Merge remote-tracking branch 'upstream/master' into link_check

.codespellrc

@@ -0,0 +1,4 @@
+[codespell]
+skip = env,venv,*.svg
+ignore-words-list = HSI
+builtin = clear,rare

.github/dependabot.yml

@@ -0,0 +1,9 @@
+---
+# Documentation
+# https://docs.github.com/en/code-security/dependabot/dependabot-version-updates/configuration-options-for-the-dependabot.yml-file
+version: 2
+updates:
+-   package-ecosystem: github-actions
+    directory: /
+    schedule:
+        interval: monthly

.github/workflows/run_precommit.yml

@@ -0,0 +1,15 @@
+---
+name: pre-commit
+
+on:
+    pull_request:
+    push:
+        branches: [main]
+
+jobs:
+    pre-commit:
+        runs-on: ubuntu-latest
+        steps:
+        -   uses: actions/checkout@v4
+        -   uses: actions/setup-python@v5
+        -   uses: pre-commit/[email protected]

.github/workflows/update_precommit_hooks.yml

@@ -0,0 +1,53 @@
+---
+name: Update precommit hooks
+
+
+on:
+
+# Uses the cron schedule for github actions
+#
+# https://docs.github.com/en/free-pro-team@latest/actions/reference/events-that-trigger-workflows#scheduled-events
+#
+#            ┌───────────── minute (0 - 59)
+#            │ ┌───────────── hour (0 - 23)
+#            │ │ ┌───────────── day of the month (1 - 31)
+#            │ │ │ ┌───────────── month (1 - 12 or JAN-DEC)
+#            │ │ │ │ ┌───────────── day of the week (0 - 6 or SUN-SAT)
+#            │ │ │ │ │
+#            │ │ │ │ │
+#            │ │ │ │ │
+#            * * * * *
+    schedule:
+    -   cron: 0 0 * 1,7 * # january and july
+
+  # Allows you to run this workflow manually from the Actions tab
+    workflow_dispatch:
+
+jobs:
+    update_precommit_hooks:
+
+    # only run on upstream repo
+        if: github.repository_owner == 'SIMEXP'
+
+        runs-on: ubuntu-latest
+        steps:
+        -   name: Checkout repo
+            uses: actions/checkout@v4
+        -   name: Set up Python
+            uses: actions/setup-python@v5
+            with:
+                python-version: '3.12'
+                allow-prereleases: false
+        -   name: Install pre-commit
+            run: pip install pre-commit
+        -   name: Update pre-commit hooks
+            run: pre-commit autoupdate
+        -   name: Create Pull Request
+            uses: peter-evans/create-pull-request@v5
+            with:
+                commit-message: pre-commit hooks auto-update
+                base: main
+                token: ${{ secrets.GITHUB_TOKEN }}
+                delete-branch: true
+                title: '[BOT] update pre-commit hooks'
+                body: done via this [GitHub Action](https://github.com/${{ github.repository_owner }}/reproschema /blob/main/.github/workflows/update_precommit_hooks.yml)

.pre-commit-config.yaml

@@ -2,13 +2,19 @@
 # See https://pre-commit.com/hooks.html for more hooks
 repos:
 -   repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v2.0.0
+    rev: v4.5.0
     hooks:
     -   id: trailing-whitespace
     -   id: end-of-file-fixer
     -   id: check-yaml
+    -   id: check-json
+    -   id: check-ast
     -   id: check-added-large-files
 -   repo: https://github.com/psf/black
-    rev: 19.3b0
+    rev: 24.3.0
     hooks:
     -   id: black
+-   repo: https://github.com/codespell-project/codespell
+    rev: v2.2.6
+    hooks:
+    -   id: codespell

docs/01_introduction.md

@@ -35,7 +35,7 @@ these questionnaires. However, these resources are often used to make data
 consistent and reusable after, rather than during data collection. However,
 harmonizing data after acquisition is resource intensive and this approach can
 create a mismatch between collected and submitted data due to human error during
-the harmonization process. To faciliate tedious harmonization efforts, several
+the harmonization process. To facilitate tedious harmonization efforts, several
 projects, over the last two decades, have developed technologies to automatically
 or interactively align and harmonize data elements (e.g., BIRN mediator, OpenRefine).
 

