 2 3 Minimum age of subjects float 0 subject age min 1 subject age min 1 2 -Participants 2 4 Maximum age of subjects float 0 subject age max 1 subject age max 1 2 -Participants 2 5 Handedness of subjects radio right | left | both handedness 1 handedness 1 2 -Participants 2 6 The proportion of subjects who were male float 0 | 1 proportion male subjects 1 proportion male subjects 1 2 -Participants 2 7 Additional inclusion/exclusion criteria, if any. Including specific sampling strategies that limit inclusion to a specific group, such as laboratory members. textarea inclusion exclusion criteria 1 inclusion exclusion criteria 1 3 -Participants 2 8 Number of subjects scanned but rejected from analysis integer 0 number of rejected subjects 1 number of rejected subjects 1 2 -Participants 2 9 Was this study a comparison between subject groups? radio preset:boolean group comparison 1 group comparison 1 1 -Participants 2 10 A description of the groups being compared textarea group description group_comparison == 1 group description 1 2 -MRI acquisition 3 1 Manufacturer of MRI scanner select Siemens | Philips | General Electric Manufacturer scanner make 1 scanner make 1 1 Describe your acquisition parameters -MRI acquisition 3 2 Model of MRI scanner textarea ManufacturersModelName scanner model 1 scanner model 1 1 -MRI acquisition 3 3 Field strength of MRI scanner Tesla float 0 MagneticFieldStrength field strength 1 field strength 1 1 -MRI acquisition 3 4 Description of pulse sequence used for fMRI select Gradient echo | Spin echo | Mutliband gradient echo | MPRAGE | MP2RAGE | FLASH PulseSequenceType pulse sequence 1 pulse sequence 1 1 -MRI acquisition 3 5 Description of parallel imaging method and parameters textarea parallel imaging 1 parallel imaging 1 3 -MRI acquisition 3 6 Imaging field of view Millimeters float field of view 1 field of view 1 2 -MRI acquisition 3 7 Matrix size for MRI acquisition integer matrix size 1 matrix size 1 2 -MRI acquisition 3 8 Distance between slices (includes skip or distance factor). Millimeters float 0 slice thickness 1 slice thickness 1 1 -MRI acquisition 3 9 The size of the skipped area between slices. Millimeters float 0 skip factor 1 skip factor 1 2 -MRI acquisition 3 10 The orientation of slices radio axial | sagittal | frontal acquisition orientation 1 acquisition orientation 1 2 -MRI acquisition 3 11 Order of acquisition of slices select ascending | descending | interleaved SliceTiming order of acquisition 1 order of acquisition 1 3 -MRI acquisition 3 12 Repetition time (TR) Milliseconds float 0 RepetitionTime repetition time 1 repetition time 1 1 -MRI acquisition 3 13 Echo time (TE) Milliseconds float 0 EchoTime echo time 1 echo time 1 1 -MRI acquisition 3 14 Flip angle Degrees float 0 FlipAngle flip angle 1 flip angle 1 2 -Preprocessing 4 1 If a single software package was used for all analyses, specify that here select preset:mri_softwares SoftwareName software package 1 software package 1 1 Describe your preprocessing -Preprocessing 4 2 Version of software package used textarea SoftwareVersion software version 1 software version 1 1 -Preprocessing 4 3 Specify order of preprocessing operations textarea order of preprocessing operations 1 order of preprocessing operations 1 2 -Preprocessing 4 4 Describe quality control measures textarea quality control 1 quality control 1 3 -Preprocessing 4 5 Was B0 distortion correction used? radio preset:boolean used b0 unwarping 1 used b0 unwarping 1 2 -Preprocessing 4 6 Specify software used for distortion correction if different from the main package select preset:mri_softwares b0 unwarping software used_b0_unwarping == 1 b0 unwarping software 1 3 -Preprocessing 4 7 Was slice timing correction used? radio preset:boolean used slice timing correction 1 used slice timing correction 1 1 -Preprocessing 4 8 Specify software used for slice timing correction if different from the main package textarea slice timing correction software used_slice_timing_correction == 1 slice timing correction software 1 3 -Preprocessing 4 9 Was motion correction used? radio preset:boolean used motion correction 1 used motion correction 1 1 -Preprocessing 4 10 Specify software used for motion correction if different from the main package select preset:mri_softwares motion correction software used_motion_correction == 1 motion correction software 1 3 -Preprocessing 4 11 Reference scan used for motion correction textarea motion correction reference used_motion_correction == 1 motion correction reference 1 3 -Preprocessing 4 12 Similarity metric used for motion correction select preset:cost_functions motion correction metric used_motion_correction == 1 motion correction metric 1 3 -Preprocessing 4 13 Interpolation method used for motion correction select preset:interpolations motion correction interpolation used_motion_correction == 1 motion correction interpolation 1 3 -Preprocessing 4 14 Was motion-susceptibility correction used? radio preset:boolean used motion susceptibiity correction 1 used motion susceptibiity correction 1 3 -Intersubject registration 5 1 Were subjects registered to a common stereotactic space? radio preset:boolean used intersubject registration 1 used intersubject registration 1 1 Describe your spatial normalization -Intersubject registration 5 2 Specify software used for intersubject registration if different from main package select preset:mri_softwares intersubject registration software used_intersubject_registration == 1 intersubject registration software 1 2 -Intersubject registration 5 3 Was linear or nonlinear registration used? select linear | non-linear intersubject transformation type used_intersubject_registration == 1 intersubject transformation type 1 1 -Intersubject registration 5 4 If nonlinear registration was used, describe transform method textarea nonlinear transform type used_intersubject_registration == 1 nonlinear transform type 1 2 -Intersubject registration 5 5 Similarity metric used for intersubject registration textarea transform similarity metric used_intersubject_registration == 1 transform similarity metric 1 3 -Intersubject registration 5 6 Interpolation method used for intersubject registration select preset:interpolations interpolation method used_intersubject_registration == 1 interpolation method 1 2 -Intersubject registration 5 7 What type of image was used to determine the transformation to the atlas? textarea object image type used_intersubject_registration == 1 object image type 1 1 -Intersubject registration 5 8 Were the functional images coregistered to the subject's structural image? radio preset:boolean functional coregistered to structural 1 functional coregistered to structural 1 2 -Intersubject registration 5 9 Method used to coregister functional to structural images textarea functional coregistration method functional_coregistered_to_structural == 1 functional coregistration method 1 3 -Intersubject registration 5 10 Name of coordinate space for registration target select MNI | Talairach | MNI2Tal coordinate space 1 coordinate space 1 1 -Intersubject registration 5 11 Name of target template image textarea target template image 1 target template image 1 2 -Intersubject registration 5 12 Voxel size of target template Millimeters float 0 target resolution 1 target resolution 1 1 -Intersubject registration 5 13 Was spatial smoothing applied? radio preset:boolean used smoothing 1 used smoothing 1 1 -Intersubject registration 5 14 Describe the type of smoothing applied text smoothing type used_smoothing == 1 smoothing type 1 1 -Intersubject registration 5 15 The full-width at half-maximum of the smoothing kernel Millimeters float smoothing fwhm used_smoothing == 1 smoothing fwhm 1 1 -Intersubject registration 5 16 Voxel size in mm of the resampled, atlas-space images float 0 resampled voxel size 1 resampled voxel size 1 1 -Individual subject modeling 6 1 Type of group model used radio Regression intrasubject model type 1 intrasubject model type 1 1 Describe your model specification at the subejct level -Individual subject modeling 6 2 Estimation method used for model select ordinary least squares | generalized least squares intrasubject estimation type 1 intrasubject estimation type 1 1 -Individual subject modeling 6 3 Software used for intrasubject modeling if different from overall package select preset:mri_softwares intrasubject modeling software 1 intrasubject modeling software 1 2 -Individual subject modeling 6 4 Nature of HRF model select double gamma | Fourrier set | FIR hemodynamic response function 1 hemodynamic response function 1 2 -Individual subject modeling 6 5 Were temporal derivatives included? radio preset:boolean used temporal derivatives 1 used temporal derivatives 1 2 -Individual subject modeling 6 6 Were dispersion derivatives included? radio preset:boolean used dispersion derivatives 1 used dispersion derivatives 1 3 -Individual subject modeling 6 7 Were motion regressors included? radio preset:boolean used motion regressors 1 used motion regressors 1 2 -Individual subject modeling 6 8 Was a reaction time regressor included? radio preset:boolean used reaction time regressor 1 used reaction time regressor 1 2 -Individual subject modeling 6 9 Were any regressors specifically orthogonalized with respect to others? radio preset:boolean used orthogonalization 1 used orthogonalization 1 1 -Individual subject modeling 6 10 If orthogonalization was used, describe here textarea orthogonalization description used_orthogonalization == 1 orthogonalization description 1 2 -Individual subject modeling 6 11 Was high pass filtering applied? radio preset:boolean used high pass filter 1 used high pass filter 1 1 -Individual subject modeling 6 12 Describe method used for high pass filtering textarea high pass filter method used_high_pass_filter == 1 high pass filter method 1 2 -Individual subject modeling 6 13 What autocorrelation model was used (or 'none' if none was used) textarea autocorrelation model 1 autocorrelation model 1 2 -Individual subject modeling 6 14 Exactly what terms are subtracted from what? textarea contrast definition 1 contrast definition 1 1 -Individual subject modeling 6 15 Link to Cognitive Atlas definition of this contrast Define these in terms of task or stimulus conditions (e.g., 'one-back task with objects versus zero-back task with objects') instead of underlying psychological concepts (e.g., 'working memory'). textarea contrast definition cogatlas 1 contrast definition cogatlas 1 3 -Group modeling 7 1 Type of group model used select Regression group model type 1 group model type 1 1 Describe the group level analysis -Group modeling 7 2 Estimation method used for model select ordinary least squares | generalized least squares group estimation type 1 group estimation type 1 1 -Group modeling 7 3 Software used for group modeling if different from overall package select preset:mri_softwares group modeling software 1 group modeling software 1 2 -Group modeling 7 4 Type of inference for group model select random effect | mixed effect | fixed effect group inference type 1 group inference type 1 1 -Group modeling 7 5 If more than 2-levels, describe the levels and assumptions of the model. For example, are variances assumed equal between groups. textarea group model multilevel 1 group model multilevel 1 3 -Group modeling 7 6 Was this a repeated measures design at the group level? radio preset:boolean group repeated measures 1 group repeated measures 1 1 -Group modeling 7 7 If multiple measurements per subject, list method to account for within subject correlation, exact assumptions made about correlation/variance textarea group repeated measures method group_repeated_measures == 1 group repeated measures method 1 3 -Group inference 8 1 Type of statistic that is the basis of the inference select Z | T | F | X2 | PostProb | NonparametricP | MonteCarloP group statistic type 1 group statistic type 1 2 Describe your statistical inference -Group inference 8 2 Parameters of the null distribution of the test statisic. Typically degrees of freedom (should be clear from the test statistic what these are). float group statistic parameters 1 group statistic parameters 1 1 -Group inference 8 3 Noise smoothness for statistical inference This is the estimated smoothness used with Random Field Theory or a simulation-based inference method. float 0 group smoothness fwhm 1 group smoothness fwhm 1 1 +activity_pref_label activity_order item_order question unit details field_type choices item item_pref_label visibility item_description include mandatory preamble bids_status bids_file bids_key bids_key_for_unit UUID +Experimental design 1 1 Type of design select blocked | event_related | hybrid block/event type_of_design type of design 1 type of design 1 1 Describe your experimental design 8e2cf1e8-6328-49fc-85d3-38d405a4cc91 +Experimental design 1 2 Number of imaging runs acquired integer 0 number of imaging runs 1 number of imaging runs 1 2 e969343d-3ca8-4cdf-afcc-b681a545144a +Experimental design 1 3 Number of blocks, trials or experimental units per imaging run integer 0 number of experimental units 1 number of experimental units 1 2 2d5111f6-ed50-4428-946b-6b9287896e27 +Experimental design 1 4 Length of each imaging run seconds float 0 length of runs 1 length of runs 1 2 27fd0fa4-75ff-47c0-8092-17d1056e3d37 +Experimental design 1 5 For blocked designs, length of blocks seconds float 0 length of blocks type_of_design in [0, 2] length of blocks 1 2 46569ab0-d730-488f-9486-3f00f90ba211 +Experimental design 1 6 Length of individual trials seconds float 0 length of trials 1 length of trials 1 2 dd65fbb8-1c54-4cc1-b1ec-5530ab6e02e6 +Experimental design 1 7 Was the design optimized for efficiency? radio preset:boolean optimization 1 optimization 1 2 92062e6c-5ff4-4e55-a2a6-2d7cc7ae272c +Experimental design 1 8 What method was used for optimization? textarea optimization method optimization == 1 optimization method 1 3 5b2910fe-cfa5-404c-a8dc-9bca47876746 +Participants 2 1 Number of subjects entering into the analysis integer 0 number of subjects 1 number of subjects 1 1 Describe your participant sample a06822dd-9f8b-4d36-8802-d11bd1e0ce81 +Participants 2 2 Mean age of subjects float 0 subject age mean 1 subject age mean 1 1 bfa6d6fb-4854-4063-bf9f-08e9c24c0337 +Participants 2 3 Minimum age of subjects float 0 subject age min 1 subject age min 1 2 3c9ada14-5ee8-472e-97aa-d8f0c5e699e0 +Participants 2 4 Maximum age of subjects float 0 subject age max 1 subject age max 1 2 e13e03d9-8074-43af-b8f1-afcf0f7c53da +Participants 2 5 Handedness of subjects radio right | left | both handedness 1 handedness 1 2 193c5710-f15a-4b32-83cb-ebaeee9b6b90 +Participants 2 6 The proportion of subjects who were male float 0 | 1 proportion male subjects 1 proportion male subjects 1 2 4da6dc89-a32b-471d-927a-21e437ded0a6 +Participants 2 7 Additional inclusion/exclusion criteria, if any. Including specific sampling strategies that limit inclusion to a specific group, such as laboratory members. textarea inclusion exclusion criteria 1 inclusion exclusion criteria 1 3 61c6e866-8733-4599-93dd-ee7601874f08 +Participants 2 8 Number of subjects scanned but rejected from analysis integer 0 number of rejected subjects 1 number of rejected subjects 1 2 a0d63a78-4017-4c85-9b28-4322b8fbfdd1 +Participants 2 9 Was this study a comparison between subject groups? radio preset:boolean group comparison 1 group comparison 1 1 b587a1e6-65a8-42b8-b2ae-3dfc05edbd4a +Participants 2 10 A description of the groups being compared textarea group description group_comparison == 1 group description 1 2 f140953d-b6bd-45ed-bbe6-9387659a252f +MRI acquisition 3 1 Manufacturer of MRI scanner select Siemens | Philips | General Electric | other Manufacturer scanner make 1 scanner make 1 1 Describe your acquisition parameters 8e0dd443-efc6-49ef-b783-cbd6e3cda4eb +MRI acquisition 3 2 Model of MRI scanner textarea ManufacturersModelName scanner model 1 scanner model 1 1 2087da57-f9c8-4446-9a77-efa1957acd20 +MRI acquisition 3 3 Field strength of MRI scanner Tesla float 0 MagneticFieldStrength field strength 1 field strength 1 1 7543b22d-07db-4b5a-8796-30b5904b552d +MRI acquisition 3 4 Description of pulse sequence used for fMRI select Gradient echo | Spin echo | Mutliband gradient echo | MPRAGE | MP2RAGE | FLASH PulseSequenceType pulse sequence 1 pulse sequence 1 1 5f2c2e3b-f17a-4d50-bf57-df65661fe199 +MRI acquisition 3 5 Description of parallel imaging method and parameters textarea parallel imaging 1 parallel imaging 1 3 f8d53fef-12a3-429a-9dcc-b19339850577 +MRI acquisition 3 6 Imaging field of view Millimeters float field of view 1 field of view 1 2 a204e1e7-82e5-4bff-9d5e-785ba72404c9 +MRI acquisition 3 7 Matrix size for MRI acquisition integer matrix size 1 matrix size 1 2 2477fc28-85f1-41ca-9a2a-f98cd250f800 +MRI acquisition 3 8 Distance between slices (includes skip or distance factor). Millimeters float 0 slice thickness 1 slice thickness 1 1 22e835fd-1940-4379-80ac-a88491950d08 +MRI acquisition 3 9 The size of the skipped area between slices. Millimeters float 0 skip factor 1 skip factor 1 2 dd82553d-335c-404e-8c27-dc95c58c1456 +MRI acquisition 3 10 The orientation of slices radio axial | sagittal | frontal acquisition orientation 1 acquisition orientation 1 2 191f098d-8aca-4cf5-bdd2-8f2e4fafc494 +MRI acquisition 3 11 Order of acquisition of slices select ascending | descending | interleaved SliceTiming order of acquisition 1 order of acquisition 1 3 34099ae2-819c-4e10-baaf-a7017c9393e1 +MRI acquisition 3 12 Repetition time (TR) Milliseconds float 0 RepetitionTime repetition time 1 repetition time 1 1 ae069155-1c4d-45b6-a9ae-210f33fc8aac +MRI acquisition 3 13 Echo time (TE) Milliseconds float 0 EchoTime echo time 1 echo time 1 1 4ed3dd1e-c121-4f71-a499-8693c32811da +MRI acquisition 3 14 Flip angle Degrees float 0 FlipAngle flip angle 1 flip angle 1 2 b7cd770d-a881-47a9-abe0-794a9f147654 +Preprocessing 4 1 If a single software package was used for all analyses, specify that here select preset:mri_softwares SoftwareName software package 1 software package 1 1 Describe your preprocessing 563bc956-277d-41f2-a68e-c529a4fceb94 +Preprocessing 4 2 Version of software package used textarea SoftwareVersion software version 1 software version 1 1 724d9e55-efca-4cb9-9339-1325c3c30f74 +Preprocessing 4 3 Specify order of preprocessing operations textarea order of preprocessing operations 1 order of preprocessing operations 1 2 5303df62-5ec3-4ef1-b0e2-d29be74a78a3 +Preprocessing 4 4 Describe quality control measures textarea quality control 1 quality control 1 3 d3f5adb3-6fd8-447d-b950-74c0c8c3ed73 +Preprocessing 4 5 Was B0 distortion correction used? radio preset:boolean used b0 unwarping 1 used b0 unwarping 1 2 e694f278-c996-4b4f-9036-7f8681418fd5 +Preprocessing 4 6 Specify software used for distortion correction if different from the main package select preset:mri_softwares b0 unwarping software used_b0_unwarping == 1 b0 unwarping software 1 3 2a21d849-3a13-4582-bc9b-db9c860f7d5b +Preprocessing 4 7 Was slice timing correction used? radio preset:boolean used slice timing correction 1 used slice timing correction 1 1 7a9fc02b-d130-4728-aef0-0d517b06e754 +Preprocessing 4 8 Specify software used for slice timing correction if different from the main package select preset:mri_softwares slice timing correction software used_slice_timing_correction == 1 slice timing correction software 1 3 d492a1e4-17be-4c40-a83a-5462532f19da +Preprocessing 4 9 Was motion correction used? radio preset:boolean used motion correction 1 used motion correction 1 1 7900736f-5566-46ea-becd-4a25bbd0e77a +Preprocessing 4 10 Specify software used for motion correction if different from the main package select preset:mri_softwares motion correction software used_motion_correction == 1 motion correction software 1 3 c2567427-3f72-46ad-991c-3e8181a8f73f +Preprocessing 4 11 Reference scan used for motion correction textarea motion correction reference used_motion_correction == 1 motion correction reference 1 3 afd06405-39fc-48a8-8773-8887f4a267a5 +Preprocessing 4 12 Similarity metric used for motion correction select preset:cost_functions motion correction metric used_motion_correction == 1 motion correction metric 1 3 d12f8e07-8788-41c9-83a8-f08f1457c734 +Preprocessing 4 13 Interpolation method used for motion correction select preset:interpolations motion correction interpolation used_motion_correction == 1 motion correction interpolation 1 3 0bb02f83-db82-4afb-b1cf-7ce3ae03a926 +Preprocessing 4 14 Was motion-susceptibility correction used? radio preset:boolean used motion susceptibiity correction 1 used motion susceptibiity correction 1 3 609d194c-33c4-48f7-a34d-2e984d7f8ee8 +Intersubject registration 5 1 Were subjects registered to a common stereotactic space? radio preset:boolean used intersubject registration 1 used intersubject registration 1 1 Describe your spatial normalization 0ec88003-df12-4090-9a12-f52ad93e15d6 +Intersubject registration 5 2 Specify software used for intersubject registration if different from main package select preset:mri_softwares intersubject registration software used_intersubject_registration == 1 intersubject registration software 1 2 101b8a20-4f17-4aa5-8776-17eab2ebda6b +Intersubject registration 5 3 Was linear or nonlinear registration used? select linear | non-linear intersubject transformation type used_intersubject_registration == 1 intersubject transformation type 1 1 9e814686-8632-4460-8a5a-6f13c972c2e6 +Intersubject registration 5 4 If nonlinear registration was used, describe transform method textarea nonlinear transform type used_intersubject_registration == 1 nonlinear transform type 1 2 59be2536-c299-4e96-aac7-d854b653f003 +Intersubject registration 5 5 Similarity metric used for intersubject registration textarea transform similarity metric used_intersubject_registration == 1 transform similarity metric 1 3 4cd51429-19ec-4a7f-80cb-071f241cc89c +Intersubject registration 5 6 Interpolation method used for intersubject registration select preset:interpolations interpolation method used_intersubject_registration == 1 interpolation method 1 2 127aaa05-a1ef-40b6-bf7a-7faffbba5587 +Intersubject registration 5 7 What type of image was used to determine the transformation to the atlas? textarea object image type used_intersubject_registration == 1 object image type 1 1 cdd9e5dc-ac7c-4a89-b47d-4ab8705fb23e +Intersubject registration 5 8 Were the functional images coregistered to the subject's structural image? radio preset:boolean functional coregistered to structural 1 functional coregistered to structural 1 2 d06f3d30-ebaf-45da-bd5c-0653cf957431 +Intersubject registration 5 9 Method used to coregister functional to structural images textarea functional coregistration method functional_coregistered_to_structural == 1 functional coregistration method 1 3 11c87f60-4ba5-4916-868f-015813e5bbb5 +Intersubject registration 5 10 Name of coordinate space for registration target select MNI | Talairach | MNI2Tal | other coordinate space 1 coordinate space 1 1 cd90b95a-96fd-445a-ba7c-be0e59b5afd8 +Intersubject registration 5 11 Name of target template image textarea target template image 1 target template image 1 2 11fb168c-fd45-48f2-b965-fb51e77906f8 +Intersubject registration 5 12 Voxel size of target template Millimeters float 0 target resolution 1 target resolution 1 1 c55f66aa-1d3d-459a-9780-21afc720d969 +Intersubject registration 5 13 Was spatial smoothing applied? radio preset:boolean used smoothing 1 used smoothing 1 1 d70017f8-9848-4aca-afc3-efc2f25e66a2 +Intersubject registration 5 14 Describe the type of smoothing applied textarea smoothing type used_smoothing == 1 smoothing type 1 1 d55441ad-488f-462e-ade5-9085bc4a0bd7 +Intersubject registration 5 15 The full-width at half-maximum of the smoothing kernel Millimeters float 0 smoothing fwhm used_smoothing == 1 smoothing fwhm 1 1 27bc5893-bac0-4327-8bdf-e31e3e4be19c +Intersubject registration 5 16 Voxel size in mm of the resampled, atlas-space images float 0 resampled voxel size 1 resampled voxel size 1 1 e33bbdbc-71a5-4989-9ca9-0e67f40106ea +Individual subject modeling 6 1 Type of group model used radio Regression | other intrasubject model type 1 intrasubject model type 1 1 Describe your model specification at the subejct level ae754ba8-05e7-4a65-83c2-ae0fb803b762 +Individual subject modeling 6 2 Estimation method used for model select ordinary least squares | generalized least squares | other intrasubject estimation type 1 intrasubject estimation type 1 1 2d7e49e9-f7e6-455c-9771-ac306a123fff +Individual subject modeling 6 3 Software used for intrasubject modeling if different from overall package select preset:mri_softwares intrasubject modeling software 1 intrasubject modeling software 1 2 247e4704-af69-48c8-9ce4-96909560f3e5 +Individual subject modeling 6 4 Nature of HRF model select spm HRF | glover HRF | double gamma | Fourrier set | Finite Impulse Response | FLOBS | other hemodynamic response function 1 hemodynamic response function 1 2 793d6278-ff64-45c4-85a2-ac44c2839489 +Individual subject modeling 6 5 Were temporal derivatives included? radio preset:boolean used temporal derivatives 1 used temporal derivatives 1 2 6d4c0751-cbb3-4f7d-852e-5667e282267b +Individual subject modeling 6 6 Were dispersion derivatives included? radio preset:boolean used dispersion derivatives 1 used dispersion derivatives 1 3 8bf99177-de69-4a10-92cf-db898f7a58e0 +Individual subject modeling 6 7 Were motion regressors included? radio preset:boolean used motion regressors 1 used motion regressors 1 2 d1b37e2e-ac7b-4d00-a1c7-944123bf632f +Individual subject modeling 6 8 Was a reaction time regressor included? radio preset:boolean used reaction time regressor 1 used reaction time regressor 1 2 e63c2d6c-602d-40dd-b3c5-d1c56c97bc80 +Individual subject modeling 6 9 Were any regressors specifically orthogonalized with respect to others? radio preset:boolean used orthogonalization 1 used orthogonalization 1 1 fafcb7eb-73b9-4d96-b5bb-6e9f431dbfda +Individual subject modeling 6 10 If orthogonalization was used, describe here textarea orthogonalization description used_orthogonalization == 1 orthogonalization description 1 2 8e0f9232-881c-405e-a2ad-09ee9558197b +Individual subject modeling 6 11 Was high pass filtering applied? radio preset:boolean used high pass filter 1 used high pass filter 1 1 816d4399-04d8-4ce4-bbee-103a575d395e +Individual subject modeling 6 12 Describe method used for high pass filtering textarea high pass filter method used_high_pass_filter == 1 high pass filter method 1 2 5b3d1c3d-0d36-44e1-939f-cacf45e173a4 +Individual subject modeling 6 13 What autocorrelation model was used ? select SPM: global approximate AR(1) | SPM: FAST | FSL: locally regularized autocorrelation function | AFNI: ARMA | none | other autocorrelation model 1 autocorrelation model 1 2 37d9669d-1991-430c-b833-0d2ae88548ab +Individual subject modeling 6 14 Exactly what terms are subtracted from what? textarea contrast definition 1 contrast definition 1 1 c550179e-f8da-490e-a68c-87818cc5d06a +Individual subject modeling 6 15 Link to Cognitive Atlas definition of this contrast Define these in terms of task or stimulus conditions (e.g., 'one-back task with objects versus zero-back task with objects') instead of underlying psychological concepts (e.g., 'working memory'). textarea contrast definition cogatlas 1 contrast definition cogatlas 1 3 45340be0-df1a-4706-b8f6-644b54864d42 +Group modeling 7 1 Type of group model used select Regression group model type 1 group model type 1 1 Describe the group level analysis 34042982-ca4d-4ca4-8621-cf194ce77ed7 +Group modeling 7 2 Estimation method used for model select ordinary least squares | generalized least squares group estimation type 1 group estimation type 1 1 d616403c-8da4-40a5-ac78-ae1fda43b8ba +Group modeling 7 3 Software used for group modeling if different from overall package select preset:mri_softwares group modeling software 1 group modeling software 1 2 92c9b96d-3f7e-4577-a91b-4b33be61454f +Group modeling 7 4 Type of inference for group model select random effect | mixed effect | fixed effect group inference type 1 group inference type 1 1 b5c321cf-b2d4-4354-a460-1502881c204d +Group modeling 7 5 If more than 2-levels, describe the levels and assumptions of the model. For example, are variances assumed equal between groups. textarea group model multilevel 1 group model multilevel 1 3 4f6db1a2-bcbf-48c5-b582-8dfca49aea5e +Group modeling 7 6 Was this a repeated measures design at the group level? radio preset:boolean group repeated measures 1 group repeated measures 1 1 22c64bc3-57b1-439a-85ca-8ba5b562832a +Group modeling 7 7 If multiple measurements per subject, list method to account for within subject correlation, exact assumptions made about correlation/variance textarea group repeated measures method group_repeated_measures == 1 group repeated measures method 1 3 7d760371-ae1b-4819-9dd6-98bce210614c +Group inference 8 1 Type of statistic that is the basis of the inference select Z | T | F | X2 | PostProb | Non-parametric Permutations | Monte Carlo Permutations group statistic type 1 group statistic type 1 2 Describe your statistical inference b01e61a4-43cc-44c4-91b9-ec395ee50850 +Group inference 8 2 Parameters of the null distribution of the test statisic. Typically degrees of freedom (should be clear from the test statistic what these are). float group statistic parameters 1 group statistic parameters 1 1 819a80f2-1f18-48d1-821c-249248b0ef53 +Group inference 8 3 Noise smoothness for statistical inference This is the estimated smoothness used with Random Field Theory or a simulation-based inference method. float 0 group smoothness fwhm 1 group smoothness fwhm 1 1 c305a2d4-a926-4764-b401-c2933cacfcb0 diff --git a/ecobidas/item.py b/ecobidas/item.py index 2cc00bad..5684d735 100644 --- a/ecobidas/item.py +++ b/ecobidas/item.py @@ -148,18 +148,11 @@ def define_new_item(item_info: dict) -> Item: output_dir="items", ) - question = item_info["question"] - if "id" in item_info and item_info["id"] != "": - question = item_info["id"] + " - " + question + item.set_question(item_info["question"]) + if "details" in item_info and item_info["details"] != "": - question = ( - question - + "
      details
      " - + str(item_info["details"]) - + "
      " - ) - - item.set_question(question) + item.schema["details"] = {"en": f"{item_info['details']}"} + item.schema_order.append("details") item = define_choices(item, field_type=item_info["field_type"], choices=item_info["choices"]) item = define_unit(item, item_info["unit"]) diff --git a/tests/data/activities/activity_2/items/number_of_subjects.jsonld b/tests/data/activities/activity_2/items/number_of_subjects.jsonld index 3d949131..3d869bef 100644 --- a/tests/data/activities/activity_2/items/number_of_subjects.jsonld +++ b/tests/data/activities/activity_2/items/number_of_subjects.jsonld @@ -12,7 +12,7 @@ "inputType": "number" }, "question": { - "en": "1.1 - Number of subjects entering into the analysis" + "en": "Number of subjects entering into the analysis" }, "responseOptions": { "valueType": "xsd:integer" diff --git a/tests/data/activities/activity_3/items/integer_item.jsonld b/tests/data/activities/activity_3/items/integer_item.jsonld index f2a25d89..75d23579 100644 --- a/tests/data/activities/activity_3/items/integer_item.jsonld +++ b/tests/data/activities/activity_3/items/integer_item.jsonld @@ -12,7 +12,7 @@ "inputType": "number" }, "question": { - "en": "2.1 - This is an integer item" + "en": "This is an integer item" }, "responseOptions": { "valueType": "xsd:integer" diff --git a/tests/data/activities/activity_3/items/slider_item.jsonld b/tests/data/activities/activity_3/items/slider_item.jsonld index c0a876cf..1733cbc0 100644 --- a/tests/data/activities/activity_3/items/slider_item.jsonld +++ b/tests/data/activities/activity_3/items/slider_item.jsonld @@ -12,7 +12,7 @@ "inputType": "slider" }, "question": { - "en": "2.2 - This is a slider item" + "en": "This is a slider item" }, "responseOptions": { "valueType": "xsd:integer", diff --git a/tests/data/activities/activity_4/items/TEXT.jsonld b/tests/data/activities/activity_4/items/TEXT.jsonld index 571f3c8c..e28e9b95 100644 --- a/tests/data/activities/activity_4/items/TEXT.jsonld +++ b/tests/data/activities/activity_4/items/TEXT.jsonld @@ -12,7 +12,7 @@ "inputType": "text" }, "question": { - "en": "3.1 - This is a text item" + "en": "This is a text item" }, "responseOptions": { "valueType": "xsd:string", diff --git a/tests/data/activities/activity_4/items/float_item.jsonld b/tests/data/activities/activity_4/items/float_item.jsonld index db4a3131..f4bb2d7e 100644 --- a/tests/data/activities/activity_4/items/float_item.jsonld +++ b/tests/data/activities/activity_4/items/float_item.jsonld @@ -12,7 +12,7 @@ "inputType": "float" }, "question": { - "en": "3.3 - This is a float item" + "en": "This is a float item" }, "responseOptions": { "valueType": "xsd:float" diff --git a/tests/data/activities/activity_4/items/multitext_item.jsonld b/tests/data/activities/activity_4/items/multitext_item.jsonld index ec8b3c3d..39c0de32 100644 --- a/tests/data/activities/activity_4/items/multitext_item.jsonld +++ b/tests/data/activities/activity_4/items/multitext_item.jsonld @@ -12,7 +12,7 @@ "inputType": "multitext" }, "question": { - "en": "3.2 - This is a multitext item" + "en": "This is a multitext item" }, "responseOptions": { "valueType": "xsd:string", diff --git a/tests/data/activities/select_activity/items/mri_softwares.jsonld b/tests/data/activities/select_activity/items/mri_softwares.jsonld index b1b2752b..aa54b067 100644 --- a/tests/data/activities/select_activity/items/mri_softwares.jsonld +++ b/tests/data/activities/select_activity/items/mri_softwares.jsonld @@ -12,7 +12,7 @@ "inputType": "select" }, "question": { - "en": "4.6 - mri software" + "en": "mri software" }, "responseOptions": { "valueType": "xsd:integer", diff --git a/tests/data/activities/select_activity/items/radio_item.jsonld b/tests/data/activities/select_activity/items/radio_item.jsonld index 22386dd9..463220ca 100644 --- a/tests/data/activities/select_activity/items/radio_item.jsonld +++ b/tests/data/activities/select_activity/items/radio_item.jsonld @@ -12,7 +12,7 @@ "inputType": "radio" }, "question": { - "en": "4.1 - radio item - one answer allowed" + "en": "radio item - one answer allowed" }, "responseOptions": { "valueType": "xsd:integer", diff --git a/tests/data/activities/select_activity/items/radio_item_multiple_choice.jsonld b/tests/data/activities/select_activity/items/radio_item_multiple_choice.jsonld index dca97be7..689221d3 100644 --- a/tests/data/activities/select_activity/items/radio_item_multiple_choice.jsonld +++ b/tests/data/activities/select_activity/items/radio_item_multiple_choice.jsonld @@ -12,7 +12,7 @@ "inputType": "radio" }, "question": { - "en": "4.2 - radio item - several answers allowed" + "en": "radio item - several answers allowed" }, "responseOptions": { "valueType": "xsd:integer", diff --git a/tests/data/activities/select_activity/items/select_item.jsonld b/tests/data/activities/select_activity/items/select_item.jsonld index f8ab3475..22150d44 100644 --- a/tests/data/activities/select_activity/items/select_item.jsonld +++ b/tests/data/activities/select_activity/items/select_item.jsonld @@ -12,7 +12,7 @@ "inputType": "select" }, "question": { - "en": "4.3 - select item - one answer allowed" + "en": "select item - one answer allowed" }, "responseOptions": { "valueType": "xsd:integer", diff --git a/tests/data/activities/select_activity/items/select_item_multiple_choice.jsonld b/tests/data/activities/select_activity/items/select_item_multiple_choice.jsonld index 766f5e12..66b626de 100644 --- a/tests/data/activities/select_activity/items/select_item_multiple_choice.jsonld +++ b/tests/data/activities/select_activity/items/select_item_multiple_choice.jsonld @@ -12,7 +12,7 @@ "inputType": "select" }, "question": { - "en": "4.4 - select item - several answer allowed" + "en": "select item - several answer allowed" }, "responseOptions": { "valueType": "xsd:integer", diff --git a/tests/data/activities/select_activity/items/yes_no_do_not_know.jsonld b/tests/data/activities/select_activity/items/yes_no_do_not_know.jsonld index a3e9954e..e26c58f0 100644 --- a/tests/data/activities/select_activity/items/yes_no_do_not_know.jsonld +++ b/tests/data/activities/select_activity/items/yes_no_do_not_know.jsonld @@ -12,7 +12,7 @@ "inputType": "radio" }, "question": { - "en": "4.5 - yes or no" + "en": "yes or no" }, "responseOptions": { "valueType": "xsd:integer", diff --git a/tests/data/activities/visibility/items/base.jsonld b/tests/data/activities/visibility/items/base.jsonld index a0ac0d9a..e94234ea 100644 --- a/tests/data/activities/visibility/items/base.jsonld +++ b/tests/data/activities/visibility/items/base.jsonld @@ -12,7 +12,7 @@ "inputType": "radio" }, "question": { - "en": "5.1 - select one answer" + "en": "select one answer" }, "responseOptions": { "valueType": "xsd:integer", diff --git a/tests/data/activities/visibility/items/base0.jsonld b/tests/data/activities/visibility/items/base0.jsonld index 061abdde..e3d33d43 100644 --- a/tests/data/activities/visibility/items/base0.jsonld +++ b/tests/data/activities/visibility/items/base0.jsonld @@ -12,7 +12,7 @@ "inputType": "text" }, "question": { - "en": "5.3 - this should only show if you selected \u2018no\u2019" + "en": "this should only show if you selected \u2018no\u2019" }, "responseOptions": { "valueType": "xsd:string", diff --git a/tests/data/activities/visibility/items/base1.jsonld b/tests/data/activities/visibility/items/base1.jsonld index 5c700309..f3627aae 100644 --- a/tests/data/activities/visibility/items/base1.jsonld +++ b/tests/data/activities/visibility/items/base1.jsonld @@ -12,7 +12,7 @@ "inputType": "text" }, "question": { - "en": "5.2 - this should only show if you selected \u2018yes\u2019" + "en": "this should only show if you selected \u2018yes\u2019" }, "responseOptions": { "valueType": "xsd:string", diff --git a/tests/data/activities/visibility/items/multi_2_or_5.jsonld b/tests/data/activities/visibility/items/multi_2_or_5.jsonld index 58ce1333..bbfd7285 100644 --- a/tests/data/activities/visibility/items/multi_2_or_5.jsonld +++ b/tests/data/activities/visibility/items/multi_2_or_5.jsonld @@ -12,7 +12,7 @@ "inputType": "text" }, "question": { - "en": "5.7 - should appear for answers 2 or 5" + "en": "should appear for answers 2 or 5" }, "responseOptions": { "valueType": "xsd:string", diff --git a/tests/data/activities/visibility/items/multi_gt_5.jsonld b/tests/data/activities/visibility/items/multi_gt_5.jsonld index 57851507..7bd033ce 100644 --- a/tests/data/activities/visibility/items/multi_gt_5.jsonld +++ b/tests/data/activities/visibility/items/multi_gt_5.jsonld @@ -12,7 +12,7 @@ "inputType": "text" }, "question": { - "en": "5.5 - should appear for answers greater than 5" + "en": "should appear for answers greater than 5" }, "responseOptions": { "valueType": "xsd:string", diff --git a/tests/data/activities/visibility/items/multi_lt_2.jsonld b/tests/data/activities/visibility/items/multi_lt_2.jsonld index 530e9322..e6277e66 100644 --- a/tests/data/activities/visibility/items/multi_lt_2.jsonld +++ b/tests/data/activities/visibility/items/multi_lt_2.jsonld @@ -12,7 +12,7 @@ "inputType": "text" }, "question": { - "en": "5.6 - should appear for answers less than 2" + "en": "should appear for answers less than 2" }, "responseOptions": { "valueType": "xsd:string", diff --git a/tests/data/activities/visibility/items/radio_vis.jsonld b/tests/data/activities/visibility/items/radio_vis.jsonld index 2b024ae4..e6aeb769 100644 --- a/tests/data/activities/visibility/items/radio_vis.jsonld +++ b/tests/data/activities/visibility/items/radio_vis.jsonld @@ -12,7 +12,7 @@ "inputType": "radio" }, "question": { - "en": "5.4 - select one or several answer" + "en": "select one or several answer" }, "responseOptions": { "valueType": "xsd:integer", diff --git a/tests/data/activities/visibility/items/select_boolean.jsonld b/tests/data/activities/visibility/items/select_boolean.jsonld index 7445bfd1..34e32b3e 100644 --- a/tests/data/activities/visibility/items/select_boolean.jsonld +++ b/tests/data/activities/visibility/items/select_boolean.jsonld @@ -12,7 +12,7 @@ "inputType": "select" }, "question": { - "en": "5.8 - select one answer" + "en": "select one answer" }, "responseOptions": { "valueType": "xsd:integer", diff --git a/tests/data/activities/visibility/items/select_boolean0.jsonld b/tests/data/activities/visibility/items/select_boolean0.jsonld index c520e8f7..1473c66f 100644 --- a/tests/data/activities/visibility/items/select_boolean0.jsonld +++ b/tests/data/activities/visibility/items/select_boolean0.jsonld @@ -12,7 +12,7 @@ "inputType": "text" }, "question": { - "en": "5.10 - this should only show if you selected \u2018no\u2019" + "en": "this should only show if you selected \u2018no\u2019" }, "responseOptions": { "valueType": "xsd:string", diff --git a/tests/data/activities/visibility/items/select_boolean1.jsonld b/tests/data/activities/visibility/items/select_boolean1.jsonld index 81bee605..083c34bc 100644 --- a/tests/data/activities/visibility/items/select_boolean1.jsonld +++ b/tests/data/activities/visibility/items/select_boolean1.jsonld @@ -12,7 +12,7 @@ "inputType": "text" }, "question": { - "en": "5.9 - this should only show if you selected \u2018yes\u2019" + "en": "this should only show if you selected \u2018yes\u2019" }, "responseOptions": { "valueType": "xsd:string", diff --git a/tests/data/protocols/test_schema.jsonld b/tests/data/protocols/test_schema.jsonld index 198efb70..757d6169 100644 --- a/tests/data/protocols/test_schema.jsonld +++ b/tests/data/protocols/test_schema.jsonld @@ -2,16 +2,12 @@ "@context": "https://raw.githubusercontent.com/ReproNim/reproschema/1.0.0-rc4/contexts/generic", "@type": "reproschema:Protocol", "@id": "test_schema.jsonld", + "schemaVersion": "1.0.0-rc4", + "version": "0.0.1", "prefLabel": { "en": "test" }, "description": "test", - "schemaVersion": "1.0.0-rc4", - "version": "0.0.1", - "landingPage": { - "@id": "../README_eCOBIDAS-en.md", - "inLanguage": "en" - }, "preamble": { "en": "" }, @@ -90,5 +86,9 @@ "reproschema:AutoAdvance", "reproschema:AllowExport" ] + }, + "landingPage": { + "@id": "../README_eCOBIDAS-en.md", + "inLanguage": "en" } } diff --git a/tests/test_convert_to_schema.py b/tests/test_convert_to_schema.py index 4d9adfec..9aeeff9a 100644 --- a/tests/test_convert_to_schema.py +++ b/tests/test_convert_to_schema.py @@ -15,16 +15,17 @@ def data_path(): def test_create_schema(tmp_path): this_schema = Path(__file__).parent / "inputs" / "test.tsv" - # out_dir = Path(__file__).parent / "outputs" + out_dir = Path(__file__).parent / "outputs" + # out_dir = tmp_path print("\n") - create_schema(this_schema, tmp_path) + create_schema(this_schema, out_dir) # Check protocol protocol_folder = "protocols" - output_file = tmp_path / "test" / protocol_folder / "test_schema.jsonld" + output_file = out_dir / "test" / protocol_folder / "test_schema.jsonld" protocol_content = read_json(output_file) data_file = data_path() / protocol_folder / "test_schema.jsonld" @@ -79,7 +80,7 @@ def test_create_schema(tmp_path): this_activity_folder = os.path.join(activities_folder, activity_name) - output_file = tmp_path / "test" / this_activity_folder / f"{activity_name}_schema.jsonld" + output_file = out_dir / "test" / this_activity_folder / f"{activity_name}_schema.jsonld" activity_content = read_json(output_file) data_file = data_path() / this_activity_folder / f"{activity_name}_schema.jsonld" expected = read_json(data_file) @@ -90,7 +91,7 @@ def test_create_schema(tmp_path): item_list = activity["items"] for item in item_list: - output_file = tmp_path / "test" / this_activity_folder / "items" / f"{item}.jsonld" + output_file = out_dir / "test" / this_activity_folder / "items" / f"{item}.jsonld" item_content = read_json(output_file) data_file = data_path() / this_activity_folder / "items" / f"{item}.jsonld" expected = read_json(data_file) diff --git a/ui/LICENSE b/ui/LICENSE new file mode 100644 index 00000000..f288702d --- /dev/null +++ b/ui/LICENSE @@ -0,0 +1,674 @@ + GNU GENERAL PUBLIC LICENSE + Version 3, 29 June 2007 + + Copyright (C) 2007 Free Software Foundation, Inc. + Everyone is permitted to copy and distribute verbatim copies + of this license document, but changing it is not allowed. + + Preamble + + The GNU General Public License is a free, copyleft license for +software and other kinds of works. + + The licenses for most software and other practical works are designed +to take away your freedom to share and change the works. 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Interpretation of Sections 15 and 16. + + If the disclaimer of warranty and limitation of liability provided +above cannot be given local legal effect according to their terms, +reviewing courts shall apply local law that most closely approximates +an absolute waiver of all civil liability in connection with the +Program, unless a warranty or assumption of liability accompanies a +copy of the Program in return for a fee. + + END OF TERMS AND CONDITIONS + + How to Apply These Terms to Your New Programs + + If you develop a new program, and you want it to be of the greatest +possible use to the public, the best way to achieve this is to make it +free software which everyone can redistribute and change under these terms. + + To do so, attach the following notices to the program. It is safest +to attach them to the start of each source file to most effectively +state the exclusion of warranty; and each file should have at least +the "copyright" line and a pointer to where the full notice is found. + + + Copyright (C) + + This program is free software: you can redistribute it and/or modify + it under the terms of the GNU General Public License as published by + the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + + This program is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU General Public License for more details. + + You should have received a copy of the GNU General Public License + along with this program. If not, see . + +Also add information on how to contact you by electronic and paper mail. + + If the program does terminal interaction, make it output a short +notice like this when it starts in an interactive mode: + + Copyright (C) + This program comes with ABSOLUTELY NO WARRANTY; for details type `show w'. + This is free software, and you are welcome to redistribute it + under certain conditions; type `show c' for details. + +The hypothetical commands `show w' and `show c' should show the appropriate +parts of the General Public License. Of course, your program's commands +might be different; for a GUI interface, you would use an "about box". + + You should also get your employer (if you work as a programmer) or school, +if any, to sign a "copyright disclaimer" for the program, if necessary. +For more information on this, and how to apply and follow the GNU GPL, see +. + + The GNU General Public License does not permit incorporating your program +into proprietary programs. If your program is a subroutine library, you +may consider it more useful to permit linking proprietary applications with +the library. If this is what you want to do, use the GNU Lesser General +Public License instead of this License. But first, please read +. diff --git a/ui/README.md b/ui/README.md index 2cbb4114..772eda3d 100644 --- a/ui/README.md +++ b/ui/README.md @@ -11,3 +11,10 @@ flask --app ecobidas_ui --debug run + + + diff --git a/ui/ecobidas_ui/protocol.py b/ui/ecobidas_ui/protocol.py index 9f1ff37a..ae5c1b89 100644 --- a/ui/ecobidas_ui/protocol.py +++ b/ui/ecobidas_ui/protocol.py @@ -4,8 +4,9 @@ import pandas as pd from ecobidas_ui.forms import UploadForm, generate_form -from ecobidas_ui.modules import ( +from ecobidas_ui.utils import ( LANG, + allowed_file, get_landing_page, get_nav_bar_content, get_protocol, @@ -20,8 +21,6 @@ bp = Blueprint("protocol", __name__, url_prefix="/protocol") -ALLOWED_EXTENSIONS = {"tsv", "json"} - def update_visibility(items: dict[str, Any], form): for item, values in items.items(): @@ -39,7 +38,7 @@ def update_visibility(items: dict[str, Any], form): return items -@bp.route("/protocol/", methods=["GET", "POST"]) +@bp.route("/", methods=["GET", "POST"]) def protocol(protocol_name: str) -> str: protocol_content = get_protocol(protocol_name) @@ -58,7 +57,7 @@ def protocol(protocol_name: str) -> str: ) -@bp.get("/protocol//") +@bp.get("//") def activity_get(protocol_name, activity_name) -> str: activities, activity, items = prep_activity_page(protocol_name, activity_name) @@ -85,7 +84,7 @@ def activity_get(protocol_name, activity_name) -> str: ) -@bp.post("/protocol//") +@bp.post("//") def activity_post(protocol_name, activity_name) -> str: activities, activity, items = prep_activity_page(protocol_name, activity_name) @@ -170,7 +169,3 @@ def activity_post(protocol_name, activity_name) -> str: completed_items=completed_items, upload_form=upload_form, ) - - -def allowed_file(filename): - return "." in filename and filename.rsplit(".", 1)[1].lower() in ALLOWED_EXTENSIONS diff --git a/ui/ecobidas_ui/templates/about.html b/ui/ecobidas_ui/templates/about.html index f65fd260..a36f35d6 100644 --- a/ui/ecobidas_ui/templates/about.html +++ b/ui/ecobidas_ui/templates/about.html @@ -1 +1,127 @@ -{% extends 'base.html' %} {% block content %} {% endblock %} +{% extends 'base.html' %} + +{% block title %} eCOBIDAS - About {% endblock %} + +{% block content %} +
      +
      +
      +

      Have any questions? Something is missing? Let us know.