docs/30_schema.md

@@ -9,7 +9,7 @@ include:
 We have used schema.org classes and properties where it maps on to the needs of
 the model and extended the model with NIDM elements to harmonize across ReproNim
 projects.
-1. Allowing for structued nested elements in a schema
+1. Allowing for structured nested elements in a schema
 `Protocol > Activity > [Activity | Field > ResponseOption]`. This nested
 structure provides a flexible schema to represent nested activities, which are
 common in biomedical and other domains.
@@ -38,7 +38,7 @@ used.
 participant.
 1. Allowing for user interface (UI) elements that allow interaction between the schema
 and any implementation that allows collecting data using the schema. By providing
-some additional UI elements the provider can guide an implementor to allow for
+some additional UI elements the provider can guide an implementer to allow for
 more complex data collection behavior.
 
 The [ReproSchema-UI](https://repronim.org/reproschema-ui) is a prototype implementation of an UI that leverages these

docs/41_create_new_protocol.md

@@ -6,7 +6,7 @@ Ready for your first ReproSchema project?! We are going to use the [Reproschema
 
 1. Prerequisite: Ensure you have Git and Cookiecutter installed on your system. If not, please refer to the installation guides for Git and Cookiecutter.
 2. Generate Your Repository: Use the Reproschema Protocol Cookiecutter to create a new repository for your research protocol. Run the following command in your terminal:
-    
+
 ```bash
 cookiecutter gh:ReproNim/reproschema-protocol-cookiecutter
 ```

docs/42_adopt_assessments.md

@@ -1,12 +1,12 @@
-# Adopting Assessments from the reproschema-library 
+# Adopting Assessments from the reproschema-library
 
 This part focuses on how to select and integrate assessments from the reproschema-library into your research protocol, an essential step in crafting a comprehensive study. The chosen assessments are to be placed in the `activities` folder within your repository. This folder serves as the central hub for various assessments or activities that collectively form your research protocol.
 
 Each activity or assessment within this `activities` folder is typically structured around a file named with a suffix `_schema`. This file defines the overall framework of the assessment. Accompanying this, if an assessment comprises specific questions, these are organized in a subfolder titled `items` within the respective activity's directory. It's important to note that if an assessment is directly taken from the ReproSchema-library without any customization, the creation of an `items` subfolder is not necessary, as the itemized questions are predefined in the library.
 
 To illustrate this process, we will use two specific types of assessments from [reproschema-library](https://github.com/ReproNim/reproschema-library): `demographics` and `psychological questions`. The latter represents a composite assessment created from multiple pre-existing assessments within the library. This example demonstrates how to combine different elements from the library to construct a bespoke assessment tailored to the unique demands of your research protocol.
 
-## Step 1: Understand the structure of a *_schema file throught this [exemplar file](https://github.com/ReproNim/reproschema-protocol-cookiecutter/blob/main/%7B%7Bcookiecutter.protocol_name%7D%7D/activities/Activity1/activity1_schema)
+## Step 1: Understand the structure of a *_schema file through this [exemplar file](https://github.com/ReproNim/reproschema-protocol-cookiecutter/blob/main/%7B%7Bcookiecutter.protocol_name%7D%7D/activities/Activity1/activity1_schema)
 
 1. **Context (@context)**: This field provides references to the context definitions. In this schema, it links to the generic context of ReproSchema and the specific context for the items in the repository, defined by the URL with the "rl" key. This context helps to interpret the terms used within the schema.
 2. **Type (@type)**: Defined as "reproschema:Activity," this indicates the nature of the document, specifying that it is an activity within the ReproSchema framework.
@@ -34,7 +34,7 @@ This step involves precise modifications, particularly in the `@context` and `ad
 
     Labeling this link as "demo" directs the schema to the location in the ReproSchema-library where items for demographics and background information are defined. We use the link with a specific commit ID to ensure the consistency of the assessment version. This contextual link allows the schema to access the detailed structures and definitions needed for each demographic item.
 
-2. **Customizing "addProperties" for Demographic Variables**: 
+2. **Customizing "addProperties" for Demographic Variables**:
 
     In the "addProperties" section, we define each variable that corresponds to a demographic question. For example:
 
@@ -141,8 +141,8 @@ Different from `demograpgics`, `psychological_questionnaire_schema` combines ass
             "isAbout": "demo:clinical_history_psychiatry"
         }
         ```
-    
+
     - The `order` array specifies the sequence in which these assessments will appear in the questionnaire, ensuring a logical flow for participants.
     - The `shuffle` setting is `false`, maintaining the defined order, and allow includes functionalities like auto-advance between assessments and data export.
 
-See the outcome [here](https://github.com/ReproNim/reproschema-demo-protocol/blob/main/activities/2_psychological/psychological_questionnaire_schema)
+See the outcome [here](https://github.com/ReproNim/reproschema-demo-protocol/blob/main/activities/2_psychological/psychological_questionnaire_schema)

docs/46_tools.md

@@ -1,6 +1,6 @@
 # Toolkit
 
-In the world of research data management, flexibility and compatibility are key. Understanding this, we provide specialized tools designed to create, validata schemas, and convert data between ReproSchema format and REDCap CSV format. Whether you're transitioning from REDCap to ReproSchema or vice versa, these tools ensure a smooth and efficient conversion process, preserving the integrity and structure of your data.
+In the world of research data management, flexibility and compatibility are key. Understanding this, we provide specialized tools designed to create, validate schemas, and convert data between ReproSchema format and REDCap CSV format. Whether you're transitioning from REDCap to ReproSchema or vice versa, these tools ensure a smooth and efficient conversion process, preserving the integrity and structure of your data.
 
 ## Install reproschema-py
 
@@ -52,7 +52,7 @@ reproschema reproschema2redcap <input_dir_path> <output_csv_filename>
   cd reproschema-demo-protocol
   pwd
   ```
-  
+
   In this case,  the output from `pwd` (which shows your current directory path)should be your `<input_dir_path>`.
 - `<output_csv_filename>`: The name of the output CSV file where the converted data will be saved.
 
@@ -66,7 +66,7 @@ Before the conversion, ensure you have the following:
 
 **YAML Configuration File**:
 
-- Download [templates/redcap2rs.yaml](templates/redcap2rs.yaml) and fill it out with your protocol details.
+- Download [templates/redcap2rs.yaml](https://github.com/ReproNim/reproschema-py/blob/ab7c051dbd4ebfce92917ce154a8053343a011e7/templates/redcap2rs.yaml) and fill it out with your protocol details.
 
 ### YAML File Configuration
 
@@ -90,4 +90,4 @@ The `redcap2reproschema` function has been integrated into a CLI tool, use the f
 reproschema redcap2reproschema path/to/your_redcap_data_dic.csv path/to/your_redcap2rs.yaml
 ```
 
-Those tools can also be used as Python functions. For detailed instructions, please visit [reproschema-py](https://github.com/ReproNim/reproschema-py). 
+Those tools can also be used as Python functions. For detailed instructions, please visit [reproschema-py](https://github.com/ReproNim/reproschema-py).

docs/98_FAQ.md

@@ -108,10 +108,10 @@ Now say you would like to use this JSON file to represent a piece of linked-data
 
 You now have a valid JSON-LD. If you want to make sure it is valid, you can copy-paste that into the [JSON-LD playground](https://json-ld.org/playground/). If you to to visualize the "linked" aspect of that data, you can click on the `Visualized` tab and this will give you a graph where that connects the different nodes (piece of information to one another).
 