      + +

      Why this project?

      +

      + Poor methods and results description hinders the reproducibility and the + replicability of research. It also makes it hard to compare new and old + results and generally increases inefficiency in the research process. + This project is built on the hope that improving methods and results + reporting could improve our research. +

      +

      + Follow the link if you want to know more about the + motivations behind this project. +

      +

      Background

      +

      + This checklist is a project to make a user friendly checklist out the + best practices + report of + the Committee on Best Practices in Data Analysis and Sharing (COBIDAS) of the + Organization for Human Brain Mapping. +

      +

      + This is very much of a work in progress but the next step is to expand + the list to cover all the items of the COBIDAS report for fMRI as well + as for the recent + extension to EEG and MEG. +

      +

      Want to help?

      +

      + We are currently working on trying to expand the number of items used in + the checklist. All of this work is done in google spreadsheets: the + spreadsheet for each section is accessible by clicking on the + Source + at the top of each page. +

      +

      Want to know more?

      +

      + Most of the information concerning this project can be found on this + github repository. +

      +

      + If you want to be kept posted about the progress of the project, you can + join our + google group +

      +

      + From more frequent updates and behind the scenes, come and join us on + the + cobidas_checklist channel on the brainhack + + + channel. + +

      +

      + There is also an OSF project to + centralize all the information and repos. +

      +

      + We have a + list + of short, middle, long term goals: if you are interested by any of those + get in touch. Many of them do not necessarily require super-advanced + technical skills (except maybe a certain love for working with + spreadsheet and wanting them to be super organized). +

      +

      Contributors

      +

      + The list of the people involved in this project can be found + here. +

      +
      +
      +
      +{% endblock %} diff --git a/ui/ecobidas_ui/templates/auth/login.html b/ui/ecobidas_ui/templates/auth/login.html index fdd4b28e..f40b0047 100644 --- a/ui/ecobidas_ui/templates/auth/login.html +++ b/ui/ecobidas_ui/templates/auth/login.html @@ -1,6 +1,6 @@ -{% extends 'base.html' %} {% block header %} -

      {% block title %}Log In{% endblock %}

      -{% endblock %} {% block content %} +{% extends 'base.html' %} + +{% block content %}
      diff --git a/ui/ecobidas_ui/templates/auth/register.html b/ui/ecobidas_ui/templates/auth/register.html index e13922dd..e36a1af7 100644 --- a/ui/ecobidas_ui/templates/auth/register.html +++ b/ui/ecobidas_ui/templates/auth/register.html @@ -1,6 +1,6 @@ -{% extends 'base.html' %} {% block header %} -

      {% block title %}Register{% endblock %}

      -{% endblock %} {% block content %} +{% extends 'base.html' %} + +{% block content %} diff --git a/ui/ecobidas_ui/templates/base.html b/ui/ecobidas_ui/templates/base.html index 138bae4b..17dcff07 100644 --- a/ui/ecobidas_ui/templates/base.html +++ b/ui/ecobidas_ui/templates/base.html @@ -12,6 +12,11 @@ rel="stylesheet" href="{{ url_for('static', filename='style.css') }}" /> + + @@ -38,38 +43,38 @@
      -
      {% block header %}{% endblock %}
      - - {% with messages = get_flashed_messages() %} {% if messages %} {% for - message in messages %} -
      -
      +
  • - About + Login +
    • +
  • + About
@@ -140,10 +156,26 @@
-
-
-
-
eCOBIDAS
+
+
+
+
+ eCobidas +
+
+ + +
diff --git a/ui/ecobidas_ui/templates/index.html b/ui/ecobidas_ui/templates/index.html index fd220352..3c79b76a 100644 --- a/ui/ecobidas_ui/templates/index.html +++ b/ui/ecobidas_ui/templates/index.html @@ -1,12 +1,8 @@ -{% extends 'base.html' %} {% block title %} TBD {% endblock %} {% block content -%} - - - +{% extends 'base.html' %} + +{% block title %} eCOBIDAS {% endblock %} + +{% block content %}
@@ -14,5 +10,4 @@

TBD

- {% endblock %} diff --git a/ui/ecobidas_ui/templates/protocol.html b/ui/ecobidas_ui/templates/protocol.html index 09831912..8af5b156 100644 --- a/ui/ecobidas_ui/templates/protocol.html +++ b/ui/ecobidas_ui/templates/protocol.html @@ -1,18 +1,23 @@ {% extends 'base.html' %} {% from 'bootstrap5/form.html' import render_form %} + +{% block title %} eCOBIDAS - {{ protocol_pref_label }} {% endblock %} + {% block content %}
-

{{ protocol_pref_label }}

+

+ {{ protocol_pref_label }} +

    - {% for act in activities %} + {% for act in activities %} {% set prefix = loop.index - 1 %}
  • {{ act['name'] }}{% if prefix > 0 %}{{prefix}} - {% endif %}{{ act['name'] }}
    • {% endfor %} diff --git a/ui/ecobidas_ui/modules.py b/ui/ecobidas_ui/utils.py similarity index 88% rename from ui/ecobidas_ui/modules.py rename to ui/ecobidas_ui/utils.py index 79a54ee4..87ff25c8 100644 --- a/ui/ecobidas_ui/modules.py +++ b/ui/ecobidas_ui/utils.py @@ -10,6 +10,12 @@ LANG: str = "en" +ALLOWED_EXTENSIONS = {"tsv", "json"} + + +def allowed_file(filename): + return "." in filename and filename.rsplit(".", 1)[1].lower() in ALLOWED_EXTENSIONS + def protocol_url(protocol_name: Path) -> Path: return ( @@ -130,7 +136,7 @@ def get_items_for_activity(activity_file): properties = sort_ui_properties(properties=properties, order=order) items = {} - for item in properties: + for i, item in enumerate(properties): item_name = item["variableName"] @@ -144,10 +150,21 @@ def get_items_for_activity(activity_file): "is_answered": False, } - tmp["description"] = item_data.get("description") - tmp["question"] = item_data["question"][LANG] + tmp["question"] = f"{i + 1} - {item_data['question'][LANG]}" tmp["input_type"] = item_data["ui"]["inputType"] + tmp["description"] = ( + "
    Details" + "
      " + f"
    • item name: {item_data.get('description')}
      • " + "
    " + "
    " + ) + details = "" + if item_data.get("details"): + details = item_data["details"].get(LANG) + tmp["description"] = f"{details}
    {tmp['description']}" + if item["isVis"] == 1: tmp["visibility"] = True diff --git a/ui/pyproject.toml b/ui/pyproject.toml index cc39cf21..fa0357b9 100644 --- a/ui/pyproject.toml +++ b/ui/pyproject.toml @@ -9,7 +9,8 @@ dependencies = [ "Flask-WTF", "bootstrap-flask", "pandas", - "rich" + "rich", + "requests" ] description = "UI for eCOBIDAS" license = {text = "GPL 3.0"} diff --git a/ui/requirements.txt b/ui/requirements.txt index 90798301..07a0ae39 100644 --- a/ui/requirements.txt +++ b/ui/requirements.txt @@ -8,6 +8,10 @@ blinker==1.8.2 # via flask bootstrap-flask==2.4.0 # via ecobidas_ui (pyproject.toml) +certifi==2024.2.2 + # via requests +charset-normalizer==3.3.2 + # via requests click==8.1.7 # via flask flask==3.0.3 @@ -17,6 +21,8 @@ flask==3.0.3 # flask-wtf flask-wtf==1.2.1 # via ecobidas_ui (pyproject.toml) +idna==3.7 + # via requests itsdangerous==2.2.0 # via # flask @@ -42,12 +48,16 @@ python-dateutil==2.9.0.post0 # via pandas pytz==2024.1 # via pandas +requests==2.32.2 + # via ecobidas_ui (pyproject.toml) rich==13.7.1 # via ecobidas_ui (pyproject.toml) six==1.16.0 # via python-dateutil tzdata==2024.1 # via pandas +urllib3==2.2.1 + # via requests werkzeug==3.0.3 # via flask wtforms==3.1.2 From a06b4e40eceff74afbb373ca8302e0352484777e Mon Sep 17 00:00:00 2001 From: Remi Gau Date: Fri, 24 May 2024 11:20:29 -0400 Subject: [PATCH 15/31] update details items --- .flake8 | 2 +- cobidas_schema | 2 +- ecobidas/inputs/neurovault/neurovault.tsv | 174 +++++++++++----------- reproschema-py | 2 +- ui/ecobidas_ui/__init__.py | 12 +- ui/ecobidas_ui/templates/404.html | 3 +- ui/ecobidas_ui/templates/500.html | 1 + ui/ecobidas_ui/templates/index.html | 10 ++ ui/ecobidas_ui/templates/protocol.html | 14 ++ ui/ecobidas_ui/utils.py | 2 +- 10 files changed, 129 insertions(+), 93 deletions(-) diff --git a/.flake8 b/.flake8 index 9bc1cf29..3133b205 100644 --- a/.flake8 +++ b/.flake8 @@ -9,7 +9,7 @@ max-line-length = 150 max_complexity = 15 max_function_length = 150 max_parameters_amount = 10 -max_returns_amount = 4 +max_returns_amount = 6 # ----------------------- errors to include / exclude ----------------------- diff --git a/cobidas_schema b/cobidas_schema index 1705ce2f..1f7c4728 160000 --- a/cobidas_schema +++ b/cobidas_schema @@ -1 +1 @@ -Subproject commit 1705ce2f92b859a6b4f3c898e345caee174e6e7c +Subproject commit 1f7c4728d79df9beaa60a83dda4e465a19eb897d diff --git a/ecobidas/inputs/neurovault/neurovault.tsv b/ecobidas/inputs/neurovault/neurovault.tsv index 2226b696..327e1d07 100644 --- a/ecobidas/inputs/neurovault/neurovault.tsv +++ b/ecobidas/inputs/neurovault/neurovault.tsv @@ -1,88 +1,88 @@ activity_pref_label activity_order item_order question unit details field_type choices item item_pref_label visibility item_description include mandatory preamble bids_status bids_file bids_key bids_key_for_unit UUID -Experimental design 1 1 Type of design select blocked | event_related | hybrid block/event type_of_design type of design 1 type of design 1 1 Describe your experimental design 8e2cf1e8-6328-49fc-85d3-38d405a4cc91 -Experimental design 1 2 Number of imaging runs acquired integer 0 number of imaging runs 1 number of imaging runs 1 2 e969343d-3ca8-4cdf-afcc-b681a545144a -Experimental design 1 3 Number of blocks, trials or experimental units per imaging run integer 0 number of experimental units 1 number of experimental units 1 2 2d5111f6-ed50-4428-946b-6b9287896e27 -Experimental design 1 4 Length of each imaging run seconds float 0 length of runs 1 length of runs 1 2 27fd0fa4-75ff-47c0-8092-17d1056e3d37 -Experimental design 1 5 For blocked designs, length of blocks seconds float 0 length of blocks type_of_design in [0, 2] length of blocks 1 2 46569ab0-d730-488f-9486-3f00f90ba211 -Experimental design 1 6 Length of individual trials seconds float 0 length of trials 1 length of trials 1 2 dd65fbb8-1c54-4cc1-b1ec-5530ab6e02e6 -Experimental design 1 7 Was the design optimized for efficiency? radio preset:boolean optimization 1 optimization 1 2 92062e6c-5ff4-4e55-a2a6-2d7cc7ae272c -Experimental design 1 8 What method was used for optimization? textarea optimization method optimization == 1 optimization method 1 3 5b2910fe-cfa5-404c-a8dc-9bca47876746 -Participants 2 1 Number of subjects entering into the analysis integer 0 number of subjects 1 number of subjects 1 1 Describe your participant sample a06822dd-9f8b-4d36-8802-d11bd1e0ce81 -Participants 2 2 Mean age of subjects float 0 subject age mean 1 subject age mean 1 1 bfa6d6fb-4854-4063-bf9f-08e9c24c0337 -Participants 2 3 Minimum age of subjects float 0 subject age min 1 subject age min 1 2 3c9ada14-5ee8-472e-97aa-d8f0c5e699e0 -Participants 2 4 Maximum age of subjects float 0 subject age max 1 subject age max 1 2 e13e03d9-8074-43af-b8f1-afcf0f7c53da -Participants 2 5 Handedness of subjects radio right | left | both handedness 1 handedness 1 2 193c5710-f15a-4b32-83cb-ebaeee9b6b90 -Participants 2 6 The proportion of subjects who were male float 0 | 1 proportion male subjects 1 proportion male subjects 1 2 4da6dc89-a32b-471d-927a-21e437ded0a6 -Participants 2 7 Additional inclusion/exclusion criteria, if any. Including specific sampling strategies that limit inclusion to a specific group, such as laboratory members. textarea inclusion exclusion criteria 1 inclusion exclusion criteria 1 3 61c6e866-8733-4599-93dd-ee7601874f08 -Participants 2 8 Number of subjects scanned but rejected from analysis integer 0 number of rejected subjects 1 number of rejected subjects 1 2 a0d63a78-4017-4c85-9b28-4322b8fbfdd1 -Participants 2 9 Was this study a comparison between subject groups? radio preset:boolean group comparison 1 group comparison 1 1 b587a1e6-65a8-42b8-b2ae-3dfc05edbd4a -Participants 2 10 A description of the groups being compared textarea group description group_comparison == 1 group description 1 2 f140953d-b6bd-45ed-bbe6-9387659a252f -MRI acquisition 3 1 Manufacturer of MRI scanner select Siemens | Philips | General Electric | other Manufacturer scanner make 1 scanner make 1 1 Describe your acquisition parameters 8e0dd443-efc6-49ef-b783-cbd6e3cda4eb -MRI acquisition 3 2 Model of MRI scanner textarea ManufacturersModelName scanner model 1 scanner model 1 1 2087da57-f9c8-4446-9a77-efa1957acd20 -MRI acquisition 3 3 Field strength of MRI scanner Tesla float 0 MagneticFieldStrength field strength 1 field strength 1 1 7543b22d-07db-4b5a-8796-30b5904b552d -MRI acquisition 3 4 Description of pulse sequence used for fMRI select Gradient echo | Spin echo | Mutliband gradient echo | MPRAGE | MP2RAGE | FLASH PulseSequenceType pulse sequence 1 pulse sequence 1 1 5f2c2e3b-f17a-4d50-bf57-df65661fe199 -MRI acquisition 3 5 Description of parallel imaging method and parameters textarea parallel imaging 1 parallel imaging 1 3 f8d53fef-12a3-429a-9dcc-b19339850577 -MRI acquisition 3 6 Imaging field of view Millimeters float field of view 1 field of view 1 2 a204e1e7-82e5-4bff-9d5e-785ba72404c9 -MRI acquisition 3 7 Matrix size for MRI acquisition integer matrix size 1 matrix size 1 2 2477fc28-85f1-41ca-9a2a-f98cd250f800 -MRI acquisition 3 8 Distance between slices (includes skip or distance factor). Millimeters float 0 slice thickness 1 slice thickness 1 1 22e835fd-1940-4379-80ac-a88491950d08 -MRI acquisition 3 9 The size of the skipped area between slices. Millimeters float 0 skip factor 1 skip factor 1 2 dd82553d-335c-404e-8c27-dc95c58c1456 -MRI acquisition 3 10 The orientation of slices radio axial | sagittal | frontal acquisition orientation 1 acquisition orientation 1 2 191f098d-8aca-4cf5-bdd2-8f2e4fafc494 -MRI acquisition 3 11 Order of acquisition of slices select ascending | descending | interleaved SliceTiming order of acquisition 1 order of acquisition 1 3 34099ae2-819c-4e10-baaf-a7017c9393e1 -MRI acquisition 3 12 Repetition time (TR) Milliseconds float 0 RepetitionTime repetition time 1 repetition time 1 1 ae069155-1c4d-45b6-a9ae-210f33fc8aac -MRI acquisition 3 13 Echo time (TE) Milliseconds float 0 EchoTime echo time 1 echo time 1 1 4ed3dd1e-c121-4f71-a499-8693c32811da -MRI acquisition 3 14 Flip angle Degrees float 0 FlipAngle flip angle 1 flip angle 1 2 b7cd770d-a881-47a9-abe0-794a9f147654 -Preprocessing 4 1 If a single software package was used for all analyses, specify that here select preset:mri_softwares SoftwareName software package 1 software package 1 1 Describe your preprocessing 563bc956-277d-41f2-a68e-c529a4fceb94 -Preprocessing 4 2 Version of software package used textarea SoftwareVersion software version 1 software version 1 1 724d9e55-efca-4cb9-9339-1325c3c30f74 -Preprocessing 4 3 Specify order of preprocessing operations textarea order of preprocessing operations 1 order of preprocessing operations 1 2 5303df62-5ec3-4ef1-b0e2-d29be74a78a3 -Preprocessing 4 4 Describe quality control measures textarea quality control 1 quality control 1 3 d3f5adb3-6fd8-447d-b950-74c0c8c3ed73 -Preprocessing 4 5 Was B0 distortion correction used? radio preset:boolean used b0 unwarping 1 used b0 unwarping 1 2 e694f278-c996-4b4f-9036-7f8681418fd5 -Preprocessing 4 6 Specify software used for distortion correction if different from the main package select preset:mri_softwares b0 unwarping software used_b0_unwarping == 1 b0 unwarping software 1 3 2a21d849-3a13-4582-bc9b-db9c860f7d5b -Preprocessing 4 7 Was slice timing correction used? radio preset:boolean used slice timing correction 1 used slice timing correction 1 1 7a9fc02b-d130-4728-aef0-0d517b06e754 -Preprocessing 4 8 Specify software used for slice timing correction if different from the main package select preset:mri_softwares slice timing correction software used_slice_timing_correction == 1 slice timing correction software 1 3 d492a1e4-17be-4c40-a83a-5462532f19da -Preprocessing 4 9 Was motion correction used? radio preset:boolean used motion correction 1 used motion correction 1 1 7900736f-5566-46ea-becd-4a25bbd0e77a -Preprocessing 4 10 Specify software used for motion correction if different from the main package select preset:mri_softwares motion correction software used_motion_correction == 1 motion correction software 1 3 c2567427-3f72-46ad-991c-3e8181a8f73f -Preprocessing 4 11 Reference scan used for motion correction textarea motion correction reference used_motion_correction == 1 motion correction reference 1 3 afd06405-39fc-48a8-8773-8887f4a267a5 -Preprocessing 4 12 Similarity metric used for motion correction select preset:cost_functions motion correction metric used_motion_correction == 1 motion correction metric 1 3 d12f8e07-8788-41c9-83a8-f08f1457c734 -Preprocessing 4 13 Interpolation method used for motion correction select preset:interpolations motion correction interpolation used_motion_correction == 1 motion correction interpolation 1 3 0bb02f83-db82-4afb-b1cf-7ce3ae03a926 -Preprocessing 4 14 Was motion-susceptibility correction used? radio preset:boolean used motion susceptibiity correction 1 used motion susceptibiity correction 1 3 609d194c-33c4-48f7-a34d-2e984d7f8ee8 -Intersubject registration 5 1 Were subjects registered to a common stereotactic space? radio preset:boolean used intersubject registration 1 used intersubject registration 1 1 Describe your spatial normalization 0ec88003-df12-4090-9a12-f52ad93e15d6 -Intersubject registration 5 2 Specify software used for intersubject registration if different from main package select preset:mri_softwares intersubject registration software used_intersubject_registration == 1 intersubject registration software 1 2 101b8a20-4f17-4aa5-8776-17eab2ebda6b -Intersubject registration 5 3 Was linear or nonlinear registration used? select linear | non-linear intersubject transformation type used_intersubject_registration == 1 intersubject transformation type 1 1 9e814686-8632-4460-8a5a-6f13c972c2e6 -Intersubject registration 5 4 If nonlinear registration was used, describe transform method textarea nonlinear transform type used_intersubject_registration == 1 nonlinear transform type 1 2 59be2536-c299-4e96-aac7-d854b653f003 -Intersubject registration 5 5 Similarity metric used for intersubject registration textarea transform similarity metric used_intersubject_registration == 1 transform similarity metric 1 3 4cd51429-19ec-4a7f-80cb-071f241cc89c -Intersubject registration 5 6 Interpolation method used for intersubject registration select preset:interpolations interpolation method used_intersubject_registration == 1 interpolation method 1 2 127aaa05-a1ef-40b6-bf7a-7faffbba5587 -Intersubject registration 5 7 What type of image was used to determine the transformation to the atlas? textarea object image type used_intersubject_registration == 1 object image type 1 1 cdd9e5dc-ac7c-4a89-b47d-4ab8705fb23e -Intersubject registration 5 8 Were the functional images coregistered to the subject's structural image? radio preset:boolean functional coregistered to structural 1 functional coregistered to structural 1 2 d06f3d30-ebaf-45da-bd5c-0653cf957431 -Intersubject registration 5 9 Method used to coregister functional to structural images textarea functional coregistration method functional_coregistered_to_structural == 1 functional coregistration method 1 3 11c87f60-4ba5-4916-868f-015813e5bbb5 -Intersubject registration 5 10 Name of coordinate space for registration target select MNI | Talairach | MNI2Tal | other coordinate space 1 coordinate space 1 1 cd90b95a-96fd-445a-ba7c-be0e59b5afd8 -Intersubject registration 5 11 Name of target template image textarea target template image 1 target template image 1 2 11fb168c-fd45-48f2-b965-fb51e77906f8 -Intersubject registration 5 12 Voxel size of target template Millimeters float 0 target resolution 1 target resolution 1 1 c55f66aa-1d3d-459a-9780-21afc720d969 -Intersubject registration 5 13 Was spatial smoothing applied? radio preset:boolean used smoothing 1 used smoothing 1 1 d70017f8-9848-4aca-afc3-efc2f25e66a2 -Intersubject registration 5 14 Describe the type of smoothing applied textarea smoothing type used_smoothing == 1 smoothing type 1 1 d55441ad-488f-462e-ade5-9085bc4a0bd7 -Intersubject registration 5 15 The full-width at half-maximum of the smoothing kernel Millimeters float 0 smoothing fwhm used_smoothing == 1 smoothing fwhm 1 1 27bc5893-bac0-4327-8bdf-e31e3e4be19c -Intersubject registration 5 16 Voxel size in mm of the resampled, atlas-space images float 0 resampled voxel size 1 resampled voxel size 1 1 e33bbdbc-71a5-4989-9ca9-0e67f40106ea -Individual subject modeling 6 1 Type of group model used radio Regression | other intrasubject model type 1 intrasubject model type 1 1 Describe your model specification at the subejct level ae754ba8-05e7-4a65-83c2-ae0fb803b762 -Individual subject modeling 6 2 Estimation method used for model select ordinary least squares | generalized least squares | other intrasubject estimation type 1 intrasubject estimation type 1 1 2d7e49e9-f7e6-455c-9771-ac306a123fff -Individual subject modeling 6 3 Software used for intrasubject modeling if different from overall package select preset:mri_softwares intrasubject modeling software 1 intrasubject modeling software 1 2 247e4704-af69-48c8-9ce4-96909560f3e5 -Individual subject modeling 6 4 Nature of HRF model select spm HRF | glover HRF | double gamma | Fourrier set | Finite Impulse Response | FLOBS | other hemodynamic response function 1 hemodynamic response function 1 2 793d6278-ff64-45c4-85a2-ac44c2839489 -Individual subject modeling 6 5 Were temporal derivatives included? radio preset:boolean used temporal derivatives 1 used temporal derivatives 1 2 6d4c0751-cbb3-4f7d-852e-5667e282267b -Individual subject modeling 6 6 Were dispersion derivatives included? radio preset:boolean used dispersion derivatives 1 used dispersion derivatives 1 3 8bf99177-de69-4a10-92cf-db898f7a58e0 -Individual subject modeling 6 7 Were motion regressors included? radio preset:boolean used motion regressors 1 used motion regressors 1 2 d1b37e2e-ac7b-4d00-a1c7-944123bf632f -Individual subject modeling 6 8 Was a reaction time regressor included? radio preset:boolean used reaction time regressor 1 used reaction time regressor 1 2 e63c2d6c-602d-40dd-b3c5-d1c56c97bc80 -Individual subject modeling 6 9 Were any regressors specifically orthogonalized with respect to others? radio preset:boolean used orthogonalization 1 used orthogonalization 1 1 fafcb7eb-73b9-4d96-b5bb-6e9f431dbfda -Individual subject modeling 6 10 If orthogonalization was used, describe here textarea orthogonalization description used_orthogonalization == 1 orthogonalization description 1 2 8e0f9232-881c-405e-a2ad-09ee9558197b -Individual subject modeling 6 11 Was high pass filtering applied? radio preset:boolean used high pass filter 1 used high pass filter 1 1 816d4399-04d8-4ce4-bbee-103a575d395e -Individual subject modeling 6 12 Describe method used for high pass filtering textarea high pass filter method used_high_pass_filter == 1 high pass filter method 1 2 5b3d1c3d-0d36-44e1-939f-cacf45e173a4 -Individual subject modeling 6 13 What autocorrelation model was used ? select SPM: global approximate AR(1) | SPM: FAST | FSL: locally regularized autocorrelation function | AFNI: ARMA | none | other autocorrelation model 1 autocorrelation model 1 2 37d9669d-1991-430c-b833-0d2ae88548ab -Individual subject modeling 6 14 Exactly what terms are subtracted from what? textarea contrast definition 1 contrast definition 1 1 c550179e-f8da-490e-a68c-87818cc5d06a -Individual subject modeling 6 15 Link to Cognitive Atlas definition of this contrast Define these in terms of task or stimulus conditions (e.g., 'one-back task with objects versus zero-back task with objects') instead of underlying psychological concepts (e.g., 'working memory'). textarea contrast definition cogatlas 1 contrast definition cogatlas 1 3 45340be0-df1a-4706-b8f6-644b54864d42 -Group modeling 7 1 Type of group model used select Regression group model type 1 group model type 1 1 Describe the group level analysis 34042982-ca4d-4ca4-8621-cf194ce77ed7 -Group modeling 7 2 Estimation method used for model select ordinary least squares | generalized least squares group estimation type 1 group estimation type 1 1 d616403c-8da4-40a5-ac78-ae1fda43b8ba -Group modeling 7 3 Software used for group modeling if different from overall package select preset:mri_softwares group modeling software 1 group modeling software 1 2 92c9b96d-3f7e-4577-a91b-4b33be61454f -Group modeling 7 4 Type of inference for group model select random effect | mixed effect | fixed effect group inference type 1 group inference type 1 1 b5c321cf-b2d4-4354-a460-1502881c204d -Group modeling 7 5 If more than 2-levels, describe the levels and assumptions of the model. For example, are variances assumed equal between groups. textarea group model multilevel 1 group model multilevel 1 3 4f6db1a2-bcbf-48c5-b582-8dfca49aea5e -Group modeling 7 6 Was this a repeated measures design at the group level? radio preset:boolean group repeated measures 1 group repeated measures 1 1 22c64bc3-57b1-439a-85ca-8ba5b562832a -Group modeling 7 7 If multiple measurements per subject, list method to account for within subject correlation, exact assumptions made about correlation/variance textarea group repeated measures method group_repeated_measures == 1 group repeated measures method 1 3 7d760371-ae1b-4819-9dd6-98bce210614c -Group inference 8 1 Type of statistic that is the basis of the inference select Z | T | F | X2 | PostProb | Non-parametric Permutations | Monte Carlo Permutations group statistic type 1 group statistic type 1 2 Describe your statistical inference b01e61a4-43cc-44c4-91b9-ec395ee50850 -Group inference 8 2 Parameters of the null distribution of the test statisic. Typically degrees of freedom (should be clear from the test statistic what these are). float group statistic parameters 1 group statistic parameters 1 1 819a80f2-1f18-48d1-821c-249248b0ef53 -Group inference 8 3 Noise smoothness for statistical inference This is the estimated smoothness used with Random Field Theory or a simulation-based inference method. float 0 group smoothness fwhm 1 group smoothness fwhm 1 1 c305a2d4-a926-4764-b401-c2933cacfcb0 +Experimental design 1 1 Type of design select blocked | event_related | hybrid block/event type_of_design type of design 1 type of design 1 1 Describe your experimental design 76c35f93-23e1-43b7-8f47-59b9e229cb71 +Experimental design 1 2 Number of imaging runs acquired integer 0 number of imaging runs 1 number of imaging runs 1 2 77423b25-3ee4-472b-bb25-8e9415189030 +Experimental design 1 3 Number of blocks, trials or experimental units per imaging run integer 0 number of experimental units 1 number of experimental units 1 2 131a5855-3fad-4b69-a9dd-a842cd7742d3 +Experimental design 1 4 Length of each imaging run seconds float 0 length of runs 1 length of runs 1 2 0b12a719-f6b8-4d1b-a353-d888d2d2fc7d +Experimental design 1 5 For blocked designs, length of blocks seconds float 0 length of blocks type_of_design in [0, 2] length of blocks 1 2 4e963713-4274-4cc3-addd-5b04f612b082 +Experimental design 1 6 Length of individual trials seconds float 0 length of trials 1 length of trials 1 2 63f7be62-80d4-4e8a-8dbb-dcb4441234de +Experimental design 1 7 Was the design optimized for efficiency? radio preset:boolean optimization 1 optimization 1 2 4bc92eea-ce45-40ce-8b2b-add6d5683585 +Experimental design 1 8 What method was used for optimization? textarea optimization method optimization == 1 optimization method 1 3 dbea3306-ad68-41de-8f5c-626bf878636d +Participants 2 1 Number of subjects entering into the analysis integer 0 number of subjects 1 number of subjects 1 1 Describe your participant sample 44bcca72-a745-4b9f-917b-2571eb73a695 +Participants 2 2 Mean age of subjects float 0 subject age mean 1 subject age mean 1 1 648db98e-e5ec-41a5-b6d4-f762bf8be2ea +Participants 2 3 Minimum age of subjects float 0 subject age min 1 subject age min 1 2 2a202af9-86c7-4cd0-95f6-2cf328608f54 +Participants 2 4 Maximum age of subjects float 0 subject age max 1 subject age max 1 2 933b1e07-9af1-4d99-adf9-81d8669dbe44 +Participants 2 5 Handedness of subjects radio right | left | both handedness 1 handedness 1 2 906b037e-b686-44a6-8440-5a05df6fe63c +Participants 2 6 The proportion of subjects who were male float 0 | 1 proportion male subjects 1 proportion male subjects 1 2 640df132-8c2e-4cd4-beee-97d9d64336a3 +Participants 2 7 Additional inclusion/exclusion criteria, if any. Including specific sampling strategies that limit inclusion to a specific group, such as laboratory members. textarea inclusion exclusion criteria 1 inclusion exclusion criteria 1 3 e061db40-8413-4ba0-ab20-1eeb89658a25 +Participants 2 8 Number of subjects scanned but rejected from analysis integer 0 number of rejected subjects 1 number of rejected subjects 1 2 6cc3460e-826f-4faf-bb4e-e66d78ab68af +Participants 2 9 Was this study a comparison between subject groups? radio preset:boolean group comparison 1 group comparison 1 1 0374fada-67e6-4d57-abf8-b0e4bd894ac4 +Participants 2 10 A description of the groups being compared textarea group description group_comparison == 1 group description 1 2 b27a7735-0393-479a-a9ee-f9e17decf720 +MRI acquisition 3 1 Manufacturer of MRI scanner select Siemens | Philips | General Electric | other Manufacturer scanner make 1 scanner make 1 1 Describe your acquisition parameters 19204f74-3646-4777-9a62-edff13947f59 +MRI acquisition 3 2 Model of MRI scanner textarea ManufacturersModelName scanner model 1 scanner model 1 1 3adcef71-b057-46ea-84e1-402c2deea39f +MRI acquisition 3 3 Field strength of MRI scanner Tesla float 0 MagneticFieldStrength field strength 1 field strength 1 1 2e7f18e2-b2e3-4310-9eb8-ff666e7383c2 +MRI acquisition 3 4 Description of pulse sequence used for fMRI select Gradient echo | Spin echo | Mutliband gradient echo | MPRAGE | MP2RAGE | FLASH PulseSequenceType pulse sequence 1 pulse sequence 1 1 20fc355f-0588-4a10-b185-851277ddc64f +MRI acquisition 3 5 Description of parallel imaging method and parameters textarea parallel imaging 1 parallel imaging 1 3 4bf06822-ee53-4e60-86bd-c54a5b8378e0 +MRI acquisition 3 6 Imaging field of view Millimeters float field of view 1 field of view 1 2 68b5c8e0-166b-42a8-ab33-9496d15e7859 +MRI acquisition 3 7 Matrix size for MRI acquisition integer matrix size 1 matrix size 1 2 4178e14e-a5f0-483a-a35f-5f7bb52d30e3 +MRI acquisition 3 8 Distance between slices (includes skip or distance factor). Millimeters float 0 slice thickness 1 slice thickness 1 1 e6b7971a-89f2-4b6a-b4c9-49fa6c4de697 +MRI acquisition 3 9 The size of the skipped area between slices. Millimeters float 0 skip factor 1 skip factor 1 2 bd9b28e1-58cf-4104-8694-350a504e9709 +MRI acquisition 3 10 The orientation of slices radio axial | sagittal | frontal acquisition orientation 1 acquisition orientation 1 2 8b5c1b46-64d5-4c36-aa19-154bd0e40a34 +MRI acquisition 3 11 Order of acquisition of slices select ascending | descending | interleaved SliceTiming order of acquisition 1 order of acquisition 1 3 37295a62-8084-42b2-b794-9bee8333b357 +MRI acquisition 3 12 Repetition time (TR) Milliseconds float 0 RepetitionTime repetition time 1 repetition time 1 1 fa71b4f7-015d-4d06-8728-fb5ef9591b71 +MRI acquisition 3 13 Echo time (TE) Milliseconds float 0 EchoTime echo time 1 echo time 1 1 a28a83be-cd4b-411e-9701-e0e711b28b05 +MRI acquisition 3 14 Flip angle Degrees float 0 FlipAngle flip angle 1 flip angle 1 2 653320d7-0dd3-412b-8464-f744d04a5f44 +Preprocessing 4 1 If a single software package was used for all analyses, specify that here select preset:mri_softwares SoftwareName software package 1 software package 1 1 Describe your preprocessing b92221e5-1b47-4692-81dd-c3c694e5f908 +Preprocessing 4 2 Version of software package used textarea SoftwareVersion software version 1 software version 1 1 c20093b4-df39-40d4-8610-ede0e4113b3f +Preprocessing 4 3 Specify order of preprocessing operations textarea order of preprocessing operations 1 order of preprocessing operations 1 2 af64fcae-c41e-4401-ab3a-3b162bf90933 +Preprocessing 4 4 Describe quality control measures textarea quality control 1 quality control 1 3 4fc681b9-9db9-4061-92b5-6a0396907ab3 +Preprocessing 4 5 Was B0 distortion correction used? radio preset:boolean used b0 unwarping 1 used b0 unwarping 1 2 5eea934f-4d84-49a5-bc79-b5ab6335d9de +Preprocessing 4 6 Specify software used for distortion correction if different from the main package select preset:mri_softwares b0 unwarping software used_b0_unwarping == 1 b0 unwarping software 1 3 7aa549bb-4c74-4859-82e6-e928e91787c4 +Preprocessing 4 7 Was slice timing correction used? radio preset:boolean used slice timing correction 1 used slice timing correction 1 1 90653c26-2d61-4e37-92e9-8a021d1a29b3 +Preprocessing 4 8 Specify software used for slice timing correction if different from the main package select preset:mri_softwares slice timing correction software used_slice_timing_correction == 1 slice timing correction software 1 3 e75c9a32-ec5a-4f3d-b048-57491f34b1bb +Preprocessing 4 9 Was motion correction used? radio preset:boolean used motion correction 1 used motion correction 1 1 ec63383c-0173-4c54-ba5b-0ff432d3e252 +Preprocessing 4 10 Specify software used for motion correction if different from the main package select preset:mri_softwares motion correction software used_motion_correction == 1 motion correction software 1 3 b4b0dd7d-1ac4-432f-a074-34b78ab021d0 +Preprocessing 4 11 Reference scan used for motion correction textarea motion correction reference used_motion_correction == 1 motion correction reference 1 3 b23f32cf-f81c-4d2b-b577-853c8da5e6c8 +Preprocessing 4 12 Similarity metric used for motion correction select preset:cost_functions motion correction metric used_motion_correction == 1 motion correction metric 1 3 24afd5d5-78fa-4a52-b196-654ddb3c9064 +Preprocessing 4 13 Interpolation method used for motion correction select preset:interpolations motion correction interpolation used_motion_correction == 1 motion correction interpolation 1 3 bd4f2aa3-7397-46bc-b63c-22f09431ac82 +Preprocessing 4 14 Was motion-susceptibility correction used? radio preset:boolean used motion susceptibiity correction 1 used motion susceptibiity correction 1 3 062960a8-0022-47ca-908b-c7fb6b89296b +Intersubject registration 5 1 Were subjects registered to a common stereotactic space? radio preset:boolean used intersubject registration 1 used intersubject registration 1 1 Describe your spatial normalization 1c13e108-0fe1-4d19-a707-9279f469a0e1 +Intersubject registration 5 2 Specify software used for intersubject registration if different from main package select preset:mri_softwares intersubject registration software used_intersubject_registration == 1 intersubject registration software 1 2 28b6d7fc-4168-48be-b6c7-fe518f9a7733 +Intersubject registration 5 3 Was linear or nonlinear registration used? select linear | non-linear intersubject transformation type used_intersubject_registration == 1 intersubject transformation type 1 1 dbbcba6b-2445-486a-b039-086f90f7f8c1 +Intersubject registration 5 4 If nonlinear registration was used, describe transform method textarea nonlinear transform type used_intersubject_registration == 1 and nonlinear_transform_type == 1 nonlinear transform type 1 2 b8cbc6b9-a3bd-4426-a2ef-860cf597f548 +Intersubject registration 5 5 Similarity metric used for intersubject registration textarea transform similarity metric used_intersubject_registration == 1 transform similarity metric 1 3 72e0b864-6950-4a15-a3ca-d6c6cc9264a8 +Intersubject registration 5 6 Interpolation method used for intersubject registration select preset:interpolations interpolation method used_intersubject_registration == 1 interpolation method 1 2 83a4f5ff-cd97-47a7-b272-e496ac1ad344 +Intersubject registration 5 7 What type of image was used to determine the transformation to the atlas? textarea object image type used_intersubject_registration == 1 object image type 1 1 0cbd4a83-80df-49ce-a3b3-50c5a63a723f +Intersubject registration 5 8 Were the functional images coregistered to the subject's structural image? radio preset:boolean functional coregistered to structural 1 functional coregistered to structural 1 2 331cfc44-6eb3-4c5b-ae7b-66dd6515e7a0 +Intersubject registration 5 9 Method used to coregister functional to structural images textarea functional coregistration method functional_coregistered_to_structural == 1 functional coregistration method 1 3 bcd0b566-2e73-4287-bc8f-2e370f43c03f +Intersubject registration 5 10 Name of coordinate space for registration target select MNI | Talairach | MNI2Tal | other coordinate space 1 coordinate space 1 1 6b8719e2-fde6-4805-a3a9-3a1dbc08df8e +Intersubject registration 5 11 Name of target template image textarea target template image 1 target template image 1 2 12331e78-51d6-47dd-8828-987de0333fdc +Intersubject registration 5 12 Voxel size of target template Millimeters float 0 target resolution 1 target resolution 1 1 265de527-ca2e-4ebe-a544-3224c7e89f3b +Intersubject registration 5 13 Was spatial smoothing applied? radio preset:boolean used smoothing 1 used smoothing 1 1 dc37a8a9-f2cf-4ed6-8610-028e92a6ec1f +Intersubject registration 5 14 Describe the type of smoothing applied textarea smoothing type used_smoothing == 1 smoothing type 1 1 bb9e0a6a-2d75-4604-89d5-54abee080ead +Intersubject registration 5 15 The full-width at half-maximum of the smoothing kernel Millimeters float 0 smoothing fwhm used_smoothing == 1 smoothing fwhm 1 1 68e4d3a2-447b-4cd3-baa1-4a131b9c41b1 +Intersubject registration 5 16 Voxel size in mm of the resampled, atlas-space images float 0 resampled voxel size 1 resampled voxel size 1 1 a64d9450-49d4-4bd5-9728-eb97a224a2b2 +Individual subject modeling 6 1 Type of group model used radio Regression | other intrasubject model type 1 intrasubject model type 1 1 Describe your model specification at the subejct level d1682682-6067-4014-aea8-651852c23ef1 +Individual subject modeling 6 2 Estimation method used for model select ordinary least squares | generalized least squares | other intrasubject estimation type 1 intrasubject estimation type 1 1 a9e542ec-fe76-4650-b54c-be144ccda2e3 +Individual subject modeling 6 3 Software used for intrasubject modeling if different from overall package select preset:mri_softwares intrasubject modeling software 1 intrasubject modeling software 1 2 93163af2-bb3a-407b-b632-18083ec4438c +Individual subject modeling 6 4 Nature of HRF model select spm HRF | glover HRF | double gamma | Fourrier set | Finite Impulse Response | FLOBS | other hemodynamic response function 1 hemodynamic response function 1 2 2cfdadcb-1aae-4653-ad09-69462b6f4bee +Individual subject modeling 6 5 Were temporal derivatives included? radio preset:boolean used temporal derivatives 1 used temporal derivatives 1 2 65c08e93-7d9f-4292-a346-750f2dee9123 +Individual subject modeling 6 6 Were dispersion derivatives included? radio preset:boolean used dispersion derivatives 1 used dispersion derivatives 1 3 1947cdad-aa5c-4747-9ea8-f72297b3fe3e +Individual subject modeling 6 7 Were motion regressors included? radio preset:boolean used motion regressors 1 used motion regressors 1 2 de73a483-2858-477d-b885-f9d64f35c97c +Individual subject modeling 6 8 Was a reaction time regressor included? radio preset:boolean used reaction time regressor 1 used reaction time regressor 1 2 7434909b-ec95-42c0-8a7f-7a785261dbde +Individual subject modeling 6 9 Were any regressors specifically orthogonalized with respect to others? radio preset:boolean used orthogonalization 1 used orthogonalization 1 1 0471ddd2-b424-4ef6-9586-dc7978a366b5 +Individual subject modeling 6 10 If orthogonalization was used, describe here textarea orthogonalization description used_orthogonalization == 1 orthogonalization description 1 2 d101653a-5004-4ccb-b15f-e5583512a08c +Individual subject modeling 6 11 Was high pass filtering applied? radio preset:boolean used high pass filter 1 used high pass filter 1 1 717f2fa9-580e-4498-96fa-acb6bf102691 +Individual subject modeling 6 12 Describe method used for high pass filtering textarea high pass filter method used_high_pass_filter == 1 high pass filter method 1 2 d1f221c9-ed0b-4fd6-bcfa-9dcdfed26709 +Individual subject modeling 6 13 What autocorrelation model was used ? select SPM: global approximate AR(1) | SPM: FAST | FSL: locally regularized autocorrelation function | AFNI: ARMA | none | other autocorrelation model 1 autocorrelation model 1 2 c662a33b-e242-4103-a2d2-9be9d1fd6ce1 +Individual subject modeling 6 14 Exactly what terms are subtracted from what? textarea contrast definition 1 contrast definition 1 1 d560f08a-62bf-4b56-b1e6-2599f906fb8a +Individual subject modeling 6 15 Link to Cognitive Atlas definition of this contrast Define these in terms of task or stimulus conditions (e.g., 'one-back task with objects versus zero-back task with objects') instead of underlying psychological concepts (e.g., 'working memory'). textarea contrast definition cogatlas 1 contrast definition cogatlas 1 3 f5dcb0b5-b94f-4dd9-81da-4abe4d6d923e +Group modeling 7 1 Type of group model used select Regression group model type 1 group model type 1 1 Describe the group level analysis 47d74a02-a1df-450a-89be-332e45acb1be +Group modeling 7 2 Estimation method used for model select ordinary least squares | generalized least squares group estimation type 1 group estimation type 1 1 01dbd376-3d69-4ac3-8779-45ff1e49796b +Group modeling 7 3 Software used for group modeling if different from overall package select preset:mri_softwares group modeling software 1 group modeling software 1 2 d617fa7d-219b-4ff1-9db2-f10ae3f29804 +Group modeling 7 4 Type of inference for group model select random effect | mixed effect | fixed effect group inference type 1 group inference type 1 1 012e837d-c1dc-4ae0-bdf5-234f410ca22d +Group modeling 7 5 If more than 2-levels, describe the levels and assumptions of the model. For example, are variances assumed equal between groups. textarea group model multilevel 1 group model multilevel 1 3 405903ff-8328-4733-852c-eac907750247 +Group modeling 7 6 Was this a repeated measures design at the group level? radio preset:boolean group repeated measures 1 group repeated measures 1 1 95d970ce-1ac2-4bb5-99fa-c6c07898ca20 +Group modeling 7 7 If multiple measurements per subject, list method to account for within subject correlation, exact assumptions made about correlation/variance textarea group repeated measures method group_repeated_measures == 1 group repeated measures method 1 3 66c51b5e-1992-4a30-8736-caa8f0c4736d +Group inference 8 1 Type of statistic that is the basis of the inference select Z | T | F | X2 | PostProb | Non-parametric Permutations | Monte Carlo Permutations group statistic type 1 group statistic type 1 2 Describe your statistical inference 3dfae2e3-4dfe-4fe7-a29d-1f3eaeec1950 +Group inference 8 2 Parameters of the null distribution of the test statisic. Typically degrees of freedom (should be clear from the test statistic what these are). float group statistic parameters 1 group statistic parameters 1 1 39e4fad9-00c7-45cf-a74a-b9c408514121 +Group inference 8 3 Noise smoothness for statistical inference This is the estimated smoothness used with Random Field Theory or a simulation-based inference method. float 0 group smoothness fwhm 1 group smoothness fwhm 1 1 4236b5c2-7e75-49c3-aa93-c1c1853f8162 diff --git a/reproschema-py b/reproschema-py index f61cf2f8..1043ffe1 160000 --- a/reproschema-py +++ b/reproschema-py @@ -1 +1 @@ -Subproject commit f61cf2f80ff86faa2dffc1ddf4e6b7a4dce76f3c +Subproject commit 1043ffe1d6a5fbc8393bc587281a9741170f6a87 diff --git a/ui/ecobidas_ui/__init__.py b/ui/ecobidas_ui/__init__.py index 94ec69f0..5d4919e8 100644 --- a/ui/ecobidas_ui/__init__.py +++ b/ui/ecobidas_ui/__init__.py @@ -1,7 +1,7 @@ from logging.config import dictConfig from pathlib import Path -from flask import Flask, render_template +from flask import Flask, flash, render_template from flask_bootstrap import Bootstrap5 from flask_wtf import CSRFProtect @@ -68,6 +68,16 @@ def create_app(test_config=None): def index() -> str: return render_template("index.html") + @app.route("/export") + def export() -> str: + flash("Not implemented yet!") + return render_template("index.html") + + @app.route("/generate") + def generate() -> str: + flash("Not implemented yet!") + return render_template("index.html") + @app.errorhandler(404) def page_not_found(e): return render_template("404.html"), 404 diff --git a/ui/ecobidas_ui/templates/404.html b/ui/ecobidas_ui/templates/404.html index 2b792a20..c196c766 100644 --- a/ui/ecobidas_ui/templates/404.html +++ b/ui/ecobidas_ui/templates/404.html @@ -7,7 +7,8 @@

    Page not found (Error 404)

    -

    Go to search page

    + +

    Go to home page

diff --git a/ui/ecobidas_ui/templates/500.html b/ui/ecobidas_ui/templates/500.html index fa47eb51..54defb2f 100644 --- a/ui/ecobidas_ui/templates/500.html +++ b/ui/ecobidas_ui/templates/500.html @@ -7,6 +7,7 @@

Internal server error (500)

+

Go to search page

diff --git a/ui/ecobidas_ui/templates/index.html b/ui/ecobidas_ui/templates/index.html index 3c79b76a..7ae6f3a8 100644 --- a/ui/ecobidas_ui/templates/index.html +++ b/ui/ecobidas_ui/templates/index.html @@ -7,6 +7,16 @@

TBD

+ +

+ "Lorem ipsum dolor sit amet, consectetur adipiscing elit, sed do eiusmod + tempor incididunt ut labore et dolore magna aliqua. Ut enim ad minim + veniam, quis nostrud exercitation ullamco laboris nisi ut aliquip ex ea + commodo consequat. Duis aute irure dolor in reprehenderit in voluptate + velit esse cillum dolore eu fugiat nulla pariatur. Excepteur sint + occaecat cupidatat non proident, sunt in culpa qui officia deserunt + mollit anim id est laborum." +

diff --git a/ui/ecobidas_ui/templates/protocol.html b/ui/ecobidas_ui/templates/protocol.html index 8af5b156..8cf318ee 100644 --- a/ui/ecobidas_ui/templates/protocol.html +++ b/ui/ecobidas_ui/templates/protocol.html @@ -21,6 +21,20 @@

> {% endfor %} +
  • + +
    • +
  • + +

    • diff --git a/ui/ecobidas_ui/utils.py b/ui/ecobidas_ui/utils.py index 87ff25c8..7603dbb1 100644 --- a/ui/ecobidas_ui/utils.py +++ b/ui/ecobidas_ui/utils.py @@ -154,7 +154,7 @@ def get_items_for_activity(activity_file): tmp["input_type"] = item_data["ui"]["inputType"] tmp["description"] = ( - "
    Details" + "
    Details" "
      " f"
    • item name: {item_data.get('description')}
      • " "
    " From 4e2346d86bd4e719a55d26fa3c9af291f89add39 Mon Sep 17 00:00:00 2001 From: Remi Gau Date: Fri, 24 May 2024 22:32:11 -0400 Subject: [PATCH 16/31] update visbility handling --- ecobidas/download_tsv.py | 20 +++ ecobidas/inputs/neurovault/neurovault.tsv | 174 +++++++++++----------- ui/ecobidas_ui/protocol.py | 28 ++-- 3 files changed, 126 insertions(+), 96 deletions(-) diff --git a/ecobidas/download_tsv.py b/ecobidas/download_tsv.py index 2cc2dc74..792503ce 100644 --- a/ecobidas/download_tsv.py +++ b/ecobidas/download_tsv.py @@ -1,5 +1,6 @@ #!/usr/bin/env python3 """Download the content of the different google spreadsheet in the inputs folder.""" +import ast import json from pathlib import Path @@ -95,6 +96,25 @@ def validate_downloaded_file(file: str | Path) -> None: f"\nThe following columns are missing from the data dictionary: {sorted(extra_columns)}" ) + invalid_vis = [] + visibility = df.visibility.values + for vis in visibility: + if not is_valid_python(vis): + invalid_vis.append(vis) + if invalid_vis: + logger.warning(f"\nThe following visibility are not valid python:\n{invalid_vis}") + + +def is_valid_python(code): + try: + ast.parse(code) + except SyntaxError: + return False + except ValueError as exc: + print(f"{exc}: {code}") + return True + return True + def main() -> None: # validates files diff --git a/ecobidas/inputs/neurovault/neurovault.tsv b/ecobidas/inputs/neurovault/neurovault.tsv index 327e1d07..c9a9c56c 100644 --- a/ecobidas/inputs/neurovault/neurovault.tsv +++ b/ecobidas/inputs/neurovault/neurovault.tsv @@ -1,88 +1,88 @@ activity_pref_label activity_order item_order question unit details field_type choices item item_pref_label visibility item_description include mandatory preamble bids_status bids_file bids_key bids_key_for_unit UUID -Experimental design 1 1 Type of design select blocked | event_related | hybrid block/event type_of_design type of design 1 type of design 1 1 Describe your experimental design 76c35f93-23e1-43b7-8f47-59b9e229cb71 -Experimental design 1 2 Number of imaging runs acquired integer 0 number of imaging runs 1 number of imaging runs 1 2 77423b25-3ee4-472b-bb25-8e9415189030 -Experimental design 1 3 Number of blocks, trials or experimental units per imaging run integer 0 number of experimental units 1 number of experimental units 1 2 131a5855-3fad-4b69-a9dd-a842cd7742d3 -Experimental design 1 4 Length of each imaging run seconds float 0 length of runs 1 length of runs 1 2 0b12a719-f6b8-4d1b-a353-d888d2d2fc7d -Experimental design 1 5 For blocked designs, length of blocks seconds float 0 length of blocks type_of_design in [0, 2] length of blocks 1 2 4e963713-4274-4cc3-addd-5b04f612b082 -Experimental design 1 6 Length of individual trials seconds float 0 length of trials 1 length of trials 1 2 63f7be62-80d4-4e8a-8dbb-dcb4441234de -Experimental design 1 7 Was the design optimized for efficiency? radio preset:boolean optimization 1 optimization 1 2 4bc92eea-ce45-40ce-8b2b-add6d5683585 -Experimental design 1 8 What method was used for optimization? textarea optimization method optimization == 1 optimization method 1 3 dbea3306-ad68-41de-8f5c-626bf878636d -Participants 2 1 Number of subjects entering into the analysis integer 0 number of subjects 1 number of subjects 1 1 Describe your participant sample 44bcca72-a745-4b9f-917b-2571eb73a695 -Participants 2 2 Mean age of subjects float 0 subject age mean 1 subject age mean 1 1 648db98e-e5ec-41a5-b6d4-f762bf8be2ea -Participants 2 3 Minimum age of subjects float 0 subject age min 1 subject age min 1 2 2a202af9-86c7-4cd0-95f6-2cf328608f54 -Participants 2 4 Maximum age of subjects float 0 subject age max 1 subject age max 1 2 933b1e07-9af1-4d99-adf9-81d8669dbe44 -Participants 2 5 Handedness of subjects radio right | left | both handedness 1 handedness 1 2 906b037e-b686-44a6-8440-5a05df6fe63c -Participants 2 6 The proportion of subjects who were male float 0 | 1 proportion male subjects 1 proportion male subjects 1 2 640df132-8c2e-4cd4-beee-97d9d64336a3 -Participants 2 7 Additional inclusion/exclusion criteria, if any. Including specific sampling strategies that limit inclusion to a specific group, such as laboratory members. textarea inclusion exclusion criteria 1 inclusion exclusion criteria 1 3 e061db40-8413-4ba0-ab20-1eeb89658a25 -Participants 2 8 Number of subjects scanned but rejected from analysis integer 0 number of rejected subjects 1 number of rejected subjects 1 2 6cc3460e-826f-4faf-bb4e-e66d78ab68af -Participants 2 9 Was this study a comparison between subject groups? radio preset:boolean group comparison 1 group comparison 1 1 0374fada-67e6-4d57-abf8-b0e4bd894ac4 -Participants 2 10 A description of the groups being compared textarea group description group_comparison == 1 group description 1 2 b27a7735-0393-479a-a9ee-f9e17decf720 -MRI acquisition 3 1 Manufacturer of MRI scanner select Siemens | Philips | General Electric | other Manufacturer scanner make 1 scanner make 1 1 Describe your acquisition parameters 19204f74-3646-4777-9a62-edff13947f59 -MRI acquisition 3 2 Model of MRI scanner textarea ManufacturersModelName scanner model 1 scanner model 1 1 3adcef71-b057-46ea-84e1-402c2deea39f -MRI acquisition 3 3 Field strength of MRI scanner Tesla float 0 MagneticFieldStrength field strength 1 field strength 1 1 2e7f18e2-b2e3-4310-9eb8-ff666e7383c2 -MRI acquisition 3 4 Description of pulse sequence used for fMRI select Gradient echo | Spin echo | Mutliband gradient echo | MPRAGE | MP2RAGE | FLASH PulseSequenceType pulse sequence 1 pulse sequence 1 1 20fc355f-0588-4a10-b185-851277ddc64f -MRI acquisition 3 5 Description of parallel imaging method and parameters textarea parallel imaging 1 parallel imaging 1 3 4bf06822-ee53-4e60-86bd-c54a5b8378e0 -MRI acquisition 3 6 Imaging field of view Millimeters float field of view 1 field of view 1 2 68b5c8e0-166b-42a8-ab33-9496d15e7859 -MRI acquisition 3 7 Matrix size for MRI acquisition integer matrix size 1 matrix size 1 2 4178e14e-a5f0-483a-a35f-5f7bb52d30e3 -MRI acquisition 3 8 Distance between slices (includes skip or distance factor). Millimeters float 0 slice thickness 1 slice thickness 1 1 e6b7971a-89f2-4b6a-b4c9-49fa6c4de697 -MRI acquisition 3 9 The size of the skipped area between slices. Millimeters float 0 skip factor 1 skip factor 1 2 bd9b28e1-58cf-4104-8694-350a504e9709 -MRI acquisition 3 10 The orientation of slices radio axial | sagittal | frontal acquisition orientation 1 acquisition orientation 1 2 8b5c1b46-64d5-4c36-aa19-154bd0e40a34 -MRI acquisition 3 11 Order of acquisition of slices select ascending | descending | interleaved SliceTiming order of acquisition 1 order of acquisition 1 3 37295a62-8084-42b2-b794-9bee8333b357 -MRI acquisition 3 12 Repetition time (TR) Milliseconds float 0 RepetitionTime repetition time 1 repetition time 1 1 fa71b4f7-015d-4d06-8728-fb5ef9591b71 -MRI acquisition 3 13 Echo time (TE) Milliseconds float 0 EchoTime echo time 1 echo time 1 1 a28a83be-cd4b-411e-9701-e0e711b28b05 -MRI acquisition 3 14 Flip angle Degrees float 0 FlipAngle flip angle 1 flip angle 1 2 653320d7-0dd3-412b-8464-f744d04a5f44 -Preprocessing 4 1 If a single software package was used for all analyses, specify that here select preset:mri_softwares SoftwareName software package 1 software package 1 1 Describe your preprocessing b92221e5-1b47-4692-81dd-c3c694e5f908 -Preprocessing 4 2 Version of software package used textarea SoftwareVersion software version 1 software version 1 1 c20093b4-df39-40d4-8610-ede0e4113b3f -Preprocessing 4 3 Specify order of preprocessing operations textarea order of preprocessing operations 1 order of preprocessing operations 1 2 af64fcae-c41e-4401-ab3a-3b162bf90933 -Preprocessing 4 4 Describe quality control measures textarea quality control 1 quality control 1 3 4fc681b9-9db9-4061-92b5-6a0396907ab3 -Preprocessing 4 5 Was B0 distortion correction used? radio preset:boolean used b0 unwarping 1 used b0 unwarping 1 2 5eea934f-4d84-49a5-bc79-b5ab6335d9de -Preprocessing 4 6 Specify software used for distortion correction if different from the main package select preset:mri_softwares b0 unwarping software used_b0_unwarping == 1 b0 unwarping software 1 3 7aa549bb-4c74-4859-82e6-e928e91787c4 -Preprocessing 4 7 Was slice timing correction used? radio preset:boolean used slice timing correction 1 used slice timing correction 1 1 90653c26-2d61-4e37-92e9-8a021d1a29b3 -Preprocessing 4 8 Specify software used for slice timing correction if different from the main package select preset:mri_softwares slice timing correction software used_slice_timing_correction == 1 slice timing correction software 1 3 e75c9a32-ec5a-4f3d-b048-57491f34b1bb -Preprocessing 4 9 Was motion correction used? radio preset:boolean used motion correction 1 used motion correction 1 1 ec63383c-0173-4c54-ba5b-0ff432d3e252 -Preprocessing 4 10 Specify software used for motion correction if different from the main package select preset:mri_softwares motion correction software used_motion_correction == 1 motion correction software 1 3 b4b0dd7d-1ac4-432f-a074-34b78ab021d0 -Preprocessing 4 11 Reference scan used for motion correction textarea motion correction reference used_motion_correction == 1 motion correction reference 1 3 b23f32cf-f81c-4d2b-b577-853c8da5e6c8 -Preprocessing 4 12 Similarity metric used for motion correction select preset:cost_functions motion correction metric used_motion_correction == 1 motion correction metric 1 3 24afd5d5-78fa-4a52-b196-654ddb3c9064 -Preprocessing 4 13 Interpolation method used for motion correction select preset:interpolations motion correction interpolation used_motion_correction == 1 motion correction interpolation 1 3 bd4f2aa3-7397-46bc-b63c-22f09431ac82 -Preprocessing 4 14 Was motion-susceptibility correction used? radio preset:boolean used motion susceptibiity correction 1 used motion susceptibiity correction 1 3 062960a8-0022-47ca-908b-c7fb6b89296b -Intersubject registration 5 1 Were subjects registered to a common stereotactic space? radio preset:boolean used intersubject registration 1 used intersubject registration 1 1 Describe your spatial normalization 1c13e108-0fe1-4d19-a707-9279f469a0e1 -Intersubject registration 5 2 Specify software used for intersubject registration if different from main package select preset:mri_softwares intersubject registration software used_intersubject_registration == 1 intersubject registration software 1 2 28b6d7fc-4168-48be-b6c7-fe518f9a7733 -Intersubject registration 5 3 Was linear or nonlinear registration used? select linear | non-linear intersubject transformation type used_intersubject_registration == 1 intersubject transformation type 1 1 dbbcba6b-2445-486a-b039-086f90f7f8c1 -Intersubject registration 5 4 If nonlinear registration was used, describe transform method textarea nonlinear transform type used_intersubject_registration == 1 and nonlinear_transform_type == 1 nonlinear transform type 1 2 b8cbc6b9-a3bd-4426-a2ef-860cf597f548 -Intersubject registration 5 5 Similarity metric used for intersubject registration textarea transform similarity metric used_intersubject_registration == 1 transform similarity metric 1 3 72e0b864-6950-4a15-a3ca-d6c6cc9264a8 -Intersubject registration 5 6 Interpolation method used for intersubject registration select preset:interpolations interpolation method used_intersubject_registration == 1 interpolation method 1 2 83a4f5ff-cd97-47a7-b272-e496ac1ad344 -Intersubject registration 5 7 What type of image was used to determine the transformation to the atlas? textarea object image type used_intersubject_registration == 1 object image type 1 1 0cbd4a83-80df-49ce-a3b3-50c5a63a723f -Intersubject registration 5 8 Were the functional images coregistered to the subject's structural image? radio preset:boolean functional coregistered to structural 1 functional coregistered to structural 1 2 331cfc44-6eb3-4c5b-ae7b-66dd6515e7a0 -Intersubject registration 5 9 Method used to coregister functional to structural images textarea functional coregistration method functional_coregistered_to_structural == 1 functional coregistration method 1 3 bcd0b566-2e73-4287-bc8f-2e370f43c03f -Intersubject registration 5 10 Name of coordinate space for registration target select MNI | Talairach | MNI2Tal | other coordinate space 1 coordinate space 1 1 6b8719e2-fde6-4805-a3a9-3a1dbc08df8e -Intersubject registration 5 11 Name of target template image textarea target template image 1 target template image 1 2 12331e78-51d6-47dd-8828-987de0333fdc -Intersubject registration 5 12 Voxel size of target template Millimeters float 0 target resolution 1 target resolution 1 1 265de527-ca2e-4ebe-a544-3224c7e89f3b -Intersubject registration 5 13 Was spatial smoothing applied? radio preset:boolean used smoothing 1 used smoothing 1 1 dc37a8a9-f2cf-4ed6-8610-028e92a6ec1f -Intersubject registration 5 14 Describe the type of smoothing applied textarea smoothing type used_smoothing == 1 smoothing type 1 1 bb9e0a6a-2d75-4604-89d5-54abee080ead -Intersubject registration 5 15 The full-width at half-maximum of the smoothing kernel Millimeters float 0 smoothing fwhm used_smoothing == 1 smoothing fwhm 1 1 68e4d3a2-447b-4cd3-baa1-4a131b9c41b1 -Intersubject registration 5 16 Voxel size in mm of the resampled, atlas-space images float 0 resampled voxel size 1 resampled voxel size 1 1 a64d9450-49d4-4bd5-9728-eb97a224a2b2 -Individual subject modeling 6 1 Type of group model used radio Regression | other intrasubject model type 1 intrasubject model type 1 1 Describe your model specification at the subejct level d1682682-6067-4014-aea8-651852c23ef1 -Individual subject modeling 6 2 Estimation method used for model select ordinary least squares | generalized least squares | other intrasubject estimation type 1 intrasubject estimation type 1 1 a9e542ec-fe76-4650-b54c-be144ccda2e3 -Individual subject modeling 6 3 Software used for intrasubject modeling if different from overall package select preset:mri_softwares intrasubject modeling software 1 intrasubject modeling software 1 2 93163af2-bb3a-407b-b632-18083ec4438c -Individual subject modeling 6 4 Nature of HRF model select spm HRF | glover HRF | double gamma | Fourrier set | Finite Impulse Response | FLOBS | other hemodynamic response function 1 hemodynamic response function 1 2 2cfdadcb-1aae-4653-ad09-69462b6f4bee -Individual subject modeling 6 5 Were temporal derivatives included? radio preset:boolean used temporal derivatives 1 used temporal derivatives 1 2 65c08e93-7d9f-4292-a346-750f2dee9123 -Individual subject modeling 6 6 Were dispersion derivatives included? radio preset:boolean used dispersion derivatives 1 used dispersion derivatives 1 3 1947cdad-aa5c-4747-9ea8-f72297b3fe3e -Individual subject modeling 6 7 Were motion regressors included? radio preset:boolean used motion regressors 1 used motion regressors 1 2 de73a483-2858-477d-b885-f9d64f35c97c -Individual subject modeling 6 8 Was a reaction time regressor included? radio preset:boolean used reaction time regressor 1 used reaction time regressor 1 2 7434909b-ec95-42c0-8a7f-7a785261dbde -Individual subject modeling 6 9 Were any regressors specifically orthogonalized with respect to others? radio preset:boolean used orthogonalization 1 used orthogonalization 1 1 0471ddd2-b424-4ef6-9586-dc7978a366b5 -Individual subject modeling 6 10 If orthogonalization was used, describe here textarea orthogonalization description used_orthogonalization == 1 orthogonalization description 1 2 d101653a-5004-4ccb-b15f-e5583512a08c -Individual subject modeling 6 11 Was high pass filtering applied? radio preset:boolean used high pass filter 1 used high pass filter 1 1 717f2fa9-580e-4498-96fa-acb6bf102691 -Individual subject modeling 6 12 Describe method used for high pass filtering textarea high pass filter method used_high_pass_filter == 1 high pass filter method 1 2 d1f221c9-ed0b-4fd6-bcfa-9dcdfed26709 -Individual subject modeling 6 13 What autocorrelation model was used ? select SPM: global approximate AR(1) | SPM: FAST | FSL: locally regularized autocorrelation function | AFNI: ARMA | none | other autocorrelation model 1 autocorrelation model 1 2 c662a33b-e242-4103-a2d2-9be9d1fd6ce1 -Individual subject modeling 6 14 Exactly what terms are subtracted from what? textarea contrast definition 1 contrast definition 1 1 d560f08a-62bf-4b56-b1e6-2599f906fb8a -Individual subject modeling 6 15 Link to Cognitive Atlas definition of this contrast Define these in terms of task or stimulus conditions (e.g., 'one-back task with objects versus zero-back task with objects') instead of underlying psychological concepts (e.g., 'working memory'). textarea contrast definition cogatlas 1 contrast definition cogatlas 1 3 f5dcb0b5-b94f-4dd9-81da-4abe4d6d923e -Group modeling 7 1 Type of group model used select Regression group model type 1 group model type 1 1 Describe the group level analysis 47d74a02-a1df-450a-89be-332e45acb1be -Group modeling 7 2 Estimation method used for model select ordinary least squares | generalized least squares group estimation type 1 group estimation type 1 1 01dbd376-3d69-4ac3-8779-45ff1e49796b -Group modeling 7 3 Software used for group modeling if different from overall package select preset:mri_softwares group modeling software 1 group modeling software 1 2 d617fa7d-219b-4ff1-9db2-f10ae3f29804 -Group modeling 7 4 Type of inference for group model select random effect | mixed effect | fixed effect group inference type 1 group inference type 1 1 012e837d-c1dc-4ae0-bdf5-234f410ca22d -Group modeling 7 5 If more than 2-levels, describe the levels and assumptions of the model. For example, are variances assumed equal between groups. textarea group model multilevel 1 group model multilevel 1 3 405903ff-8328-4733-852c-eac907750247 -Group modeling 7 6 Was this a repeated measures design at the group level? radio preset:boolean group repeated measures 1 group repeated measures 1 1 95d970ce-1ac2-4bb5-99fa-c6c07898ca20 -Group modeling 7 7 If multiple measurements per subject, list method to account for within subject correlation, exact assumptions made about correlation/variance textarea group repeated measures method group_repeated_measures == 1 group repeated measures method 1 3 66c51b5e-1992-4a30-8736-caa8f0c4736d -Group inference 8 1 Type of statistic that is the basis of the inference select Z | T | F | X2 | PostProb | Non-parametric Permutations | Monte Carlo Permutations group statistic type 1 group statistic type 1 2 Describe your statistical inference 3dfae2e3-4dfe-4fe7-a29d-1f3eaeec1950 -Group inference 8 2 Parameters of the null distribution of the test statisic. Typically degrees of freedom (should be clear from the test statistic what these are). float group statistic parameters 1 group statistic parameters 1 1 39e4fad9-00c7-45cf-a74a-b9c408514121 -Group inference 8 3 Noise smoothness for statistical inference This is the estimated smoothness used with Random Field Theory or a simulation-based inference method. float 0 group smoothness fwhm 1 group smoothness fwhm 1 1 4236b5c2-7e75-49c3-aa93-c1c1853f8162 +Experimental design 1 1 Type of design select blocked | event_related | hybrid block/event type_of_design type of design 1 type of design 1 1 Describe your experimental design #NAME? +Experimental design 1 2 Number of imaging runs acquired integer 0 number of imaging runs 1 number of imaging runs 1 2 #NAME? +Experimental design 1 3 Number of blocks, trials or experimental units per imaging run integer 0 number of experimental units 1 number of experimental units 1 2 #NAME? +Experimental design 1 4 Length of each imaging run seconds float 0 length of runs 1 length of runs 1 2 #NAME? +Experimental design 1 5 For blocked designs, length of blocks seconds float 0 length of blocks type_of_design in [0, 2] length of blocks 1 2 #NAME? +Experimental design 1 6 Length of individual trials seconds float 0 length of trials 1 length of trials 1 2 #NAME? +Experimental design 1 7 Was the design optimized for efficiency? radio preset:boolean optimization 1 optimization 1 2 #NAME? +Experimental design 1 8 What method was used for optimization? textarea optimization method optimization == 1 optimization method 1 3 #NAME? +Participants 2 1 Number of subjects entering into the analysis integer 0 number of subjects 1 number of subjects 1 1 Describe your participant sample #NAME? +Participants 2 2 Mean age of subjects float 0 subject age mean 1 subject age mean 1 1 #NAME? +Participants 2 3 Minimum age of subjects float 0 subject age min 1 subject age min 1 2 #NAME? +Participants 2 4 Maximum age of subjects float 0 subject age max 1 subject age max 1 2 #NAME? +Participants 2 5 Handedness of subjects radio right | left | both handedness 1 handedness 1 2 #NAME? +Participants 2 6 The proportion of subjects who were male float 0 | 1 proportion male subjects 1 proportion male subjects 1 2 #NAME? +Participants 2 7 Additional inclusion/exclusion criteria, if any. Including specific sampling strategies that limit inclusion to a specific group, such as laboratory members. textarea inclusion exclusion criteria 1 inclusion exclusion criteria 1 3 #NAME? +Participants 2 8 Number of subjects scanned but rejected from analysis integer 0 number of rejected subjects 1 number of rejected subjects 1 2 #NAME? +Participants 2 9 Was this study a comparison between subject groups? radio preset:boolean group comparison 1 group comparison 1 1 #NAME? +Participants 2 10 A description of the groups being compared textarea group description group_comparison == 1 group description 1 2 #NAME? +MRI acquisition 3 1 Manufacturer of MRI scanner select Siemens | Philips | General Electric | other Manufacturer scanner make 1 scanner make 1 1 Describe your acquisition parameters #NAME? +MRI acquisition 3 2 Model of MRI scanner textarea ManufacturersModelName scanner model 1 scanner model 1 1 #NAME? +MRI acquisition 3 3 Field strength of MRI scanner Tesla float 0 MagneticFieldStrength field strength 1 field strength 1 1 #NAME? +MRI acquisition 3 4 Description of pulse sequence used for fMRI select Gradient echo | Spin echo | Mutliband gradient echo | MPRAGE | MP2RAGE | FLASH PulseSequenceType pulse sequence 1 pulse sequence 1 1 #NAME? +MRI acquisition 3 5 Description of parallel imaging method and parameters textarea parallel imaging 1 parallel imaging 1 3 #NAME? +MRI acquisition 3 6 Imaging field of view Millimeters float field of view 1 field of view 1 2 #NAME? +MRI acquisition 3 7 Matrix size for MRI acquisition integer matrix size 1 matrix size 1 2 #NAME? +MRI acquisition 3 8 Distance between slices (includes skip or distance factor). Millimeters float 0 slice thickness 1 slice thickness 1 1 #NAME? +MRI acquisition 3 9 The size of the skipped area between slices. Millimeters float 0 skip factor 1 skip factor 1 2 #NAME? +MRI acquisition 3 10 The orientation of slices radio axial | sagittal | frontal acquisition orientation 1 acquisition orientation 1 2 #NAME? +MRI acquisition 3 11 Order of acquisition of slices select ascending | descending | interleaved SliceTiming order of acquisition 1 order of acquisition 1 3 #NAME? +MRI acquisition 3 12 Repetition time (TR) Milliseconds float 0 RepetitionTime repetition time 1 repetition time 1 1 #NAME? +MRI acquisition 3 13 Echo time (TE) Milliseconds float 0 EchoTime echo time 1 echo time 1 1 #NAME? +MRI acquisition 3 14 Flip angle Degrees float 0 FlipAngle flip angle 1 flip angle 1 2 #NAME? +Preprocessing 4 1 If a single software package was used for all analyses, specify that here select preset:mri_softwares SoftwareName software package 1 software package 1 1 Describe your preprocessing #NAME? +Preprocessing 4 2 Version of software package used textarea SoftwareVersion software version 1 software version 1 1 #NAME? +Preprocessing 4 3 Specify order of preprocessing operations textarea order of preprocessing operations 1 order of preprocessing operations 1 2 #NAME? +Preprocessing 4 4 Describe quality control measures textarea quality control 1 quality control 1 3 #NAME? +Preprocessing 4 5 Was B0 distortion correction used? radio preset:boolean used b0 unwarping 1 used b0 unwarping 1 2 #NAME? +Preprocessing 4 6 Specify software used for distortion correction if different from the main package select preset:mri_softwares b0 unwarping software used_b0_unwarping == 1 b0 unwarping software 1 3 #NAME? +Preprocessing 4 7 Was slice timing correction used? radio preset:boolean used slice timing correction 1 used slice timing correction 1 1 #NAME? +Preprocessing 4 8 Specify software used for slice timing correction if different from the main package select preset:mri_softwares slice timing correction software used_slice_timing_correction == 1 slice timing correction software 1 3 #NAME? +Preprocessing 4 9 Was motion correction used? radio preset:boolean used motion correction 1 used motion correction 1 1 #NAME? +Preprocessing 4 10 Specify software used for motion correction if different from the main package select preset:mri_softwares motion correction software used_motion_correction == 1 motion correction software 1 3 #NAME? +Preprocessing 4 11 Reference scan used for motion correction textarea motion correction reference used_motion_correction == 1 motion correction reference 1 3 #NAME? +Preprocessing 4 12 Similarity metric used for motion correction select preset:cost_functions motion correction metric used_motion_correction == 1 motion correction metric 1 3 #NAME? +Preprocessing 4 13 Interpolation method used for motion correction select preset:interpolations motion correction interpolation used_motion_correction == 1 motion correction interpolation 1 3 #NAME? +Preprocessing 4 14 Was motion-susceptibility correction used? radio preset:boolean used motion susceptibiity correction 1 used motion susceptibiity correction 1 3 #NAME? +Intersubject registration 5 1 Were subjects registered to a common stereotactic space? radio preset:boolean used intersubject registration 1 used intersubject registration 1 1 Describe your spatial normalization #NAME? +Intersubject registration 5 2 Specify software used for intersubject registration if different from main package select preset:mri_softwares intersubject registration software used_intersubject_registration == 1 intersubject registration software 1 2 #NAME? +Intersubject registration 5 3 Was linear or nonlinear registration used? select linear | non-linear intersubject transformation type used_intersubject_registration == 1 intersubject transformation type 1 1 #NAME? +Intersubject registration 5 4 If nonlinear registration was used, describe transform method textarea nonlinear transform type used_intersubject_registration == 1 and nonlinear_transform_type == 1 nonlinear transform type 1 2 #NAME? +Intersubject registration 5 5 Similarity metric used for intersubject registration textarea transform similarity metric used_intersubject_registration == 1 transform similarity metric 1 3 #NAME? +Intersubject registration 5 6 Interpolation method used for intersubject registration select preset:interpolations interpolation method used_intersubject_registration == 1 interpolation method 1 2 #NAME? +Intersubject registration 5 7 What type of image was used to determine the transformation to the atlas? textarea object image type used_intersubject_registration == 1 object image type 1 1 #NAME? +Intersubject registration 5 8 Were the functional images coregistered to the subject's structural image? radio preset:boolean functional coregistered to structural 1 functional coregistered to structural 1 2 #NAME? +Intersubject registration 5 9 Method used to coregister functional to structural images textarea functional coregistration method functional_coregistered_to_structural == 1 functional coregistration method 1 3 #NAME? +Intersubject registration 5 10 Name of coordinate space for registration target select MNI | Talairach | MNI2Tal | other coordinate space 1 coordinate space 1 1 #NAME? +Intersubject registration 5 11 Name of target template image textarea target template image 1 target template image 1 2 #NAME? +Intersubject registration 5 12 Voxel size of target template Millimeters float 0 target resolution 1 target resolution 1 1 #NAME? +Intersubject registration 5 13 Was spatial smoothing applied? radio preset:boolean used smoothing 1 used smoothing 1 1 #NAME? +Intersubject registration 5 14 Describe the type of smoothing applied textarea smoothing type used_smoothing == 1 smoothing type 1 1 #NAME? +Intersubject registration 5 15 The full-width at half-maximum of the smoothing kernel Millimeters float 0 smoothing fwhm used_smoothing == 1 smoothing fwhm 1 1 #NAME? +Intersubject registration 5 16 Voxel size in mm of the resampled, atlas-space images float 0 resampled voxel size 1 resampled voxel size 1 1 #NAME? +Individual subject modeling 6 1 Type of group model used radio Regression | other intrasubject model type 1 intrasubject model type 1 1 Describe your model specification at the subejct level #NAME? +Individual subject modeling 6 2 Estimation method used for model select ordinary least squares | generalized least squares | other intrasubject estimation type 1 intrasubject estimation type 1 1 #NAME? +Individual subject modeling 6 3 Software used for intrasubject modeling if different from overall package select preset:mri_softwares intrasubject modeling software 1 intrasubject modeling software 1 2 #NAME? +Individual subject modeling 6 4 Nature of HRF model select spm HRF | glover HRF | double gamma | Fourrier set | Finite Impulse Response | FLOBS | other hemodynamic response function 1 hemodynamic response function 1 2 #NAME? +Individual subject modeling 6 5 Were temporal derivatives included? radio preset:boolean used temporal derivatives 1 used temporal derivatives 1 2 #NAME? +Individual subject modeling 6 6 Were dispersion derivatives included? radio preset:boolean used dispersion derivatives 1 used dispersion derivatives 1 3 #NAME? +Individual subject modeling 6 7 Were motion regressors included? radio preset:boolean used motion regressors 1 used motion regressors 1 2 #NAME? +Individual subject modeling 6 8 Was a reaction time regressor included? radio preset:boolean used reaction time regressor 1 used reaction time regressor 1 2 #NAME? +Individual subject modeling 6 9 Were any regressors specifically orthogonalized with respect to others? radio preset:boolean used orthogonalization 1 used orthogonalization 1 1 #NAME? +Individual subject modeling 6 10 If orthogonalization was used, describe here textarea orthogonalization description used_orthogonalization == 1 orthogonalization description 1 2 #NAME? +Individual subject modeling 6 11 Was high pass filtering applied? radio preset:boolean used high pass filter 1 used high pass filter 1 1 #NAME? +Individual subject modeling 6 12 Describe method used for high pass filtering textarea high pass filter method used_high_pass_filter == 1 high pass filter method 1 2 #NAME? +Individual subject modeling 6 13 What autocorrelation model was used ? select SPM: global approximate AR(1) | SPM: FAST | FSL: locally regularized autocorrelation function | AFNI: ARMA | none | other autocorrelation model 1 autocorrelation model 1 2 #NAME? +Individual subject modeling 6 14 Exactly what terms are subtracted from what? textarea contrast definition 1 contrast definition 1 1 #NAME? +Individual subject modeling 6 15 Link to Cognitive Atlas definition of this contrast Define these in terms of task or stimulus conditions (e.g., 'one-back task with objects versus zero-back task with objects') instead of underlying psychological concepts (e.g., 'working memory'). textarea contrast definition cogatlas 1 contrast definition cogatlas 1 3 #NAME? +Group modeling 7 1 Type of group model used select Regression group model type 1 group model type 1 1 Describe the group level analysis #NAME? +Group modeling 7 2 Estimation method used for model select ordinary least squares | generalized least squares group estimation type 1 group estimation type 1 1 #NAME? +Group modeling 7 3 Software used for group modeling if different from overall package select preset:mri_softwares group modeling software 1 group modeling software 1 2 #NAME? +Group modeling 7 4 Type of inference for group model select random effect | mixed effect | fixed effect group inference type 1 group inference type 1 1 #NAME? +Group modeling 7 5 If more than 2-levels, describe the levels and assumptions of the model. For example, are variances assumed equal between groups. textarea group model multilevel 1 group model multilevel 1 3 #NAME? +Group modeling 7 6 Was this a repeated measures design at the group level? radio preset:boolean group repeated measures 1 group repeated measures 1 1 #NAME? +Group modeling 7 7 If multiple measurements per subject, list method to account for within subject correlation, exact assumptions made about correlation/variance textarea group repeated measures method group_repeated_measures == 1 group repeated measures method 1 3 #NAME? +Group inference 8 1 Type of statistic that is the basis of the inference select Z | T | F | X2 | PostProb | Non-parametric Permutations | Monte Carlo Permutations group statistic type 1 group statistic type 1 2 Describe your statistical inference #NAME? +Group inference 8 2 Parameters of the null distribution of the test statisic. Typically degrees of freedom (should be clear from the test statistic what these are). float group statistic parameters 1 group statistic parameters 1 1 #NAME? +Group inference 8 3 Noise smoothness for statistical inference This is the estimated smoothness used with Random Field Theory or a simulation-based inference method. float 0 group smoothness fwhm 1 group smoothness fwhm 1 1 #NAME? diff --git a/ui/ecobidas_ui/protocol.py b/ui/ecobidas_ui/protocol.py index ae5c1b89..cbd0c051 100644 --- a/ui/ecobidas_ui/protocol.py +++ b/ui/ecobidas_ui/protocol.py @@ -23,18 +23,28 @@ def update_visibility(items: dict[str, Any], form): + """Evaluate visibility condition of each item and make item visible if necessary.""" + # assign response to a variable with same name as the item it comees from + for key, value in form.data.items(): + if key not in items: + continue + if not value: + value = None + string_to_eval = f"{key} = {value}" + exec(string_to_eval) + + # evaluate visibility for item, values in items.items(): isVis = values["isVis"] if isinstance(isVis, str): - isVis = isVis.replace(" ", "").split("==") - # if len(isVis) > 2: - # app.logger.warning("More than 1 '=='") - # if len(isVis) < 2: - # app.logger.warning(f"Unsupported JavaScript expression: {isVis}") - if len(isVis) == 2 and form[isVis[0]].data: - response = int(form[isVis[0]].data) - expected = int(isVis[1]) - items[item]["visibility"] = response == expected + try: + items[item]["visibility"] = eval(isVis) + except Exception as exc: + # actually log this + print(f"Could not evaluate '{eval(isVis)}' as a valid python expression") + print(exc) + items[item]["visibility"] = False + return items From 91e0a21efccab01eed360186c103e3ff4dd032a1 Mon Sep 17 00:00:00 2001 From: Remi Gau Date: Sat, 25 May 2024 15:48:33 -0400 Subject: [PATCH 17/31] upload bold json --- inputs/bids_template/participants.json | 2 +- .../task-auditoryLocalizer_bold.json | 80 +++++++ pyproject.toml | 2 +- ui/README.md | 3 + ui/ecobidas_ui/about.py | 2 +- ui/ecobidas_ui/forms.py | 8 +- ui/ecobidas_ui/protocol.py | 197 ++++++++++++------ ui/ecobidas_ui/templates/base.html | 13 ++ ui/ecobidas_ui/templates/protocol.html | 52 ++++- ui/ecobidas_ui/utils.py | 42 +++- ui/tests/test_utils.py | 60 ++++++ 11 files changed, 394 insertions(+), 67 deletions(-) create mode 100755 inputs/bids_template/task-auditoryLocalizer_bold.json create mode 100644 ui/tests/test_utils.py diff --git a/inputs/bids_template/participants.json b/inputs/bids_template/participants.json index 4f6f9ff0..5cc2a253 100644 --- a/inputs/bids_template/participants.json +++ b/inputs/bids_template/participants.json @@ -14,7 +14,7 @@ "Description": "There should have been a description here, but there wasn't. :(" }, "participant_id": { - "Annottations": { + "Annotations": { "IsAbout": { "TermURL": "nb:ParticipantID", "Label": "" diff --git a/inputs/bids_template/task-auditoryLocalizer_bold.json b/inputs/bids_template/task-auditoryLocalizer_bold.json new file mode 100755 index 00000000..d61f4425 --- /dev/null +++ b/inputs/bids_template/task-auditoryLocalizer_bold.json @@ -0,0 +1,80 @@ +{ + "AcquisitionMatrixPE": 136, + "AcquisitionNumber": 1, + "AcquisitionTime": "11:06:33.777500", + "BandwidthPerPixelPhaseEncode": 37.388, + "BaseResolution": 134, + "BodyPartExamined": "BRAIN", + "CoilCombinationMethod": "Sum of Squares", + "CoilString": "A32", + "ConsistencyInfo": "N4_VE12U_LATEST_20181126", + "ConversionSoftware": "dcm2niix", + "ConversionSoftwareVersion": "v1.0.20220720", + "DerivedVendorReportedEchoSpacing": 0.000589997, + "DeviceSerialNumber": "79116", + "DwellTime": 1.8e-6, + "EchoTime": 0.022, + "EchoTrainLength": 45, + "EffectiveEchoSpacing": 0.000196666, + "FlipAngle": 70, + "HeudiconvVersion": "0.12.2", + "ImageComments": "Unaliased MB2/PE2/LB", + "ImageOrientationPatientDICOM": [ + 0.999976, 0.00314557, 0.00619129, -0.000174468, 0.902631, -0.430415 + ], + "ImageOrientationText": "Tra>Cor(-25.5)>Sag(0.4)", + "ImageType": ["ORIGINAL", "PRIMARY", "M", "MB", "ND", "MOSAIC"], + "ImagingFrequency": 297.161, + "InPlanePhaseEncodingDirectionDICOM": "COL", + "InstitutionAddress": "Allee du 6 Aout 8,Liege,Liege,BE,4000", + "InstitutionName": "CRC Liege", + "InstitutionalDepartmentName": "Department", + "MRAcquisitionType": "2D", + "MagneticFieldStrength": 7, + "Manufacturer": "Siemens", + "ManufacturersModelName": "Terra", + "MatrixCoilMode": "GRAPPA", + "Modality": "MR", + "MultibandAccelerationFactor": 2, + "NonlinearGradientCorrection": false, + "ParallelReductionFactorInPlane": 3, + "PartialFourier": 1, + "PatientPosition": "HFS", + "PercentPhaseFOV": 101.493, + "PercentSampling": 100, + "PhaseEncodingDirection": "j-", + "PhaseEncodingSteps": 135, + "PhaseResolution": 1, + "PixelBandwidth": 2075, + "ProcedureStepDescription": "BLAM", + "ProtocolName": "cmrr_mbep2d_p3_mb2_1.6iso_AABrain", + "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", + "ReceiveCoilName": "1Tx32Rx_Head", + "ReconMatrixPE": 136, + "RefLinesPE": 36, + "RepetitionTime": 1.8, + "SAR": 0.0728539, + "ScanOptions": "FS\\EXT", + "ScanningSequence": "EP", + "SequenceName": "epfid2d1_136", + "SequenceVariant": "SK\\SS\\OSP", + "SeriesDescription": "cmrr_mbep2d_p3_mb2_1.6iso_AABrain", + "SeriesNumber": 11, + "ShimSetting": [180, 191, -50, 81, 46, -213, -216, -65], + "SliceThickness": 1.6, + "SliceTiming": [ + 0, 0.85, 1.7, 0.75, 1.6, 0.65, 1.5, 0.55, 1.4, 0.45, 1.3, 0.35, 1.2, 0.25, + 1.1, 0.15, 1, 0.05, 0.9, 1.75, 0.8, 1.65, 0.7, 1.55, 0.6, 1.45, 0.5, 1.35, + 0.4, 1.25, 0.3, 1.15, 0.2, 1.05, 0.1, 0.95, 0, 0.85, 1.7, 0.75, 1.6, 0.65, + 1.5, 0.55, 1.4, 0.45, 1.3, 0.35, 1.2, 0.25, 1.1, 0.15, 1, 0.05, 0.9, 1.75, + 0.8, 1.65, 0.7, 1.55, 0.6, 1.45, 0.5, 1.35, 0.4, 1.25, 0.3, 1.15, 0.2, 1.05, + 0.1, 0.95 + ], + "SoftwareVersions": "syngo MR E12", + "SpacingBetweenSlices": 1.6, + "StationName": "AWP79116", + "TaskName": "auditoryLocalizer", + "TotalReadoutTime": 0.0265499, + "TxRefAmp": 204.476, + "WipMemBlock": "892ba1da-48b0-4d69-9197-d97ef06e2eeb||Sequence: R016 ve12u/SP01_R016a r/af3652dd; Apr 1 2021 14:05:17 by eja" +} diff --git a/pyproject.toml b/pyproject.toml index 3402d887..50a32ad7 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -38,7 +38,7 @@ ecobidas = "ecobidas.cli:cli" line-length = 100 [tool.codespell] -ignore-words-list = "jist,softwares,te,fwe,als" +ignore-words-list = "jist,softwares,te,fwe,als,nd" skip = "./.git,*.svg,reproschema-ui,node_modules,env,reproschema-py,htmlcov,package-lock.json" [tool.hatch.build.hooks.vcs] diff --git a/ui/README.md b/ui/README.md index 772eda3d..3501d332 100644 --- a/ui/README.md +++ b/ui/README.md @@ -18,3 +18,6 @@ flask --app ecobidas_ui --debug run https://github.com/helloflask/bootstrap-flask https://bootstrap-flask.readthedocs.io/ --> + + +🚧 diff --git a/ui/ecobidas_ui/about.py b/ui/ecobidas_ui/about.py index dce45834..0e2eb59c 100644 --- a/ui/ecobidas_ui/about.py +++ b/ui/ecobidas_ui/about.py @@ -3,6 +3,6 @@ bp = Blueprint("about", __name__) -@bp.route("/about") +@bp.route("/about", methods=["GET", "POST"]) def about() -> str: return render_template("about.html") diff --git a/ui/ecobidas_ui/forms.py b/ui/ecobidas_ui/forms.py index c0d5dcfc..f4ba1987 100644 --- a/ui/ecobidas_ui/forms.py +++ b/ui/ecobidas_ui/forms.py @@ -1,4 +1,5 @@ from flask_wtf import FlaskForm +from flask_wtf.file import FileField, FileRequired from markupsafe import Markup from wtforms import ( DateField, @@ -16,11 +17,16 @@ from wtforms.validators import DataRequired, NumberRange -class UploadForm(FlaskForm): +class UploadParticipantsForm(FlaskForm): participants = MultipleFileField("Upload participants.tsv and participants.json") submit = SubmitField("Upload") +class UploadBoldJsonForm(FlaskForm): + bold_json = FileField("Upload bold.json", validators=[FileRequired()]) + submit_bold_json = SubmitField("Upload") + + def generate_form(items=None, prefix=None): class DyanmicForm(FlaskForm): diff --git a/ui/ecobidas_ui/protocol.py b/ui/ecobidas_ui/protocol.py index cbd0c051..b5bd294f 100644 --- a/ui/ecobidas_ui/protocol.py +++ b/ui/ecobidas_ui/protocol.py @@ -2,17 +2,19 @@ from pathlib import Path from typing import Any -import pandas as pd -from ecobidas_ui.forms import UploadForm, generate_form +from ecobidas_ui.forms import UploadBoldJsonForm, UploadParticipantsForm, generate_form from ecobidas_ui.utils import ( LANG, allowed_file, + extract_values_participants, get_landing_page, get_nav_bar_content, get_protocol, prep_activity_page, protocol_url, update_format, + validate_participants_json, + validate_participants_tsv, ) from flask import Blueprint, current_app, flash, redirect, render_template, request from markupsafe import Markup @@ -31,7 +33,11 @@ def update_visibility(items: dict[str, Any], form): if not value: value = None string_to_eval = f"{key} = {value}" - exec(string_to_eval) + try: + exec(string_to_eval) + except Exception as exc: + print(f"Could not execute '{string_to_eval}' as a valid python statement.") + print(exc) # evaluate visibility for item, values in items.items(): @@ -41,7 +47,7 @@ def update_visibility(items: dict[str, Any], form): items[item]["visibility"] = eval(isVis) except Exception as exc: # actually log this - print(f"Could not evaluate '{eval(isVis)}' as a valid python expression") + print(f"Could not evaluate '{eval(isVis)}' as a valid python expression.") print(exc) items[item]["visibility"] = False @@ -72,9 +78,9 @@ def activity_get(protocol_name, activity_name) -> str: activities, activity, items = prep_activity_page(protocol_name, activity_name) - upload_form = None - if protocol_name == "neurovault" and activity_name == "participants": - upload_form = UploadForm(prefix="upload-") + upload_participants_form, upload_acquisition_form = generate_additional_forms( + protocol_name, activity_name + ) form = generate_form(items=items, prefix=activity_name) @@ -90,7 +96,8 @@ def activity_get(protocol_name, activity_name) -> str: form=form, nb_items=nb_items, completed_items=completed_items, - upload_form=upload_form, + upload_participants_form=upload_participants_form, + upload_acquisition_form=upload_acquisition_form, ) @@ -99,51 +106,38 @@ def activity_post(protocol_name, activity_name) -> str: activities, activity, items = prep_activity_page(protocol_name, activity_name) - upload_form = None - if protocol_name == "neurovault" and activity_name == "participants": - upload_form = UploadForm(prefix="upload-") + upload_participants_form, upload_acquisition_form = generate_additional_forms( + protocol_name, activity_name + ) form = generate_form(items=items, prefix=activity_name) - if upload_form and upload_form.participants.data: - - nb_files_uploaded = len(upload_form.participants.data) - participants_json_uploaded = any( - file.filename == "participants.json" for file in upload_form.participants.data - ) - participants_tsv_uploaded = any( - file.filename == "participants.tsv" for file in upload_form.participants.data - ) + if ( + upload_participants_form + and upload_participants_form.is_submitted() + and upload_participants_form.participants.data + ): - if nb_files_uploaded != 2: - message = "2 files must be uploaded." - if not participants_json_uploaded: - message = "No 'participants.json' was uploaded." - if not participants_tsv_uploaded: - message = "No 'participants.tsv' was uploaded." - - if ( - nb_files_uploaded != 2 - or not participants_json_uploaded - or not participants_tsv_uploaded - ): + if message := validate_participants_form(upload_participants_form): flash(message) return redirect(request.url) - for file in upload_form.participants.data: + for file in upload_participants_form.participants.data: if allowed_file(file.filename): filename = secure_filename(file.filename) file.save(Path(current_app.config["UPLOAD_FOLDER"]) / filename) - participants_tsv = pd.read_csv( - Path(current_app.config["UPLOAD_FOLDER"]) / "participants.tsv", sep="\t" - ) - with open(Path(current_app.config["UPLOAD_FOLDER"]) / "participants.json") as f: - participants_json = json.load(f) + tsv_file = Path(current_app.config["UPLOAD_FOLDER"]) / "participants.tsv" + if not validate_participants_tsv(tsv_file): + flash( + Markup( + "

    The 'participants.tsv' does not seem to be valid: 'participant_id' column is missing.