-If you want to visualize a more complex graph, we can try that with one of the JSON-LD file that describe one of the `protocols` of the reproschema like the one [here](https://github.com/ReproNim/reproschema/blob/master/protocols/VoicePilot/VoicePilot_schema). Actually if you want to test get the raw content of the file you should click on `Raw`. You can then either use the raw content of the file or the URL of this raw file which should be something like:
+If you want to visualize a more complex graph, we can try that with one of the JSON-LD file that describe one of the `protocols` of the reproschema like the one [here](https://github.com/ReproNim/reproschema/blob/741e295d998037629c213ef41cffaaf177f4d014/examples/protocols/protocol1.jsonld). Actually if you want to test get the raw content of the file you should click on `Raw`. You can then either use the raw content of the file or the URL of this raw file which should be something like:
 
 ```
-https://raw.githubusercontent.com/ReproNim/reproschema/master/protocols/VoicePilot/VoicePilot_schema
+https://raw.githubusercontent.com/ReproNim/reproschema/741e295d998037629c213ef41cffaaf177f4d014/examples/protocols/protocol1.jsonld
 ```
 
 directly into the [JSON-LD playground](https://json-ld.org/playground/) to see whether it is a valid JSON-LD and how the different elements are connected.
@@ -175,10 +175,10 @@ If you just want to view a protocol or activity you are developing using the `re
 
 If you are hosting a schema on github, make sure that you are passing the URL of the **raw** content of the schema. For example, our demo protocol can be accessed at this URL:
 
-[https://github.com/ReproNim/demo-protocol/blob/master/VoicePilot/VoicePilot_schema](https://github.com/ReproNim/demo-protocol/blob/master/VoicePilot/VoicePilot_schema)
+[https://github.com/ReproNim/reproschema-demo-protocol/blob/7ed1ae49279f75acdd57380fff1f8aaff2c7b511/reproschema_demo_protocol/reproschema_demo_protocol_schema](https://github.com/ReproNim/reproschema-demo-protocol/blob/7ed1ae49279f75acdd57380fff1f8aaff2c7b511/reproschema_demo_protocol/reproschema_demo_protocol_schema)
 
 But to get access to the raw content of that file you must click on the `Raw` button once you have opened that page on github that will open this URL:
 
-[https://raw.githubusercontent.com/ReproNim/demo-protocol/master/VoicePilot/VoicePilot_schema](https://raw.githubusercontent.com/ReproNim/demo-protocol/master/VoicePilot/VoicePilot_schema).
+[https://raw.githubusercontent.com/ReproNim/reproschema-demo-protocol/7ed1ae49279f75acdd57380fff1f8aaff2c7b511/reproschema_demo_protocol/reproschema_demo_protocol_schema](https://raw.githubusercontent.com/ReproNim/reproschema-demo-protocol/7ed1ae49279f75acdd57380fff1f8aaff2c7b511/reproschema_demo_protocol/reproschema_demo_protocol_schema).
 
 If you want to visualize the graph represented by the JSON-LD file, we explain how to do this in [From JSON to JSON-LD](#from-json-to-json-ld).

docs/index.md

@@ -16,7 +16,7 @@ our [FAQ](./98_FAQ.md). You do not need an in depth understanding of what those
 things are to use the ReproSchema but some "big picture" conceptual understanding
 could save you from a lot of confusion. 😉
 
-- Not sure how the project is organized? Check out the [project structure](./20_project_structure)
+- Not sure how the project is organized? Check out the [project structure](./20_project_structure.md)
 page.
 
 ## How to cite

mkdocs.yml

@@ -20,8 +20,8 @@ nav:
   - Project structure: "20_project_structure.md"
   - Schema: "30_schema.md"
   - User Guide:
-      - Create a research protocol: "41_create_new_protocol.md" 
-      - Adopt assessments from the library: "42_adopt_assessments.md" 
+      - Create a research protocol: "41_create_new_protocol.md"
+      - Adopt assessments from the library: "42_adopt_assessments.md"
       - Create new assessments for a protocol: "43_create_new_assess.md"
       - Add a feedback section: "44_setup_feedback.md"
       - Finalize the protocol: "45_finalize_protocol.md"

terms/Field

@@ -139,4 +139,3 @@
         }
     ]
 }
-

terms/unitOptions

@@ -9,4 +9,4 @@
         "@id": "reproschema:UnitOption"
         }
     ]
-}
+}