    " + ) + ) + return redirect(request.url) - if not participants_json.get("participant_id") or not participants_json[ - "participant_id" - ].get("Annotations"): + json_file = Path(current_app.config["UPLOAD_FOLDER"]) / "participants.json" + if not validate_participants_json(json_file): flash( Markup( "

    The 'participants.json' was not annotated. " @@ -154,28 +148,115 @@ def activity_post(protocol_name, activity_name) -> str: ) return redirect(request.url) - print(participants_tsv) - print(participants_json) + form.number_of_subjects.data = extract_values_participants( + tsv_file, value="number_of_subjects" + ) + form.subject_age_mean.data = extract_values_participants(tsv_file, value="subject_age_mean") + form.subject_age_min.data = extract_values_participants(tsv_file, value="subject_age_min") + form.subject_age_max.data = extract_values_participants(tsv_file, value="subject_age_max") - elif form.is_submitted(): + # TODO + form.proportion_male_subjects.data = 0.5 items = update_visibility(items, form) + items = update_format(items, form) + form = generate_form(items, prefix=activity_name) + form.number_of_subjects.data = extract_values_participants( + tsv_file, target="number_of_subjects" + ) + form.subject_age_mean.data = extract_values_participants( + tsv_file, target="subject_age_mean" + ) + form.subject_age_min.data = extract_values_participants(tsv_file, vtarget="subject_age_min") + form.subject_age_max.data = extract_values_participants(tsv_file, target="subject_age_max") + form.proportion_male_subjects.data = 0.5 + + if upload_acquisition_form.validate_on_submit(): + + f = upload_acquisition_form.bold_json.data + filename = secure_filename(f.filename) + + if not allowed_file(filename): + message = "No '_bold.json' was uploaded." + flash(message) + return redirect(request.url) + + f.save(Path(current_app.instance_path) / filename) + + with open(Path(current_app.instance_path) / filename) as f: + bold_json = json.load(f) + + for key in bold_json: + if key in form: + form[key].data = bold_json[key] + + items = update_visibility(items, form) items = update_format(items, form) + form = generate_form(items, prefix=activity_name) + + for key in bold_json: + if key in form: + form[key].data = bold_json[key] + + elif form.is_submitted(): + items = update_visibility(items, form) + items = update_format(items, form) form = generate_form(items, prefix=activity_name) - completed_items = sum(bool(i["is_answered"]) for i in items.values()) - nb_items = sum(bool(i["visibility"]) for i in items.values()) - - return render_template( - "protocol.html", - protocol_pref_label=protocol_name, - activity_pref_label=activity["prefLabel"][LANG], - activity_preamble=Markup(activity["preamble"][LANG]), - activities=activities, - form=form, - nb_items=nb_items, - completed_items=completed_items, - upload_form=upload_form, - ) + completed_items = sum(bool(i["is_answered"]) for i in items.values()) + nb_items = sum(bool(i["visibility"]) for i in items.values()) + + return render_template( + "protocol.html", + protocol_pref_label=protocol_name, + activity_pref_label=activity["prefLabel"][LANG], + activity_preamble=Markup(activity["preamble"][LANG]), + activities=activities, + form=form, + nb_items=nb_items, + completed_items=completed_items, + upload_participants_form=upload_participants_form, + upload_acquisition_form=upload_acquisition_form, + ) + + +def validate_participants_form(upload_participants_form): + nb_files_uploaded = len(upload_participants_form.participants.data) + participants_json_uploaded = any( + file.filename == "participants.json" for file in upload_participants_form.participants.data + ) + participants_tsv_uploaded = any( + file.filename == "participants.tsv" for file in upload_participants_form.participants.data + ) + + if nb_files_uploaded != 2: + message = "2 files must be uploaded." + if not participants_json_uploaded: + message = "No 'participants.json' was uploaded." + if not participants_tsv_uploaded: + message = "No 'participants.tsv' was uploaded." + + if nb_files_uploaded != 2 or not participants_json_uploaded or not participants_tsv_uploaded: + + return message + + else: + return "" + + +def generate_additional_forms(protocol_name, activity_name): + + upload_participants_form = None + upload_acquisition_form = None + + if protocol_name != "neurovault": + return upload_participants_form, upload_acquisition_form + + if activity_name == "participants": + upload_participants_form = UploadParticipantsForm(prefix="upload-") + if activity_name == "mri_acquisition": + upload_acquisition_form = UploadBoldJsonForm(prefix="mri_acquisition-") + + return upload_participants_form, upload_acquisition_form diff --git a/ui/ecobidas_ui/templates/base.html b/ui/ecobidas_ui/templates/base.html index 17dcff07..dad901a5 100644 --- a/ui/ecobidas_ui/templates/base.html +++ b/ui/ecobidas_ui/templates/base.html @@ -42,6 +42,19 @@ +

    +
    +
    + +
    +
    +
    +
    {% with messages = get_flashed_messages() %} {% if messages %} {% for diff --git a/ui/ecobidas_ui/templates/protocol.html b/ui/ecobidas_ui/templates/protocol.html index 8cf318ee..2c590008 100644 --- a/ui/ecobidas_ui/templates/protocol.html +++ b/ui/ecobidas_ui/templates/protocol.html @@ -55,9 +55,55 @@

    {{ activity_pref_label }}

    >

    - {{ activity_preamble }} {% if upload_form %} -
    {{ render_form(upload_form) }}
    - {% endif %} + {{ activity_preamble }} + +
    +
    + {% if upload_participants_form %} +
    +
    + +
    +

    + To fill in this form faster you can upload a + participants.tsv file formatted according to the + BIDS specification + along with a participants.json file containing column + annotations generated by + the neurobagel annotation tool. +

    + {{ render_form(upload_participants_form) }} +
    + {% endif %} {% if upload_acquisition_form %} +
    +
    + +
    +

    + To fill in this form faster you can upload a + *_bold.json file formatted according to the + BIDS specification + containing the metadata for your fMRI runs. +

    + {{ render_form(upload_acquisition_form) }} +
    + {% endif %} +
    +
    Path: @@ -217,3 +218,40 @@ def get_choices(item_data): except KeyError: choices = {} return choices + + +def validate_participants_json(file: Path): + with open(file) as f: + participants_json = json.load(f) + return bool( + participants_json.get("participant_id") + and participants_json["participant_id"].get("Annotations") + ) + + +def validate_participants_tsv(file: Path): + df = pd.read_csv(file, sep="\t") + return "participant_id" in df.columns + + +def extract_values_participants(df, json_content, target): + if isinstance(df, Path): + df = pd.read_csv(df, sep="\t") + + if target == "number_of_subjects": + return len(df) + + column = next( + ( + key + for key, value in json_content.items() + if value["Annotations"]["IsAbout"]["TermURL"] == "nb:Age" + ), + None, + ) + if target == "subject_age_mean": + return df[column].mean() + if target == "subject_age_min": + return df[column].min() + if target == "subject_age_max": + return df[column].max() diff --git a/ui/tests/test_utils.py b/ui/tests/test_utils.py new file mode 100644 index 00000000..8dd27ef8 --- /dev/null +++ b/ui/tests/test_utils.py @@ -0,0 +1,60 @@ +import pandas as pd +from ecobidas_ui.utils import extract_values_participants + + +def test_extract_values_participants(): + tsv = pd.DataFrame( + { + "age": [ + 26, + 24, + 27, + 20, + 22, + 26, + 24, + 21, + 26, + 21, + 24, + 22, + 21, + 30, + 24, + 19, + ], + "sex": [ + "F", + "M", + "F", + "F", + "M,", + "F", + "M", + "M", + "M", + "F", + "F", + "F", + "F", + "F", + "F", + "M", + ], + } + ) + + json_content = { + "age": { + "Annotations": { + "IsAbout": {"TermURL": "nb:Age", "Label": ""}, + "Transformation": {"TermURL": "nb:FromInt", "Label": "integer data"}, + "MissingValues": ["", "n/a", " "], + } + } + } + + assert extract_values_participants(tsv, json_content, target="number_of_subjects") == 16 + assert extract_values_participants(tsv, json_content, target="subject_age_min") == 19 + assert extract_values_participants(tsv, json_content, target="subject_age_max") == 30 + # assert mean==23.5625 From af5f34bfeb7ba923801dd7493ad6b237e8574705 Mon Sep 17 00:00:00 2001 From: Remi Gau Date: Sat, 25 May 2024 15:49:44 -0400 Subject: [PATCH 18/31] adapt size --- ui/ecobidas_ui/templates/protocol.html | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/ui/ecobidas_ui/templates/protocol.html b/ui/ecobidas_ui/templates/protocol.html index 2c590008..087d111b 100644 --- a/ui/ecobidas_ui/templates/protocol.html +++ b/ui/ecobidas_ui/templates/protocol.html @@ -86,7 +86,7 @@
    From 0f4df8255b918eca9570414d197ceb0e251bbdc4 Mon Sep 17 00:00:00 2001 From: Remi Gau Date: Mon, 27 May 2024 15:47:48 +0200 Subject: [PATCH 19/31] refactor ui --- .pre-commit-config.yaml | 6 + ecobidas/inputs/spreadsheet_google_id.yml | 6 +- ui/ecobidas_ui/__init__.py | 89 - ui/ecobidas_ui/about.py | 8 - ui/ecobidas_ui/app.py | 73 + ui/ecobidas_ui/extensions.py | 11 + ui/ecobidas_ui/initializers/__init__.py | 0 ui/ecobidas_ui/initializers/assets.py | 11 + ui/ecobidas_ui/protocol.py | 19 +- ui/ecobidas_ui/public/__init__.py | 3 + ui/ecobidas_ui/public/views.py | 27 + ui/ecobidas_ui/settings.py | 28 + .../static/css/font-awesome.min.css | 1567 +++++++++++++++++ .../static/{style.css => css/main.css} | 0 ui/ecobidas_ui/static/favicon.ico | Bin 0 -> 766 bytes ui/ecobidas_ui/static/json/faq.json | 30 + ui/ecobidas_ui/templates/401.html | 21 + ui/ecobidas_ui/templates/404.html | 14 +- ui/ecobidas_ui/templates/500.html | 15 +- ui/ecobidas_ui/templates/auth/login.html | 2 +- ui/ecobidas_ui/templates/auth/register.html | 2 +- ui/ecobidas_ui/templates/base.html | 196 --- ui/ecobidas_ui/templates/layout/base.html | 92 + ui/ecobidas_ui/templates/layout/footer.html | 25 + ui/ecobidas_ui/templates/layout/nav.html | 82 + ui/ecobidas_ui/templates/layout/svg.html | 21 + ui/ecobidas_ui/templates/protocol.html | 51 +- .../templates/{ => public}/about.html | 49 +- ui/ecobidas_ui/templates/public/faq.html | 36 + .../templates/{ => public}/index.html | 2 +- ui/ecobidas_ui/templates/side_nav.html | 28 + ui/ecobidas_ui/utils.py | 8 + ui/pyproject.toml | 6 +- ui/requirements.txt | 1 + 34 files changed, 2165 insertions(+), 364 deletions(-) delete mode 100644 ui/ecobidas_ui/about.py create mode 100644 ui/ecobidas_ui/app.py create mode 100644 ui/ecobidas_ui/extensions.py create mode 100644 ui/ecobidas_ui/initializers/__init__.py create mode 100644 ui/ecobidas_ui/initializers/assets.py create mode 100644 ui/ecobidas_ui/public/__init__.py create mode 100644 ui/ecobidas_ui/public/views.py create mode 100644 ui/ecobidas_ui/settings.py create mode 100644 ui/ecobidas_ui/static/css/font-awesome.min.css rename ui/ecobidas_ui/static/{style.css => css/main.css} (100%) create mode 100644 ui/ecobidas_ui/static/favicon.ico create mode 100644 ui/ecobidas_ui/static/json/faq.json create mode 100644 ui/ecobidas_ui/templates/401.html delete mode 100644 ui/ecobidas_ui/templates/base.html create mode 100644 ui/ecobidas_ui/templates/layout/base.html create mode 100644 ui/ecobidas_ui/templates/layout/footer.html create mode 100644 ui/ecobidas_ui/templates/layout/nav.html create mode 100644 ui/ecobidas_ui/templates/layout/svg.html rename ui/ecobidas_ui/templates/{ => public}/about.html (72%) create mode 100644 ui/ecobidas_ui/templates/public/faq.html rename ui/ecobidas_ui/templates/{ => public}/index.html (96%) create mode 100644 ui/ecobidas_ui/templates/side_nav.html diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 2e5f250b..9731853e 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -84,6 +84,12 @@ repos: - id: prettier types_or: [css, html, json] +# Check formatting HTML / Jinja +# - repo: https://github.com/thibaudcolas/curlylint + # rev: v0.13.1 + # hooks: + # - id: curlylint + # Check that Python code complies with PEP8 guidelines # flake8 uses pydocstyle to check docstrings: https://flake8.pycqa.org/en/latest/ # flake8-docstrings: https://pypi.org/project/flake8-docstrings/ diff --git a/ecobidas/inputs/spreadsheet_google_id.yml b/ecobidas/inputs/spreadsheet_google_id.yml index 8cfcbcd9..ce729378 100644 --- a/ecobidas/inputs/spreadsheet_google_id.yml +++ b/ecobidas/inputs/spreadsheet_google_id.yml @@ -19,7 +19,7 @@ eyetracking: google_id: 1aQZINzS24oYDgu6PZ8djqZQZ2s2eNs2xP6kyzHokU8o citation: https://psyarxiv.com/f6qcy/ app_link: https://remi-gau.github.io/cobidas-eyetracker/#/ - landing_page: ../README_eyetracker-en.md + landing_page: ../README_eyetracker-en.html repo: https://github.com/Remi-Gau/cobidas-eyetracker neurovault: @@ -37,7 +37,7 @@ pet: google_id: 1HS-1KOP8nE7C3MHiyRmQ6hd823cBZnCRVq0UryXvDc8 citation: https://doi.org/10.1177/0271678X20905433 app_link: https://remi-gau.github.io/cobidas-PET/#/ - landing_page: ../README_PET-en.md + landing_page: ../README_PET-en.html repo: https://github.com/Remi-Gau/cobidas-PET reexecution: @@ -46,7 +46,7 @@ reexecution: google_id: 1M9H7Bkti4OEVrYETajLbpbwY0T-QqSkpRUiwTz6-5Vc citation: https://doi.org/10.12688/f1000research.25306.2 app_link: https://remi-gau.github.io/cobidas_reexecute/#/ - landing_page: ../README_reexecute-en.md + landing_page: ../README_reexecute-en.html repo: https://github.com/Remi-Gau/cobidas_reexecute diff --git a/ui/ecobidas_ui/__init__.py b/ui/ecobidas_ui/__init__.py index 5d4919e8..e69de29b 100644 --- a/ui/ecobidas_ui/__init__.py +++ b/ui/ecobidas_ui/__init__.py @@ -1,89 +0,0 @@ -from logging.config import dictConfig -from pathlib import Path - -from flask import Flask, flash, render_template -from flask_bootstrap import Bootstrap5 -from flask_wtf import CSRFProtect - - -def create_app(test_config=None): - from ecobidas_ui import about, auth, db, protocol - - dictConfig( - { - "version": 1, - "formatters": { - "default": { - "format": "[%(asctime)s] %(levelname)s in %(module)s: %(message)s", - } - }, - "handlers": { - "wsgi": { - "class": "logging.StreamHandler", - "stream": "ext://flask.logging.wsgi_errors_stream", - "formatter": "default", - } - }, - "root": {"level": "INFO", "handlers": ["wsgi"]}, - } - ) - - # create and configure the app - UPLOAD_FOLDER = Path(__file__).parent / "tmp" - UPLOAD_FOLDER.mkdir(parents=True, exist_ok=True) - - # create and configure the app - app = Flask(__name__, instance_relative_config=True) - app.config.from_mapping( - SECRET_KEY="tO$&!|0wkamvVia0?n$NqIRVWOG", - DATABASE=Path(app.instance_path) / "flaskr.sqlite", - UPLOAD_FOLDER=UPLOAD_FOLDER, - MAX_CONTENT_LENGTH=16 * 1000 * 1000, - ) - - if test_config is None: - # load the instance config, if it exists, when not testing - app.config.from_pyfile("config.py", silent=True) - else: - # load the test config if passed in - app.config.from_mapping(test_config) - - # ensure the instance folder exists - Path(app.instance_path).mkdir(parents=True, exist_ok=True) - - # Bootstrap-Flask requires this line - bootstrap = Bootstrap5(app) # noqa - - # Flask-WTF requires this line - csrf = CSRFProtect(app) # noqa - - db.init_app(app) - - app.register_blueprint(auth.bp) - app.register_blueprint(about.bp) - app.register_blueprint(protocol.bp) - app.add_url_rule("/about", endpoint="about") - - @app.route("/", methods=["GET", "POST"]) - def index() -> str: - return render_template("index.html") - - @app.route("/export") - def export() -> str: - flash("Not implemented yet!") - return render_template("index.html") - - @app.route("/generate") - def generate() -> str: - flash("Not implemented yet!") - return render_template("index.html") - - @app.errorhandler(404) - def page_not_found(e): - return render_template("404.html"), 404 - - @app.errorhandler(500) - def internal_server_error(e): - return render_template("500.html"), 500 - - return app diff --git a/ui/ecobidas_ui/about.py b/ui/ecobidas_ui/about.py deleted file mode 100644 index 0e2eb59c..00000000 --- a/ui/ecobidas_ui/about.py +++ /dev/null @@ -1,8 +0,0 @@ -from flask import Blueprint, render_template - -bp = Blueprint("about", __name__) - - -@bp.route("/about", methods=["GET", "POST"]) -def about() -> str: - return render_template("about.html") diff --git a/ui/ecobidas_ui/app.py b/ui/ecobidas_ui/app.py new file mode 100644 index 00000000..099a6ca1 --- /dev/null +++ b/ui/ecobidas_ui/app.py @@ -0,0 +1,73 @@ +import logging +import sys + +from ecobidas_ui import auth, db, protocol, public +from ecobidas_ui.extensions import bootstrap, cache, csrf_protect, debug_toolbar +from ecobidas_ui.initializers.assets import init_assets +from flask import Flask, flash, render_template + + +def create_app(config_object="ecobidas_ui.settings"): + + # create and configure the app + app = Flask(__name__, instance_relative_config=True) + + app.config.from_object(config_object) + + register_extensions(app) + db.init_app(app) + + init_assets(app) + register_blueprints(app) + register_errorhandlers(app) + configure_logger(app) + + @app.route("/export") + def export() -> str: + flash("Not implemented yet!") + return render_template("index.html") + + @app.route("/generate") + def generate() -> str: + flash("Not implemented yet!") + return render_template("index.html") + + return app + + +def register_extensions(app): + """Register Flask extensions.""" + bootstrap.init_app(app) + csrf_protect.init_app(app) + cache.init_app(app) + debug_toolbar.init_app(app) + return None + + +def register_blueprints(app): + """Register Flask blueprints.""" + app.register_blueprint(public.views.blueprint) + app.register_blueprint(auth.bp) + app.register_blueprint(protocol.bp) + return None + + +def register_errorhandlers(app): + """Register error handlers.""" + + def render_error(error): + """Render error template.""" + # If a HTTPException, pull the `code` attribute; default to 500 + error_code = getattr(error, "code", 500) + return render_template(f"{error_code}.html"), error_code + + for errcode in [401, 404, 500]: + app.errorhandler(errcode)(render_error) + return None + + +def configure_logger(app): + """Configure loggers.""" + handler = logging.StreamHandler(sys.stdout) + if not app.logger.handlers: + app.logger.addHandler(handler) diff --git a/ui/ecobidas_ui/extensions.py b/ui/ecobidas_ui/extensions.py new file mode 100644 index 00000000..6b4ace46 --- /dev/null +++ b/ui/ecobidas_ui/extensions.py @@ -0,0 +1,11 @@ +"""Extensions module. Each extension is initialized in the app factory located in app.py.""" + +from flask_bootstrap import Bootstrap5 +from flask_caching import Cache +from flask_debugtoolbar import DebugToolbarExtension +from flask_wtf import CSRFProtect + +bootstrap = Bootstrap5() +csrf_protect = CSRFProtect() +cache = Cache() +debug_toolbar = DebugToolbarExtension() diff --git a/ui/ecobidas_ui/initializers/__init__.py b/ui/ecobidas_ui/initializers/__init__.py new file mode 100644 index 00000000..e69de29b diff --git a/ui/ecobidas_ui/initializers/assets.py b/ui/ecobidas_ui/initializers/assets.py new file mode 100644 index 00000000..ccd99e40 --- /dev/null +++ b/ui/ecobidas_ui/initializers/assets.py @@ -0,0 +1,11 @@ +from ecobidas_ui import settings +from flask_assets import Bundle, Environment + +# consolidated css bundle +css_bundle = Bundle("css/font-awesome.min.css") + + +def init_assets(app): + app.config["ASSETS_DEBUG"] = settings.DEBUG + webassets = Environment(app) + webassets.register("css", css_bundle) diff --git a/ui/ecobidas_ui/protocol.py b/ui/ecobidas_ui/protocol.py index b5bd294f..ed2ab69e 100644 --- a/ui/ecobidas_ui/protocol.py +++ b/ui/ecobidas_ui/protocol.py @@ -69,10 +69,19 @@ def protocol(protocol_name: str) -> str: protocol_pref_label=protocol_name, protocol_preamble=protocol_content["preamble"][LANG], activities=activities, - landing_page=Markup(landing_page), + landing_page=landing_page, + show_export_button=show_export_button(protocol_name), ) +def show_export_button(protocol_name): + print(protocol_name) + if protocol_name in ["neurovault", "cobidas"]: + return True + else: + return False + + @bp.get("//") def activity_get(protocol_name, activity_name) -> str: @@ -91,13 +100,14 @@ def activity_get(protocol_name, activity_name) -> str: "protocol.html", protocol_pref_label=protocol_name, activity_pref_label=activity["prefLabel"][LANG], - activity_preamble=Markup(activity["preamble"][LANG]), + activity_preamble=activity["preamble"][LANG], activities=activities, form=form, nb_items=nb_items, completed_items=completed_items, upload_participants_form=upload_participants_form, upload_acquisition_form=upload_acquisition_form, + show_export_button=show_export_button(protocol_name), ) @@ -142,7 +152,7 @@ def activity_post(protocol_name, activity_name) -> str: Markup( "

    The 'participants.json' was not annotated. " "Annotate your data with " - "the neurobagel online annotation tool

    " ) ) @@ -212,13 +222,14 @@ def activity_post(protocol_name, activity_name) -> str: "protocol.html", protocol_pref_label=protocol_name, activity_pref_label=activity["prefLabel"][LANG], - activity_preamble=Markup(activity["preamble"][LANG]), + activity_preamble=activity["preamble"][LANG], activities=activities, form=form, nb_items=nb_items, completed_items=completed_items, upload_participants_form=upload_participants_form, upload_acquisition_form=upload_acquisition_form, + show_export_button=show_export_button(protocol_name), ) diff --git a/ui/ecobidas_ui/public/__init__.py b/ui/ecobidas_ui/public/__init__.py new file mode 100644 index 00000000..05af8588 --- /dev/null +++ b/ui/ecobidas_ui/public/__init__.py @@ -0,0 +1,3 @@ +"""The public module, including the homepage and user auth.""" + +from . import views # noqa diff --git a/ui/ecobidas_ui/public/views.py b/ui/ecobidas_ui/public/views.py new file mode 100644 index 00000000..4d874025 --- /dev/null +++ b/ui/ecobidas_ui/public/views.py @@ -0,0 +1,27 @@ +"""Public section, including homepage and signup.""" + +import json + +from ecobidas_ui.settings import STATIC_FOLDER +from flask import Blueprint, current_app, render_template + +blueprint = Blueprint("public", __name__, static_folder="../static") + + +@blueprint.route("/", methods=["GET", "POST"]) +def home(): + """Home page.""" + current_app.logger.info("Hello from the home page!") + return render_template("public/index.html") + + +@blueprint.route("/faq/") +def faq(): + data = json.load(open(STATIC_FOLDER / "json" / "faq.json")) + return render_template("public/faq.html", data=data) + + +@blueprint.route("/about/") +def about(): + """About page.""" + return render_template("public/about.html") diff --git a/ui/ecobidas_ui/settings.py b/ui/ecobidas_ui/settings.py new file mode 100644 index 00000000..42e8cd6d --- /dev/null +++ b/ui/ecobidas_ui/settings.py @@ -0,0 +1,28 @@ +from pathlib import Path + +from environs import Env + +env = Env() +env.read_env() + +ROOT_DIR = Path(__file__).parent + +# Static content +STATIC_FOLDER = ROOT_DIR / "static" + +# Templates +TEMPLATE_FOLDER = ROOT_DIR / "templates" + +UPLOAD_FOLDER = Path(__file__).parent / "tmp" +UPLOAD_FOLDER.mkdir(parents=True, exist_ok=True) + +# ---- SETUP INSTRUCTIONS AND APP BEHAVIOR #### + +# ------ App-level configuration ### +DEBUG = True + +PROTOTYPE = True + +SECRET_KEY = env.str("SECRET_KEY") + +CACHE_TYPE = "flask_caching.backends.SimpleCache" # Can be "MemcachedCache", "RedisCache", etc. diff --git a/ui/ecobidas_ui/static/css/font-awesome.min.css b/ui/ecobidas_ui/static/css/font-awesome.min.css new file mode 100644 index 00000000..cbe88b5e --- /dev/null +++ b/ui/ecobidas_ui/static/css/font-awesome.min.css @@ -0,0 +1,1567 @@ +/*! + * Font Awesome 4.1.0 by @davegandy - http://fontawesome.io - @fontawesome + * License - http://fontawesome.io/license (Font: SIL OFL 1.1, CSS: MIT License) + */ +@font-face { + font-family: "FontAwesome"; + src: url("../fonts/fontawesome-webfont.eot?v=4.1.0"); + src: + url("../fonts/fontawesome-webfont.eot?#iefix&v=4.1.0") + format("embedded-opentype"), + url("../fonts/fontawesome-webfont.woff?v=4.1.0") format("woff"), + url("../fonts/fontawesome-webfont.ttf?v=4.1.0") format("truetype"), + url("../fonts/fontawesome-webfont.svg?v=4.1.0#fontawesomeregular") + format("svg"); + font-weight: normal; + font-style: normal; +} +.fa { + display: inline-block; + font-family: FontAwesome; + font-style: normal; + font-weight: normal; + line-height: 1; + -webkit-font-smoothing: antialiased; + -moz-osx-font-smoothing: grayscale; +} +.fa-lg { + font-size: 1.33333333em; + line-height: 0.75em; + vertical-align: -15%; +} +.fa-2x { + font-size: 2em; +} +.fa-3x { + font-size: 3em; +} +.fa-4x { + font-size: 4em; +} +.fa-5x { + font-size: 5em; +} +.fa-fw { + width: 1.28571429em; + text-align: center; +} +.fa-ul { + padding-left: 0; + margin-left: 2.14285714em; + list-style-type: none; +} +.fa-ul > li { + position: relative; +} +.fa-li { + position: absolute; + left: -2.14285714em; + width: 2.14285714em; + top: 0.14285714em; + text-align: center; +} +.fa-li.fa-lg { + left: -1.85714286em; +} +.fa-border { + padding: 0.2em 0.25em 0.15em; + border: solid 0.08em #eee; + border-radius: 0.1em; +} +.pull-right { + float: right; +} +.pull-left { + float: left; +} +.fa.pull-left { + margin-right: 0.3em; +} +.fa.pull-right { + margin-left: 0.3em; +} +.fa-spin { + -webkit-animation: spin 2s infinite linear; + -moz-animation: spin 2s infinite linear; + -o-animation: spin 2s infinite linear; + animation: spin 2s infinite linear; +} +@-moz-keyframes spin { + 0% { + -moz-transform: rotate(0deg); + } + 100% { + -moz-transform: rotate(359deg); + } +} +@-webkit-keyframes spin { + 0% { + -webkit-transform: rotate(0deg); + } + 100% { + -webkit-transform: rotate(359deg); + } +} +@-o-keyframes spin { + 0% { + -o-transform: rotate(0deg); + } + 100% { + -o-transform: rotate(359deg); + } +} +@keyframes spin { + 0% { + -webkit-transform: rotate(0deg); + transform: rotate(0deg); + } + 100% { + -webkit-transform: rotate(359deg); + transform: rotate(359deg); + } +} +.fa-rotate-90 { + filter: progid:DXImageTransform.Microsoft.BasicImage(rotation=1); + -webkit-transform: rotate(90deg); + -moz-transform: rotate(90deg); + -ms-transform: rotate(90deg); + -o-transform: rotate(90deg); + transform: rotate(90deg); +} +.fa-rotate-180 { + filter: progid:DXImageTransform.Microsoft.BasicImage(rotation=2); + -webkit-transform: rotate(180deg); + -moz-transform: rotate(180deg); + -ms-transform: rotate(180deg); + -o-transform: rotate(180deg); + transform: rotate(180deg); +} +.fa-rotate-270 { + filter: progid:DXImageTransform.Microsoft.BasicImage(rotation=3); + -webkit-transform: rotate(270deg); + -moz-transform: rotate(270deg); + -ms-transform: rotate(270deg); + -o-transform: rotate(270deg); + transform: rotate(270deg); +} +.fa-flip-horizontal { + filter: progid:DXImageTransform.Microsoft.BasicImage(rotation=0, mirror=1); + -webkit-transform: scale(-1, 1); + -moz-transform: scale(-1, 1); + -ms-transform: scale(-1, 1); + -o-transform: scale(-1, 1); + transform: scale(-1, 1); +} +.fa-flip-vertical { + filter: progid:DXImageTransform.Microsoft.BasicImage(rotation=2, mirror=1); + -webkit-transform: scale(1, -1); + -moz-transform: scale(1, -1); + -ms-transform: scale(1, -1); + -o-transform: scale(1, -1); + transform: scale(1, -1); +} +.fa-stack { + position: relative; + display: inline-block; + width: 2em; + height: 2em; + line-height: 2em; + vertical-align: middle; +} +.fa-stack-1x, +.fa-stack-2x { + position: absolute; + left: 0; + width: 100%; + text-align: center; +} +.fa-stack-1x { + line-height: inherit; +} +.fa-stack-2x { + font-size: 2em; +} +.fa-inverse { + color: #fff; +} +.fa-glass:before { + content: "\f000"; +} +.fa-music:before { + content: "\f001"; +} +.fa-search:before { + content: "\f002"; +} +.fa-envelope-o:before { + content: "\f003"; +} +.fa-heart:before { + content: "\f004"; +} +.fa-star:before { + content: "\f005"; +} +.fa-star-o:before { + content: "\f006"; +} +.fa-user:before { + content: "\f007"; +} +.fa-film:before { + content: "\f008"; +} +.fa-th-large:before { + content: "\f009"; +} +.fa-th:before { + content: "\f00a"; +} +.fa-th-list:before { + content: "\f00b"; +} +.fa-check:before { + content: "\f00c"; +} +.fa-times:before { + content: "\f00d"; +} +.fa-search-plus:before { + content: "\f00e"; +} +.fa-search-minus:before { + content: "\f010"; +} +.fa-power-off:before { + content: "\f011"; +} +.fa-signal:before { + content: "\f012"; +} +.fa-gear:before, +.fa-cog:before { + content: "\f013"; +} +.fa-trash-o:before { + content: "\f014"; +} +.fa-home:before { + content: "\f015"; +} +.fa-file-o:before { + content: "\f016"; +} +.fa-clock-o:before { + content: "\f017"; +} +.fa-road:before { + content: "\f018"; +} +.fa-download:before { + content: "\f019"; +} +.fa-arrow-circle-o-down:before { + content: "\f01a"; +} +.fa-arrow-circle-o-up:before { + content: "\f01b"; +} +.fa-inbox:before { + content: "\f01c"; +} +.fa-play-circle-o:before { + content: "\f01d"; +} +.fa-rotate-right:before, +.fa-repeat:before { + content: "\f01e"; +} +.fa-refresh:before { + content: "\f021"; +} +.fa-list-alt:before { + content: "\f022"; +} +.fa-lock:before { + content: "\f023"; +} +.fa-flag:before { + content: "\f024"; +} +.fa-headphones:before { + content: "\f025"; +} +.fa-volume-off:before { + content: "\f026"; +} +.fa-volume-down:before { + content: "\f027"; +} +.fa-volume-up:before { + content: "\f028"; +} +.fa-qrcode:before { + content: "\f029"; +} +.fa-barcode:before { + content: "\f02a"; +} +.fa-tag:before { + content: "\f02b"; +} +.fa-tags:before { + content: "\f02c"; +} +.fa-book:before { + content: "\f02d"; +} +.fa-bookmark:before { + content: "\f02e"; +} +.fa-print:before { + content: "\f02f"; +} +.fa-camera:before { + content: "\f030"; +} +.fa-font:before { + content: "\f031"; +} +.fa-bold:before { + content: "\f032"; +} +.fa-italic:before { + content: "\f033"; +} +.fa-text-height:before { + content: "\f034"; +} +.fa-text-width:before { + content: "\f035"; +} +.fa-align-left:before { + content: "\f036"; +} +.fa-align-center:before { + content: "\f037"; +} +.fa-align-right:before { + content: "\f038"; +} +.fa-align-justify:before { + content: "\f039"; +} +.fa-list:before { + content: "\f03a"; +} +.fa-dedent:before, +.fa-outdent:before { + content: "\f03b"; +} +.fa-indent:before { + content: "\f03c"; +} +.fa-video-camera:before { + content: "\f03d"; +} +.fa-photo:before, +.fa-image:before, +.fa-picture-o:before { + content: "\f03e"; +} +.fa-pencil:before { + content: "\f040"; +} +.fa-map-marker:before { + content: "\f041"; +} +.fa-adjust:before { + content: "\f042"; +} +.fa-tint:before { + content: "\f043"; +} +.fa-edit:before, +.fa-pencil-square-o:before { + content: "\f044"; +} +.fa-share-square-o:before { + content: "\f045"; +} +.fa-check-square-o:before { + content: "\f046"; +} +.fa-arrows:before { + content: "\f047"; +} +.fa-step-backward:before { + content: "\f048"; +} +.fa-fast-backward:before { + content: "\f049"; +} +.fa-backward:before { + content: "\f04a"; +} +.fa-play:before { + content: "\f04b"; +} +.fa-pause:before { + content: "\f04c"; +} +.fa-stop:before { + content: "\f04d"; +} +.fa-forward:before { + content: "\f04e"; +} +.fa-fast-forward:before { + content: "\f050"; +} +.fa-step-forward:before { + content: "\f051"; +} +.fa-eject:before { + content: "\f052"; +} +.fa-chevron-left:before { + content: "\f053"; +} +.fa-chevron-right:before { + content: "\f054"; +} +.fa-plus-circle:before { + content: "\f055"; +} +.fa-minus-circle:before { + content: "\f056"; +} +.fa-times-circle:before { + content: "\f057"; +} +.fa-check-circle:before { + content: "\f058"; +} +.fa-question-circle:before { + content: "\f059"; +} +.fa-info-circle:before { + content: "\f05a"; +} +.fa-crosshairs:before { + content: "\f05b"; +} +.fa-times-circle-o:before { + content: "\f05c"; +} +.fa-check-circle-o:before { + content: "\f05d"; +} +.fa-ban:before { + content: "\f05e"; +} +.fa-arrow-left:before { + content: "\f060"; +} +.fa-arrow-right:before { + content: "\f061"; +} +.fa-arrow-up:before { + content: "\f062"; +} +.fa-arrow-down:before { + content: "\f063"; +} +.fa-mail-forward:before, +.fa-share:before { + content: "\f064"; +} +.fa-expand:before { + content: "\f065"; +} +.fa-compress:before { + content: "\f066"; +} +.fa-plus:before { + content: "\f067"; +} +.fa-minus:before { + content: "\f068"; +} +.fa-asterisk:before { + content: "\f069"; +} +.fa-exclamation-circle:before { + content: "\f06a"; +} +.fa-gift:before { + content: "\f06b"; +} +.fa-leaf:before { + content: "\f06c"; +} +.fa-fire:before { + content: "\f06d"; +} +.fa-eye:before { + content: "\f06e"; +} +.fa-eye-slash:before { + content: "\f070"; +} +.fa-warning:before, +.fa-exclamation-triangle:before { + content: "\f071"; +} +.fa-plane:before { + content: "\f072"; +} +.fa-calendar:before { + content: "\f073"; +} +.fa-random:before { + content: "\f074"; +} +.fa-comment:before { + content: "\f075"; +} +.fa-magnet:before { + content: "\f076"; +} +.fa-chevron-up:before { + content: "\f077"; +} +.fa-chevron-down:before { + content: "\f078"; +} +.fa-retweet:before { + content: "\f079"; +} +.fa-shopping-cart:before { + content: "\f07a"; +} +.fa-folder:before { + content: "\f07b"; +} +.fa-folder-open:before { + content: "\f07c"; +} +.fa-arrows-v:before { + content: "\f07d"; +} +.fa-arrows-h:before { + content: "\f07e"; +} +.fa-bar-chart-o:before { + content: "\f080"; +} +.fa-twitter-square:before { + content: "\f081"; +} +.fa-facebook-square:before { + content: "\f082"; +} +.fa-camera-retro:before { + content: "\f083"; +} +.fa-key:before { + content: "\f084"; +} +.fa-gears:before, +.fa-cogs:before { + content: "\f085"; +} +.fa-comments:before { + content: "\f086"; +} +.fa-thumbs-o-up:before { + content: "\f087"; +} +.fa-thumbs-o-down:before { + content: "\f088"; +} +.fa-star-half:before { + content: "\f089"; +} +.fa-heart-o:before { + content: "\f08a"; +} +.fa-sign-out:before { + content: "\f08b"; +} +.fa-linkedin-square:before { + content: "\f08c"; +} +.fa-thumb-tack:before { + content: "\f08d"; +} +.fa-external-link:before { + content: "\f08e"; +} +.fa-sign-in:before { + content: "\f090"; +} +.fa-trophy:before { + content: "\f091"; +} +.fa-github-square:before { + content: "\f092"; +} +.fa-upload:before { + content: "\f093"; +} +.fa-lemon-o:before { + content: "\f094"; +} +.fa-phone:before { + content: "\f095"; +} +.fa-square-o:before { + content: "\f096"; +} +.fa-bookmark-o:before { + content: "\f097"; +} +.fa-phone-square:before { + content: "\f098"; +} +.fa-twitter:before { + content: "\f099"; +} +.fa-facebook:before { + content: "\f09a"; +} +.fa-github:before { + content: "\f09b"; +} +.fa-unlock:before { + content: "\f09c"; +} +.fa-credit-card:before { + content: "\f09d"; +} +.fa-rss:before { + content: "\f09e"; +} +.fa-hdd-o:before { + content: "\f0a0"; +} +.fa-bullhorn:before { + content: "\f0a1"; +} +.fa-bell:before { + content: "\f0f3"; +} +.fa-certificate:before { + content: "\f0a3"; +} +.fa-hand-o-right:before { + content: "\f0a4"; +} +.fa-hand-o-left:before { + content: "\f0a5"; +} +.fa-hand-o-up:before { + content: "\f0a6"; +} +.fa-hand-o-down:before { + content: "\f0a7"; +} +.fa-arrow-circle-left:before { + content: "\f0a8"; +} +.fa-arrow-circle-right:before { + content: "\f0a9"; +} +.fa-arrow-circle-up:before { + content: "\f0aa"; +} +.fa-arrow-circle-down:before { + content: "\f0ab"; +} +.fa-globe:before { + content: "\f0ac"; +} +.fa-wrench:before { + content: "\f0ad"; +} +.fa-tasks:before { + content: "\f0ae"; +} +.fa-filter:before { + content: "\f0b0"; +} +.fa-briefcase:before { + content: "\f0b1"; +} +.fa-arrows-alt:before { + content: "\f0b2"; +} +.fa-group:before, +.fa-users:before { + content: "\f0c0"; +} +.fa-chain:before, +.fa-link:before { + content: "\f0c1"; +} +.fa-cloud:before { + content: "\f0c2"; +} +.fa-flask:before { + content: "\f0c3"; +} +.fa-cut:before, +.fa-scissors:before { + content: "\f0c4"; +} +.fa-copy:before, +.fa-files-o:before { + content: "\f0c5"; +} +.fa-paperclip:before { + content: "\f0c6"; +} +.fa-save:before, +.fa-floppy-o:before { + content: "\f0c7"; +} +.fa-square:before { + content: "\f0c8"; +} +.fa-navicon:before, +.fa-reorder:before, +.fa-bars:before { + content: "\f0c9"; +} +.fa-list-ul:before { + content: "\f0ca"; +} +.fa-list-ol:before { + content: "\f0cb"; +} +.fa-strikethrough:before { + content: "\f0cc"; +} +.fa-underline:before { + content: "\f0cd"; +} +.fa-table:before { + content: "\f0ce"; +} +.fa-magic:before { + content: "\f0d0"; +} +.fa-truck:before { + content: "\f0d1"; +} +.fa-pinterest:before { + content: "\f0d2"; +} +.fa-pinterest-square:before { + content: "\f0d3"; +} +.fa-google-plus-square:before { + content: "\f0d4"; +} +.fa-google-plus:before { + content: "\f0d5"; +} +.fa-money:before { + content: "\f0d6"; +} +.fa-caret-down:before { + content: "\f0d7"; +} +.fa-caret-up:before { + content: "\f0d8"; +} +.fa-caret-left:before { + content: "\f0d9"; +} +.fa-caret-right:before { + content: "\f0da"; +} +.fa-columns:before { + content: "\f0db"; +} +.fa-unsorted:before, +.fa-sort:before { + content: "\f0dc"; +} +.fa-sort-down:before, +.fa-sort-desc:before { + content: "\f0dd"; +} +.fa-sort-up:before, +.fa-sort-asc:before { + content: "\f0de"; +} +.fa-envelope:before { + content: "\f0e0"; +} +.fa-linkedin:before { + content: "\f0e1"; +} +.fa-rotate-left:before, +.fa-undo:before { + content: "\f0e2"; +} +.fa-legal:before, +.fa-gavel:before { + content: "\f0e3"; +} +.fa-dashboard:before, +.fa-tachometer:before { + content: "\f0e4"; +} +.fa-comment-o:before { + content: "\f0e5"; +} +.fa-comments-o:before { + content: "\f0e6"; +} +.fa-flash:before, +.fa-bolt:before { + content: "\f0e7"; +} +.fa-sitemap:before { + content: "\f0e8"; +} +.fa-umbrella:before { + content: "\f0e9"; +} +.fa-paste:before, +.fa-clipboard:before { + content: "\f0ea"; +} +.fa-lightbulb-o:before { + content: "\f0eb"; +} +.fa-exchange:before { + content: "\f0ec"; +} +.fa-cloud-download:before { + content: "\f0ed"; +} +.fa-cloud-upload:before { + content: "\f0ee"; +} +.fa-user-md:before { + content: "\f0f0"; +} +.fa-stethoscope:before { + content: "\f0f1"; +} +.fa-suitcase:before { + content: "\f0f2"; +} +.fa-bell-o:before { + content: "\f0a2"; +} +.fa-coffee:before { + content: "\f0f4"; +} +.fa-cutlery:before { + content: "\f0f5"; +} +.fa-file-text-o:before { + content: "\f0f6"; +} +.fa-building-o:before { + content: "\f0f7"; +} +.fa-hospital-o:before { + content: "\f0f8"; +} +.fa-ambulance:before { + content: "\f0f9"; +} +.fa-medkit:before { + content: "\f0fa"; +} +.fa-fighter-jet:before { + content: "\f0fb"; +} +.fa-beer:before { + content: "\f0fc"; +} +.fa-h-square:before { + content: "\f0fd"; +} +.fa-plus-square:before { + content: "\f0fe"; +} +.fa-angle-double-left:before { + content: "\f100"; +} +.fa-angle-double-right:before { + content: "\f101"; +} +.fa-angle-double-up:before { + content: "\f102"; +} +.fa-angle-double-down:before { + content: "\f103"; +} +.fa-angle-left:before { + content: "\f104"; +} +.fa-angle-right:before { + content: "\f105"; +} +.fa-angle-up:before { + content: "\f106"; +} +.fa-angle-down:before { + content: "\f107"; +} +.fa-desktop:before { + content: "\f108"; +} +.fa-laptop:before { + content: "\f109"; +} +.fa-tablet:before { + content: "\f10a"; +} +.fa-mobile-phone:before, +.fa-mobile:before { + content: "\f10b"; +} +.fa-circle-o:before { + content: "\f10c"; +} +.fa-quote-left:before { + content: "\f10d"; +} +.fa-quote-right:before { + content: "\f10e"; +} +.fa-spinner:before { + content: "\f110"; +} +.fa-circle:before { + content: "\f111"; +} +.fa-mail-reply:before, +.fa-reply:before { + content: "\f112"; +} +.fa-github-alt:before { + content: "\f113"; +} +.fa-folder-o:before { + content: "\f114"; +} +.fa-folder-open-o:before { + content: "\f115"; +} +.fa-smile-o:before { + content: "\f118"; +} +.fa-frown-o:before { + content: "\f119"; +} +.fa-meh-o:before { + content: "\f11a"; +} +.fa-gamepad:before { + content: "\f11b"; +} +.fa-keyboard-o:before { + content: "\f11c"; +} +.fa-flag-o:before { + content: "\f11d"; +} +.fa-flag-checkered:before { + content: "\f11e"; +} +.fa-terminal:before { + content: "\f120"; +} +.fa-code:before { + content: "\f121"; +} +.fa-mail-reply-all:before, +.fa-reply-all:before { + content: "\f122"; +} +.fa-star-half-empty:before, +.fa-star-half-full:before, +.fa-star-half-o:before { + content: "\f123"; +} +.fa-location-arrow:before { + content: "\f124"; +} +.fa-crop:before { + content: "\f125"; +} +.fa-code-fork:before { + content: "\f126"; +} +.fa-unlink:before, +.fa-chain-broken:before { + content: "\f127"; +} +.fa-question:before { + content: "\f128"; +} +.fa-info:before { + content: "\f129"; +} +.fa-exclamation:before { + content: "\f12a"; +} +.fa-superscript:before { + content: "\f12b"; +} +.fa-subscript:before { + content: "\f12c"; +} +.fa-eraser:before { + content: "\f12d"; +} +.fa-puzzle-piece:before { + content: "\f12e"; +} +.fa-microphone:before { + content: "\f130"; +} +.fa-microphone-slash:before { + content: "\f131"; +} +.fa-shield:before { + content: "\f132"; +} +.fa-calendar-o:before { + content: "\f133"; +} +.fa-fire-extinguisher:before { + content: "\f134"; +} +.fa-rocket:before { + content: "\f135"; +} +.fa-maxcdn:before { + content: "\f136"; +} +.fa-chevron-circle-left:before { + content: "\f137"; +} +.fa-chevron-circle-right:before { + content: "\f138"; +} +.fa-chevron-circle-up:before { + content: "\f139"; +} +.fa-chevron-circle-down:before { + content: "\f13a"; +} +.fa-html5:before { + content: "\f13b"; +} +.fa-css3:before { + content: "\f13c"; +} +.fa-anchor:before { + content: "\f13d"; +} +.fa-unlock-alt:before { + content: "\f13e"; +} +.fa-bullseye:before { + content: "\f140"; +} +.fa-ellipsis-h:before { + content: "\f141"; +} +.fa-ellipsis-v:before { + content: "\f142"; +} +.fa-rss-square:before { + content: "\f143"; +} +.fa-play-circle:before { + content: "\f144"; +} +.fa-ticket:before { + content: "\f145"; +} +.fa-minus-square:before { + content: "\f146"; +} +.fa-minus-square-o:before { + content: "\f147"; +} +.fa-level-up:before { + content: "\f148"; +} +.fa-level-down:before { + content: "\f149"; +} +.fa-check-square:before { + content: "\f14a"; +} +.fa-pencil-square:before { + content: "\f14b"; +} +.fa-external-link-square:before { + content: "\f14c"; +} +.fa-share-square:before { + content: "\f14d"; +} +.fa-compass:before { + content: "\f14e"; +} +.fa-toggle-down:before, +.fa-caret-square-o-down:before { + content: "\f150"; +} +.fa-toggle-up:before, +.fa-caret-square-o-up:before { + content: "\f151"; +} +.fa-toggle-right:before, +.fa-caret-square-o-right:before { + content: "\f152"; +} +.fa-euro:before, +.fa-eur:before { + content: "\f153"; +} +.fa-gbp:before { + content: "\f154"; +} +.fa-dollar:before, +.fa-usd:before { + content: "\f155"; +} +.fa-rupee:before, +.fa-inr:before { + content: "\f156"; +} +.fa-cny:before, +.fa-rmb:before, +.fa-yen:before, +.fa-jpy:before { + content: "\f157"; +} +.fa-ruble:before, +.fa-rouble:before, +.fa-rub:before { + content: "\f158"; +} +.fa-won:before, +.fa-krw:before { + content: "\f159"; +} +.fa-bitcoin:before, +.fa-btc:before { + content: "\f15a"; +} +.fa-file:before { + content: "\f15b"; +} +.fa-file-text:before { + content: "\f15c"; +} +.fa-sort-alpha-asc:before { + content: "\f15d"; +} +.fa-sort-alpha-desc:before { + content: "\f15e"; +} +.fa-sort-amount-asc:before { + content: "\f160"; +} +.fa-sort-amount-desc:before { + content: "\f161"; +} +.fa-sort-numeric-asc:before { + content: "\f162"; +} +.fa-sort-numeric-desc:before { + content: "\f163"; +} +.fa-thumbs-up:before { + content: "\f164"; +} +.fa-thumbs-down:before { + content: "\f165"; +} +.fa-youtube-square:before { + content: "\f166"; +} +.fa-youtube:before { + content: "\f167"; +} +.fa-xing:before { + content: "\f168"; +} +.fa-xing-square:before { + content: "\f169"; +} +.fa-youtube-play:before { + content: "\f16a"; +} +.fa-dropbox:before { + content: "\f16b"; +} +.fa-stack-overflow:before { + content: "\f16c"; +} +.fa-instagram:before { + content: "\f16d"; +} +.fa-flickr:before { + content: "\f16e"; +} +.fa-adn:before { + content: "\f170"; +} +.fa-bitbucket:before { + content: "\f171"; +} +.fa-bitbucket-square:before { + content: "\f172"; +} +.fa-tumblr:before { + content: "\f173"; +} +.fa-tumblr-square:before { + content: "\f174"; +} +.fa-long-arrow-down:before { + content: "\f175"; +} +.fa-long-arrow-up:before { + content: "\f176"; +} +.fa-long-arrow-left:before { + content: "\f177"; +} +.fa-long-arrow-right:before { + content: "\f178"; +} +.fa-apple:before { + content: "\f179"; +} +.fa-windows:before { + content: "\f17a"; +} +.fa-android:before { + content: "\f17b"; +} +.fa-linux:before { + content: "\f17c"; +} +.fa-dribbble:before { + content: "\f17d"; +} +.fa-skype:before { + content: "\f17e"; +} +.fa-foursquare:before { + content: "\f180"; +} +.fa-trello:before { + content: "\f181"; +} +.fa-female:before { + content: "\f182"; +} +.fa-male:before { + content: "\f183"; +} +.fa-gittip:before { + content: "\f184"; +} +.fa-sun-o:before { + content: "\f185"; +} +.fa-moon-o:before { + content: "\f186"; +} +.fa-archive:before { + content: "\f187"; +} +.fa-bug:before { + content: "\f188"; +} +.fa-vk:before { + content: "\f189"; +} +.fa-weibo:before { + content: "\f18a"; +} +.fa-renren:before { + content: "\f18b"; +} +.fa-pagelines:before { + content: "\f18c"; +} +.fa-stack-exchange:before { + content: "\f18d"; +} +.fa-arrow-circle-o-right:before { + content: "\f18e"; +} +.fa-arrow-circle-o-left:before { + content: "\f190"; +} +.fa-toggle-left:before, +.fa-caret-square-o-left:before { + content: "\f191"; +} +.fa-dot-circle-o:before { + content: "\f192"; +} +.fa-wheelchair:before { + content: "\f193"; +} +.fa-vimeo-square:before { + content: "\f194"; +} +.fa-turkish-lira:before, +.fa-try:before { + content: "\f195"; +} +.fa-plus-square-o:before { + content: "\f196"; +} +.fa-space-shuttle:before { + content: "\f197"; +} +.fa-slack:before { + content: "\f198"; +} +.fa-envelope-square:before { + content: "\f199"; +} +.fa-wordpress:before { + content: "\f19a"; +} +.fa-openid:before { + content: "\f19b"; +} +.fa-institution:before, +.fa-bank:before, +.fa-university:before { + content: "\f19c"; +} +.fa-mortar-board:before, +.fa-graduation-cap:before { + content: "\f19d"; +} +.fa-yahoo:before { + content: "\f19e"; +} +.fa-google:before { + content: "\f1a0"; +} +.fa-reddit:before { + content: "\f1a1"; +} +.fa-reddit-square:before { + content: "\f1a2"; +} +.fa-stumbleupon-circle:before { + content: "\f1a3"; +} +.fa-stumbleupon:before { + content: "\f1a4"; +} +.fa-delicious:before { + content: "\f1a5"; +} +.fa-digg:before { + content: "\f1a6"; +} +.fa-pied-piper-square:before, +.fa-pied-piper:before { + content: "\f1a7"; +} +.fa-pied-piper-alt:before { + content: "\f1a8"; +} +.fa-drupal:before { + content: "\f1a9"; +} +.fa-joomla:before { + content: "\f1aa"; +} +.fa-language:before { + content: "\f1ab"; +} +.fa-fax:before { + content: "\f1ac"; +} +.fa-building:before { + content: "\f1ad"; +} +.fa-child:before { + content: "\f1ae"; +} +.fa-paw:before { + content: "\f1b0"; +} +.fa-spoon:before { + content: "\f1b1"; +} +.fa-cube:before { + content: "\f1b2"; +} +.fa-cubes:before { + content: "\f1b3"; +} +.fa-behance:before { + content: "\f1b4"; +} +.fa-behance-square:before { + content: "\f1b5"; +} +.fa-steam:before { + content: "\f1b6"; +} +.fa-steam-square:before { + content: "\f1b7"; +} +.fa-recycle:before { + content: "\f1b8"; +} +.fa-automobile:before, +.fa-car:before { + content: "\f1b9"; +} +.fa-cab:before, +.fa-taxi:before { + content: "\f1ba"; +} +.fa-tree:before { + content: "\f1bb"; +} +.fa-spotify:before { + content: "\f1bc"; +} +.fa-deviantart:before { + content: "\f1bd"; +} +.fa-soundcloud:before { + content: "\f1be"; +} +.fa-database:before { + content: "\f1c0"; +} +.fa-file-pdf-o:before { + content: "\f1c1"; +} +.fa-file-word-o:before { + content: "\f1c2"; +} +.fa-file-excel-o:before { + content: "\f1c3"; +} +.fa-file-powerpoint-o:before { + content: "\f1c4"; +} +.fa-file-photo-o:before, +.fa-file-picture-o:before, +.fa-file-image-o:before { + content: "\f1c5"; +} +.fa-file-zip-o:before, +.fa-file-archive-o:before { + content: "\f1c6"; +} +.fa-file-sound-o:before, +.fa-file-audio-o:before { + content: "\f1c7"; +} +.fa-file-movie-o:before, +.fa-file-video-o:before { + content: "\f1c8"; +} +.fa-file-code-o:before { + content: "\f1c9"; +} +.fa-vine:before { + content: "\f1ca"; +} +.fa-codepen:before { + content: "\f1cb"; +} +.fa-jsfiddle:before { + content: "\f1cc"; +} +.fa-life-bouy:before, +.fa-life-saver:before, +.fa-support:before, +.fa-life-ring:before { + content: "\f1cd"; +} +.fa-circle-o-notch:before { + content: "\f1ce"; +} +.fa-ra:before, +.fa-rebel:before { + content: "\f1d0"; +} +.fa-ge:before, +.fa-empire:before { + content: "\f1d1"; +} +.fa-git-square:before { + content: "\f1d2"; +} +.fa-git:before { + content: "\f1d3"; +} +.fa-hacker-news:before { + content: "\f1d4"; +} +.fa-tencent-weibo:before { + content: "\f1d5"; +} +.fa-qq:before { + content: "\f1d6"; +} +.fa-wechat:before, +.fa-weixin:before { + content: "\f1d7"; +} +.fa-send:before, +.fa-paper-plane:before { + content: "\f1d8"; +} +.fa-send-o:before, +.fa-paper-plane-o:before { + content: "\f1d9"; +} +.fa-history:before { + content: "\f1da"; +} +.fa-circle-thin:before { + content: "\f1db"; +} +.fa-header:before { + content: "\f1dc"; +} +.fa-paragraph:before { + content: "\f1dd"; +} +.fa-sliders:before { + content: "\f1de"; +} +.fa-share-alt:before { + content: "\f1e0"; +} +.fa-share-alt-square:before { + content: "\f1e1"; +} +.fa-bomb:before { + content: "\f1e2"; +} diff --git a/ui/ecobidas_ui/static/style.css b/ui/ecobidas_ui/static/css/main.css similarity index 100% rename from ui/ecobidas_ui/static/style.css rename to ui/ecobidas_ui/static/css/main.css diff --git a/ui/ecobidas_ui/static/favicon.ico b/ui/ecobidas_ui/static/favicon.ico new file mode 100644 index 0000000000000000000000000000000000000000..be74abd69ad6a32de7375df13cab9354798e328f GIT binary patch literal 766 zcmc(dze~eV5XUd2fg&jH87YDYDQKxq1{4b-_ydP-wqS9vgGh17QXQQAwOE{VaBvi* zmu^z9t({y-&1ey8Y_x;?x+`BviV9;aRjMgZ8M*!jgkRrFqSI9;F zHyfX@Az|AvVmn~YWWZP`0&JWEY~BFm?*Vq}VD7&_%x%MP$p`D`4JMC!K|B7pt?Mmp zUJAB7rxMXS6=!P+AtLU9V)J#61WPxwipRXCHO{BJ`l{m53#=t97a!znv~vfmr|AaP zRGIT7#0FyJy3Z*hL{GQp-0TRhX8UzZ)+>%?mK0^goaX4Q;x +{% block page_title %}500 Error - Unauthorized{% endblock %} + +{% block content %} +
    +
    +
    + +

    + You are not authorized to see this page. Please + log in or + create a new account. +

    +

    + Want to go home instead? +

    +
    +
    +
    +{% endblock %} diff --git a/ui/ecobidas_ui/templates/404.html b/ui/ecobidas_ui/templates/404.html index c196c766..7e446981 100644 --- a/ui/ecobidas_ui/templates/404.html +++ b/ui/ecobidas_ui/templates/404.html @@ -1,14 +1,16 @@ -{% extends 'base.html' %} +{% extends 'layout/base.html' %} -{% block title %} 404 Error - Page Not Found {% endblock %} +{% block title %}404 Error - Page Not Found{% endblock %} {% block content %}
    -
    -

    Page not found (Error 404)

    - -

    Go to home page

    +
    + +

    Sorry, that page doesn't exist.

    +

    + Want to go home instead? +

    diff --git a/ui/ecobidas_ui/templates/500.html b/ui/ecobidas_ui/templates/500.html index 54defb2f..b3594f29 100644 --- a/ui/ecobidas_ui/templates/500.html +++ b/ui/ecobidas_ui/templates/500.html @@ -1,14 +1,19 @@ -{% extends 'base.html' %} +{% extends 'layout/base.html' %} -{% block title %} 500 Error - Internal Server Error {% endblock %} +{% block title %}500 Error - Internal Server Error{% endblock %} {% block content %}
    -
    -

    Internal server error (500)

    +
    -

    Go to search page

    +

    + Sorry, something went wrong on our system. Don't panic, we are fixing + it! Please try again later. +

    +

    + Want to go home instead? +

    diff --git a/ui/ecobidas_ui/templates/auth/login.html b/ui/ecobidas_ui/templates/auth/login.html index f40b0047..6cfe371d 100644 --- a/ui/ecobidas_ui/templates/auth/login.html +++ b/ui/ecobidas_ui/templates/auth/login.html @@ -1,4 +1,4 @@ -{% extends 'base.html' %} +{% extends 'layout/base.html' %} {% block content %} diff --git a/ui/ecobidas_ui/templates/auth/register.html b/ui/ecobidas_ui/templates/auth/register.html index e36a1af7..b5cbc764 100644 --- a/ui/ecobidas_ui/templates/auth/register.html +++ b/ui/ecobidas_ui/templates/auth/register.html @@ -1,4 +1,4 @@ -{% extends 'base.html' %} +{% extends 'layout/base.html' %} {% block content %} diff --git a/ui/ecobidas_ui/templates/base.html b/ui/ecobidas_ui/templates/base.html deleted file mode 100644 index dad901a5..00000000 --- a/ui/ecobidas_ui/templates/base.html +++ /dev/null @@ -1,196 +0,0 @@ - - - - - - - {% block title %} {% endblock %} - - {{ bootstrap.load_css() }} - - - - - - - - - - - - - - - - - - - -
    -
    -
    - -
    -
    -
    - -
    -
    - {% with messages = get_flashed_messages() %} {% if messages %} {% for - message in messages %} - - {% endfor %} {% endif %} {% endwith %} -
    -
    - -
    -
    - -
    - -
    -
    - {% block content %} {% endblock %} -
    -
    - - - {{ bootstrap.load_js() }} -
    - - -
    -
    -
    -
    -
    - eCobidas -
    -
    - - -
    -
    -
    -
    -
    - diff --git a/ui/ecobidas_ui/templates/layout/base.html b/ui/ecobidas_ui/templates/layout/base.html new file mode 100644 index 00000000..520a01b2 --- /dev/null +++ b/ui/ecobidas_ui/templates/layout/base.html @@ -0,0 +1,92 @@ + + + + + + + {% block title %} {% endblock %} + + + + + {{ bootstrap.load_css() }} {% assets "css" %} + + {% endassets %} + + + + + {% include "layout/svg.html" %} + +
    +
    +
    + +
    +
    +
    + + {% with messages = get_flashed_messages() %} + + {% if messages %} + + {% for message in messages %} +
    +
    + +
    +
    + {% endfor %} + + {% endif %} + + {% endwith %} + +
    + {% include "layout/nav.html" %} + +
    +
    + {% block content %} + + {% endblock %} +
    +
    + + + {{ bootstrap.load_js() }} +
    + + + {% include "layout/footer.html" %} + diff --git a/ui/ecobidas_ui/templates/layout/footer.html b/ui/ecobidas_ui/templates/layout/footer.html new file mode 100644 index 00000000..60b14cd8 --- /dev/null +++ b/ui/ecobidas_ui/templates/layout/footer.html @@ -0,0 +1,25 @@ +
    +
    +
    +
    +
    eCobidas
    +
    + + +
    +
    +
    +
    +
    diff --git a/ui/ecobidas_ui/templates/layout/nav.html b/ui/ecobidas_ui/templates/layout/nav.html new file mode 100644 index 00000000..ef4e2ad9 --- /dev/null +++ b/ui/ecobidas_ui/templates/layout/nav.html @@ -0,0 +1,82 @@ +
    + +
    diff --git a/ui/ecobidas_ui/templates/layout/svg.html b/ui/ecobidas_ui/templates/layout/svg.html new file mode 100644 index 00000000..655bc1d1 --- /dev/null +++ b/ui/ecobidas_ui/templates/layout/svg.html @@ -0,0 +1,21 @@ + + + + + + + + + + + diff --git a/ui/ecobidas_ui/templates/protocol.html b/ui/ecobidas_ui/templates/protocol.html index 087d111b..1f7408b9 100644 --- a/ui/ecobidas_ui/templates/protocol.html +++ b/ui/ecobidas_ui/templates/protocol.html @@ -1,4 +1,6 @@ -{% extends 'base.html' %} {% from 'bootstrap5/form.html' import render_form %} +{% extends 'layout/base.html' %} + +{% from 'bootstrap5/form.html' import render_form %} {% block title %} eCOBIDAS - {{ protocol_pref_label }} {% endblock %} @@ -9,39 +11,15 @@

    {{ protocol_pref_label }}

    -
    - -
    + {% include "side_nav.html" %}
    +
    - {% if landing_page %} {{ protocol_preamble }} {{ landing_page }} {% else - %} + {% if landing_page %} {{ protocol_preamble|safe }} {{ landing_page|safe }} + {% else %}

    {{ activity_pref_label }}

    + + {% if form %}

    {{ activity_pref_label }}

    >{{ completed_items }} / {{ nb_items }} items completed

    - - {{ activity_preamble }} + {% endif %} {{ activity_preamble|safe }}
    @@ -72,11 +49,12 @@
    participants.tsv file formatted according to the BIDS specification along with a participants.json file containing column annotations generated by - the neurobagel annotation tool.

    @@ -95,6 +73,7 @@
    *_bold.json file formatted according to the BIDS specification containing the metadata for your fMRI runs. @@ -105,14 +84,14 @@
    + {% if form %}
    {{ render_form(form) }}
    - - {% endif %} + {% endif %} {% endif %}
    diff --git a/ui/ecobidas_ui/templates/about.html b/ui/ecobidas_ui/templates/public/about.html similarity index 72% rename from ui/ecobidas_ui/templates/about.html rename to ui/ecobidas_ui/templates/public/about.html index a36f35d6..b581b65d 100644 --- a/ui/ecobidas_ui/templates/about.html +++ b/ui/ecobidas_ui/templates/public/about.html @@ -1,4 +1,4 @@ -{% extends 'base.html' %} +{% extends 'layout/base.html' %} {% block title %} eCOBIDAS - About {% endblock %} @@ -10,22 +10,28 @@

    Have any questions? Something is missing? Let us know.

    • drop us an email on our - google group.
    • open an issue this - github repository. + github repository.
    • leave a message on the cobidas_checklist channel on the brainhack channel. @@ -42,7 +48,9 @@

      Why this project?

      Follow the link if you want to know more about the - motivations behind this project.

      @@ -50,12 +58,17 @@

      Background

      This checklist is a project to make a user friendly checklist out the best practices - report of - the Committee on Best Practices in Data Analysis and Sharing (report + of the Committee on Best Practices in Data Analysis and Sharing (COBIDAS) of the - Organization for Human Brain Mapping.

      @@ -63,7 +76,9 @@

      Background

      This is very much of a work in progress but the next step is to expand the list to cover all the items of the COBIDAS report for fMRI as well as for the recent - extension to EEG and MEG. + extension to EEG and MEG.

      Want to help?

      @@ -76,12 +91,16 @@

      Want to help?

      Want to know more?

      Most of the information concerning this project can be found on this - github repository. + github repository.

      If you want to be kept posted about the progress of the project, you can join our - google group

      @@ -91,6 +110,7 @@

      Want to know more?

      cobidas_checklist channel on the brainhack Want to know more?

      - There is also an OSF project to - centralize all the information and repos. + There is also an OSF + project to centralize all the information and repos.

      We have a - list of short, middle, long term goals: if you are interested by any of those @@ -118,6 +140,7 @@

      Contributors

      The list of the people involved in this project can be found here.

      diff --git a/ui/ecobidas_ui/templates/public/faq.html b/ui/ecobidas_ui/templates/public/faq.html new file mode 100644 index 00000000..a004c667 --- /dev/null +++ b/ui/ecobidas_ui/templates/public/faq.html @@ -0,0 +1,36 @@ +{% extends "layout/base.html" %} {% block title %} eCOBIDAS - FAQ {% endblock %} +{% block content %} +
      +
      +
      + {% set count = [0] %} {% for s in data['sections'] %} +

      {{ s['name'] }}

      + {% for item in s['questions'] %} {% set _ = count.append(count.pop()+1) %} +
      +
      +

      + +

      +
      +
      {{ item['a']|safe }}
      +
      +
      +
      + {% endfor %} {% endfor %} +
      +
      + {% endblock %} +
      diff --git a/ui/ecobidas_ui/templates/index.html b/ui/ecobidas_ui/templates/public/index.html similarity index 96% rename from ui/ecobidas_ui/templates/index.html rename to ui/ecobidas_ui/templates/public/index.html index 7ae6f3a8..32c9b55a 100644 --- a/ui/ecobidas_ui/templates/index.html +++ b/ui/ecobidas_ui/templates/public/index.html @@ -1,4 +1,4 @@ -{% extends 'base.html' %} +{% extends 'layout/base.html' %} {% block title %} eCOBIDAS {% endblock %} diff --git a/ui/ecobidas_ui/templates/side_nav.html b/ui/ecobidas_ui/templates/side_nav.html new file mode 100644 index 00000000..0e9519b2 --- /dev/null +++ b/ui/ecobidas_ui/templates/side_nav.html @@ -0,0 +1,28 @@ +
      + +
      diff --git a/ui/ecobidas_ui/utils.py b/ui/ecobidas_ui/utils.py index 0a26adb2..75898d7f 100644 --- a/ui/ecobidas_ui/utils.py +++ b/ui/ecobidas_ui/utils.py @@ -6,6 +6,7 @@ import pandas as pd import requests +from flask import flash from markupsafe import escape from rich import print @@ -255,3 +256,10 @@ def extract_values_participants(df, json_content, target): return df[column].min() if target == "subject_age_max": return df[column].max() + + +def flash_errors(form, category="warning"): + """Flash all errors for a form.""" + for field, errors in form.errors.items(): + for error in errors: + flash(f"{getattr(form, field).label.text} - {error}", category) diff --git a/ui/pyproject.toml b/ui/pyproject.toml index fa0357b9..9d0c7cf6 100644 --- a/ui/pyproject.toml +++ b/ui/pyproject.toml @@ -7,10 +7,14 @@ authors = [{name = "Remi Gau"}] dependencies = [ "flask", "Flask-WTF", + "Flask-Assets", "bootstrap-flask", "pandas", "rich", - "requests" + "requests", + "Flask-Caching", + "Flask-DebugToolbar", + "environs" ] description = "UI for eCOBIDAS" license = {text = "GPL 3.0"} diff --git a/ui/requirements.txt b/ui/requirements.txt index 07a0ae39..302b83bb 100644 --- a/ui/requirements.txt +++ b/ui/requirements.txt @@ -4,6 +4,7 @@ # # pip-compile --output-file=requirements.txt --strip-extras pyproject.toml # +Flask-Assets blinker==1.8.2 # via flask bootstrap-flask==2.4.0 From b51104f651e7e0e2a439d5b003cc5cf3d551ee8b Mon Sep 17 00:00:00 2001 From: Remi Gau Date: Mon, 27 May 2024 21:44:18 +0200 Subject: [PATCH 20/31] refactor tests --- .flake8 | 2 +- ecobidas/generate_landing_page.py | 22 -- ecobidas/templates/contact.j2 | 16 - ecobidas/templates/how_to_use.j2 | 14 - ecobidas/templates/landing_page.j2 | 14 - ecobidas/templates/want_to_help.j2 | 6 - ecobidas/templates/want_to_know_more.j2 | 9 - ecobidas/templates/why_this_project.j2 | 11 - ecobidas/utils.py | 2 +- tests/data/protocols/test_schema.jsonld | 2 +- tests/test_generate_files.py | 6 - tests/test_utils.py | 4 +- ui/ecobidas_ui/app.py | 27 +- ui/ecobidas_ui/auth/__init__.py | 3 + ui/ecobidas_ui/{auth.py => auth/views.py} | 14 +- ui/ecobidas_ui/protocols/__init__.py | 3 + ui/ecobidas_ui/{ => protocols}/forms.py | 28 +- ui/ecobidas_ui/protocols/utils.py | 282 ++++++++++++++++++ .../{protocol.py => protocols/views.py} | 197 +++++++----- ui/ecobidas_ui/settings.py | 2 +- .../static/images/BIDS_logo_black.svg | 1 + ui/ecobidas_ui/templates/extra_forms.html | 51 ++++ ui/ecobidas_ui/templates/layout/base.html | 20 +- ui/ecobidas_ui/templates/layout/footer.html | 1 + ui/ecobidas_ui/templates/protocol.html | 69 +---- ui/ecobidas_ui/utils.py | 264 ---------------- ui/tests/__init__.py | 0 ui/tests/conftest.py | 41 --- ui/tests/data.sql | 8 - ui/tests/protocols/__init__.py | 0 ui/tests/{ => protocols}/test_utils.py | 33 +- 31 files changed, 561 insertions(+), 591 deletions(-) delete mode 100644 ecobidas/generate_landing_page.py delete mode 100644 ecobidas/templates/contact.j2 delete mode 100644 ecobidas/templates/how_to_use.j2 delete mode 100644 ecobidas/templates/landing_page.j2 delete mode 100644 ecobidas/templates/want_to_help.j2 delete mode 100644 ecobidas/templates/want_to_know_more.j2 delete mode 100644 ecobidas/templates/why_this_project.j2 create mode 100644 ui/ecobidas_ui/auth/__init__.py rename ui/ecobidas_ui/{auth.py => auth/views.py} (87%) create mode 100644 ui/ecobidas_ui/protocols/__init__.py rename ui/ecobidas_ui/{ => protocols}/forms.py (87%) create mode 100644 ui/ecobidas_ui/protocols/utils.py rename ui/ecobidas_ui/{protocol.py => protocols/views.py} (58%) create mode 100644 ui/ecobidas_ui/static/images/BIDS_logo_black.svg create mode 100644 ui/ecobidas_ui/templates/extra_forms.html create mode 100644 ui/tests/__init__.py delete mode 100644 ui/tests/conftest.py delete mode 100644 ui/tests/data.sql create mode 100644 ui/tests/protocols/__init__.py rename ui/tests/{ => protocols}/test_utils.py (58%) diff --git a/.flake8 b/.flake8 index 3133b205..46a95fe5 100644 --- a/.flake8 +++ b/.flake8 @@ -9,7 +9,7 @@ max-line-length = 150 max_complexity = 15 max_function_length = 150 max_parameters_amount = 10 -max_returns_amount = 6 +max_returns_amount = 7 # ----------------------- errors to include / exclude ----------------------- diff --git a/ecobidas/generate_landing_page.py b/ecobidas/generate_landing_page.py deleted file mode 100644 index a9c70347..00000000 --- a/ecobidas/generate_landing_page.py +++ /dev/null @@ -1,22 +0,0 @@ -"""Generates a typical landing page in english for an app.""" - -from pathlib import Path - -from ecobidas.template_manager import TemplateManager - - -def main(output_dir: Path | None = None) -> None: - if output_dir is None: - output_dir = Path() / "output" - - TemplateManager.initialize() - - template = TemplateManager.env.get_template("landing_page.j2") - - rendered_template = template.render() - with open(output_dir / "landing_page.html", "w") as out: - out.write(f"{rendered_template}") - - -if __name__ == "__main__": - main() diff --git a/ecobidas/templates/contact.j2 b/ecobidas/templates/contact.j2 deleted file mode 100644 index b63ed38e..00000000 --- a/ecobidas/templates/contact.j2 +++ /dev/null @@ -1,16 +0,0 @@ -

      Have any questions? Something is missing? Let us know.

      - diff --git a/ecobidas/templates/how_to_use.j2 b/ecobidas/templates/how_to_use.j2 deleted file mode 100644 index b8274636..00000000 --- a/ecobidas/templates/how_to_use.j2 +++ /dev/null @@ -1,14 +0,0 @@ -

      How to use it

      -

      - You can navigate each section on the left and then answer the questions - corresponding to your design, acquisition, analysis... - This is meant to make sure that you have not forgotten any of the essential - information in the methods and results parts of your article. -

      -

      - At the end, you can click on Export (bottom left) to get a zip file - containing machine readable jsonld files that captures information about - your method/results section: our next step is to use this to automate the - part of the methods writing and to submit the information alongside data - submission to data archives. -

      diff --git a/ecobidas/templates/landing_page.j2 b/ecobidas/templates/landing_page.j2 deleted file mode 100644 index af5a188c..00000000 --- a/ecobidas/templates/landing_page.j2 +++ /dev/null @@ -1,14 +0,0 @@ -
      -
      -

      Information Collection Protocol

      - {% include 'how_to_use.j2' %} - {% include 'contact.j2' %} - {% include 'why_this_project.j2' %} -

      Background

      - {% include 'want_to_help.j2' %} - {% include 'want_to_know_more.j2' %} -

      Contributors

      -

      License

      -

      The protocol is licensed CC-BY-4.0

      -
      -
      diff --git a/ecobidas/templates/want_to_help.j2 b/ecobidas/templates/want_to_help.j2 deleted file mode 100644 index 6ec752da..00000000 --- a/ecobidas/templates/want_to_help.j2 +++ /dev/null @@ -1,6 +0,0 @@ -

      Want to help?

      -

      - We are looking for people to give us feedback or help us move forward. - If you are interested, check our - documentation for contributors. -

      diff --git a/ecobidas/templates/want_to_know_more.j2 b/ecobidas/templates/want_to_know_more.j2 deleted file mode 100644 index 92588091..00000000 --- a/ecobidas/templates/want_to_know_more.j2 +++ /dev/null @@ -1,9 +0,0 @@ -

      Want to know more?

      -

      - Most of the information concerning this project can be found in - our documentation. -

      -

      - If you want to be kept posted about the progress of the project, - check our contact page -

      diff --git a/ecobidas/templates/why_this_project.j2 b/ecobidas/templates/why_this_project.j2 deleted file mode 100644 index 4814ea92..00000000 --- a/ecobidas/templates/why_this_project.j2 +++ /dev/null @@ -1,11 +0,0 @@ -

      Why this project?

      -

      - Poor methods and results description hinders the reproducibility and the replicability of research. - It also makes it hard to compare new and old results and generally increases inefficiency in the research process. - This project is built on the hope that improving methods and results reporting could improve our research. -

      -

      - Follow the link if you want to know more about the - motivations behind this project. -

      diff --git a/ecobidas/utils.py b/ecobidas/utils.py index fac70318..1cd21159 100644 --- a/ecobidas/utils.py +++ b/ecobidas/utils.py @@ -55,7 +55,7 @@ def get_landing_page(schema_info: dict[str, str]) -> str: if schema_info["landing_page"]: return schema_info["landing_page"] else: - return "../README_eCOBIDAS-en.md" + return "../README_eCOBIDAS-en.html" def get_schema_info(this_schema: str | Path) -> dict[str, str]: diff --git a/tests/data/protocols/test_schema.jsonld b/tests/data/protocols/test_schema.jsonld index 757d6169..66f2adc0 100644 --- a/tests/data/protocols/test_schema.jsonld +++ b/tests/data/protocols/test_schema.jsonld @@ -88,7 +88,7 @@ ] }, "landingPage": { - "@id": "../README_eCOBIDAS-en.md", + "@id": "../README_eCOBIDAS-en.html", "inLanguage": "en" } } diff --git a/tests/test_generate_files.py b/tests/test_generate_files.py index 56b4604a..e9dd0008 100644 --- a/tests/test_generate_files.py +++ b/tests/test_generate_files.py @@ -1,4 +1,3 @@ -from ecobidas.generate_landing_page import main as landing_page_main from ecobidas.macros import main as app_list_table_main @@ -6,8 +5,3 @@ def test_generate_table(tmp_path): app_list_table_main(tmp_path) assert (tmp_path / "apps_table.md").exists() assert (tmp_path / "preset_responses_table.md").exists() - - -def test_landing_page(tmp_path): - landing_page_main(tmp_path) - assert (tmp_path / "landing_page.html").exists() diff --git a/tests/test_utils.py b/tests/test_utils.py index 279f4092..864b35bb 100644 --- a/tests/test_utils.py +++ b/tests/test_utils.py @@ -38,8 +38,8 @@ def test_get_output_dir(tmp_path): "this_schema, filename", [ ("neurovault", "../README_eCOBIDAS-en.html"), - ("test", "../README_eCOBIDAS-en.md"), - ("pet", "../README_PET-en.md"), + ("test", "../README_eCOBIDAS-en.html"), + ("pet", "../README_PET-en.html"), ], ) def test_get_landing_page(this_schema, filename): diff --git a/ui/ecobidas_ui/app.py b/ui/ecobidas_ui/app.py index 099a6ca1..fb08aaf5 100644 --- a/ui/ecobidas_ui/app.py +++ b/ui/ecobidas_ui/app.py @@ -1,8 +1,11 @@ import logging import sys -from ecobidas_ui import auth, db, protocol, public -from ecobidas_ui.extensions import bootstrap, cache, csrf_protect, debug_toolbar +from ecobidas_ui import auth, db, protocols, public +from ecobidas_ui._version import version +from ecobidas_ui.extensions import bootstrap, csrf_protect + +# from ecobidas_ui.extensions import cache, debug_toolbar from ecobidas_ui.initializers.assets import init_assets from flask import Flask, flash, render_template @@ -22,15 +25,19 @@ def create_app(config_object="ecobidas_ui.settings"): register_errorhandlers(app) configure_logger(app) + @app.context_processor + def inject_version(): + return dict(version=version) + @app.route("/export") def export() -> str: - flash("Not implemented yet!") - return render_template("index.html") + flash("'Export' not implemented yet!", category="warning") + return render_template("public/index.html") @app.route("/generate") def generate() -> str: - flash("Not implemented yet!") - return render_template("index.html") + flash("'Generate' Not implemented yet!", category="warning") + return render_template("public/index.html") return app @@ -39,16 +46,16 @@ def register_extensions(app): """Register Flask extensions.""" bootstrap.init_app(app) csrf_protect.init_app(app) - cache.init_app(app) - debug_toolbar.init_app(app) + # cache.init_app(app) + # debug_toolbar.init_app(app) return None def register_blueprints(app): """Register Flask blueprints.""" app.register_blueprint(public.views.blueprint) - app.register_blueprint(auth.bp) - app.register_blueprint(protocol.bp) + app.register_blueprint(auth.views.blueprint) + app.register_blueprint(protocols.views.blueprint) return None diff --git a/ui/ecobidas_ui/auth/__init__.py b/ui/ecobidas_ui/auth/__init__.py new file mode 100644 index 00000000..05af8588 --- /dev/null +++ b/ui/ecobidas_ui/auth/__init__.py @@ -0,0 +1,3 @@ +"""The public module, including the homepage and user auth.""" + +from . import views # noqa diff --git a/ui/ecobidas_ui/auth.py b/ui/ecobidas_ui/auth/views.py similarity index 87% rename from ui/ecobidas_ui/auth.py rename to ui/ecobidas_ui/auth/views.py index 571eebac..30824f72 100644 --- a/ui/ecobidas_ui/auth.py +++ b/ui/ecobidas_ui/auth/views.py @@ -4,10 +4,10 @@ from flask import Blueprint, flash, g, redirect, render_template, request, session, url_for from werkzeug.security import check_password_hash, generate_password_hash -bp = Blueprint("auth", __name__, url_prefix="/auth") +blueprint = Blueprint("auth", __name__, url_prefix="/auth") -@bp.route("/register", methods=("GET", "POST")) +@blueprint.route("/register", methods=("GET", "POST")) def register(): if request.method == "POST": username = request.form["username"] @@ -32,12 +32,12 @@ def register(): else: return redirect(url_for("auth.login")) - flash(error) + flash(error, category="warning") return render_template("auth/register.html") -@bp.route("/login", methods=("GET", "POST")) +@blueprint.route("/login", methods=("GET", "POST")) def login(): if request.method == "POST": username = request.form["username"] @@ -56,12 +56,12 @@ def login(): session["user_id"] = user["id"] return redirect(url_for("index")) - flash(error) + flash(error, category="warning") return render_template("auth/login.html") -@bp.before_app_request +@blueprint.before_app_request def load_logged_in_user(): user_id = session.get("user_id") @@ -71,7 +71,7 @@ def load_logged_in_user(): g.user = get_db().execute("SELECT * FROM user WHERE id = ?", (user_id,)).fetchone() -@bp.route("/logout") +@blueprint.route("/logout") def logout(): session.clear() return redirect(url_for("index")) diff --git a/ui/ecobidas_ui/protocols/__init__.py b/ui/ecobidas_ui/protocols/__init__.py new file mode 100644 index 00000000..05af8588 --- /dev/null +++ b/ui/ecobidas_ui/protocols/__init__.py @@ -0,0 +1,3 @@ +"""The public module, including the homepage and user auth.""" + +from . import views # noqa diff --git a/ui/ecobidas_ui/forms.py b/ui/ecobidas_ui/protocols/forms.py similarity index 87% rename from ui/ecobidas_ui/forms.py rename to ui/ecobidas_ui/protocols/forms.py index f4ba1987..60b3d2eb 100644 --- a/ui/ecobidas_ui/forms.py +++ b/ui/ecobidas_ui/protocols/forms.py @@ -1,12 +1,11 @@ from flask_wtf import FlaskForm -from flask_wtf.file import FileField, FileRequired +from flask_wtf.file import FileAllowed, FileField, FileRequired, MultipleFileField from markupsafe import Markup from wtforms import ( DateField, DecimalField, HiddenField, IntegerField, - MultipleFileField, RadioField, SelectField, SelectMultipleField, @@ -18,16 +17,25 @@ class UploadParticipantsForm(FlaskForm): - participants = MultipleFileField("Upload participants.tsv and participants.json") + participants = MultipleFileField( + "Upload participants.tsv and participants.json", + validators=[ + FileRequired(), + FileAllowed(["tsv", "json"], "File must be '.tsv' and '.json' files."), + ], + ) submit = SubmitField("Upload") class UploadBoldJsonForm(FlaskForm): - bold_json = FileField("Upload bold.json", validators=[FileRequired()]) + bold_json = FileField( + "Upload bold.json", + validators=[FileRequired(), FileAllowed(["json"], "The file must be a '.json' file.")], + ) submit_bold_json = SubmitField("Upload") -def generate_form(items=None, prefix=None): +def generate_form(items=None, prefix=None, obj=None) -> FlaskForm: class DyanmicForm(FlaskForm): pass @@ -115,12 +123,6 @@ class DyanmicForm(FlaskForm): elif input_type == "slider": - # FieldType = DecimalRangeField - # render_kw["value"]= "50.0" - # render_kw["min"]= "0.0" - # render_kw["max"]= "100.0" - # render_kw["step"]= "0.5" - min_label = float(item["choices"][0][1]) max_label = float(item["choices"][-1][1]) @@ -147,10 +149,10 @@ class DyanmicForm(FlaskForm): setattr(form, "submit", SubmitField("Save")) # noqa B010 - return form() + return form(obj=obj) -def add_choice_based_items(form, prefix, item_name, item): +def add_choice_based_items(form: FlaskForm, prefix: str, item_name: str, item: dict) -> FlaskForm: question = f"{item['question']} {item['unit']}" diff --git a/ui/ecobidas_ui/protocols/utils.py b/ui/ecobidas_ui/protocols/utils.py new file mode 100644 index 00000000..fae13cc3 --- /dev/null +++ b/ui/ecobidas_ui/protocols/utils.py @@ -0,0 +1,282 @@ +# functions to be used by the routes +import json +from functools import lru_cache +from pathlib import Path +from typing import Any + +import pandas as pd +import requests +from ecobidas_ui.utils import LANG +from flask import flash +from markupsafe import escape +from rich import print + +ALLOWED_EXTENSIONS = {".tsv", ".json"} + + +def local_cobidas_schema(): + return Path(__file__).parents[3] / "cobidas_schema" + + +def allowed_file(filename: str | Path): + return Path(filename).suffix in ALLOWED_EXTENSIONS + + +def protocol_url(protocol_name: Path) -> Path: + return ( + local_cobidas_schema() + / "schemas" + / protocol_name + / "protocols" + / f"{protocol_name}_schema.jsonld" + ) + + +@lru_cache +def get_protocol(protocol_name: str) -> dict[str, Any]: + file = protocol_url(protocol_name) + with open(file) as f: + content = json.load(f) + return content + + +def get_item(file: Path) -> dict[str, Any]: + with open(file) as f: + content = json.load(f) + return content + + +@lru_cache +def query_choices(url: str) -> None | dict[str, Any]: + try: + data = requests.get(url).json() + except Exception as exc: + print(exc) + data = None + return data + + +@lru_cache +def get_landing_page(url: Path) -> None | dict[str, Any]: + try: + if str(url).startswith("https:"): + data = requests.get(url) + else: + data = Path(url).read_text() + except Exception as exc: + print(exc) + data = None + return data + + +def get_nav_bar_content( + protocol_name: str, activity_name: str | None = None +) -> list[dict[str, str]]: + protocol_content = get_protocol(protocol_name) + + order = protocol_content["ui"]["order"] + properties = protocol_content["ui"]["addProperties"] + properties = sort_ui_properties(properties=properties, order=order) + + activities = [ + {"name": "Start", "link": "#", "class": "nav-link active"}, + ] + activities.extend( + { + "name": activity["prefLabel"][LANG], + "link": f"/protocol/{protocol_name}/{activity['variableName']}", + "class": "nav-link", + } + for activity in properties + ) + + if activity_name: + activities[0]["link"] = f"/protocol/{protocol_name}" + activities[0]["class"] = "nav-link" + for activity in activities: + if activity["name"] == activity_name: + activity["link"] = "#" + activity["class"] = "nav-link active" + + return activities + + +def update_format(items: dict[str, Any], form): + for i in items: + if form[i].data: + items[i]["is_answered"] = True + return items + + +def prep_activity_page(protocol_name: str, activity_name: str): + protocol_name = escape(protocol_name) + activity_name = escape(activity_name) + + protocol_content = get_protocol(protocol_name) + properties = protocol_content["ui"]["addProperties"] + is_about_activity = "" + for activity in properties: + if activity["variableName"] == activity_name: + is_about_activity = activity["isAbout"] + break + activity_file = protocol_url(protocol_name).parent / is_about_activity + + with open(activity_file) as f: + activity = json.load(f) + + activities = get_nav_bar_content(protocol_name, activity["prefLabel"][LANG]) + + items = get_items_for_activity(activity_file) + + return activities, activity, items + + +@lru_cache +def get_items_for_activity(activity_file): + with open(activity_file) as f: + activity = json.load(f) + + order = activity["ui"]["order"] + properties = activity["ui"]["addProperties"] + properties = sort_ui_properties(properties=properties, order=order) + + items = {} + for i, item in enumerate(properties): + + item_name = item["variableName"] + + item_data = get_item(activity_file.parent / item["isAbout"]) + + tmp = { + "visibility": False, + "required": False, + "isVis": item["isVis"], + "choices": get_choices(item_data), + "is_answered": False, + } + + tmp["question"] = f"{i + 1} - {item_data['question'][LANG]}" + tmp["input_type"] = item_data["ui"]["inputType"] + + tmp["description"] = ( + "
      Details" + "
        " + f"
      • item name: {item_data.get('description')}
        • " + "
      " + "
      " + ) + details = "" + if item_data.get("details"): + details = item_data["details"].get(LANG) + tmp["description"] = f"{details}
      {tmp['description']}" + + if item["isVis"] == 1: + tmp["visibility"] = True + + if item["requiredValue"]: + tmp["required"] = True + + if response_options := item_data.get("responseOptions"): + try: + unit = f"({response_options['unitOptions'][0]['prefLabel'][LANG]})" + except KeyError: + unit = "" + tmp["unit"] = unit + + tmp["min"] = response_options.get("minValue") + tmp["max"] = response_options.get("maxValue") + + try: + is_multiple = response_options.get("multipleChoice", False) + except KeyError: + is_multiple = False + tmp["is_multiple"] = is_multiple + + else: + tmp["unit"] = "" + tmp["min"] = None + tmp["max"] = None + tmp["is_multiple"] = None + + items[item_name] = tmp + + return items + + +def sort_ui_properties(properties: list[dict[str, Any]], order: list[str]) -> list[dict[str, Any]]: + tmp = [] + for i in order: + for prop in properties: + if prop["isAbout"] == i: + tmp.append(prop) + break + return tmp + + +def get_choices(item_data): + try: + choices = item_data["responseOptions"]["choices"] + if isinstance(choices, str): + # hack to load local data + if "https://raw.githubusercontent.com/ohbm/cobidas_schema/master/" in choices: + choices = choices.replace( + "https://raw.githubusercontent.com/ohbm/cobidas_schema/master/", + str(local_cobidas_schema()) + "/", + ) + with open(choices) as f: + choices = json.load(f) + else: + choices = query_choices(choices) + choices = choices["choices"] + choices = [(x["value"], x["name"][LANG]) for x in choices] + except KeyError: + choices = {} + return choices + + +def validate_participants_json(file: Path): + with open(file) as f: + participants_json = json.load(f) + return bool( + participants_json.get("participant_id") + and participants_json["participant_id"].get("Annotations") + ) + + +def validate_participants_tsv(file: Path): + df = pd.read_csv(file, sep="\t") + return "participant_id" in df.columns + + +def extract_values_participants(df, json_content): + + if isinstance(df, Path): + df = pd.read_csv(df, sep="\t") + + age_column = next( + ( + key + for key, value in json_content.items() + if value["Annotations"]["IsAbout"]["TermURL"] == "nb:Age" + ), + None, + ) + + return Found(df, age_column) + + +class Found: + + def __init__(self, df, age_column) -> None: + self.number_of_subjects = len(df) + self.subject_age_mean = df[age_column].mean() + self.subject_age_min = df[age_column].min() + self.subject_age_max = df[age_column].max() + self.proportion_male_subjects = None + + +def flash_errors(form, category="warning"): + """Flash all errors for a form.""" + for field, errors in form.errors.items(): + for error in errors: + flash(f"{getattr(form, field).label.text} - {error}", category) diff --git a/ui/ecobidas_ui/protocol.py b/ui/ecobidas_ui/protocols/views.py similarity index 58% rename from ui/ecobidas_ui/protocol.py rename to ui/ecobidas_ui/protocols/views.py index ed2ab69e..10b1063a 100644 --- a/ui/ecobidas_ui/protocol.py +++ b/ui/ecobidas_ui/protocols/views.py @@ -2,8 +2,8 @@ from pathlib import Path from typing import Any -from ecobidas_ui.forms import UploadBoldJsonForm, UploadParticipantsForm, generate_form -from ecobidas_ui.utils import ( +from ecobidas_ui.protocols.forms import UploadBoldJsonForm, UploadParticipantsForm, generate_form +from ecobidas_ui.protocols.utils import ( LANG, allowed_file, extract_values_participants, @@ -17,11 +17,11 @@ validate_participants_tsv, ) from flask import Blueprint, current_app, flash, redirect, render_template, request +from flask_wtf import FlaskForm from markupsafe import Markup -from rich import print from werkzeug.utils import secure_filename -bp = Blueprint("protocol", __name__, url_prefix="/protocol") +blueprint = Blueprint("protocol", __name__, url_prefix="/protocol") def update_visibility(items: dict[str, Any], form): @@ -36,8 +36,9 @@ def update_visibility(items: dict[str, Any], form): try: exec(string_to_eval) except Exception as exc: - print(f"Could not execute '{string_to_eval}' as a valid python statement.") - print(exc) + current_app.logger.error( + f"Could not execute '{string_to_eval}' as a valid python statement.\n{exc}" + ) # evaluate visibility for item, values in items.items(): @@ -47,14 +48,15 @@ def update_visibility(items: dict[str, Any], form): items[item]["visibility"] = eval(isVis) except Exception as exc: # actually log this - print(f"Could not evaluate '{eval(isVis)}' as a valid python expression.") - print(exc) + current_app.logger.error( + f"Could not evaluate '{eval(isVis)}' as a valid python expression.\n{exc}" + ) items[item]["visibility"] = False return items -@bp.route("/", methods=["GET", "POST"]) +@blueprint.route("/", methods=["GET", "POST"]) def protocol(protocol_name: str) -> str: protocol_content = get_protocol(protocol_name) @@ -75,21 +77,18 @@ def protocol(protocol_name: str) -> str: def show_export_button(protocol_name): - print(protocol_name) if protocol_name in ["neurovault", "cobidas"]: return True else: return False -@bp.get("//") +@blueprint.get("//") def activity_get(protocol_name, activity_name) -> str: activities, activity, items = prep_activity_page(protocol_name, activity_name) - upload_participants_form, upload_acquisition_form = generate_additional_forms( - protocol_name, activity_name - ) + upload_participants_form, extra_form = generate_extra_forms(protocol_name, activity_name) form = generate_form(items=items, prefix=activity_name) @@ -106,33 +105,36 @@ def activity_get(protocol_name, activity_name) -> str: nb_items=nb_items, completed_items=completed_items, upload_participants_form=upload_participants_form, - upload_acquisition_form=upload_acquisition_form, + upload_acquisition_form=extra_form, show_export_button=show_export_button(protocol_name), ) -@bp.post("//") +@blueprint.post("//") def activity_post(protocol_name, activity_name) -> str: + current_app.logger.info(f"{protocol_name}-{activity_name}") activities, activity, items = prep_activity_page(protocol_name, activity_name) - upload_participants_form, upload_acquisition_form = generate_additional_forms( - protocol_name, activity_name - ) + upload_participants_form, extra_form = generate_extra_forms(protocol_name, activity_name) form = generate_form(items=items, prefix=activity_name) if ( upload_participants_form and upload_participants_form.is_submitted() - and upload_participants_form.participants.data + and upload_participants_form.validate_on_submit() ): if message := validate_participants_form(upload_participants_form): - flash(message) + flash(message, category="warning") return redirect(request.url) - for file in upload_participants_form.participants.data: + data = upload_participants_form.participants.data + if not isinstance(data, list): + data = [data] + + for file in data: if allowed_file(file.filename): filename = secure_filename(file.filename) file.save(Path(current_app.config["UPLOAD_FOLDER"]) / filename) @@ -142,7 +144,8 @@ def activity_post(protocol_name, activity_name) -> str: flash( Markup( "

      The 'participants.tsv' does not seem to be valid: 'participant_id' column is missing.

      " - ) + ), + category="warning", ) return redirect(request.url) @@ -154,66 +157,55 @@ def activity_post(protocol_name, activity_name) -> str: "Annotate your data with " "the neurobagel online annotation tool

      " - ) + ), + category="warning", ) return redirect(request.url) - form.number_of_subjects.data = extract_values_participants( - tsv_file, value="number_of_subjects" + form, items, fields = process_participants_form( + form, activity_name, items, tsv_file, json_file ) - form.subject_age_mean.data = extract_values_participants(tsv_file, value="subject_age_mean") - form.subject_age_min.data = extract_values_participants(tsv_file, value="subject_age_min") - form.subject_age_max.data = extract_values_participants(tsv_file, value="subject_age_max") - # TODO - form.proportion_male_subjects.data = 0.5 + if not fields: + message = "No field could be updated." + flash(message, category="warning") + return redirect(request.url) - items = update_visibility(items, form) - items = update_format(items, form) - form = generate_form(items, prefix=activity_name) + message = f"The following fields were updated: {fields}" + flash(message, category="success") - form.number_of_subjects.data = extract_values_participants( - tsv_file, target="number_of_subjects" - ) - form.subject_age_mean.data = extract_values_participants( - tsv_file, target="subject_age_mean" - ) - form.subject_age_min.data = extract_values_participants(tsv_file, vtarget="subject_age_min") - form.subject_age_max.data = extract_values_participants(tsv_file, target="subject_age_max") - form.proportion_male_subjects.data = 0.5 + if extra_form and extra_form.is_submitted() and extra_form.validate_on_submit(): - if upload_acquisition_form.validate_on_submit(): + data = extra_form.bold_json.data + if not isinstance(data, list): + data = [data] - f = upload_acquisition_form.bold_json.data - filename = secure_filename(f.filename) + uploaded_files = [] + for file in data: + if allowed_file(file.filename): + filename = secure_filename(file.filename) + file.save(Path(current_app.config["UPLOAD_FOLDER"]) / filename) + uploaded_files.append(filename) + else: + message = "No '_bold.json' was uploaded." + flash(message, category="warning") + return redirect(request.url) + + form, items, fields = process_acquisition_form( + form, activity_name, items, filename=Path(current_app.instance_path) / uploaded_files[0] + ) - if not allowed_file(filename): - message = "No '_bold.json' was uploaded." - flash(message) + if not fields: + message = "No field could be updated." + flash(message, category="warning") return redirect(request.url) - f.save(Path(current_app.instance_path) / filename) - - with open(Path(current_app.instance_path) / filename) as f: - bold_json = json.load(f) - - for key in bold_json: - if key in form: - form[key].data = bold_json[key] - - items = update_visibility(items, form) - items = update_format(items, form) - form = generate_form(items, prefix=activity_name) - - for key in bold_json: - if key in form: - form[key].data = bold_json[key] + message = f"The following fields were updated: {fields}" + flash(message, category="success") elif form.is_submitted(): - items = update_visibility(items, form) - items = update_format(items, form) - form = generate_form(items, prefix=activity_name) + form, items = update_items_and_forms(form, items, activity_name) completed_items = sum(bool(i["is_answered"]) for i in items.values()) nb_items = sum(bool(i["visibility"]) for i in items.values()) @@ -228,36 +220,36 @@ def activity_post(protocol_name, activity_name) -> str: nb_items=nb_items, completed_items=completed_items, upload_participants_form=upload_participants_form, - upload_acquisition_form=upload_acquisition_form, + upload_acquisition_form=extra_form, show_export_button=show_export_button(protocol_name), ) def validate_participants_form(upload_participants_form): nb_files_uploaded = len(upload_participants_form.participants.data) + if nb_files_uploaded != 2: + message = f"2 files must be uploaded. Received: {nb_files_uploaded}" + return message + participants_json_uploaded = any( file.filename == "participants.json" for file in upload_participants_form.participants.data ) + if not participants_json_uploaded: + message = "No 'participants.json' was uploaded." + return message + participants_tsv_uploaded = any( file.filename == "participants.tsv" for file in upload_participants_form.participants.data ) - - if nb_files_uploaded != 2: - message = "2 files must be uploaded." - if not participants_json_uploaded: - message = "No 'participants.json' was uploaded." if not participants_tsv_uploaded: message = "No 'participants.tsv' was uploaded." - - if nb_files_uploaded != 2 or not participants_json_uploaded or not participants_tsv_uploaded: - return message else: return "" -def generate_additional_forms(protocol_name, activity_name): +def generate_extra_forms(protocol_name, activity_name) -> tuple[FlaskForm | None]: upload_participants_form = None upload_acquisition_form = None @@ -271,3 +263,52 @@ def generate_additional_forms(protocol_name, activity_name): upload_acquisition_form = UploadBoldJsonForm(prefix="mri_acquisition-") return upload_participants_form, upload_acquisition_form + + +def process_acquisition_form(form: FlaskForm, activity_name: str, items, filename): + """Use uploaded bold.json to prefill the form.""" + with open(filename) as f: + bold_json = json.load(f) + + found = JsonMeta(bold_json) + + fields = [] + for key in found.__dir__(): + if not getattr(found, key) or key not in form: + continue + fields.append(key) + + form, items = update_items_and_forms(form, items, activity_name, obj=found) + + return form, items, fields + + +class JsonMeta: + + def __init__(self, json_content) -> None: + + for key in json_content: + self.__setattr__(key, json_content[key]) + + +def process_participants_form(form: FlaskForm, activity_name: str, items, tsv_file, json_file): + json_content = json.load(open(json_file)) + + found = extract_values_participants(tsv_file, json_content=json_content) + + fields = [] + for key in found.__dir__(): + if not getattr(found, key) or key not in form: + continue + fields.append(key) + + form, items = update_items_and_forms(form, items, activity_name, obj=found) + + return form, items, fields + + +def update_items_and_forms(form: FlaskForm, items, activity_name: str, obj=None): + items = update_visibility(items, form) + items = update_format(items, form) + form = generate_form(items, prefix=activity_name, obj=obj) + return form, items diff --git a/ui/ecobidas_ui/settings.py b/ui/ecobidas_ui/settings.py index 42e8cd6d..40539c48 100644 --- a/ui/ecobidas_ui/settings.py +++ b/ui/ecobidas_ui/settings.py @@ -25,4 +25,4 @@ SECRET_KEY = env.str("SECRET_KEY") -CACHE_TYPE = "flask_caching.backends.SimpleCache" # Can be "MemcachedCache", "RedisCache", etc. +# CACHE_TYPE = "flask_caching.backends.SimpleCache" # Can be "MemcachedCache", "RedisCache", etc. diff --git a/ui/ecobidas_ui/static/images/BIDS_logo_black.svg b/ui/ecobidas_ui/static/images/BIDS_logo_black.svg new file mode 100644 index 00000000..9f1718f7 --- /dev/null +++ b/ui/ecobidas_ui/static/images/BIDS_logo_black.svg @@ -0,0 +1 @@ +Ресурс 2 diff --git a/ui/ecobidas_ui/templates/extra_forms.html b/ui/ecobidas_ui/templates/extra_forms.html new file mode 100644 index 00000000..e3771097 --- /dev/null +++ b/ui/ecobidas_ui/templates/extra_forms.html @@ -0,0 +1,51 @@ +
      +
      + {% if upload_participants_form %} +
      +
      + BIDS +
      +

      + To fill in this form faster you can upload a + participants.tsv file formatted according to the + BIDS specification + along with a participants.json file containing column + annotations generated by + the neurobagel annotation tool. +

      + {{ render_form(upload_participants_form) }} +
      + {% endif %} {% if upload_acquisition_form %} +
      +
      + BIDS +
      +

      + To fill in this form faster you can upload a + *_bold.json file formatted according to the + BIDS specification + containing the metadata for your fMRI runs. +

      + {{ render_form(upload_acquisition_form) }} +
      + {% endif %} +
      +
      diff --git a/ui/ecobidas_ui/templates/layout/base.html b/ui/ecobidas_ui/templates/layout/base.html index 520a01b2..239ba9bf 100644 --- a/ui/ecobidas_ui/templates/layout/base.html +++ b/ui/ecobidas_ui/templates/layout/base.html @@ -6,8 +6,10 @@ {% block title %} {% endblock %} - - + {{ bootstrap.load_css() }} {% assets "css" %} @@ -34,15 +36,15 @@

      🚧 This website is under construction !!!!!! 🚧

    - {% with messages = get_flashed_messages() %} + {% with messages = get_flashed_messages(with_categories=true) %} {% if messages %} - {% for message in messages %} + {% for category, message in messages %}
    diff --git a/ui/ecobidas_ui/utils.py b/ui/ecobidas_ui/utils.py index 75898d7f..d527089b 100644 --- a/ui/ecobidas_ui/utils.py +++ b/ui/ecobidas_ui/utils.py @@ -1,265 +1 @@ -# functions to be used by the routes -import json -from functools import lru_cache -from pathlib import Path -from typing import Any - -import pandas as pd -import requests -from flask import flash -from markupsafe import escape -from rich import print - LANG: str = "en" - -ALLOWED_EXTENSIONS = {".tsv", ".json"} - - -def allowed_file(filename): - return Path(filename).suffix in ALLOWED_EXTENSIONS - - -def protocol_url(protocol_name: Path) -> Path: - return ( - Path(__file__).parents[2] - / "cobidas_schema" - / "schemas" - / protocol_name - / "protocols" - / f"{protocol_name}_schema.jsonld" - ) - - -@lru_cache -def get_protocol(protocol_name: str) -> dict[str, Any]: - file = protocol_url(protocol_name) - with open(file) as f: - content = json.load(f) - return content - - -def get_item(file: Path) -> dict[str, Any]: - with open(file) as f: - content = json.load(f) - return content - - -@lru_cache -def query_choices(url: str) -> None | dict[str, Any]: - try: - data = requests.get(url).json() - except Exception as exc: - print(exc) - data = None - return data - - -@lru_cache -def get_landing_page(url: Path) -> None | dict[str, Any]: - try: - if str(url).startswith("https:"): - data = requests.get(url) - else: - data = Path(url).read_text() - except Exception as exc: - print(exc) - data = None - return data - - -def get_nav_bar_content( - protocol_name: str, activity_name: str | None = None -) -> list[dict[str, str]]: - protocol_content = get_protocol(protocol_name) - - order = protocol_content["ui"]["order"] - properties = protocol_content["ui"]["addProperties"] - properties = sort_ui_properties(properties=properties, order=order) - - activities = [ - {"name": "Start", "link": "#", "class": "nav-link active"}, - ] - activities.extend( - { - "name": activity["prefLabel"][LANG], - "link": f"/protocol/{protocol_name}/{activity['variableName']}", - "class": "nav-link", - } - for activity in properties - ) - - if activity_name: - activities[0]["link"] = f"/protocol/{protocol_name}" - activities[0]["class"] = "nav-link" - for activity in activities: - if activity["name"] == activity_name: - activity["link"] = "#" - activity["class"] = "nav-link active" - - return activities - - -def update_format(items: dict[str, Any], form): - for i in items: - if form[i].data: - items[i]["is_answered"] = True - return items - - -def prep_activity_page(protocol_name, activity_name): - protocol_name = escape(protocol_name) - activity_name = escape(activity_name) - - protocol_content = get_protocol(protocol_name) - properties = protocol_content["ui"]["addProperties"] - for activity in properties: - if activity["variableName"] == activity_name: - is_about_activity = activity["isAbout"] - break - activity_file = protocol_url(protocol_name).parent / is_about_activity - - with open(activity_file) as f: - activity = json.load(f) - - activities = get_nav_bar_content(protocol_name, activity["prefLabel"][LANG]) - - items = get_items_for_activity(activity_file) - - return activities, activity, items - - -@lru_cache -def get_items_for_activity(activity_file): - with open(activity_file) as f: - activity = json.load(f) - - order = activity["ui"]["order"] - properties = activity["ui"]["addProperties"] - properties = sort_ui_properties(properties=properties, order=order) - - items = {} - for i, item in enumerate(properties): - - item_name = item["variableName"] - - item_data = get_item(activity_file.parent / item["isAbout"]) - - tmp = { - "visibility": False, - "required": False, - "isVis": item["isVis"], - "choices": get_choices(item_data), - "is_answered": False, - } - - tmp["question"] = f"{i + 1} - {item_data['question'][LANG]}" - tmp["input_type"] = item_data["ui"]["inputType"] - - tmp["description"] = ( - "
    Details" - "
      " - f"
    • item name: {item_data.get('description')}
      • " - "
    " - "
    " - ) - details = "" - if item_data.get("details"): - details = item_data["details"].get(LANG) - tmp["description"] = f"{details}
    {tmp['description']}" - - if item["isVis"] == 1: - tmp["visibility"] = True - - if item["requiredValue"]: - tmp["required"] = True - - if response_options := item_data.get("responseOptions"): - try: - unit = f"({response_options['unitOptions'][0]['prefLabel'][LANG]})" - except KeyError: - unit = "" - tmp["unit"] = unit - - tmp["min"] = response_options.get("minValue") - tmp["max"] = response_options.get("maxValue") - - try: - is_multiple = response_options.get("multipleChoice", False) - except KeyError: - is_multiple = False - tmp["is_multiple"] = is_multiple - - else: - tmp["unit"] = "" - tmp["min"] = None - tmp["max"] = None - tmp["is_multiple"] = None - - items[item_name] = tmp - - return items - - -def sort_ui_properties(properties: list[dict[str, Any]], order: list[str]) -> list[dict[str, Any]]: - tmp = [] - for i in order: - for prop in properties: - if prop["isAbout"] == i: - tmp.append(prop) - break - return tmp - - -def get_choices(item_data): - try: - choices = item_data["responseOptions"]["choices"] - if isinstance(choices, str): - choices = query_choices(choices)["choices"] - choices = [(x["value"], x["name"][LANG]) for x in choices] - except KeyError: - choices = {} - return choices - - -def validate_participants_json(file: Path): - with open(file) as f: - participants_json = json.load(f) - return bool( - participants_json.get("participant_id") - and participants_json["participant_id"].get("Annotations") - ) - - -def validate_participants_tsv(file: Path): - df = pd.read_csv(file, sep="\t") - return "participant_id" in df.columns - - -def extract_values_participants(df, json_content, target): - if isinstance(df, Path): - df = pd.read_csv(df, sep="\t") - - if target == "number_of_subjects": - return len(df) - - column = next( - ( - key - for key, value in json_content.items() - if value["Annotations"]["IsAbout"]["TermURL"] == "nb:Age" - ), - None, - ) - if target == "subject_age_mean": - return df[column].mean() - if target == "subject_age_min": - return df[column].min() - if target == "subject_age_max": - return df[column].max() - - -def flash_errors(form, category="warning"): - """Flash all errors for a form.""" - for field, errors in form.errors.items(): - for error in errors: - flash(f"{getattr(form, field).label.text} - {error}", category) diff --git a/ui/tests/__init__.py b/ui/tests/__init__.py new file mode 100644 index 00000000..e69de29b diff --git a/ui/tests/conftest.py b/ui/tests/conftest.py deleted file mode 100644 index 94bece32..00000000 --- a/ui/tests/conftest.py +++ /dev/null @@ -1,41 +0,0 @@ -import os -import tempfile -from pathlib import Path - -import pytest -from ecobidas_ui import create_app -from ecobidas_ui.db import get_db, init_db - -with open(Path(__file__).parent / "data.sql", "rb") as f: - _data_sql = f.read().decode("utf8") - - -@pytest.fixture -def app(): - db_fd, db_path = tempfile.mkstemp() - - app = create_app( - { - "TESTING": True, - "DATABASE": db_path, - } - ) - - with app.app_context(): - init_db() - get_db().executescript(_data_sql) - - yield app - - os.close(db_fd) - os.unlink(db_path) - - -@pytest.fixture -def client(app): - return app.test_client() - - -@pytest.fixture -def runner(app): - return app.test_cli_runner() diff --git a/ui/tests/data.sql b/ui/tests/data.sql deleted file mode 100644 index 9b680065..00000000 --- a/ui/tests/data.sql +++ /dev/null @@ -1,8 +0,0 @@ -INSERT INTO user (username, password) -VALUES - ('test', 'pbkdf2:sha256:50000$TCI4GzcX$0de171a4f4dac32e3364c7ddc7c14f3e2fa61f2d17574483f7ffbb431b4acb2f'), - ('other', 'pbkdf2:sha256:50000$kJPKsz6N$d2d4784f1b030a9761f5ccaeeaca413f27f2ecb76d6168407af962ddce849f79'); - -INSERT INTO post (title, body, author_id, created) -VALUES - ('test title', 'test' || x'0a' || 'body', 1, '2018-01-01 00:00:00'); diff --git a/ui/tests/protocols/__init__.py b/ui/tests/protocols/__init__.py new file mode 100644 index 00000000..e69de29b diff --git a/ui/tests/test_utils.py b/ui/tests/protocols/test_utils.py similarity index 58% rename from ui/tests/test_utils.py rename to ui/tests/protocols/test_utils.py index 8dd27ef8..f8f4e10b 100644 --- a/ui/tests/test_utils.py +++ b/ui/tests/protocols/test_utils.py @@ -1,5 +1,31 @@ import pandas as pd -from ecobidas_ui.utils import extract_values_participants +from ecobidas_ui.protocols.utils import ( + extract_values_participants, + get_nav_bar_content, + get_protocol, + prep_activity_page, + protocol_url, +) + + +def test_protocol_url(): + assert protocol_url("neurovault").suffix == ".jsonld" + assert protocol_url("neurovault").stem == "neurovault_schema" + + +def test_get_protocol(): + protocol_content = get_protocol("neurovault") + assert protocol_content["@id"] == "neurovault_schema.jsonld" + + +def test_get_nav_bar_content(): + nav_bar = get_nav_bar_content("neurovault", "Participants") + assert len(nav_bar) == 9 + assert nav_bar[2]["link"] == "#" + + +def test_prep_activity_page(): + activities, activity, items = prep_activity_page("neurovault", "participants") def test_extract_values_participants(): @@ -54,7 +80,4 @@ def test_extract_values_participants(): } } - assert extract_values_participants(tsv, json_content, target="number_of_subjects") == 16 - assert extract_values_participants(tsv, json_content, target="subject_age_min") == 19 - assert extract_values_participants(tsv, json_content, target="subject_age_max") == 30 - # assert mean==23.5625 + assert extract_values_participants(tsv, json_content).subject_age_min == 19 From 3519a0953d8f79fcf749bd701de4cdd2bc0ac2b0 Mon Sep 17 00:00:00 2001 From: Remi Gau Date: Mon, 27 May 2024 23:21:28 +0200 Subject: [PATCH 21/31] refactor --- ui/ecobidas_ui/app.py | 5 ++- ui/ecobidas_ui/protocols/forms.py | 19 ++++++++++ ui/ecobidas_ui/protocols/utils.py | 24 +++--------- ui/ecobidas_ui/protocols/views.py | 57 ++++++++++++++++------------ ui/ecobidas_ui/public/views.py | 3 +- ui/tests/conftest.py | 29 +++++++++++++++ ui/tests/protocols/__init__.py | 0 ui/tests/protocols/conftest.py | 60 ++++++++++++++++++++++++++++++ ui/tests/protocols/test_forms.py | 12 ++++++ ui/tests/protocols/test_utils.py | 62 +++---------------------------- ui/tests/test_app.py | 9 +++++ 11 files changed, 179 insertions(+), 101 deletions(-) create mode 100644 ui/tests/conftest.py delete mode 100644 ui/tests/protocols/__init__.py create mode 100644 ui/tests/protocols/conftest.py create mode 100644 ui/tests/protocols/test_forms.py create mode 100644 ui/tests/test_app.py diff --git a/ui/ecobidas_ui/app.py b/ui/ecobidas_ui/app.py index fb08aaf5..cb5ed344 100644 --- a/ui/ecobidas_ui/app.py +++ b/ui/ecobidas_ui/app.py @@ -1,5 +1,6 @@ import logging import sys +from pathlib import Path from ecobidas_ui import auth, db, protocols, public from ecobidas_ui._version import version @@ -13,7 +14,9 @@ def create_app(config_object="ecobidas_ui.settings"): # create and configure the app - app = Flask(__name__, instance_relative_config=True) + app = Flask( + __name__, instance_relative_config=True, instance_path=Path(__file__).parent / "instance" + ) app.config.from_object(config_object) diff --git a/ui/ecobidas_ui/protocols/forms.py b/ui/ecobidas_ui/protocols/forms.py index 60b3d2eb..f1077c8f 100644 --- a/ui/ecobidas_ui/protocols/forms.py +++ b/ui/ecobidas_ui/protocols/forms.py @@ -1,3 +1,7 @@ +import json +from pathlib import Path + +import pandas as pd from flask_wtf import FlaskForm from flask_wtf.file import FileAllowed, FileField, FileRequired, MultipleFileField from markupsafe import Markup @@ -27,6 +31,21 @@ class UploadParticipantsForm(FlaskForm): submit = SubmitField("Upload") +def validate_participants_json(participants_json: Path | str | dict): + if not isinstance(participants_json, dict): + with open(Path(participants_json)) as f: + participants_json = json.load(f) + return bool( + participants_json.get("participant_id") + and participants_json["participant_id"].get("Annotations") + ) + + +def validate_participants_tsv(file: Path | pd.DataFrame): + df = pd.read_csv(file, sep="\t") + return "participant_id" in df.columns + + class UploadBoldJsonForm(FlaskForm): bold_json = FileField( "Upload bold.json", diff --git a/ui/ecobidas_ui/protocols/utils.py b/ui/ecobidas_ui/protocols/utils.py index fae13cc3..a103e74d 100644 --- a/ui/ecobidas_ui/protocols/utils.py +++ b/ui/ecobidas_ui/protocols/utils.py @@ -101,9 +101,10 @@ def get_nav_bar_content( return activities -def update_format(items: dict[str, Any], form): +def update_format(items: dict[str, Any], form_data): + for i in items: - if form[i].data: + if form_data[i]: items[i]["is_answered"] = True return items @@ -234,20 +235,6 @@ def get_choices(item_data): return choices -def validate_participants_json(file: Path): - with open(file) as f: - participants_json = json.load(f) - return bool( - participants_json.get("participant_id") - and participants_json["participant_id"].get("Annotations") - ) - - -def validate_participants_tsv(file: Path): - df = pd.read_csv(file, sep="\t") - return "participant_id" in df.columns - - def extract_values_participants(df, json_content): if isinstance(df, Path): @@ -268,10 +255,11 @@ def extract_values_participants(df, json_content): class Found: def __init__(self, df, age_column) -> None: - self.number_of_subjects = len(df) - self.subject_age_mean = df[age_column].mean() + self.number_of_subjects = int(len(df)) + self.subject_age_mean = float(df[age_column].mean()) self.subject_age_min = df[age_column].min() self.subject_age_max = df[age_column].max() + # TODO Actually compute the percent male self.proportion_male_subjects = None diff --git a/ui/ecobidas_ui/protocols/views.py b/ui/ecobidas_ui/protocols/views.py index 10b1063a..2692c184 100644 --- a/ui/ecobidas_ui/protocols/views.py +++ b/ui/ecobidas_ui/protocols/views.py @@ -2,7 +2,13 @@ from pathlib import Path from typing import Any -from ecobidas_ui.protocols.forms import UploadBoldJsonForm, UploadParticipantsForm, generate_form +from ecobidas_ui.protocols.forms import ( + UploadBoldJsonForm, + UploadParticipantsForm, + generate_form, + validate_participants_json, + validate_participants_tsv, +) from ecobidas_ui.protocols.utils import ( LANG, allowed_file, @@ -13,8 +19,6 @@ prep_activity_page, protocol_url, update_format, - validate_participants_json, - validate_participants_tsv, ) from flask import Blueprint, current_app, flash, redirect, render_template, request from flask_wtf import FlaskForm @@ -24,10 +28,10 @@ blueprint = Blueprint("protocol", __name__, url_prefix="/protocol") -def update_visibility(items: dict[str, Any], form): +def update_visibility(items: dict[str, Any], form_data): """Evaluate visibility condition of each item and make item visible if necessary.""" # assign response to a variable with same name as the item it comees from - for key, value in form.data.items(): + for key, value in form_data.items(): if key not in items: continue if not value: @@ -126,14 +130,14 @@ def activity_post(protocol_name, activity_name) -> str: and upload_participants_form.validate_on_submit() ): - if message := validate_participants_form(upload_participants_form): - flash(message, category="warning") - return redirect(request.url) - data = upload_participants_form.participants.data if not isinstance(data, list): data = [data] + if message := validate_participants_form(data): + flash(message, category="warning") + return redirect(request.url) + for file in data: if allowed_file(file.filename): filename = secure_filename(file.filename) @@ -162,6 +166,7 @@ def activity_post(protocol_name, activity_name) -> str: ) return redirect(request.url) + # TODO values in fields for participant data are not updated. form, items, fields = process_participants_form( form, activity_name, items, tsv_file, json_file ) @@ -192,7 +197,10 @@ def activity_post(protocol_name, activity_name) -> str: return redirect(request.url) form, items, fields = process_acquisition_form( - form, activity_name, items, filename=Path(current_app.instance_path) / uploaded_files[0] + form, + activity_name, + items, + filename=Path(current_app.config["UPLOAD_FOLDER"]) / uploaded_files[0], ) if not fields: @@ -205,7 +213,7 @@ def activity_post(protocol_name, activity_name) -> str: elif form.is_submitted(): - form, items = update_items_and_forms(form, items, activity_name) + form, items = update_items_and_forms(form.data, items, activity_name) completed_items = sum(bool(i["is_answered"]) for i in items.values()) nb_items = sum(bool(i["visibility"]) for i in items.values()) @@ -225,22 +233,18 @@ def activity_post(protocol_name, activity_name) -> str: ) -def validate_participants_form(upload_participants_form): - nb_files_uploaded = len(upload_participants_form.participants.data) +def validate_participants_form(data): + nb_files_uploaded = len(data) if nb_files_uploaded != 2: message = f"2 files must be uploaded. Received: {nb_files_uploaded}" return message - participants_json_uploaded = any( - file.filename == "participants.json" for file in upload_participants_form.participants.data - ) + participants_json_uploaded = any(file.filename == "participants.json" for file in data) if not participants_json_uploaded: message = "No 'participants.json' was uploaded." return message - participants_tsv_uploaded = any( - file.filename == "participants.tsv" for file in upload_participants_form.participants.data - ) + participants_tsv_uploaded = any(file.filename == "participants.tsv" for file in data) if not participants_tsv_uploaded: message = "No 'participants.tsv' was uploaded." return message @@ -278,7 +282,7 @@ def process_acquisition_form(form: FlaskForm, activity_name: str, items, filenam continue fields.append(key) - form, items = update_items_and_forms(form, items, activity_name, obj=found) + form, items = update_items_and_forms(form.data, items, activity_name, obj=found) return form, items, fields @@ -302,13 +306,18 @@ def process_participants_form(form: FlaskForm, activity_name: str, items, tsv_fi continue fields.append(key) - form, items = update_items_and_forms(form, items, activity_name, obj=found) + form, items = update_items_and_forms(form.data, items, activity_name, obj=found) return form, items, fields -def update_items_and_forms(form: FlaskForm, items, activity_name: str, obj=None): - items = update_visibility(items, form) - items = update_format(items, form) +def update_items_and_forms(form_data: dict, items, activity_name: str, obj=None): + if obj is not None: + for key in obj.__dir__(): + if key in form_data: + form_data[key] = getattr(obj, key) + + items = update_visibility(items, form_data) + items = update_format(items, form_data) form = generate_form(items, prefix=activity_name, obj=obj) return form, items diff --git a/ui/ecobidas_ui/public/views.py b/ui/ecobidas_ui/public/views.py index 4d874025..88829745 100644 --- a/ui/ecobidas_ui/public/views.py +++ b/ui/ecobidas_ui/public/views.py @@ -3,7 +3,7 @@ import json from ecobidas_ui.settings import STATIC_FOLDER -from flask import Blueprint, current_app, render_template +from flask import Blueprint, render_template blueprint = Blueprint("public", __name__, static_folder="../static") @@ -11,7 +11,6 @@ @blueprint.route("/", methods=["GET", "POST"]) def home(): """Home page.""" - current_app.logger.info("Hello from the home page!") return render_template("public/index.html") diff --git a/ui/tests/conftest.py b/ui/tests/conftest.py new file mode 100644 index 00000000..44452705 --- /dev/null +++ b/ui/tests/conftest.py @@ -0,0 +1,29 @@ +import pytest +from ecobidas_ui.app import create_app + + +@pytest.fixture() +def app(): + app = create_app() + app.config.update( + { + "TESTING": True, + } + ) + + # other setup can go here + + yield app + + # clean up / reset resources here + + +@pytest.fixture() +def client(app): + return app.test_client() + + +@pytest.fixture +def app_context(app): + with app.app_context(): + yield diff --git a/ui/tests/protocols/__init__.py b/ui/tests/protocols/__init__.py deleted file mode 100644 index e69de29b..00000000 diff --git a/ui/tests/protocols/conftest.py b/ui/tests/protocols/conftest.py new file mode 100644 index 00000000..2da42613 --- /dev/null +++ b/ui/tests/protocols/conftest.py @@ -0,0 +1,60 @@ +import pandas as pd +import pytest + + +@pytest.fixture +def participants_json(): + return { + "participant_id": {"Annotations": {"IsAbout": {"TermURL": "", "Label": ""}}}, + "age": { + "Annotations": { + "IsAbout": {"TermURL": "nb:Age", "Label": ""}, + "Transformation": {"TermURL": "nb:FromInt", "Label": "integer data"}, + "MissingValues": ["", "n/a", " "], + } + }, + } + + +@pytest.fixture +def participants_df(): + return pd.DataFrame( + { + "age": [ + 26, + 24, + 27, + 20, + 22, + 26, + 24, + 21, + 26, + 21, + 24, + 22, + 21, + 30, + 24, + 19, + ], + "sex": [ + "F", + "M", + "F", + "F", + "M,", + "F", + "M", + "M", + "M", + "F", + "F", + "F", + "F", + "F", + "F", + "M", + ], + } + ) diff --git a/ui/tests/protocols/test_forms.py b/ui/tests/protocols/test_forms.py new file mode 100644 index 00000000..1884ace7 --- /dev/null +++ b/ui/tests/protocols/test_forms.py @@ -0,0 +1,12 @@ +import pandas as pd +from ecobidas_ui.protocols.forms import validate_participants_json, validate_participants_tsv + + +def test_validate_participants_tsv(participants_df): + assert validate_participants_tsv(participants_df) + assert not validate_participants_tsv(pd.DataFrame()) + + +def test_validate_participants_json(participants_json): + assert validate_participants_json(participants_json) + assert not validate_participants_json({}) diff --git a/ui/tests/protocols/test_utils.py b/ui/tests/protocols/test_utils.py index f8f4e10b..53736209 100644 --- a/ui/tests/protocols/test_utils.py +++ b/ui/tests/protocols/test_utils.py @@ -1,4 +1,4 @@ -import pandas as pd +import pytest from ecobidas_ui.protocols.utils import ( extract_values_participants, get_nav_bar_content, @@ -24,60 +24,10 @@ def test_get_nav_bar_content(): assert nav_bar[2]["link"] == "#" -def test_prep_activity_page(): - activities, activity, items = prep_activity_page("neurovault", "participants") +@pytest.mark.parametrize("activity_name", ["participants", "mri_acquisition"]) +def test_prep_activity_page(activity_name): + activities, activity, items = prep_activity_page("neurovault", activity_name) -def test_extract_values_participants(): - tsv = pd.DataFrame( - { - "age": [ - 26, - 24, - 27, - 20, - 22, - 26, - 24, - 21, - 26, - 21, - 24, - 22, - 21, - 30, - 24, - 19, - ], - "sex": [ - "F", - "M", - "F", - "F", - "M,", - "F", - "M", - "M", - "M", - "F", - "F", - "F", - "F", - "F", - "F", - "M", - ], - } - ) - - json_content = { - "age": { - "Annotations": { - "IsAbout": {"TermURL": "nb:Age", "Label": ""}, - "Transformation": {"TermURL": "nb:FromInt", "Label": "integer data"}, - "MissingValues": ["", "n/a", " "], - } - } - } - - assert extract_values_participants(tsv, json_content).subject_age_min == 19 +def test_extract_values_participants(participants_df, participants_json): + assert extract_values_participants(participants_df, participants_json).subject_age_min == 19 diff --git a/ui/tests/test_app.py b/ui/tests/test_app.py new file mode 100644 index 00000000..7cc2db04 --- /dev/null +++ b/ui/tests/test_app.py @@ -0,0 +1,9 @@ +def test_request_example(client): + response = client.get("/") + assert b"eCOBIDAS" in response.data + response = client.get("/faq/") + assert b"FAQ" in response.data + response = client.get("/about/") + assert b"about" in response.data + response = client.get("/protocols/neurovault/mri_acquisition") + assert b"neurovault" in response.data From 07d6ba39c358eb5377dfa4590fbed6fcc5b0eff8 Mon Sep 17 00:00:00 2001 From: Remi Gau Date: Tue, 28 May 2024 01:25:54 +0200 Subject: [PATCH 22/31] generate and download methods --- .pre-commit-config.yaml | 4 +++ .../mri/preprocessing/brain-extraction.md | 7 ----- .../mri/preprocessing/coregistration.md | 8 ----- .../mri/preprocessing/intensity-norm.md | 11 ------- .../mri/preprocessing/operations-performed.md | 5 ---- .../preprocessing/quality-control-reports.md | 6 ---- .../mri/preprocessing/segmentation.md | 7 ----- .../preprocessing/slice-timing-correction.md | 8 ----- .../mri/preprocessing/smoothing.md | 13 -------- .../boilerplate/mri/preprocessing/software.md | 6 ---- .../mri/preprocessing/t1-stabilization.md | 6 ---- .../mri/preprocessing/volume-censoring.md | 10 ------- ui/ecobidas_ui/app.py | 10 ++----- ui/ecobidas_ui/generate/__init__.py | 3 ++ ui/ecobidas_ui/generate/views.py | 30 +++++++++++++++++++ ui/ecobidas_ui/protocols/views.py | 10 +++++-- ui/ecobidas_ui/templates/405.html | 17 +++++++++++ .../templates/generate/device_info.html | 3 ++ ui/ecobidas_ui/templates/generate/index.html | 22 ++++++++++++++ .../templates/generate/institution.html | 2 ++ .../generate/meeg/device_channel_count.tmp | 1 + .../generate/meeg/device_channels.tmp | 2 ++ .../generate/meeg/device_freq_config.tmp | 1 + .../generate/meeg/dewar_positioning.tmp | 1 + .../generate/meeg/eeg_channel_placement.tmp | 1 + .../templates/generate/meeg/eeg_report.tmp | 13 ++++++++ .../generate/meeg/head_coil_frequency.tmp | 1 + .../generate/meeg/head_localisation.tmp | 1 + .../templates/generate/meeg/meg_report.tmp | 21 +++++++++++++ .../generate/meeg/recording_properties.tmp | 1 + .../generate/mri/acquisition/info.html | 8 +++++ .../acquisition/inplane_spatial_encoding.html | 6 ++++ .../mri/acquisition/rf_contrasts.html | 1 + .../mri/acquisition/scanner_hardware.html | 10 +++++++ .../generate/mri/acquisition/sequence.html | 4 +++ .../mri/acquisition/slice_acceleration.html | 2 ++ .../mri/acquisition/timing_parameters.html | 2 ++ .../mri/preprocessing/brain-extraction.html | 3 ++ .../mri/preprocessing/coregistration.html | 5 ++++ .../mri/preprocessing/intensity-norm.html | 5 ++++ .../preprocessing/operations-performed.html | 1 + .../quality-control-reports.html | 2 ++ .../mri/preprocessing/segmentation.html | 3 ++ .../slice-timing-correction.html | 4 +++ .../generate/mri/preprocessing/smoothing.html | 3 ++ .../generate/mri/preprocessing/software.html | 1 + .../mri/preprocessing/t1-stabilization.html | 2 ++ .../mri/preprocessing/volume-censoring.html | 5 ++++ ui/ecobidas_ui/templates/generate/report.html | 17 +++++++++++ .../templates/generate/task_name.html | 1 + ui/ecobidas_ui/templates/layout/base.html | 4 +-- ui/ecobidas_ui/templates/side_nav.html | 2 +- ui/pyproject.toml | 3 +- 53 files changed, 224 insertions(+), 101 deletions(-) delete mode 100644 inputs/boilerplate/mri/preprocessing/brain-extraction.md delete mode 100644 inputs/boilerplate/mri/preprocessing/coregistration.md delete mode 100644 inputs/boilerplate/mri/preprocessing/intensity-norm.md delete mode 100644 inputs/boilerplate/mri/preprocessing/operations-performed.md delete mode 100644 inputs/boilerplate/mri/preprocessing/quality-control-reports.md delete mode 100644 inputs/boilerplate/mri/preprocessing/segmentation.md delete mode 100644 inputs/boilerplate/mri/preprocessing/slice-timing-correction.md delete mode 100644 inputs/boilerplate/mri/preprocessing/smoothing.md delete mode 100644 inputs/boilerplate/mri/preprocessing/software.md delete mode 100644 inputs/boilerplate/mri/preprocessing/t1-stabilization.md delete mode 100644 inputs/boilerplate/mri/preprocessing/volume-censoring.md create mode 100644 ui/ecobidas_ui/generate/__init__.py create mode 100644 ui/ecobidas_ui/generate/views.py create mode 100644 ui/ecobidas_ui/templates/405.html create mode 100644 ui/ecobidas_ui/templates/generate/device_info.html create mode 100644 ui/ecobidas_ui/templates/generate/index.html create mode 100644 ui/ecobidas_ui/templates/generate/institution.html create mode 100644 ui/ecobidas_ui/templates/generate/meeg/device_channel_count.tmp create mode 100644 ui/ecobidas_ui/templates/generate/meeg/device_channels.tmp create mode 100644 ui/ecobidas_ui/templates/generate/meeg/device_freq_config.tmp create mode 100644 ui/ecobidas_ui/templates/generate/meeg/dewar_positioning.tmp create mode 100644 ui/ecobidas_ui/templates/generate/meeg/eeg_channel_placement.tmp create mode 100644 ui/ecobidas_ui/templates/generate/meeg/eeg_report.tmp create mode 100644 ui/ecobidas_ui/templates/generate/meeg/head_coil_frequency.tmp create mode 100644 ui/ecobidas_ui/templates/generate/meeg/head_localisation.tmp create mode 100644 ui/ecobidas_ui/templates/generate/meeg/meg_report.tmp create mode 100644 ui/ecobidas_ui/templates/generate/meeg/recording_properties.tmp create mode 100644 ui/ecobidas_ui/templates/generate/mri/acquisition/info.html create mode 100644 ui/ecobidas_ui/templates/generate/mri/acquisition/inplane_spatial_encoding.html create mode 100644 ui/ecobidas_ui/templates/generate/mri/acquisition/rf_contrasts.html create mode 100644 ui/ecobidas_ui/templates/generate/mri/acquisition/scanner_hardware.html create mode 100644 ui/ecobidas_ui/templates/generate/mri/acquisition/sequence.html create mode 100644 ui/ecobidas_ui/templates/generate/mri/acquisition/slice_acceleration.html create mode 100644 ui/ecobidas_ui/templates/generate/mri/acquisition/timing_parameters.html create mode 100644 ui/ecobidas_ui/templates/generate/mri/preprocessing/brain-extraction.html create mode 100644 ui/ecobidas_ui/templates/generate/mri/preprocessing/coregistration.html create mode 100644 ui/ecobidas_ui/templates/generate/mri/preprocessing/intensity-norm.html create mode 100644 ui/ecobidas_ui/templates/generate/mri/preprocessing/operations-performed.html create mode 100644 ui/ecobidas_ui/templates/generate/mri/preprocessing/quality-control-reports.html create mode 100644 ui/ecobidas_ui/templates/generate/mri/preprocessing/segmentation.html create mode 100644 ui/ecobidas_ui/templates/generate/mri/preprocessing/slice-timing-correction.html create mode 100644 ui/ecobidas_ui/templates/generate/mri/preprocessing/smoothing.html create mode 100644 ui/ecobidas_ui/templates/generate/mri/preprocessing/software.html create mode 100644 ui/ecobidas_ui/templates/generate/mri/preprocessing/t1-stabilization.html create mode 100644 ui/ecobidas_ui/templates/generate/mri/preprocessing/volume-censoring.html create mode 100644 ui/ecobidas_ui/templates/generate/report.html create mode 100644 ui/ecobidas_ui/templates/generate/task_name.html diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 9731853e..04f84a8c 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -83,6 +83,10 @@ repos: hooks: - id: prettier types_or: [css, html, json] + exclude: | + (?x)^( + ui/ecobidas_ui/static/css/font-awesome.min.css + )$ # Check formatting HTML / Jinja # - repo: https://github.com/thibaudcolas/curlylint diff --git a/inputs/boilerplate/mri/preprocessing/brain-extraction.md b/inputs/boilerplate/mri/preprocessing/brain-extraction.md deleted file mode 100644 index ed67bc41..00000000 --- a/inputs/boilerplate/mri/preprocessing/brain-extraction.md +++ /dev/null @@ -1,7 +0,0 @@ -# Template text for skull stripping/brain extraction - -Brain extraction/Skull stripping was performed using `bet_method` -(`bet_software` version `bet_version`) with the following parameters: -`bet_parameters`. {if bet_manual_edit != ''} `bet_manual_edit`. else `` - -## Example diff --git a/inputs/boilerplate/mri/preprocessing/coregistration.md b/inputs/boilerplate/mri/preprocessing/coregistration.md deleted file mode 100644 index c8adf168..00000000 --- a/inputs/boilerplate/mri/preprocessing/coregistration.md +++ /dev/null @@ -1,8 +0,0 @@ -# Coregistration - -As part of the coregistration, the `func-anat_coreg__source_volume` scan was -aligned to the `func-anat_coreg_target_volume` scan using -`func-anat_coreg_method` in `func-anat_coreg_software` `func-anat_coreg_version` -(cost function: `func-anat_coreg_cost_function`, df: `func-anat_coreg_dof`) - -## Example diff --git a/inputs/boilerplate/mri/preprocessing/intensity-norm.md b/inputs/boilerplate/mri/preprocessing/intensity-norm.md deleted file mode 100644 index 9fa49751..00000000 --- a/inputs/boilerplate/mri/preprocessing/intensity-norm.md +++ /dev/null @@ -1,11 +0,0 @@ -# Normalization - -{if intensity_normalization} `intensity_normalization_choice` intensity -normalization was performed. - -{if structural_intensity_correction} T1 images were bias field corrected. - -{if functional_intensity_correction} Functional images were intensity corrected -to reduce interleaved acquisition artifacts. - -## Example diff --git a/inputs/boilerplate/mri/preprocessing/operations-performed.md b/inputs/boilerplate/mri/preprocessing/operations-performed.md deleted file mode 100644 index ca390c1e..00000000 --- a/inputs/boilerplate/mri/preprocessing/operations-performed.md +++ /dev/null @@ -1,5 +0,0 @@ -# Operations performed + order of operation - -The following preprocessing steps were performed: `order_of_operation`. - -## Example diff --git a/inputs/boilerplate/mri/preprocessing/quality-control-reports.md b/inputs/boilerplate/mri/preprocessing/quality-control-reports.md deleted file mode 100644 index ab86269c..00000000 --- a/inputs/boilerplate/mri/preprocessing/quality-control-reports.md +++ /dev/null @@ -1,6 +0,0 @@ -# Quality control reports - -The following measures were taken to control image quality: -`quality_control_reports`. - -## Example diff --git a/inputs/boilerplate/mri/preprocessing/segmentation.md b/inputs/boilerplate/mri/preprocessing/segmentation.md deleted file mode 100644 index 7fde938f..00000000 --- a/inputs/boilerplate/mri/preprocessing/segmentation.md +++ /dev/null @@ -1,7 +0,0 @@ -# Segmentation - -Structural images were segmented using `segmentation_software` -`segmentation_version` by `segmentation_method` with the following parameters: -`segmentation_parameters` - -## Example diff --git a/inputs/boilerplate/mri/preprocessing/slice-timing-correction.md b/inputs/boilerplate/mri/preprocessing/slice-timing-correction.md deleted file mode 100644 index 14b2b8ad..00000000 --- a/inputs/boilerplate/mri/preprocessing/slice-timing-correction.md +++ /dev/null @@ -1,8 +0,0 @@ -# Slice timing correction - -Slice timing correction was implemented in `stc_software` (`stc_version`) and -applied using `stc_method`. Individual slices were realigned with slice -`stc_reference` as a reference. As interpolation method, `stc_interpolation` -interpolation was used. - -## Example diff --git a/inputs/boilerplate/mri/preprocessing/smoothing.md b/inputs/boilerplate/mri/preprocessing/smoothing.md deleted file mode 100644 index 1e238dfe..00000000 --- a/inputs/boilerplate/mri/preprocessing/smoothing.md +++ /dev/null @@ -1,13 +0,0 @@ -# Smoothing - -`smoothing_target_space` were smoothed using `smoothing_software` -(`smoothing_version`) using a `smoothing_type` (FWHM = `smoothing_size` mm) with -a `filtering_approach`. - -## Example - -Native volumes were smoothed using SPM (SPM12 - r7487) using a gaussian (FWHM = -8 mm) fixed kernel. - -Template surfaces were smoothed using Freeesurfer (6.0) using a gaussian (FWHM = -8 mm) with iterative smoothing until the desired FWHM was reached. diff --git a/inputs/boilerplate/mri/preprocessing/software.md b/inputs/boilerplate/mri/preprocessing/software.md deleted file mode 100644 index b3b25cfe..00000000 --- a/inputs/boilerplate/mri/preprocessing/software.md +++ /dev/null @@ -1,6 +0,0 @@ -# Preprocessing software - -Raw fMRI data were preprocessed using `preprocessing_software` -`preprocessing_software_version`. - -## Example diff --git a/inputs/boilerplate/mri/preprocessing/t1-stabilization.md b/inputs/boilerplate/mri/preprocessing/t1-stabilization.md deleted file mode 100644 index 1418a877..00000000 --- a/inputs/boilerplate/mri/preprocessing/t1-stabilization.md +++ /dev/null @@ -1,6 +0,0 @@ -# T1 stabilization - -For each functional run, the first `t1_stabilization` volumes were removed to -discard unsteady signals. - -## Example diff --git a/inputs/boilerplate/mri/preprocessing/volume-censoring.md b/inputs/boilerplate/mri/preprocessing/volume-censoring.md deleted file mode 100644 index 5764dc10..00000000 --- a/inputs/boilerplate/mri/preprocessing/volume-censoring.md +++ /dev/null @@ -1,10 +0,0 @@ -#Template text for volume_censoring - -{if volume_censoring_used == 1} - -Volume censoring was applied using `volume_censoring_method` -(`volume_censoring_software` version `volume_censoring_version`) with the -following criteria `volume_censoring_criteria` {if interpolation == 'none'} and -`interpolation` interpolation. - -## Example diff --git a/ui/ecobidas_ui/app.py b/ui/ecobidas_ui/app.py index cb5ed344..c35040a8 100644 --- a/ui/ecobidas_ui/app.py +++ b/ui/ecobidas_ui/app.py @@ -2,7 +2,7 @@ import sys from pathlib import Path -from ecobidas_ui import auth, db, protocols, public +from ecobidas_ui import auth, db, generate, protocols, public from ecobidas_ui._version import version from ecobidas_ui.extensions import bootstrap, csrf_protect @@ -37,11 +37,6 @@ def export() -> str: flash("'Export' not implemented yet!", category="warning") return render_template("public/index.html") - @app.route("/generate") - def generate() -> str: - flash("'Generate' Not implemented yet!", category="warning") - return render_template("public/index.html") - return app @@ -59,6 +54,7 @@ def register_blueprints(app): app.register_blueprint(public.views.blueprint) app.register_blueprint(auth.views.blueprint) app.register_blueprint(protocols.views.blueprint) + app.register_blueprint(generate.views.blueprint) return None @@ -71,7 +67,7 @@ def render_error(error): error_code = getattr(error, "code", 500) return render_template(f"{error_code}.html"), error_code - for errcode in [401, 404, 500]: + for errcode in [401, 404, 405, 500]: app.errorhandler(errcode)(render_error) return None diff --git a/ui/ecobidas_ui/generate/__init__.py b/ui/ecobidas_ui/generate/__init__.py new file mode 100644 index 00000000..05af8588 --- /dev/null +++ b/ui/ecobidas_ui/generate/__init__.py @@ -0,0 +1,3 @@ +"""The public module, including the homepage and user auth.""" + +from . import views # noqa diff --git a/ui/ecobidas_ui/generate/views.py b/ui/ecobidas_ui/generate/views.py new file mode 100644 index 00000000..2682f3b6 --- /dev/null +++ b/ui/ecobidas_ui/generate/views.py @@ -0,0 +1,30 @@ +"""Public section, including homepage and signup.""" + +import json +from pathlib import Path + +from flask import Blueprint, current_app, render_template, send_from_directory +from markdownify import markdownify as md + +blueprint = Blueprint("generate", __name__, url_prefix="/generate") + + +def dummmy_data(): + with open( + "/home/remi/github/cobidas_chckls/inputs/bids_template/task-auditoryLocalizer_bold.json" + ) as f: + data = json.load(f) + return data + + +@blueprint.route("/", methods=["GET", "POST"]) +def generate(): + return render_template("generate/index.html", **dummmy_data()) + + +@blueprint.route("/download", methods=["GET"]) +def download(): + tmp = md(render_template("generate/report.html"), heading_style="ATX") + with open(Path(current_app.config["UPLOAD_FOLDER"]) / "report.md", "w") as f: + f.write(tmp) + return send_from_directory(current_app.config["UPLOAD_FOLDER"], "report.md") diff --git a/ui/ecobidas_ui/protocols/views.py b/ui/ecobidas_ui/protocols/views.py index 2692c184..098f363e 100644 --- a/ui/ecobidas_ui/protocols/views.py +++ b/ui/ecobidas_ui/protocols/views.py @@ -258,12 +258,16 @@ def generate_extra_forms(protocol_name, activity_name) -> tuple[FlaskForm | None upload_participants_form = None upload_acquisition_form = None - if protocol_name != "neurovault": + if protocol_name not in ["neurovault", "cobidas"]: return upload_participants_form, upload_acquisition_form - if activity_name == "participants": + if (protocol_name == "neurovault" and activity_name == "participants") or ( + protocol_name == "cobidas" and activity_name == "sample" + ): upload_participants_form = UploadParticipantsForm(prefix="upload-") - if activity_name == "mri_acquisition": + if (protocol_name == "neurovault" and activity_name == "mri_acquisition") or ( + protocol_name == "cobidas" and activity_name == "common_parameters" + ): upload_acquisition_form = UploadBoldJsonForm(prefix="mri_acquisition-") return upload_participants_form, upload_acquisition_form diff --git a/ui/ecobidas_ui/templates/405.html b/ui/ecobidas_ui/templates/405.html new file mode 100644 index 00000000..23529a41 --- /dev/null +++ b/ui/ecobidas_ui/templates/405.html @@ -0,0 +1,17 @@ +{% extends 'layout/base.html' %} + +{% block title %}405 Error -Method Not Allowed{% endblock %} + +{% block content %} +
    +
    +
    + +

    The method is not allowed for the requested URL.

    +

    + Want to go home instead? +

    +
    +
    +
    +{% endblock %} diff --git a/ui/ecobidas_ui/templates/generate/device_info.html b/ui/ecobidas_ui/templates/generate/device_info.html new file mode 100644 index 00000000..19426591 --- /dev/null +++ b/ui/ecobidas_ui/templates/generate/device_info.html @@ -0,0 +1,3 @@ +Recordings were acquired using the {{ManufacturersModelName}} system from +{{Manufacturer}}, with serial number {{DeviceSerialNumber}}. The software +version was {{SoftwareVersions}}. diff --git a/ui/ecobidas_ui/templates/generate/index.html b/ui/ecobidas_ui/templates/generate/index.html new file mode 100644 index 00000000..87ff341f --- /dev/null +++ b/ui/ecobidas_ui/templates/generate/index.html @@ -0,0 +1,22 @@ +{% extends 'layout/base.html' %} + +{% block title %} eCOBIDAS {% endblock %} + +{% block content %} +
    +
    +
    +
    + + + +
    + +

    Report

    +
    {% include 'generate/report.html' %}
    +
    +
    +
    +{% endblock %} diff --git a/ui/ecobidas_ui/templates/generate/institution.html b/ui/ecobidas_ui/templates/generate/institution.html new file mode 100644 index 00000000..7a70e904 --- /dev/null +++ b/ui/ecobidas_ui/templates/generate/institution.html @@ -0,0 +1,2 @@ +The recordings were performed in the {{InstitutionName}}, +{{InstitutionalDepartmentName}}, {{InstitutionAddress}}. diff --git a/ui/ecobidas_ui/templates/generate/meeg/device_channel_count.tmp b/ui/ecobidas_ui/templates/generate/meeg/device_channel_count.tmp new file mode 100644 index 00000000..e51784cd --- /dev/null +++ b/ui/ecobidas_ui/templates/generate/meeg/device_channel_count.tmp @@ -0,0 +1 @@ +There were {{MEGChannelCount}} MEG channels, {{MEGREFChannelCount}} of which where MEG reference channels. diff --git a/ui/ecobidas_ui/templates/generate/meeg/device_channels.tmp b/ui/ecobidas_ui/templates/generate/meeg/device_channels.tmp new file mode 100644 index 00000000..69584869 --- /dev/null +++ b/ui/ecobidas_ui/templates/generate/meeg/device_channels.tmp @@ -0,0 +1,2 @@ +Data was collected with {{EEGChannelCount}} EEG channels, {{EOGChannelCount}} EOG channels, +{{ECGChannelCount}} ECG channels and {{EMGChannelCount}} EMG channels recorded simultaneously. diff --git a/ui/ecobidas_ui/templates/generate/meeg/device_freq_config.tmp b/ui/ecobidas_ui/templates/generate/meeg/device_freq_config.tmp new file mode 100644 index 00000000..83d3b108 --- /dev/null +++ b/ui/ecobidas_ui/templates/generate/meeg/device_freq_config.tmp @@ -0,0 +1 @@ +Power line and sampling frequencies were {{PowerLineFrequency}} Hz and {{SamplingFrequency}} Hz, respectively. diff --git a/ui/ecobidas_ui/templates/generate/meeg/dewar_positioning.tmp b/ui/ecobidas_ui/templates/generate/meeg/dewar_positioning.tmp new file mode 100644 index 00000000..2e8a62a2 --- /dev/null +++ b/ui/ecobidas_ui/templates/generate/meeg/dewar_positioning.tmp @@ -0,0 +1 @@ +The dewar was positioned {{DewarPosition}} during the scan. diff --git a/ui/ecobidas_ui/templates/generate/meeg/eeg_channel_placement.tmp b/ui/ecobidas_ui/templates/generate/meeg/eeg_channel_placement.tmp new file mode 100644 index 00000000..78d6b451 --- /dev/null +++ b/ui/ecobidas_ui/templates/generate/meeg/eeg_channel_placement.tmp @@ -0,0 +1 @@ +Channels were placed according to the {{EEGPlacementScheme}} with a {{EEGGround}}. The {{EEGReference}} were used as the reference. diff --git a/ui/ecobidas_ui/templates/generate/meeg/eeg_report.tmp b/ui/ecobidas_ui/templates/generate/meeg/eeg_report.tmp new file mode 100644 index 00000000..5ed7b7f9 --- /dev/null +++ b/ui/ecobidas_ui/templates/generate/meeg/eeg_report.tmp @@ -0,0 +1,13 @@ +{% include 'task_name.tmp' %} + +{% include 'institution.tmp' %} + +{% include 'device_info.tmp' %} + +{% include 'device_freq_config.tmp' %} + +{% include 'device_channels.tmp' %} + +{% include 'eeg_channel_placement.tmp' %} + +{% include 'recording_properties.tmp' %} diff --git a/ui/ecobidas_ui/templates/generate/meeg/head_coil_frequency.tmp b/ui/ecobidas_ui/templates/generate/meeg/head_coil_frequency.tmp new file mode 100644 index 00000000..b6aca2a2 --- /dev/null +++ b/ui/ecobidas_ui/templates/generate/meeg/head_coil_frequency.tmp @@ -0,0 +1 @@ +Head localisation coils used frequencies of {% for f in HeadCoilFrequency %}{{f}} Hz{% if loop.last -1 %} and {% elif not loop.last %}, {% endif %}{% endfor %}. diff --git a/ui/ecobidas_ui/templates/generate/meeg/head_localisation.tmp b/ui/ecobidas_ui/templates/generate/meeg/head_localisation.tmp new file mode 100644 index 00000000..81b6a7e5 --- /dev/null +++ b/ui/ecobidas_ui/templates/generate/meeg/head_localisation.tmp @@ -0,0 +1 @@ +Head localisation was continuous. diff --git a/ui/ecobidas_ui/templates/generate/meeg/meg_report.tmp b/ui/ecobidas_ui/templates/generate/meeg/meg_report.tmp new file mode 100644 index 00000000..62c6bd2e --- /dev/null +++ b/ui/ecobidas_ui/templates/generate/meeg/meg_report.tmp @@ -0,0 +1,21 @@ +{% include 'task_name.tmp' %} + +{% include 'institution.tmp' %} + +{% include 'device_info.tmp' %} + +{% include 'device_freq_config.tmp' %} + +{% include 'device_channel_count.tmp' %} + +{% include 'device_channels.tmp' %} + +{% include 'recording_properties.tmp' %} + +{% if ContinuousHeadLocalization %} +{% include 'head_localisation.tmp' %} +{% endif %} + +{% include 'dewar_positioning.tmp' %} + +{% include 'head_coil_frequency.tmp' %} diff --git a/ui/ecobidas_ui/templates/generate/meeg/recording_properties.tmp b/ui/ecobidas_ui/templates/generate/meeg/recording_properties.tmp new file mode 100644 index 00000000..ab1a98c9 --- /dev/null +++ b/ui/ecobidas_ui/templates/generate/meeg/recording_properties.tmp @@ -0,0 +1 @@ +The experiment was recorded during {{RecordingDuration}} seconds {{RecordingType}}. diff --git a/ui/ecobidas_ui/templates/generate/mri/acquisition/info.html b/ui/ecobidas_ui/templates/generate/mri/acquisition/info.html new file mode 100644 index 00000000..caff2b83 --- /dev/null +++ b/ui/ecobidas_ui/templates/generate/mri/acquisition/info.html @@ -0,0 +1,8 @@ +The anatomical MRI data were collected with following parameters. {% include +'generate/mri/acquisition/sequence.html' %} {% include +'generate/mri/acquisition/inplane_spatial_encoding.html' %} {% include +'generate/mri/acquisition/rf_contrasts.html' %} {% include +'generate/mri/acquisition/slice_acceleration.html' %} {% include +'generate/mri/acquisition/timing_parameters.html' %} ({{n_slices}} slices +acquired in XXXX order; field of view, FOV={{fov}}mm; matrix size={{ms}}; voxel +size={{vs}}mm). diff --git a/ui/ecobidas_ui/templates/generate/mri/acquisition/inplane_spatial_encoding.html b/ui/ecobidas_ui/templates/generate/mri/acquisition/inplane_spatial_encoding.html new file mode 100644 index 00000000..4ba10853 --- /dev/null +++ b/ui/ecobidas_ui/templates/generate/mri/acquisition/inplane_spatial_encoding.html @@ -0,0 +1,6 @@ +This data was acquired using {{NumberShots}} radio-frequency excitations, with a +phase encoding direction along {{PhaseEncodingDirection}}, with an effective +echo spacing {{EffectiveEchoSpacing}} seconds and total readout time of +{{TotalReadoutTime}}, using {{ParallelAcquisitionTechnique}} parallel imaging +with a factor of {{ParallelReductionFactorInPlane}}, a partial Fourrier of +{{PartialFourier}} in the {{PartialFourierDirection}} direction. diff --git a/ui/ecobidas_ui/templates/generate/mri/acquisition/rf_contrasts.html b/ui/ecobidas_ui/templates/generate/mri/acquisition/rf_contrasts.html new file mode 100644 index 00000000..3c4daf5d --- /dev/null +++ b/ui/ecobidas_ui/templates/generate/mri/acquisition/rf_contrasts.html @@ -0,0 +1 @@ +This data was acquired using a flip angle of {{FlipAngle}}. diff --git a/ui/ecobidas_ui/templates/generate/mri/acquisition/scanner_hardware.html b/ui/ecobidas_ui/templates/generate/mri/acquisition/scanner_hardware.html new file mode 100644 index 00000000..4ade7da0 --- /dev/null +++ b/ui/ecobidas_ui/templates/generate/mri/acquisition/scanner_hardware.html @@ -0,0 +1,10 @@ +MR data were acquired on {{StationName}} with software version: +{{SoftwareVersions}}. This MRI scanner is a {{MagneticFieldStrength}}-Tesla +{{ManufacturersModelName}} from {{Manufacturer}} with serial number +{{DeviceSerialNumber}}. A {{ReceiveCoilName}} receiver coil was used with the +following characteristics for the receiver coil ReceiveCoilActiveElements +{{ReceiveCoilActiveElements}}. A {{GradientSetType}} gradient coil was used. A +{{MRTransmitCoilSequence}} transmit coid was used. A {{MatrixCoilMode}} was used +to reduce the number of independent channels by combining in analog the signals +from multiple coil elements. The following coil combination method was used +{{CoilCombinationMethod}}. diff --git a/ui/ecobidas_ui/templates/generate/mri/acquisition/sequence.html b/ui/ecobidas_ui/templates/generate/mri/acquisition/sequence.html new file mode 100644 index 00000000..7063fd0c --- /dev/null +++ b/ui/ecobidas_ui/templates/generate/mri/acquisition/sequence.html @@ -0,0 +1,4 @@ +This data was acquired using a {{SequenceVariant}} variant of {{SequenceName}}, +a {{ScanningSequence}} {{PulseSequenceType}} with options {{ScanOptions}}. {% if +NonlinearGradientCorrection %} The image(s) were corrected for gradient +nonlinearities by this scanner sequence. {% endif %} {{PulseSequenceDetails}} diff --git a/ui/ecobidas_ui/templates/generate/mri/acquisition/slice_acceleration.html b/ui/ecobidas_ui/templates/generate/mri/acquisition/slice_acceleration.html new file mode 100644 index 00000000..e185be7d --- /dev/null +++ b/ui/ecobidas_ui/templates/generate/mri/acquisition/slice_acceleration.html @@ -0,0 +1,2 @@ +For this multiband acquisition, the multiband factor was +{{MultibandAccelerationFactor}}. diff --git a/ui/ecobidas_ui/templates/generate/mri/acquisition/timing_parameters.html b/ui/ecobidas_ui/templates/generate/mri/acquisition/timing_parameters.html new file mode 100644 index 00000000..01c9d3a3 --- /dev/null +++ b/ui/ecobidas_ui/templates/generate/mri/acquisition/timing_parameters.html @@ -0,0 +1,2 @@ +repetition time, TR={{tr}}ms; echo time, TE={{EchoTime}}ms; inversion time, +TE={{InversionTime}}ms; SliceTiming SliceEncodingDirection DwellTime diff --git a/ui/ecobidas_ui/templates/generate/mri/preprocessing/brain-extraction.html b/ui/ecobidas_ui/templates/generate/mri/preprocessing/brain-extraction.html new file mode 100644 index 00000000..8a037fd4 --- /dev/null +++ b/ui/ecobidas_ui/templates/generate/mri/preprocessing/brain-extraction.html @@ -0,0 +1,3 @@ +Brain extraction/Skull stripping was performed using {{ bet_method }} {{ +bet_software }} (version {{ bet_version}}) with the following parameters: {{ +bet_parameters }}. diff --git a/ui/ecobidas_ui/templates/generate/mri/preprocessing/coregistration.html b/ui/ecobidas_ui/templates/generate/mri/preprocessing/coregistration.html new file mode 100644 index 00000000..9e850cdf --- /dev/null +++ b/ui/ecobidas_ui/templates/generate/mri/preprocessing/coregistration.html @@ -0,0 +1,5 @@ +As part of the coregistration, the {{ func-anat_coreg__source_volume }} scan was +aligned to the {{ func-anat_coreg_target_volume }} scan using {{ +func-anat_coreg_method }} in {{ func-anat_coreg_software }} {{ +func-anat_coreg_version }} (cost function: {{ func-anat_coreg_cost_function }} +df: {{ func-anat_coreg_dof }}) diff --git a/ui/ecobidas_ui/templates/generate/mri/preprocessing/intensity-norm.html b/ui/ecobidas_ui/templates/generate/mri/preprocessing/intensity-norm.html new file mode 100644 index 00000000..837ad65b --- /dev/null +++ b/ui/ecobidas_ui/templates/generate/mri/preprocessing/intensity-norm.html @@ -0,0 +1,5 @@ +{% if intensity_normalization_choice %} {{ intensity_normalization_choice }} +intensity normalization was performed. {% endif %} {% if +structural_intensity_correction %} T1 images were bias field corrected. {% endif +%} {% if functional_intensity_correction %} Functional images were intensity +corrected to reduce interleaved acquisition artifacts. {% endif %} diff --git a/ui/ecobidas_ui/templates/generate/mri/preprocessing/operations-performed.html b/ui/ecobidas_ui/templates/generate/mri/preprocessing/operations-performed.html new file mode 100644 index 00000000..0e2e242e --- /dev/null +++ b/ui/ecobidas_ui/templates/generate/mri/preprocessing/operations-performed.html @@ -0,0 +1 @@ +The following preprocessing steps were performed: {{ order_of_operation }}. diff --git a/ui/ecobidas_ui/templates/generate/mri/preprocessing/quality-control-reports.html b/ui/ecobidas_ui/templates/generate/mri/preprocessing/quality-control-reports.html new file mode 100644 index 00000000..f6fcd47b --- /dev/null +++ b/ui/ecobidas_ui/templates/generate/mri/preprocessing/quality-control-reports.html @@ -0,0 +1,2 @@ +The following measures were taken to control image quality: {{ +quality_control_reports }}. diff --git a/ui/ecobidas_ui/templates/generate/mri/preprocessing/segmentation.html b/ui/ecobidas_ui/templates/generate/mri/preprocessing/segmentation.html new file mode 100644 index 00000000..cb4c214c --- /dev/null +++ b/ui/ecobidas_ui/templates/generate/mri/preprocessing/segmentation.html @@ -0,0 +1,3 @@ +# Segmentation Structural images were segmented using {{ segmentation_software` +`segmentation_version }} by {{ segmentation_method }} with the following +parameters: `segmentation_parameters` ## Example diff --git a/ui/ecobidas_ui/templates/generate/mri/preprocessing/slice-timing-correction.html b/ui/ecobidas_ui/templates/generate/mri/preprocessing/slice-timing-correction.html new file mode 100644 index 00000000..0ba3aa4f --- /dev/null +++ b/ui/ecobidas_ui/templates/generate/mri/preprocessing/slice-timing-correction.html @@ -0,0 +1,4 @@ +Slice timing correction was implemented in {{ stc_software }} ({{ stc_version +}}) and applied using {{ stc_method }}. Individual slices were realigned with +slice {{ stc_reference }} as a reference. As interpolation method, {{ +stc_interpolation }} interpolation was used. diff --git a/ui/ecobidas_ui/templates/generate/mri/preprocessing/smoothing.html b/ui/ecobidas_ui/templates/generate/mri/preprocessing/smoothing.html new file mode 100644 index 00000000..d36622d9 --- /dev/null +++ b/ui/ecobidas_ui/templates/generate/mri/preprocessing/smoothing.html @@ -0,0 +1,3 @@ +{{ smoothing_target_space }} were smoothed using {{ smoothing_software }} ({{ +smoothing_version }}) using a {{ smoothing_type }} (FWHM = {{ smoothing_size }} +mm) with a {{ filtering_approach }}. diff --git a/ui/ecobidas_ui/templates/generate/mri/preprocessing/software.html b/ui/ecobidas_ui/templates/generate/mri/preprocessing/software.html new file mode 100644 index 00000000..f5593ec2 --- /dev/null +++ b/ui/ecobidas_ui/templates/generate/mri/preprocessing/software.html @@ -0,0 +1 @@ +Raw fMRI data were preprocessed using {{ preprocessing_software }}. diff --git a/ui/ecobidas_ui/templates/generate/mri/preprocessing/t1-stabilization.html b/ui/ecobidas_ui/templates/generate/mri/preprocessing/t1-stabilization.html new file mode 100644 index 00000000..23f5d70e --- /dev/null +++ b/ui/ecobidas_ui/templates/generate/mri/preprocessing/t1-stabilization.html @@ -0,0 +1,2 @@ +For each functional run, the first {{ t1_stabilization }} volumes were removed +to discard unsteady signals. diff --git a/ui/ecobidas_ui/templates/generate/mri/preprocessing/volume-censoring.html b/ui/ecobidas_ui/templates/generate/mri/preprocessing/volume-censoring.html new file mode 100644 index 00000000..c5d373f4 --- /dev/null +++ b/ui/ecobidas_ui/templates/generate/mri/preprocessing/volume-censoring.html @@ -0,0 +1,5 @@ +{% if volume_censoring_used %} Volume censoring was applied using {{ +volume_censoring_method` ({{ volume_censoring_software }} version {{ +volume_censoring_version }}) with the following criteria {{ +volume_censoring_criteria }} {% if interpolation %} and `interpolation }} +interpolation {% endif %}. {% endif %} diff --git a/ui/ecobidas_ui/templates/generate/report.html b/ui/ecobidas_ui/templates/generate/report.html new file mode 100644 index 00000000..78c24b8d --- /dev/null +++ b/ui/ecobidas_ui/templates/generate/report.html @@ -0,0 +1,17 @@ +

    Institution

    +{% include 'generate/institution.html' %} + +

    Acquisition

    + +

    Scanner

    +{% include 'generate/device_info.html' %} {% include +'generate/mri/acquisition/scanner_hardware.html' %} + +

    Anatomical scans

    +{% include 'generate/mri/acquisition/info.html' %} + +

    Functional scans

    +{% include 'generate/task_name.html' %} {% include +'generate/mri/acquisition/info.html' %} + +

    Preprocessing

    diff --git a/ui/ecobidas_ui/templates/generate/task_name.html b/ui/ecobidas_ui/templates/generate/task_name.html new file mode 100644 index 00000000..08c8ec38 --- /dev/null +++ b/ui/ecobidas_ui/templates/generate/task_name.html @@ -0,0 +1 @@ +The following data correspond to the {{TaskName}} task. diff --git a/ui/ecobidas_ui/templates/layout/base.html b/ui/ecobidas_ui/templates/layout/base.html index 239ba9bf..a35edb49 100644 --- a/ui/ecobidas_ui/templates/layout/base.html +++ b/ui/ecobidas_ui/templates/layout/base.html @@ -14,10 +14,10 @@ {{ bootstrap.load_css() }} {% assets "css" %} {% endassets %} - + > diff --git a/ui/ecobidas_ui/templates/side_nav.html b/ui/ecobidas_ui/templates/side_nav.html index 0e9519b2..310cb657 100644 --- a/ui/ecobidas_ui/templates/side_nav.html +++ b/ui/ecobidas_ui/templates/side_nav.html @@ -16,7 +16,7 @@ -
  • - -
    • - -

    Report

    -
    {% include 'generate/report.html' %}
    -
    -
    -
    -{% endblock %} diff --git a/ui/ecobidas_ui/templates/generate/institution.jinja b/ui/ecobidas_ui/templates/generate/institution.jinja deleted file mode 100644 index 746ad7eb..00000000 --- a/ui/ecobidas_ui/templates/generate/institution.jinja +++ /dev/null @@ -1,2 +0,0 @@ -The recordings were performed in the {{ InstitutionName }}, -{{ InstitutionalDepartmentName }}, {{ InstitutionAddress }}. diff --git a/ui/ecobidas_ui/templates/generate/meeg/device_channel_count.tmp b/ui/ecobidas_ui/templates/generate/meeg/device_channel_count.tmp deleted file mode 100644 index 8bbb120a..00000000 --- a/ui/ecobidas_ui/templates/generate/meeg/device_channel_count.tmp +++ /dev/null @@ -1 +0,0 @@ -There were {{ MEGChannelCount }} MEG channels, {{ MEGREFChannelCount }} of which where MEG reference channels. diff --git a/ui/ecobidas_ui/templates/generate/meeg/device_channels.tmp b/ui/ecobidas_ui/templates/generate/meeg/device_channels.tmp deleted file mode 100644 index 548b3821..00000000 --- a/ui/ecobidas_ui/templates/generate/meeg/device_channels.tmp +++ /dev/null @@ -1,2 +0,0 @@ -Data was collected with {{ EEGChannelCount }} EEG channels, {{ EOGChannelCount }} EOG channels, -{{ ECGChannelCount }} ECG channels and {{ EMGChannelCount }} EMG channels recorded simultaneously. diff --git a/ui/ecobidas_ui/templates/generate/meeg/device_freq_config.tmp b/ui/ecobidas_ui/templates/generate/meeg/device_freq_config.tmp deleted file mode 100644 index 2b9b85a2..00000000 --- a/ui/ecobidas_ui/templates/generate/meeg/device_freq_config.tmp +++ /dev/null @@ -1 +0,0 @@ -Power line and sampling frequencies were {{ PowerLineFrequency }} Hz and {{ SamplingFrequency }} Hz, respectively. diff --git a/ui/ecobidas_ui/templates/generate/meeg/dewar_positioning.tmp b/ui/ecobidas_ui/templates/generate/meeg/dewar_positioning.tmp deleted file mode 100644 index 2758a381..00000000 --- a/ui/ecobidas_ui/templates/generate/meeg/dewar_positioning.tmp +++ /dev/null @@ -1 +0,0 @@ -The dewar was positioned {{ DewarPosition }} during the scan. diff --git a/ui/ecobidas_ui/templates/generate/meeg/eeg_channel_placement.tmp b/ui/ecobidas_ui/templates/generate/meeg/eeg_channel_placement.tmp deleted file mode 100644 index d2dc2ffe..00000000 --- a/ui/ecobidas_ui/templates/generate/meeg/eeg_channel_placement.tmp +++ /dev/null @@ -1 +0,0 @@ -Channels were placed according to the {{ EEGPlacementScheme }} with a {{ EEGGround }}. The {{ EEGReference }} were used as the reference. diff --git a/ui/ecobidas_ui/templates/generate/meeg/eeg_report.tmp b/ui/ecobidas_ui/templates/generate/meeg/eeg_report.tmp deleted file mode 100644 index 5ed7b7f9..00000000 --- a/ui/ecobidas_ui/templates/generate/meeg/eeg_report.tmp +++ /dev/null @@ -1,13 +0,0 @@ -{% include 'task_name.tmp' %} - -{% include 'institution.tmp' %} - -{% include 'device_info.tmp' %} - -{% include 'device_freq_config.tmp' %} - -{% include 'device_channels.tmp' %} - -{% include 'eeg_channel_placement.tmp' %} - -{% include 'recording_properties.tmp' %} diff --git a/ui/ecobidas_ui/templates/generate/meeg/head_coil_frequency.tmp b/ui/ecobidas_ui/templates/generate/meeg/head_coil_frequency.tmp deleted file mode 100644 index baa5c911..00000000 --- a/ui/ecobidas_ui/templates/generate/meeg/head_coil_frequency.tmp +++ /dev/null @@ -1 +0,0 @@ -Head localisation coils used frequencies of {% for f in HeadCoilFrequency %}{{ f }} Hz{% if loop.last -1 %} and {% elif not loop.last %}, {% endif %}{% endfor %}. diff --git a/ui/ecobidas_ui/templates/generate/meeg/head_localisation.tmp b/ui/ecobidas_ui/templates/generate/meeg/head_localisation.tmp deleted file mode 100644 index 81b6a7e5..00000000 --- a/ui/ecobidas_ui/templates/generate/meeg/head_localisation.tmp +++ /dev/null @@ -1 +0,0 @@ -Head localisation was continuous. diff --git a/ui/ecobidas_ui/templates/generate/meeg/meg_report.tmp b/ui/ecobidas_ui/templates/generate/meeg/meg_report.tmp deleted file mode 100644 index 62c6bd2e..00000000 --- a/ui/ecobidas_ui/templates/generate/meeg/meg_report.tmp +++ /dev/null @@ -1,21 +0,0 @@ -{% include 'task_name.tmp' %} - -{% include 'institution.tmp' %} - -{% include 'device_info.tmp' %} - -{% include 'device_freq_config.tmp' %} - -{% include 'device_channel_count.tmp' %} - -{% include 'device_channels.tmp' %} - -{% include 'recording_properties.tmp' %} - -{% if ContinuousHeadLocalization %} -{% include 'head_localisation.tmp' %} -{% endif %} - -{% include 'dewar_positioning.tmp' %} - -{% include 'head_coil_frequency.tmp' %} diff --git a/ui/ecobidas_ui/templates/generate/meeg/recording_properties.tmp b/ui/ecobidas_ui/templates/generate/meeg/recording_properties.tmp deleted file mode 100644 index a64f8e23..00000000 --- a/ui/ecobidas_ui/templates/generate/meeg/recording_properties.tmp +++ /dev/null @@ -1 +0,0 @@ -The experiment was recorded during {{ RecordingDuration }} seconds {{ RecordingType }}. diff --git a/ui/ecobidas_ui/templates/generate/mri/acquisition/info.jinja b/ui/ecobidas_ui/templates/generate/mri/acquisition/info.jinja deleted file mode 100644 index 6c13be68..00000000 --- a/ui/ecobidas_ui/templates/generate/mri/acquisition/info.jinja +++ /dev/null @@ -1,13 +0,0 @@ -The anatomical MRI data were collected with following parameters. - -{% include 'generate/mri/acquisition/sequence.jinja' %} - -{% include 'generate/mri/acquisition/inplane_spatial_encoding.jinja' %} - -{% include 'generate/mri/acquisition/rf_contrasts.jinja' %} - -{% include 'generate/mri/acquisition/slice_acceleration.jinja' %} - -{% include 'generate/mri/acquisition/timing_parameters.jinja' %} - -({{ n_slices }} slices acquired in XXXX order; field of view, FOV={{ fov }}mm; matrix size={{ ms }}; voxel size={{ vs }}mm). diff --git a/ui/ecobidas_ui/templates/generate/mri/acquisition/inplane_spatial_encoding.jinja b/ui/ecobidas_ui/templates/generate/mri/acquisition/inplane_spatial_encoding.jinja deleted file mode 100644 index ac6068b6..00000000 --- a/ui/ecobidas_ui/templates/generate/mri/acquisition/inplane_spatial_encoding.jinja +++ /dev/null @@ -1,6 +0,0 @@ -This data was acquired using {{ NumberShots }} radio-frequency excitations, with a -phase encoding direction along {{ PhaseEncodingDirection }}, with an effective -echo spacing {{ EffectiveEchoSpacing }} seconds and total readout time of -{{ TotalReadoutTime }}, using {{ ParallelAcquisitionTechnique }} parallel imaging -with a factor of {{ ParallelReductionFactorInPlane }}, a partial Fourrier of -{{ PartialFourier }} in the {{ PartialFourierDirection }} direction. diff --git a/ui/ecobidas_ui/templates/generate/mri/acquisition/rf_contrasts.jinja b/ui/ecobidas_ui/templates/generate/mri/acquisition/rf_contrasts.jinja deleted file mode 100644 index 7a12e393..00000000 --- a/ui/ecobidas_ui/templates/generate/mri/acquisition/rf_contrasts.jinja +++ /dev/null @@ -1 +0,0 @@ -This data was acquired using a flip angle of {{ FlipAngle }}. diff --git a/ui/ecobidas_ui/templates/generate/mri/acquisition/scanner_hardware.jinja b/ui/ecobidas_ui/templates/generate/mri/acquisition/scanner_hardware.jinja deleted file mode 100644 index c9771e40..00000000 --- a/ui/ecobidas_ui/templates/generate/mri/acquisition/scanner_hardware.jinja +++ /dev/null @@ -1,10 +0,0 @@ -MR data were acquired on {{ StationName }} with software version: -{{ SoftwareVersions }}. This MRI scanner is a {{ MagneticFieldStrength }}-Tesla -{{ ManufacturersModelName }} from {{ Manufacturer }} with serial number -{{ DeviceSerialNumber }}. A {{ ReceiveCoilName }} receiver coil was used with the -following characteristics for the receiver coil ReceiveCoilActiveElements -{{ ReceiveCoilActiveElements }}. A {{ GradientSetType }} gradient coil was used. A -{{ MRTransmitCoilSequence }} transmit coid was used. A {{ MatrixCoilMode }} was used -to reduce the number of independent channels by combining in analog the signals -from multiple coil elements. The following coil combination method was used -{{ CoilCombinationMethod }}. diff --git a/ui/ecobidas_ui/templates/generate/mri/acquisition/sequence.jinja b/ui/ecobidas_ui/templates/generate/mri/acquisition/sequence.jinja deleted file mode 100644 index 82377e59..00000000 --- a/ui/ecobidas_ui/templates/generate/mri/acquisition/sequence.jinja +++ /dev/null @@ -1,7 +0,0 @@ -This data was acquired using a {{ SequenceVariant }} variant of {{ SequenceName }}, -a {{ ScanningSequence }} {{ PulseSequenceType }} with options {{ ScanOptions }}. -{# #} -{% if NonlinearGradientCorrection %} -The image(s) were corrected for gradient nonlinearities by this scanner sequence. -{% endif %} -{{ PulseSequenceDetails }} diff --git a/ui/ecobidas_ui/templates/generate/mri/acquisition/slice_acceleration.jinja b/ui/ecobidas_ui/templates/generate/mri/acquisition/slice_acceleration.jinja deleted file mode 100644 index 5bfc0674..00000000 --- a/ui/ecobidas_ui/templates/generate/mri/acquisition/slice_acceleration.jinja +++ /dev/null @@ -1 +0,0 @@ -For this multiband acquisition, the multiband factor was {{ MultibandAccelerationFactor }}. diff --git a/ui/ecobidas_ui/templates/generate/mri/acquisition/timing_parameters.jinja b/ui/ecobidas_ui/templates/generate/mri/acquisition/timing_parameters.jinja deleted file mode 100644 index 05cc3f12..00000000 --- a/ui/ecobidas_ui/templates/generate/mri/acquisition/timing_parameters.jinja +++ /dev/null @@ -1,2 +0,0 @@ -repetition time, TR={{ tr }}ms; echo time, TE={{ EchoTime }}ms; inversion time, -TE={{ InversionTime }}ms; SliceTiming SliceEncodingDirection DwellTime diff --git a/ui/ecobidas_ui/templates/generate/mri/preprocessing/brain-extraction.jinja b/ui/ecobidas_ui/templates/generate/mri/preprocessing/brain-extraction.jinja deleted file mode 100644 index c671bb04..00000000 --- a/ui/ecobidas_ui/templates/generate/mri/preprocessing/brain-extraction.jinja +++ /dev/null @@ -1,3 +0,0 @@ -Brain extraction/Skull stripping was performed using {{ bet_method }} -{{ bet_software }} (version {{ bet_version }}) with the following parameters: -{{ bet_parameters }}. diff --git a/ui/ecobidas_ui/templates/generate/mri/preprocessing/coregistration.jinja b/ui/ecobidas_ui/templates/generate/mri/preprocessing/coregistration.jinja deleted file mode 100644 index 8a8e7ed8..00000000 --- a/ui/ecobidas_ui/templates/generate/mri/preprocessing/coregistration.jinja +++ /dev/null @@ -1,4 +0,0 @@ -As part of the coregistration, the {{ func_anat_coreg_source_volume }} scan was -aligned to the {{ func_anat_coreg_target_volume }} scan using -{{ func_anat_coreg_method }} in {{ func_anat_coreg_software }} -{{ func_anat_coreg_version }} (cost function: {{ func_anat_coreg_cost_function }} df: {{ func_anat_coreg_dof }}) diff --git a/ui/ecobidas_ui/templates/generate/mri/preprocessing/intensity-norm.jinja b/ui/ecobidas_ui/templates/generate/mri/preprocessing/intensity-norm.jinja deleted file mode 100644 index 110061d2..00000000 --- a/ui/ecobidas_ui/templates/generate/mri/preprocessing/intensity-norm.jinja +++ /dev/null @@ -1,9 +0,0 @@ -{% if intensity_normalization_choice %} -{{ intensity_normalization_choice }} intensity normalization was performed. -{% endif %} -{% if structural_intensity_correction %} -T1 images were bias field corrected. -{% endif %} -{% if functional_intensity_correction %} -Functional images were intensity corrected to reduce interleaved acquisition artifacts. -{% endif %} diff --git a/ui/ecobidas_ui/templates/generate/mri/preprocessing/operations-performed.jinja b/ui/ecobidas_ui/templates/generate/mri/preprocessing/operations-performed.jinja deleted file mode 100644 index 0e2e242e..00000000 --- a/ui/ecobidas_ui/templates/generate/mri/preprocessing/operations-performed.jinja +++ /dev/null @@ -1 +0,0 @@ -The following preprocessing steps were performed: {{ order_of_operation }}. diff --git a/ui/ecobidas_ui/templates/generate/mri/preprocessing/preprocessing.jinja b/ui/ecobidas_ui/templates/generate/mri/preprocessing/preprocessing.jinja deleted file mode 100644 index 345b7574..00000000 --- a/ui/ecobidas_ui/templates/generate/mri/preprocessing/preprocessing.jinja +++ /dev/null @@ -1,19 +0,0 @@ -{% include 'generate/mri/preprocessing/operations-performed.jinja' %} - -{% include 'generate/mri/preprocessing/software.jinja' %} - -{% include 'generate/mri/preprocessing/intensity-norm.jinja' %} - -{% include 'generate/mri/preprocessing/brain-extraction.jinja' %} - -{% include 'generate/mri/preprocessing/segmentation.jinja' %} - -{% include 'generate/mri/preprocessing/t1-stabilization.jinja' %} - -{% include 'generate/mri/preprocessing/coregistration.jinja' %} - -{% include 'generate/mri/preprocessing/slice-timing-correction.jinja' %} - -{% include 'generate/mri/preprocessing/quality-control-reports.jinja' %} - -{% include 'generate/mri/preprocessing/smoothing.jinja' %} diff --git a/ui/ecobidas_ui/templates/generate/mri/preprocessing/quality-control-reports.jinja b/ui/ecobidas_ui/templates/generate/mri/preprocessing/quality-control-reports.jinja deleted file mode 100644 index 174181bc..00000000 --- a/ui/ecobidas_ui/templates/generate/mri/preprocessing/quality-control-reports.jinja +++ /dev/null @@ -1 +0,0 @@ -The following measures were taken to control image quality: {{ quality_control_reports }}. diff --git a/ui/ecobidas_ui/templates/generate/mri/preprocessing/segmentation.jinja b/ui/ecobidas_ui/templates/generate/mri/preprocessing/segmentation.jinja deleted file mode 100644 index b48d9e99..00000000 --- a/ui/ecobidas_ui/templates/generate/mri/preprocessing/segmentation.jinja +++ /dev/null @@ -1,3 +0,0 @@ -Structural images were segmented using {{ segmentation_software }} -{{ segmentation_version }} by {{ segmentation_method }} with the following -parameters: {{ segmentation_parameters }} diff --git a/ui/ecobidas_ui/templates/generate/mri/preprocessing/slice-timing-correction.jinja b/ui/ecobidas_ui/templates/generate/mri/preprocessing/slice-timing-correction.jinja deleted file mode 100644 index 2673f7fe..00000000 --- a/ui/ecobidas_ui/templates/generate/mri/preprocessing/slice-timing-correction.jinja +++ /dev/null @@ -1,3 +0,0 @@ -Slice timing correction was implemented in {{ stc_software }} ({{ stc_version }}) and applied using {{ stc_method }}. -Individual slices were realigned with slice {{ stc_reference }} as a reference. -As interpolation method, {{ stc_interpolation }} interpolation was used. diff --git a/ui/ecobidas_ui/templates/generate/mri/preprocessing/smoothing.jinja b/ui/ecobidas_ui/templates/generate/mri/preprocessing/smoothing.jinja deleted file mode 100644 index f44697e5..00000000 --- a/ui/ecobidas_ui/templates/generate/mri/preprocessing/smoothing.jinja +++ /dev/null @@ -1,3 +0,0 @@ -{{ smoothing_target_space }} were smoothed using {{ smoothing_software }} -({{ smoothing_version }}) using a {{ smoothing_type }} -(FWHM = {{ smoothing_size }} mm) with a {{ filtering_approach }}. diff --git a/ui/ecobidas_ui/templates/generate/mri/preprocessing/software.jinja b/ui/ecobidas_ui/templates/generate/mri/preprocessing/software.jinja deleted file mode 100644 index f5593ec2..00000000 --- a/ui/ecobidas_ui/templates/generate/mri/preprocessing/software.jinja +++ /dev/null @@ -1 +0,0 @@ -Raw fMRI data were preprocessed using {{ preprocessing_software }}. diff --git a/ui/ecobidas_ui/templates/generate/mri/preprocessing/t1-stabilization.jinja b/ui/ecobidas_ui/templates/generate/mri/preprocessing/t1-stabilization.jinja deleted file mode 100644 index 0df0d5b8..00000000 --- a/ui/ecobidas_ui/templates/generate/mri/preprocessing/t1-stabilization.jinja +++ /dev/null @@ -1 +0,0 @@ -For each functional run, the first {{ t1_stabilization }} volumes were removed to discard unsteady signals. diff --git a/ui/ecobidas_ui/templates/generate/mri/preprocessing/volume-censoring.jinja b/ui/ecobidas_ui/templates/generate/mri/preprocessing/volume-censoring.jinja deleted file mode 100644 index f4a8d643..00000000 --- a/ui/ecobidas_ui/templates/generate/mri/preprocessing/volume-censoring.jinja +++ /dev/null @@ -1,5 +0,0 @@ -{% if volume_censoring_used %} -Volume censoring was applied using {{ volume_censoring_method }} -({{ volume_censoring_software }} version {{ volume_censoring_version }}) -with the following criteria {{ volume_censoring_criteria }} {% if interpolation %} and {{ interpolation }} interpolation {% endif %}. -{% endif %} diff --git a/ui/ecobidas_ui/templates/generate/report.html b/ui/ecobidas_ui/templates/generate/report.html deleted file mode 100644 index d228e9f4..00000000 --- a/ui/ecobidas_ui/templates/generate/report.html +++ /dev/null @@ -1,22 +0,0 @@ -

    Institution

    -{% include 'generate/institution.jinja' %} - -

    Acquisition

    - -

    Scanner

    -{% include 'generate/device_info.jinja' %} - -{% include 'generate/mri/acquisition/scanner_hardware.jinja' %} - -

    Anatomical scans

    -{% include 'generate/mri/acquisition/info.jinja' %} - -

    Functional scans

    -{% include 'generate/task_name.jinja' %} - -{% include 'generate/mri/acquisition/info.jinja' %} - -

    Preprocessing

    -{% include 'generate/mri/preprocessing/preprocessing.jinja' %} - -

    Analysis

    diff --git a/ui/ecobidas_ui/templates/generate/task_name.jinja b/ui/ecobidas_ui/templates/generate/task_name.jinja deleted file mode 100644 index d160a961..00000000 --- a/ui/ecobidas_ui/templates/generate/task_name.jinja +++ /dev/null @@ -1 +0,0 @@ -The following data correspond to the {{ TaskName }} task. diff --git a/ui/ecobidas_ui/templates/layout/base.html b/ui/ecobidas_ui/templates/layout/base.html deleted file mode 100644 index a35edb49..00000000 --- a/ui/ecobidas_ui/templates/layout/base.html +++ /dev/null @@ -1,100 +0,0 @@ - - - - - - - {% block title %} {% endblock %} - - - - {{ bootstrap.load_css() }} {% assets "css" %} - - {% endassets %} - - - - - {% include "layout/svg.html" %} - -
    -
    -
    - -
    -
    -
    - - {% with messages = get_flashed_messages(with_categories=true) %} - - {% if messages %} - - {% for category, message in messages %} -
    -
    - -
    -
    - {% endfor %} - - {% endif %} - - {% endwith %} - -
    - {% include "layout/nav.html" %} - -
    -
    - {% block content %} - - {% endblock %} -
    -
    - - - {{ bootstrap.load_js() }} -
    - - - {% include "layout/footer.html" %} - diff --git a/ui/ecobidas_ui/templates/layout/footer.html b/ui/ecobidas_ui/templates/layout/footer.html deleted file mode 100644 index c1ba239a..00000000 --- a/ui/ecobidas_ui/templates/layout/footer.html +++ /dev/null @@ -1,26 +0,0 @@ -
    -
    -
    -
    -
    eCobidas
    -
    UI version: {{ version }}
    -
    - - -
    -
    -
    -
    -
    diff --git a/ui/ecobidas_ui/templates/layout/nav.html b/ui/ecobidas_ui/templates/layout/nav.html deleted file mode 100644 index ef4e2ad9..00000000 --- a/ui/ecobidas_ui/templates/layout/nav.html +++ /dev/null @@ -1,82 +0,0 @@ -
    - -
    diff --git a/ui/ecobidas_ui/templates/layout/svg.html b/ui/ecobidas_ui/templates/layout/svg.html deleted file mode 100644 index 655bc1d1..00000000 --- a/ui/ecobidas_ui/templates/layout/svg.html +++ /dev/null @@ -1,21 +0,0 @@ - - - - - - - - - - - diff --git a/ui/ecobidas_ui/templates/protocol.html b/ui/ecobidas_ui/templates/protocol.html deleted file mode 100644 index 0e02cabe..00000000 --- a/ui/ecobidas_ui/templates/protocol.html +++ /dev/null @@ -1,57 +0,0 @@ -{% extends 'layout/base.html' %} - -{% from 'bootstrap5/form.html' import render_form %} - -{% block title %} eCOBIDAS - {{ protocol_pref_label }} {% endblock %} - -{% block content %} -
    -
    -
    -

    - {{ protocol_pref_label }} -

    - {% include "side_nav.html" %} -
    - -
    - {% if landing_page %} - - {{ protocol_preamble|safe }} - - {{ landing_page|safe }} {% else %} -

    {{ activity_pref_label }}

    - - {% if form %} -

    - -
    - -

    - {% endif %} - - {{ activity_preamble|safe }} - - {% include "extra_forms.html" %} - - {% if form %} -
    -
    {{ render_form(form) }}
    -
    - {% endif %} - - {% endif %} -
    -
    -
    -{% endblock %} diff --git a/ui/ecobidas_ui/templates/public/about.html b/ui/ecobidas_ui/templates/public/about.html deleted file mode 100644 index b581b65d..00000000 --- a/ui/ecobidas_ui/templates/public/about.html +++ /dev/null @@ -1,150 +0,0 @@ -{% extends 'layout/base.html' %} - -{% block title %} eCOBIDAS - About {% endblock %} - -{% block content %} -
    -
    -
    -

    Have any questions? Something is missing? Let us know.

    - -

    Why this project?

    -

    - Poor methods and results description hinders the reproducibility and the - replicability of research. It also makes it hard to compare new and old - results and generally increases inefficiency in the research process. - This project is built on the hope that improving methods and results - reporting could improve our research. -

    -

    - Follow the link if you want to know more about the - motivations behind this project. -

    -

    Background

    -

    - This checklist is a project to make a user friendly checklist out the - best practices - report - of the Committee on Best Practices in Data Analysis and Sharing (COBIDAS) of the - Organization for Human Brain Mapping. -

    -

    - This is very much of a work in progress but the next step is to expand - the list to cover all the items of the COBIDAS report for fMRI as well - as for the recent - extension to EEG and MEG. -

    -

    Want to help?

    -

    - We are currently working on trying to expand the number of items used in - the checklist. All of this work is done in google spreadsheets: the - spreadsheet for each section is accessible by clicking on the - Source - at the top of each page. -

    -

    Want to know more?

    -

    - Most of the information concerning this project can be found on this - github repository. -

    -

    - If you want to be kept posted about the progress of the project, you can - join our - google group -

    -

    - From more frequent updates and behind the scenes, come and join us on - the - cobidas_checklist channel on the brainhack - - - channel. - -

    -

    - There is also an OSF - project to centralize all the information and repos. -

    -

    - We have a - list - of short, middle, long term goals: if you are interested by any of those - get in touch. Many of them do not necessarily require super-advanced - technical skills (except maybe a certain love for working with - spreadsheet and wanting them to be super organized). -

    -

    Contributors

    -

    - The list of the people involved in this project can be found - here. -

    -
    -
    -
    -{% endblock %} diff --git a/ui/ecobidas_ui/templates/public/faq.html b/ui/ecobidas_ui/templates/public/faq.html deleted file mode 100644 index a004c667..00000000 --- a/ui/ecobidas_ui/templates/public/faq.html +++ /dev/null @@ -1,36 +0,0 @@ -{% extends "layout/base.html" %} {% block title %} eCOBIDAS - FAQ {% endblock %} -{% block content %} -
    -
    -
    - {% set count = [0] %} {% for s in data['sections'] %} -

    {{ s['name'] }}

    - {% for item in s['questions'] %} {% set _ = count.append(count.pop()+1) %} -
    -
    -

    - -

    -
    -
    {{ item['a']|safe }}
    -
    -
    -
    - {% endfor %} {% endfor %} -
    -
    - {% endblock %} -
    diff --git a/ui/ecobidas_ui/templates/public/index.html b/ui/ecobidas_ui/templates/public/index.html deleted file mode 100644 index 32c9b55a..00000000 --- a/ui/ecobidas_ui/templates/public/index.html +++ /dev/null @@ -1,23 +0,0 @@ -{% extends 'layout/base.html' %} - -{% block title %} eCOBIDAS {% endblock %} - -{% block content %} -
    -
    -
    -

    TBD

    - -

    - "Lorem ipsum dolor sit amet, consectetur adipiscing elit, sed do eiusmod - tempor incididunt ut labore et dolore magna aliqua. Ut enim ad minim - veniam, quis nostrud exercitation ullamco laboris nisi ut aliquip ex ea - commodo consequat. Duis aute irure dolor in reprehenderit in voluptate - velit esse cillum dolore eu fugiat nulla pariatur. Excepteur sint - occaecat cupidatat non proident, sunt in culpa qui officia deserunt - mollit anim id est laborum." -

    -
    -
    -
    -{% endblock %} diff --git a/ui/ecobidas_ui/templates/side_nav.html b/ui/ecobidas_ui/templates/side_nav.html deleted file mode 100644 index 310cb657..00000000 --- a/ui/ecobidas_ui/templates/side_nav.html +++ /dev/null @@ -1,28 +0,0 @@ -
    - -
    diff --git a/ui/ecobidas_ui/utils.py b/ui/ecobidas_ui/utils.py deleted file mode 100644 index d527089b..00000000 --- a/ui/ecobidas_ui/utils.py +++ /dev/null @@ -1 +0,0 @@ -LANG: str = "en" diff --git a/ui/pyproject.toml b/ui/pyproject.toml deleted file mode 100644 index d5501fc0..00000000 --- a/ui/pyproject.toml +++ /dev/null @@ -1,90 +0,0 @@ -[build-system] -build-backend = "hatchling.build" -requires = ["hatchling", "hatch-vcs"] - -[project] -authors = [{name = "Remi Gau"}] -dependencies = [ - "flask", - "Flask-WTF", - "Flask-Assets", - "bootstrap-flask", - "pandas", - "rich", - "requests", - "Flask-Caching", - "Flask-DebugToolbar", - "environs", - "markdownify" -] -description = "UI for eCOBIDAS" -license = {text = "GPL 3.0"} -maintainers = [{name = "Remi Gau", email = "remi.gau2@mcgill.ca"}] -name = "ecobidas_ui" -readme = "README.md" -requires-python = ">=3.11" -# Version from setuptools_scm -# dynamic = ["version"] -version = "0.1.0" - -[project.optional-dependencies] -dev = [ - 'tox' -] -test = [ - "coverage", - "pytest>=6.0.0", - "pytest-cov" -] - -[tool.black] -line-length = 100 - -[tool.codespell] -# ignore-words-list = "" -skip = "./.git,*.svg,env," - -[tool.hatch.build.hooks.vcs] -version-file = "ecobidas_ui/_version.py" - -[tool.hatch.build.targets.wheel] -packages = ["ecobidas_ui"] - -[tool.hatch.version] -source = "vcs" - -[tool.isort] -combine_as_imports = true -line_length = 100 -profile = "black" -skip_gitignore = true - -[tool.mypy] -check_untyped_defs = true -disallow_any_generics = true -disallow_incomplete_defs = true -disallow_untyped_defs = true -enable_error_code = ["ignore-without-code", "redundant-expr"] # "truthy-bool" -no_implicit_optional = true -show_error_codes = true -# strict = true -warn_redundant_casts = true -warn_unreachable = true -warn_unused_ignores = true - -[[tool.mypy.overrides]] -ignore_missing_imports = true -module = [ - "rich" -] - -[[tool.mypy.overrides]] -ignore_errors = true -module = ['tests.*'] - -[tool.pytest.ini_options] -addopts = "-ra --strict-config --strict-markers --doctest-modules --showlocals -s -v" -doctest_optionflags = "NORMALIZE_WHITESPACE ELLIPSIS" -junit_family = "xunit2" -minversion = "6.0" -xfail_strict = true diff --git a/ui/requirements.txt b/ui/requirements.txt deleted file mode 100644 index 302b83bb..00000000 --- a/ui/requirements.txt +++ /dev/null @@ -1,67 +0,0 @@ -# -# This file is autogenerated by pip-compile with Python 3.11 -# by the following command: -# -# pip-compile --output-file=requirements.txt --strip-extras pyproject.toml -# -Flask-Assets -blinker==1.8.2 - # via flask -bootstrap-flask==2.4.0 - # via ecobidas_ui (pyproject.toml) -certifi==2024.2.2 - # via requests -charset-normalizer==3.3.2 - # via requests -click==8.1.7 - # via flask -flask==3.0.3 - # via - # bootstrap-flask - # ecobidas_ui (pyproject.toml) - # flask-wtf -flask-wtf==1.2.1 - # via ecobidas_ui (pyproject.toml) -idna==3.7 - # via requests -itsdangerous==2.2.0 - # via - # flask - # flask-wtf -jinja2==3.1.4 - # via flask -markdown-it-py==3.0.0 - # via rich -markupsafe==2.1.5 - # via - # jinja2 - # werkzeug - # wtforms -mdurl==0.1.2 - # via markdown-it-py -numpy==1.26.4 - # via pandas -pandas==2.2.2 - # via ecobidas_ui (pyproject.toml) -pygments==2.18.0 - # via rich -python-dateutil==2.9.0.post0 - # via pandas -pytz==2024.1 - # via pandas -requests==2.32.2 - # via ecobidas_ui (pyproject.toml) -rich==13.7.1 - # via ecobidas_ui (pyproject.toml) -six==1.16.0 - # via python-dateutil -tzdata==2024.1 - # via pandas -urllib3==2.2.1 - # via requests -werkzeug==3.0.3 - # via flask -wtforms==3.1.2 - # via - # bootstrap-flask - # flask-wtf diff --git a/ui/tests/__init__.py b/ui/tests/__init__.py deleted file mode 100644 index e69de29b..00000000 diff --git a/ui/tests/conftest.py b/ui/tests/conftest.py deleted file mode 100644 index 44452705..00000000 --- a/ui/tests/conftest.py +++ /dev/null @@ -1,29 +0,0 @@ -import pytest -from ecobidas_ui.app import create_app - - -@pytest.fixture() -def app(): - app = create_app() - app.config.update( - { - "TESTING": True, - } - ) - - # other setup can go here - - yield app - - # clean up / reset resources here - - -@pytest.fixture() -def client(app): - return app.test_client() - - -@pytest.fixture -def app_context(app): - with app.app_context(): - yield diff --git a/ui/tests/protocols/conftest.py b/ui/tests/protocols/conftest.py deleted file mode 100644 index 2da42613..00000000 --- a/ui/tests/protocols/conftest.py +++ /dev/null @@ -1,60 +0,0 @@ -import pandas as pd -import pytest - - -@pytest.fixture -def participants_json(): - return { - "participant_id": {"Annotations": {"IsAbout": {"TermURL": "", "Label": ""}}}, - "age": { - "Annotations": { - "IsAbout": {"TermURL": "nb:Age", "Label": ""}, - "Transformation": {"TermURL": "nb:FromInt", "Label": "integer data"}, - "MissingValues": ["", "n/a", " "], - } - }, - } - - -@pytest.fixture -def participants_df(): - return pd.DataFrame( - { - "age": [ - 26, - 24, - 27, - 20, - 22, - 26, - 24, - 21, - 26, - 21, - 24, - 22, - 21, - 30, - 24, - 19, - ], - "sex": [ - "F", - "M", - "F", - "F", - "M,", - "F", - "M", - "M", - "M", - "F", - "F", - "F", - "F", - "F", - "F", - "M", - ], - } - ) diff --git a/ui/tests/protocols/test_forms.py b/ui/tests/protocols/test_forms.py deleted file mode 100644 index 1884ace7..00000000 --- a/ui/tests/protocols/test_forms.py +++ /dev/null @@ -1,12 +0,0 @@ -import pandas as pd -from ecobidas_ui.protocols.forms import validate_participants_json, validate_participants_tsv - - -def test_validate_participants_tsv(participants_df): - assert validate_participants_tsv(participants_df) - assert not validate_participants_tsv(pd.DataFrame()) - - -def test_validate_participants_json(participants_json): - assert validate_participants_json(participants_json) - assert not validate_participants_json({}) diff --git a/ui/tests/protocols/test_utils.py b/ui/tests/protocols/test_utils.py deleted file mode 100644 index 53736209..00000000 --- a/ui/tests/protocols/test_utils.py +++ /dev/null @@ -1,33 +0,0 @@ -import pytest -from ecobidas_ui.protocols.utils import ( - extract_values_participants, - get_nav_bar_content, - get_protocol, - prep_activity_page, - protocol_url, -) - - -def test_protocol_url(): - assert protocol_url("neurovault").suffix == ".jsonld" - assert protocol_url("neurovault").stem == "neurovault_schema" - - -def test_get_protocol(): - protocol_content = get_protocol("neurovault") - assert protocol_content["@id"] == "neurovault_schema.jsonld" - - -def test_get_nav_bar_content(): - nav_bar = get_nav_bar_content("neurovault", "Participants") - assert len(nav_bar) == 9 - assert nav_bar[2]["link"] == "#" - - -@pytest.mark.parametrize("activity_name", ["participants", "mri_acquisition"]) -def test_prep_activity_page(activity_name): - activities, activity, items = prep_activity_page("neurovault", activity_name) - - -def test_extract_values_participants(participants_df, participants_json): - assert extract_values_participants(participants_df, participants_json).subject_age_min == 19 diff --git a/ui/tests/test_app.py b/ui/tests/test_app.py deleted file mode 100644 index 7cc2db04..00000000 --- a/ui/tests/test_app.py +++ /dev/null @@ -1,9 +0,0 @@ -def test_request_example(client): - response = client.get("/") - assert b"eCOBIDAS" in response.data - response = client.get("/faq/") - assert b"FAQ" in response.data - response = client.get("/about/") - assert b"about" in response.data - response = client.get("/protocols/neurovault/mri_acquisition") - assert b"neurovault" in response.data diff --git a/ui/tmp/participants.json b/ui/tmp/participants.json deleted file mode 100644 index 7fe84dfb..00000000 --- a/ui/tmp/participants.json +++ /dev/null @@ -1,22 +0,0 @@ -{ - "sex": { - "LongName": "sex", - "Description": "String value indicating phenotypical sex.", - "TermURL": "http://purl.obolibrary.org/obo/PATO_0001894", - "Levels": { - "F": { - "Description": "Female", - "TermURL": "http://purl.obolibrary.org/obo/PATO_0000383" - }, - "M": { - "Description": "Male", - "TermURL": "http://purl.obolibrary.org/obo/PATO_0000384" - } - } - }, - "age": { - "LongName": "age", - "Units": "year", - "TermURL": "http://purl.obolibrary.org/obo/PATO_0000011" - } -} diff --git a/ui/tmp/participants.tsv b/ui/tmp/participants.tsv deleted file mode 100644 index 1bae496a..00000000 --- a/ui/tmp/participants.tsv +++ /dev/null @@ -1,35 +0,0 @@ -participant_id sex age -sub-01 F 29 -sub-02 M 21 -sub-03 M 18 -sub-04 F 27 -sub-05 M 24 -sub-06 M 18 -sub-07 M 19 -sub-08 F 21 -sub-09 M 18 -sub-10 F 20 -sub-11 F 26 -sub-12 F 19 -sub-13 F 23 -sub-14 F 25 -sub-15 F 22 -sub-16 M 22 -sub-17 F 18 -sub-18 F 21 -sub-19 M 21 -sub-20 F 18 -sub-21 M 18 -sub-22 M 19 -sub-23 F 20 -sub-24 M 21 -sub-25 M 18 -sub-26 F 24 -sub-27 M 25 -sub-28 M 20 -sub-29 M 20 -sub-30 F 21 -sub-31 M 41 -sub-32 F 25 -sub-33 M 23 -sub-34 F 29 diff --git a/ui/tox.ini b/ui/tox.ini deleted file mode 100644 index 4ff19c02..00000000 --- a/ui/tox.ini +++ /dev/null @@ -1,33 +0,0 @@ -; See https://tox.wiki/en -[tox] -requires = - tox>=4 -; run lint by default when just calling "tox" -env_list = lint - -; ENVIRONMENTS -; ------------ -[style] -description = common environment for style checkers (rely on pre-commit hooks) -skip_install = true -deps = - pre-commit - -; COMMANDS -; -------- -[testenv:lint] -description = install pre-commit hooks and run all linters and formatters -skip_install = true -deps = - {[style]deps} -commands = - pre-commit install - pre-commit run --all-files --show-diff-on-failure {posargs:} - -[testenv:update_dependencies] -description = update requirements.txt -skip_install = true -deps = - pip-tools -commands = - pip-compile --strip-extras -o requirements.txt pyproject.toml {posargs:} From 4fc27199280f0abf9237c8f7c6cbe740c3cde922 Mon Sep 17 00:00:00 2001 From: Remi Gau Date: Tue, 28 May 2024 15:43:55 +0200 Subject: [PATCH 27/31] update precommit --- .pre-commit-config.yaml | 4 ---- 1 file changed, 4 deletions(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 0403e4f6..9731853e 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -83,10 +83,6 @@ repos: hooks: - id: prettier types_or: [css, html, json] - # exclude: | - # (?x)^( - # ui/ecobidas_ui/static/css/font-awesome.min.css - # )$ # Check formatting HTML / Jinja # - repo: https://github.com/thibaudcolas/curlylint From 018423361e1481b8d649a319b04b7fa19132a106 Mon Sep 17 00:00:00 2001 From: Remi Gau Date: Tue, 28 May 2024 15:56:07 +0200 Subject: [PATCH 28/31] update all schemas --- cobidas_schema | 2 +- ecobidas/inputs/meeg/acquisition.tsv | 2 +- ecobidas/inputs/neurovault/neurovault.tsv | 176 ++++++++++---------- ecobidas/inputs/reexecution/reexecution.tsv | 2 +- mkdocs.yml | 6 +- 5 files changed, 94 insertions(+), 94 deletions(-) diff --git a/cobidas_schema b/cobidas_schema index c1621e78..a6753816 160000 --- a/cobidas_schema +++ b/cobidas_schema @@ -1 +1 @@ -Subproject commit c1621e7839c730963cdc735efa35ed9520b4df2a +Subproject commit a6753816ac6960e357e657378c882bb2593e3a28 diff --git a/ecobidas/inputs/meeg/acquisition.tsv b/ecobidas/inputs/meeg/acquisition.tsv index b47146cb..9a576796 100644 --- a/ecobidas/inputs/meeg/acquisition.tsv +++ b/ecobidas/inputs/meeg/acquisition.tsv @@ -20,7 +20,7 @@ Acquisition Data acquisition parameters Low- and high-pass filter characteristic Acquisition Data acquisition parameters Sampling frequency sampling_frequency sampling_frequency 21 1 1 Does the paper specify the sampling frequency? Acquisition Data acquisition parameters Continuous versus epoched acquisition? continuous_versus_epoched_acquisition? continuous_versus_epoched_acquisition 22 1 1 Does the paper specify whether continuous versus epoched acquisition was used? Acquisition Data acquisition parameters For EEG/EOG/ECG/EMG/skin conductance: report reference and ground electrode positions reference_and_ground_electrode_positions reference_and_ground_electrode_positions 23 1 1 (EEG/EOG/ECG/EMG/skin conductance) Does the paper report reference and ground electrode positions? -Acquisition Sensor position digitization EEG/EOG: manufacterer and model of the device used other_devices_for_meg other_devices_for_meg 25 1 1 (EEG/EOG) Does the paper specify the manufacterer and model of the device used for EEG/EOG - ECG?, All electrodes? +Acquisition Sensor position digitization EEG/EOG: manufacturer and model of the device used other_devices_for_meg other_devices_for_meg 25 1 1 (EEG/EOG) Does the paper specify the manufacturer and model of the device used for EEG/EOG - ECG?, All electrodes? Acquisition Sensor position digitization MEG: monitoring of head position relative to the sensor array monitoring_of_head_position monitoring_of_head_position 26 1 1 (MEG) Does the paper describe how head position relative to the sensor array was monitored? Acquisition Sensor position digitization MEG: use of head movement detection coils use_of_head_movement_detection_coils use_of_head_movement_detection_coils 27 1 1 (MEG) Does the paper specify the use of head movement detection coils? Acquisition Sensor position digitization MEG: placement of coils placement_of_coils placement_of_coils 28 1 1 (MEG) Does the paper specify the placement of coils? diff --git a/ecobidas/inputs/neurovault/neurovault.tsv b/ecobidas/inputs/neurovault/neurovault.tsv index c9a9c56c..2540a968 100644 --- a/ecobidas/inputs/neurovault/neurovault.tsv +++ b/ecobidas/inputs/neurovault/neurovault.tsv @@ -1,88 +1,88 @@ -activity_pref_label activity_order item_order question unit details field_type choices item item_pref_label visibility item_description include mandatory preamble bids_status bids_file bids_key bids_key_for_unit UUID -Experimental design 1 1 Type of design select blocked | event_related | hybrid block/event type_of_design type of design 1 type of design 1 1 Describe your experimental design #NAME? -Experimental design 1 2 Number of imaging runs acquired integer 0 number of imaging runs 1 number of imaging runs 1 2 #NAME? -Experimental design 1 3 Number of blocks, trials or experimental units per imaging run integer 0 number of experimental units 1 number of experimental units 1 2 #NAME? -Experimental design 1 4 Length of each imaging run seconds float 0 length of runs 1 length of runs 1 2 #NAME? -Experimental design 1 5 For blocked designs, length of blocks seconds float 0 length of blocks type_of_design in [0, 2] length of blocks 1 2 #NAME? -Experimental design 1 6 Length of individual trials seconds float 0 length of trials 1 length of trials 1 2 #NAME? -Experimental design 1 7 Was the design optimized for efficiency? radio preset:boolean optimization 1 optimization 1 2 #NAME? -Experimental design 1 8 What method was used for optimization? textarea optimization method optimization == 1 optimization method 1 3 #NAME? -Participants 2 1 Number of subjects entering into the analysis integer 0 number of subjects 1 number of subjects 1 1 Describe your participant sample #NAME? -Participants 2 2 Mean age of subjects float 0 subject age mean 1 subject age mean 1 1 #NAME? -Participants 2 3 Minimum age of subjects float 0 subject age min 1 subject age min 1 2 #NAME? -Participants 2 4 Maximum age of subjects float 0 subject age max 1 subject age max 1 2 #NAME? -Participants 2 5 Handedness of subjects radio right | left | both handedness 1 handedness 1 2 #NAME? -Participants 2 6 The proportion of subjects who were male float 0 | 1 proportion male subjects 1 proportion male subjects 1 2 #NAME? -Participants 2 7 Additional inclusion/exclusion criteria, if any. Including specific sampling strategies that limit inclusion to a specific group, such as laboratory members. textarea inclusion exclusion criteria 1 inclusion exclusion criteria 1 3 #NAME? -Participants 2 8 Number of subjects scanned but rejected from analysis integer 0 number of rejected subjects 1 number of rejected subjects 1 2 #NAME? -Participants 2 9 Was this study a comparison between subject groups? radio preset:boolean group comparison 1 group comparison 1 1 #NAME? -Participants 2 10 A description of the groups being compared textarea group description group_comparison == 1 group description 1 2 #NAME? -MRI acquisition 3 1 Manufacturer of MRI scanner select Siemens | Philips | General Electric | other Manufacturer scanner make 1 scanner make 1 1 Describe your acquisition parameters #NAME? -MRI acquisition 3 2 Model of MRI scanner textarea ManufacturersModelName scanner model 1 scanner model 1 1 #NAME? -MRI acquisition 3 3 Field strength of MRI scanner Tesla float 0 MagneticFieldStrength field strength 1 field strength 1 1 #NAME? -MRI acquisition 3 4 Description of pulse sequence used for fMRI select Gradient echo | Spin echo | Mutliband gradient echo | MPRAGE | MP2RAGE | FLASH PulseSequenceType pulse sequence 1 pulse sequence 1 1 #NAME? -MRI acquisition 3 5 Description of parallel imaging method and parameters textarea parallel imaging 1 parallel imaging 1 3 #NAME? -MRI acquisition 3 6 Imaging field of view Millimeters float field of view 1 field of view 1 2 #NAME? -MRI acquisition 3 7 Matrix size for MRI acquisition integer matrix size 1 matrix size 1 2 #NAME? -MRI acquisition 3 8 Distance between slices (includes skip or distance factor). Millimeters float 0 slice thickness 1 slice thickness 1 1 #NAME? -MRI acquisition 3 9 The size of the skipped area between slices. Millimeters float 0 skip factor 1 skip factor 1 2 #NAME? -MRI acquisition 3 10 The orientation of slices radio axial | sagittal | frontal acquisition orientation 1 acquisition orientation 1 2 #NAME? -MRI acquisition 3 11 Order of acquisition of slices select ascending | descending | interleaved SliceTiming order of acquisition 1 order of acquisition 1 3 #NAME? -MRI acquisition 3 12 Repetition time (TR) Milliseconds float 0 RepetitionTime repetition time 1 repetition time 1 1 #NAME? -MRI acquisition 3 13 Echo time (TE) Milliseconds float 0 EchoTime echo time 1 echo time 1 1 #NAME? -MRI acquisition 3 14 Flip angle Degrees float 0 FlipAngle flip angle 1 flip angle 1 2 #NAME? -Preprocessing 4 1 If a single software package was used for all analyses, specify that here select preset:mri_softwares SoftwareName software package 1 software package 1 1 Describe your preprocessing #NAME? -Preprocessing 4 2 Version of software package used textarea SoftwareVersion software version 1 software version 1 1 #NAME? -Preprocessing 4 3 Specify order of preprocessing operations textarea order of preprocessing operations 1 order of preprocessing operations 1 2 #NAME? -Preprocessing 4 4 Describe quality control measures textarea quality control 1 quality control 1 3 #NAME? -Preprocessing 4 5 Was B0 distortion correction used? radio preset:boolean used b0 unwarping 1 used b0 unwarping 1 2 #NAME? -Preprocessing 4 6 Specify software used for distortion correction if different from the main package select preset:mri_softwares b0 unwarping software used_b0_unwarping == 1 b0 unwarping software 1 3 #NAME? -Preprocessing 4 7 Was slice timing correction used? radio preset:boolean used slice timing correction 1 used slice timing correction 1 1 #NAME? -Preprocessing 4 8 Specify software used for slice timing correction if different from the main package select preset:mri_softwares slice timing correction software used_slice_timing_correction == 1 slice timing correction software 1 3 #NAME? -Preprocessing 4 9 Was motion correction used? radio preset:boolean used motion correction 1 used motion correction 1 1 #NAME? -Preprocessing 4 10 Specify software used for motion correction if different from the main package select preset:mri_softwares motion correction software used_motion_correction == 1 motion correction software 1 3 #NAME? -Preprocessing 4 11 Reference scan used for motion correction textarea motion correction reference used_motion_correction == 1 motion correction reference 1 3 #NAME? -Preprocessing 4 12 Similarity metric used for motion correction select preset:cost_functions motion correction metric used_motion_correction == 1 motion correction metric 1 3 #NAME? -Preprocessing 4 13 Interpolation method used for motion correction select preset:interpolations motion correction interpolation used_motion_correction == 1 motion correction interpolation 1 3 #NAME? -Preprocessing 4 14 Was motion-susceptibility correction used? radio preset:boolean used motion susceptibiity correction 1 used motion susceptibiity correction 1 3 #NAME? -Intersubject registration 5 1 Were subjects registered to a common stereotactic space? radio preset:boolean used intersubject registration 1 used intersubject registration 1 1 Describe your spatial normalization #NAME? -Intersubject registration 5 2 Specify software used for intersubject registration if different from main package select preset:mri_softwares intersubject registration software used_intersubject_registration == 1 intersubject registration software 1 2 #NAME? -Intersubject registration 5 3 Was linear or nonlinear registration used? select linear | non-linear intersubject transformation type used_intersubject_registration == 1 intersubject transformation type 1 1 #NAME? -Intersubject registration 5 4 If nonlinear registration was used, describe transform method textarea nonlinear transform type used_intersubject_registration == 1 and nonlinear_transform_type == 1 nonlinear transform type 1 2 #NAME? -Intersubject registration 5 5 Similarity metric used for intersubject registration textarea transform similarity metric used_intersubject_registration == 1 transform similarity metric 1 3 #NAME? -Intersubject registration 5 6 Interpolation method used for intersubject registration select preset:interpolations interpolation method used_intersubject_registration == 1 interpolation method 1 2 #NAME? -Intersubject registration 5 7 What type of image was used to determine the transformation to the atlas? textarea object image type used_intersubject_registration == 1 object image type 1 1 #NAME? -Intersubject registration 5 8 Were the functional images coregistered to the subject's structural image? radio preset:boolean functional coregistered to structural 1 functional coregistered to structural 1 2 #NAME? -Intersubject registration 5 9 Method used to coregister functional to structural images textarea functional coregistration method functional_coregistered_to_structural == 1 functional coregistration method 1 3 #NAME? -Intersubject registration 5 10 Name of coordinate space for registration target select MNI | Talairach | MNI2Tal | other coordinate space 1 coordinate space 1 1 #NAME? -Intersubject registration 5 11 Name of target template image textarea target template image 1 target template image 1 2 #NAME? -Intersubject registration 5 12 Voxel size of target template Millimeters float 0 target resolution 1 target resolution 1 1 #NAME? -Intersubject registration 5 13 Was spatial smoothing applied? radio preset:boolean used smoothing 1 used smoothing 1 1 #NAME? -Intersubject registration 5 14 Describe the type of smoothing applied textarea smoothing type used_smoothing == 1 smoothing type 1 1 #NAME? -Intersubject registration 5 15 The full-width at half-maximum of the smoothing kernel Millimeters float 0 smoothing fwhm used_smoothing == 1 smoothing fwhm 1 1 #NAME? -Intersubject registration 5 16 Voxel size in mm of the resampled, atlas-space images float 0 resampled voxel size 1 resampled voxel size 1 1 #NAME? -Individual subject modeling 6 1 Type of group model used radio Regression | other intrasubject model type 1 intrasubject model type 1 1 Describe your model specification at the subejct level #NAME? -Individual subject modeling 6 2 Estimation method used for model select ordinary least squares | generalized least squares | other intrasubject estimation type 1 intrasubject estimation type 1 1 #NAME? -Individual subject modeling 6 3 Software used for intrasubject modeling if different from overall package select preset:mri_softwares intrasubject modeling software 1 intrasubject modeling software 1 2 #NAME? -Individual subject modeling 6 4 Nature of HRF model select spm HRF | glover HRF | double gamma | Fourrier set | Finite Impulse Response | FLOBS | other hemodynamic response function 1 hemodynamic response function 1 2 #NAME? -Individual subject modeling 6 5 Were temporal derivatives included? radio preset:boolean used temporal derivatives 1 used temporal derivatives 1 2 #NAME? -Individual subject modeling 6 6 Were dispersion derivatives included? radio preset:boolean used dispersion derivatives 1 used dispersion derivatives 1 3 #NAME? -Individual subject modeling 6 7 Were motion regressors included? radio preset:boolean used motion regressors 1 used motion regressors 1 2 #NAME? -Individual subject modeling 6 8 Was a reaction time regressor included? radio preset:boolean used reaction time regressor 1 used reaction time regressor 1 2 #NAME? -Individual subject modeling 6 9 Were any regressors specifically orthogonalized with respect to others? radio preset:boolean used orthogonalization 1 used orthogonalization 1 1 #NAME? -Individual subject modeling 6 10 If orthogonalization was used, describe here textarea orthogonalization description used_orthogonalization == 1 orthogonalization description 1 2 #NAME? -Individual subject modeling 6 11 Was high pass filtering applied? radio preset:boolean used high pass filter 1 used high pass filter 1 1 #NAME? -Individual subject modeling 6 12 Describe method used for high pass filtering textarea high pass filter method used_high_pass_filter == 1 high pass filter method 1 2 #NAME? -Individual subject modeling 6 13 What autocorrelation model was used ? select SPM: global approximate AR(1) | SPM: FAST | FSL: locally regularized autocorrelation function | AFNI: ARMA | none | other autocorrelation model 1 autocorrelation model 1 2 #NAME? -Individual subject modeling 6 14 Exactly what terms are subtracted from what? textarea contrast definition 1 contrast definition 1 1 #NAME? -Individual subject modeling 6 15 Link to Cognitive Atlas definition of this contrast Define these in terms of task or stimulus conditions (e.g., 'one-back task with objects versus zero-back task with objects') instead of underlying psychological concepts (e.g., 'working memory'). textarea contrast definition cogatlas 1 contrast definition cogatlas 1 3 #NAME? -Group modeling 7 1 Type of group model used select Regression group model type 1 group model type 1 1 Describe the group level analysis #NAME? -Group modeling 7 2 Estimation method used for model select ordinary least squares | generalized least squares group estimation type 1 group estimation type 1 1 #NAME? -Group modeling 7 3 Software used for group modeling if different from overall package select preset:mri_softwares group modeling software 1 group modeling software 1 2 #NAME? -Group modeling 7 4 Type of inference for group model select random effect | mixed effect | fixed effect group inference type 1 group inference type 1 1 #NAME? -Group modeling 7 5 If more than 2-levels, describe the levels and assumptions of the model. For example, are variances assumed equal between groups. textarea group model multilevel 1 group model multilevel 1 3 #NAME? -Group modeling 7 6 Was this a repeated measures design at the group level? radio preset:boolean group repeated measures 1 group repeated measures 1 1 #NAME? -Group modeling 7 7 If multiple measurements per subject, list method to account for within subject correlation, exact assumptions made about correlation/variance textarea group repeated measures method group_repeated_measures == 1 group repeated measures method 1 3 #NAME? -Group inference 8 1 Type of statistic that is the basis of the inference select Z | T | F | X2 | PostProb | Non-parametric Permutations | Monte Carlo Permutations group statistic type 1 group statistic type 1 2 Describe your statistical inference #NAME? -Group inference 8 2 Parameters of the null distribution of the test statisic. Typically degrees of freedom (should be clear from the test statistic what these are). float group statistic parameters 1 group statistic parameters 1 1 #NAME? -Group inference 8 3 Noise smoothness for statistical inference This is the estimated smoothness used with Random Field Theory or a simulation-based inference method. float 0 group smoothness fwhm 1 group smoothness fwhm 1 1 #NAME? +activity_pref_label activity_order item_order question unit details field_type choices item item_pref_label visibility validation item_description include mandatory preamble bids_status bids_file bids_key bids_key_for_unit UUID +Experimental design 1 1 Type of design select blocked | event_related | hybrid block/event type_of_design type of design 1 type of design 1 1 Describe your experimental design #NAME? +Experimental design 1 2 Number of imaging runs acquired integer 0 number of imaging runs 1 number of imaging runs 1 2 #NAME? +Experimental design 1 3 Number of blocks, trials or experimental units per imaging run integer 0 number of experimental units 1 number of experimental units 1 2 #NAME? +Experimental design 1 4 Length of each imaging run seconds float 0 length of runs 1 length of runs 1 2 #NAME? +Experimental design 1 5 For blocked designs, length of blocks seconds float 0 length of blocks type_of_design in [0, 2] length of blocks 1 2 #NAME? +Experimental design 1 6 Length of individual trials seconds float 0 length of trials 1 length of trials 1 2 #NAME? +Experimental design 1 7 Was the design optimized for efficiency? radio preset:boolean optimization 1 optimization 1 2 #NAME? +Experimental design 1 8 What method was used for optimization? textarea optimization method optimization == 1 optimization method 1 3 #NAME? +Participants 2 1 Number of subjects entering into the analysis integer 0 number of subjects 1 number of subjects 1 1 Describe your participant sample #NAME? +Participants 2 2 Mean age of subjects float 0 | 120 subject_age_mean subject age mean 1 subject age mean 1 1 #NAME? +Participants 2 3 Minimum age of subjects float 0 | 120 subject_age_min subject age min 1 subject_age_min < subject_age_mean subject age min 1 2 #NAME? +Participants 2 4 Maximum age of subjects float 0 | 120 subject_age_max subject age max 1 subject_age_max > subject_age_mean subject age max 1 2 #NAME? +Participants 2 5 Handedness of subjects radio right | left | both handedness 1 handedness 1 2 #NAME? +Participants 2 6 The proportion of subjects who were male float 0 | 1 proportion male subjects 1 proportion male subjects 1 2 #NAME? +Participants 2 7 Additional inclusion/exclusion criteria, if any. Including specific sampling strategies that limit inclusion to a specific group, such as laboratory members. textarea inclusion exclusion criteria 1 inclusion exclusion criteria 1 3 #NAME? +Participants 2 8 Number of subjects scanned but rejected from analysis integer 0 number of rejected subjects 1 number of rejected subjects 1 2 #NAME? +Participants 2 9 Was this study a comparison between subject groups? radio preset:boolean group comparison 1 group comparison 1 1 #NAME? +Participants 2 10 A description of the groups being compared textarea group description group_comparison == 1 group description 1 2 #NAME? +MRI acquisition 3 1 Manufacturer of MRI scanner select Siemens | Philips | General Electric | other Manufacturer scanner make 1 scanner make 1 1 Describe your acquisition parameters #NAME? +MRI acquisition 3 2 Model of MRI scanner textarea ManufacturersModelName scanner model 1 scanner model 1 1 #NAME? +MRI acquisition 3 3 Field strength of MRI scanner Tesla float 0 | 20 MagneticFieldStrength field strength 1 field strength 1 1 #NAME? +MRI acquisition 3 4 Description of pulse sequence used for fMRI select Gradient echo | Spin echo | Mutliband gradient echo | MPRAGE | MP2RAGE | FLASH | other PulseSequenceType pulse sequence 1 pulse sequence 1 1 #NAME? +MRI acquisition 3 5 Description of parallel imaging method and parameters textarea parallel imaging 1 parallel imaging 1 3 #NAME? +MRI acquisition 3 6 Imaging field of view Millimeters float field of view 1 field of view 1 2 #NAME? +MRI acquisition 3 7 Matrix size for MRI acquisition integer matrix size 1 matrix size 1 2 #NAME? +MRI acquisition 3 8 Distance between slices (includes skip or distance factor). Millimeters float 0 slice thickness 1 slice thickness 1 1 #NAME? +MRI acquisition 3 9 The size of the skipped area between slices. Millimeters float 0 skip factor 1 skip factor 1 2 #NAME? +MRI acquisition 3 10 The orientation of slices radio axial | sagittal | frontal acquisition orientation 1 acquisition orientation 1 2 #NAME? +MRI acquisition 3 11 Order of acquisition of slices select ascending | descending | interleaved SliceTiming order of acquisition 1 order of acquisition 1 3 #NAME? +MRI acquisition 3 12 Repetition time (TR) Milliseconds float 0 RepetitionTime repetition time 1 repetition time 1 1 #NAME? +MRI acquisition 3 13 Echo time (TE) Milliseconds float 0 EchoTime echo time 1 echo time 1 1 #NAME? +MRI acquisition 3 14 Flip angle Degrees float 0 FlipAngle flip angle 1 flip angle 1 2 #NAME? +Preprocessing 4 1 If a single software package was used for all analyses, specify that here select preset:mri_softwares SoftwareName software package 1 software package 1 1 Describe your preprocessing #NAME? +Preprocessing 4 2 Version of software package used textarea SoftwareVersion software version 1 software version 1 1 #NAME? +Preprocessing 4 3 Specify order of preprocessing operations textarea order of preprocessing operations 1 order of preprocessing operations 1 2 #NAME? +Preprocessing 4 4 Describe quality control measures textarea quality control 1 quality control 1 3 #NAME? +Preprocessing 4 5 Was B0 distortion correction used? radio preset:boolean used b0 unwarping 1 used b0 unwarping 1 2 #NAME? +Preprocessing 4 6 Specify software used for distortion correction if different from the main package select preset:mri_softwares b0 unwarping software used_b0_unwarping == 1 b0 unwarping software 1 3 #NAME? +Preprocessing 4 7 Was slice timing correction used? radio preset:boolean used slice timing correction 1 used slice timing correction 1 1 #NAME? +Preprocessing 4 8 Specify software used for slice timing correction if different from the main package select preset:mri_softwares slice timing correction software used_slice_timing_correction == 1 slice timing correction software 1 3 #NAME? +Preprocessing 4 9 Was motion correction used? radio preset:boolean used motion correction 1 used motion correction 1 1 #NAME? +Preprocessing 4 10 Specify software used for motion correction if different from the main package select preset:mri_softwares motion correction software used_motion_correction == 1 motion correction software 1 3 #NAME? +Preprocessing 4 11 Reference scan used for motion correction textarea motion correction reference used_motion_correction == 1 motion correction reference 1 3 #NAME? +Preprocessing 4 12 Similarity metric used for motion correction select preset:cost_functions motion correction metric used_motion_correction == 1 motion correction metric 1 3 #NAME? +Preprocessing 4 13 Interpolation method used for motion correction select preset:interpolations motion correction interpolation used_motion_correction == 1 motion correction interpolation 1 3 #NAME? +Preprocessing 4 14 Was motion-susceptibility correction used? radio preset:boolean used motion susceptibiity correction 1 used motion susceptibiity correction 1 3 #NAME? +Intersubject registration 5 1 Were subjects registered to a common stereotactic space? radio preset:boolean used intersubject registration 1 used intersubject registration 1 1 Describe your spatial normalization #NAME? +Intersubject registration 5 2 Specify software used for intersubject registration if different from main package select preset:mri_softwares intersubject registration software used_intersubject_registration == 1 intersubject registration software 1 2 #NAME? +Intersubject registration 5 3 Was linear or nonlinear registration used? select linear | non-linear intersubject transformation type used_intersubject_registration == 1 intersubject transformation type 1 1 #NAME? +Intersubject registration 5 4 If nonlinear registration was used, describe transform method textarea nonlinear transform type used_intersubject_registration == 1 and nonlinear_transform_type == 1 nonlinear transform type 1 2 #NAME? +Intersubject registration 5 5 Similarity metric used for intersubject registration textarea transform similarity metric used_intersubject_registration == 1 transform similarity metric 1 3 #NAME? +Intersubject registration 5 6 Interpolation method used for intersubject registration select preset:interpolations interpolation method used_intersubject_registration == 1 interpolation method 1 2 #NAME? +Intersubject registration 5 7 What type of image was used to determine the transformation to the atlas? textarea object image type used_intersubject_registration == 1 object image type 1 1 #NAME? +Intersubject registration 5 8 Were the functional images coregistered to the subject's structural image? radio preset:boolean functional coregistered to structural 1 functional coregistered to structural 1 2 #NAME? +Intersubject registration 5 9 Method used to coregister functional to structural images textarea functional coregistration method functional_coregistered_to_structural == 1 functional coregistration method 1 3 #NAME? +Intersubject registration 5 10 Name of coordinate space for registration target select MNI | Talairach | MNI2Tal | other coordinate space 1 coordinate space 1 1 #NAME? +Intersubject registration 5 11 Name of target template image textarea target template image 1 target template image 1 2 #NAME? +Intersubject registration 5 12 Voxel size of target template Millimeters float 0 target resolution 1 target resolution 1 1 #NAME? +Intersubject registration 5 13 Was spatial smoothing applied? radio preset:boolean used smoothing 1 used smoothing 1 1 #NAME? +Intersubject registration 5 14 Describe the type of smoothing applied textarea smoothing type used_smoothing == 1 smoothing type 1 1 #NAME? +Intersubject registration 5 15 The full-width at half-maximum of the smoothing kernel Millimeters float 0 smoothing fwhm used_smoothing == 1 smoothing fwhm 1 1 #NAME? +Intersubject registration 5 16 Voxel size in mm of the resampled, atlas-space images float 0 resampled voxel size 1 resampled voxel size 1 1 #NAME? +Individual subject modeling 6 1 Type of group model used radio Regression | other intrasubject model type 1 intrasubject model type 1 1 Describe your model specification at the subejct level #NAME? +Individual subject modeling 6 2 Estimation method used for model select ordinary least squares | generalized least squares | other intrasubject estimation type 1 intrasubject estimation type 1 1 #NAME? +Individual subject modeling 6 3 Software used for intrasubject modeling if different from overall package select preset:mri_softwares intrasubject modeling software 1 intrasubject modeling software 1 2 #NAME? +Individual subject modeling 6 4 Nature of HRF model select spm HRF | glover HRF | double gamma | Fourrier set | Finite Impulse Response | FLOBS | other hemodynamic response function 1 hemodynamic response function 1 2 #NAME? +Individual subject modeling 6 5 Were temporal derivatives included? radio preset:boolean used temporal derivatives 1 used temporal derivatives 1 2 #NAME? +Individual subject modeling 6 6 Were dispersion derivatives included? radio preset:boolean used dispersion derivatives 1 used dispersion derivatives 1 3 #NAME? +Individual subject modeling 6 7 Were motion regressors included? radio preset:boolean used motion regressors 1 used motion regressors 1 2 #NAME? +Individual subject modeling 6 8 Was a reaction time regressor included? radio preset:boolean used reaction time regressor 1 used reaction time regressor 1 2 #NAME? +Individual subject modeling 6 9 Were any regressors specifically orthogonalized with respect to others? radio preset:boolean used orthogonalization 1 used orthogonalization 1 1 #NAME? +Individual subject modeling 6 10 If orthogonalization was used, describe here textarea orthogonalization description used_orthogonalization == 1 orthogonalization description 1 2 #NAME? +Individual subject modeling 6 11 Was high pass filtering applied? radio preset:boolean used high pass filter 1 used high pass filter 1 1 #NAME? +Individual subject modeling 6 12 Describe method used for high pass filtering textarea high pass filter method used_high_pass_filter == 1 high pass filter method 1 2 #NAME? +Individual subject modeling 6 13 What autocorrelation model was used ? select SPM: global approximate AR(1) | SPM: FAST | FSL: locally regularized autocorrelation function | AFNI: ARMA | none | other autocorrelation model 1 autocorrelation model 1 2 #NAME? +Individual subject modeling 6 14 Exactly what terms are subtracted from what? textarea contrast definition 1 contrast definition 1 1 #NAME? +Individual subject modeling 6 15 Link to Cognitive Atlas definition of this contrast Define these in terms of task or stimulus conditions (for example 'one-back task with objects versus zero-back task with objects') instead of underlying psychological concepts (for example 'working memory'). textarea contrast definition cogatlas 1 contrast definition cogatlas 1 3 #NAME? +Group modeling 7 1 Type of group model used select Regression group model type 1 group model type 1 1 Describe the group level analysis #NAME? +Group modeling 7 2 Estimation method used for model select ordinary least squares | generalized least squares | other group estimation type 1 group estimation type 1 1 #NAME? +Group modeling 7 3 Software used for group modeling if different from overall package select preset:mri_softwares group modeling software 1 group modeling software 1 2 #NAME? +Group modeling 7 4 Type of inference for group model select random effect | mixed effect | fixed effect group inference type 1 group inference type 1 1 #NAME? +Group modeling 7 5 If more than 2-levels, describe the levels and assumptions of the model. For example, are variances assumed equal between groups. textarea group model multilevel 1 group model multilevel 1 3 #NAME? +Group modeling 7 6 Was this a repeated measures design at the group level? radio preset:boolean group repeated measures 1 group repeated measures 1 1 #NAME? +Group modeling 7 7 If multiple measurements per subject, list method to account for within subject correlation, exact assumptions made about correlation/variance textarea group repeated measures method group_repeated_measures == 1 group repeated measures method 1 3 #NAME? +Group inference 8 1 Type of statistic that is the basis of the inference select Z | T | F | X2 | PostProb | Non-parametric Permutations | Monte Carlo Permutations | other group statistic type 1 group statistic type 1 2 Describe your statistical inference #NAME? +Group inference 8 2 Parameters of the null distribution of the test statisic. Typically degrees of freedom (should be clear from the test statistic what these are). float group statistic parameters 1 group statistic parameters 1 1 #NAME? +Group inference 8 3 Noise smoothness for statistical inference This is the estimated smoothness used with Random Field Theory or a simulation-based inference method. float 0 group smoothness fwhm 1 group smoothness fwhm 1 1 #NAME? diff --git a/ecobidas/inputs/reexecution/reexecution.tsv b/ecobidas/inputs/reexecution/reexecution.tsv index 56c6a8da..05adfd49 100644 --- a/ecobidas/inputs/reexecution/reexecution.tsv +++ b/ecobidas/inputs/reexecution/reexecution.tsv @@ -20,7 +20,7 @@ include activity_pref_label activity_order item_order item item_pref_label item_ 1 analysis 3 6 preprocessing_parameters_specified preprocessing parameters specified preprocessing parameters specified 1 1 Are the detailed processing parameters specified? radio yes | some details provided | no 1 analysis 3 7 analysis_reexecutable analysis reexecutable analysis reexecutable 1 1 Do you think a reasonably skilled image analyst could re-execute this analysis (including getting the specified versions of the tools and operating system indicated)? radio yes | approximately | no | I am not sure 1 statistics 4 1 statistical_tools_specified statistical tools specified statistical tools specified 1 1 Are the statistical tools / packages specified? radio preset:boolean -1 statistics 4 2 statitical_tools_and_versions statitical tools and versions statitical tools and versions 1 statistical_tools_specified == 1 List the tools and versions indicated (i.e. Stata 5.0). If more than one tool used, use a new line for each tool. textarea +1 statistics 4 2 statistical_tools_and_versions statistical tools and versions statistical tools and versions 1 statistical_tools_specified == 1 List the tools and versions indicated (i.e. Stata 5.0). If more than one tool used, use a new line for each tool. textarea 1 statistics 4 3 statistics_OS_specified statistics OS specified statistics OS specified 1 1 Is the operating system used for the statistical tool(s) specified? radio preset:boolean 1 statistics 4 4 statistics_OS_class statistics OS class statistics OS class 0 statistics_OS_specified == 1 Which class of operating system was indicated for the statistical analysis? radio preset:operating_systems 1 statistics 4 5 statistics_OS_details statistics OS details statistics OS details 0 statistics_OS_specified == 1 Describe the operating system details (i.e. specific version) provided (i.e. MacOS 10.12.6). textarea diff --git a/mkdocs.yml b/mkdocs.yml index 4ae36e18..b1357869 100644 --- a/mkdocs.yml +++ b/mkdocs.yml @@ -93,14 +93,14 @@ markdown_extensions: - md_in_html - pymdownx.details - pymdownx.emoji: - emoji_generator: !%21python/name:material.extensions.emoji.to_svg - emoji_index: !%21python/name:material.extensions.emoji.twemoji + emoji_generator: !!python/name:material.extensions.emoji.to_svg + emoji_index: !!python/name:material.extensions.emoji.twemoji - pymdownx.snippets - pymdownx.superfences: custom_fences: - name: mermaid class: mermaid - format: !%21python/name:pymdownx.superfences.fence_code_format + format: !!python/name:pymdownx.superfences.fence_code_format - tables - toc: anchorlink: true From 312e831d61f8edab38a7f88250bfa401c26cb180 Mon Sep 17 00:00:00 2001 From: Remi Gau Date: Tue, 28 May 2024 16:01:15 +0200 Subject: [PATCH 29/31] update precommit --- .pre-commit-config.yaml | 6 ------ 1 file changed, 6 deletions(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 607d7d6c..f4162e95 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -84,12 +84,6 @@ repos: - id: prettier types_or: [css, html, json] -# Check formatting HTML / Jinja -# - repo: https://github.com/thibaudcolas/curlylint - # rev: v0.13.1 - # hooks: - # - id: curlylint - # Check that Python code complies with PEP8 guidelines # flake8 uses pydocstyle to check docstrings: https://flake8.pycqa.org/en/latest/ # flake8-docstrings: https://pypi.org/project/flake8-docstrings/ From 0041650af4298af9b3e6dd71f865554ee1a1e8f4 Mon Sep 17 00:00:00 2001 From: Remi Gau Date: Tue, 28 May 2024 16:11:27 +0200 Subject: [PATCH 30/31] drop reproschema-ui --- .gitmodules | 4 ---- reproschema-ui | 1 - 2 files changed, 5 deletions(-) delete mode 160000 reproschema-ui diff --git a/.gitmodules b/.gitmodules index 319563bd..105e508b 100644 --- a/.gitmodules +++ b/.gitmodules @@ -9,7 +9,3 @@ [submodule "reproschema-py"] path = reproschema-py url = https://github.com/Remi-Gau/reproschema-py.git -[submodule "reproschema-ui"] - path = reproschema-ui - url = https://github.com/Remi-Gau/reproschema-ui.git - datalad-url = https://github.com/Remi-Gau/reproschema-ui.git diff --git a/reproschema-ui b/reproschema-ui deleted file mode 160000 index eb11cd6c..00000000 --- a/reproschema-ui +++ /dev/null @@ -1 +0,0 @@ -Subproject commit eb11cd6ce4ad250e4bf053cfe2932b466190ac73 From e279d5dec0fd340e9018c0a755c20b8c8441f6df Mon Sep 17 00:00:00 2001 From: Remi Gau Date: Tue, 28 May 2024 16:15:09 +0200 Subject: [PATCH 31/31] fix tests --- tests/test_item.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/tests/test_item.py b/tests/test_item.py index acc7c78b..86d6500e 100644 --- a/tests/test_item.py +++ b/tests/test_item.py @@ -39,7 +39,7 @@ def test_preset(): @pytest.mark.parametrize( - "input, expected", + "input_str, expected", [ ("_i[t]em-n:a m!e", "_item-na_me"), # alphanumeric with _ and - only ("item name", "item_name"), @@ -164,7 +164,7 @@ def test_get_item_info_with_only_name(): @pytest.mark.parametrize( - "input, expected", + "input_value, expected", [ (float("nan"), True), ("1", True),