diff --git a/.env.production b/.env.production deleted file mode 100644 index 25ed957..0000000 --- a/.env.production +++ /dev/null @@ -1,2 +0,0 @@ -GEN3_COMMONS_NAME=gen3 -NEXT_PUBLIC_GEN3_API=https://prometheus.data-commons.org diff --git a/.eslintignore b/.eslintignore new file mode 100644 index 0000000..905cb7e --- /dev/null +++ b/.eslintignore @@ -0,0 +1,2 @@ +*.css +node_modules diff --git a/.eslintrc.js b/.eslintrc.js index edf6734..f0f9465 100644 --- a/.eslintrc.js +++ b/.eslintrc.js @@ -23,6 +23,7 @@ module.exports = { }, plugins: ['jsx-a11y', 'react', 'react-hooks', '@typescript-eslint'], rules: { + '@typescript-eslint/no-explicit-any':['warn'], 'no-underscore-dangle': 'off', 'import/prefer-default-export': 'off', 'linebreak-style': ['error', 'unix'], diff --git a/.nvmrc b/.nvmrc index 209e3ef..016e34b 100644 --- a/.nvmrc +++ b/.nvmrc @@ -1 +1 @@ -20 +v20.17.0 diff --git a/Dockerfile b/Dockerfile index 928e5c0..3b80b98 100644 --- a/Dockerfile +++ b/Dockerfile @@ -31,17 +31,10 @@ RUN apt-get update && apt-get install -y --no-install-recommends \ && npm install -g npm@10.5.2 RUN addgroup --system --gid 1001 nextjs && adduser --system --uid 1001 nextjs -COPY ./package.json ./package-lock.json ./ -COPY ./package-lock.json ./ +COPY ./package.json ./package-lock.json ./next.config.js ./tsconfig.json ./.env.development ./tailwind.config.js ./postcss.config.js ./ COPY ./src ./src COPY ./public ./public COPY ./config ./config -COPY ./next.config.js ./ -COPY ./tsconfig.json ./ -COPY ./.env.development ./ -COPY ./.env.production ./ -COPY ./tailwind.config.js ./ -COPY ./postcss.config.js ./ RUN npm ci RUN npm install \ "@swc/core" \ diff --git a/config/gen3/alternate_colors/dark.json b/config/gen3/alternate_colors/dark.json new file mode 100644 index 0000000..492038e --- /dev/null +++ b/config/gen3/alternate_colors/dark.json @@ -0,0 +1,9 @@ +{ + "primary": "#009688", + "secondary": "#465451", + "accent": "#cba12c", + "base": "#111111", + "accentWarm": "#892115", + "accentCool": "#255990", + "chart": "#0d95A1" +} diff --git a/config/gen3/alternate_colors/pallet2.json b/config/gen3/alternate_colors/pallet2.json new file mode 100644 index 0000000..b3fb0a1 --- /dev/null +++ b/config/gen3/alternate_colors/pallet2.json @@ -0,0 +1,11 @@ + + +{ +"primary": "#edae49", +"secondary": "#772b38", +"accent": "#00798c", +"base": "#7a7a7a", +"accentWarm": "#30638e", +"accentCool": "#003d5b", +"chart": "#0d95A1" +} diff --git a/config/gen3/alternate_colors/urban.json b/config/gen3/alternate_colors/urban.json new file mode 100644 index 0000000..3d83f54 --- /dev/null +++ b/config/gen3/alternate_colors/urban.json @@ -0,0 +1,9 @@ +{ + "primary": "#2C2C54", + "secondary": "#AAABB8", + "accent": "#474787", + "base": "#ECECEC", + "accentWarm": "#892115", + "accentCool": "#255990", + "chart": "#0d95A1" +} diff --git a/config/gen3/apps/CohortDiscovery.json b/config/gen3/apps/CohortDiscovery.json new file mode 100644 index 0000000..bdb8c75 --- /dev/null +++ b/config/gen3/apps/CohortDiscovery.json @@ -0,0 +1,33 @@ +{ + "name": "CohortDiscovery", + "dataIndexes": [ + { + "dataConfig": { + "dataType": "subject", + "nodeCountTitle": "Cases" + }, + "tabTitle": "Cases", + "tabs": [ + { + "title": "Demographic", + "fields": [ + "gender", + "race", + "ethnicity", + "vital_status" + ] + }, + { + "title": "Study", + "fields": [ + "gender", + "race", + "ethnicity", + "vital_status", + "project" + ] + } + ] + } + ] +} diff --git a/config/gen3/apps/CohortDiversity.json b/config/gen3/apps/CohortDiversity.json new file mode 100644 index 0000000..a56f13a --- /dev/null +++ b/config/gen3/apps/CohortDiversity.json @@ -0,0 +1,53 @@ +{ + "datasets": { + "ground": { + "dataset": "census", + "label": "Census" + }, + "comparison": [ + { + "dataset": "MIDRC", + "label": "MIDRC Data Commons" + } + ] + }, + "fields": [ + "age_at_index", + "sex", + "race", + "ethnicity" + ], + "fieldsConfig": { + "Age_at_Index": { + "title": "Age at Index" + } + }, + "charts": { + "age_at_index": { + "chartType": "bar" + }, + "sex": { + "chartType": "bar" + }, + "race": { + "chartType": "bar" + }, + "ethnicity": { + "chartType": "bar" + } + }, + "comparisonCharts": { + "age_at_index": { + "chartType": "radarComparison" + }, + "sex": { + "chartType": "barComparison" + }, + "race": { + "chartType": "barComparison" + }, + "ethnicity": { + "chartType": "barComparison" + } + } +} diff --git a/config/gen3/colors.json b/config/gen3/colors.json index b339da3..3d83f54 100644 --- a/config/gen3/colors.json +++ b/config/gen3/colors.json @@ -1,10 +1,9 @@ { - "primary": "#3283C8", - "secondary": "#3283C8", - "accent": "#b75113", - "base": "#c0c0c0", - "accentWarm": "#25869b", - "accentCool": "#1f839b", - "chart": "#0d95A1", - "table": "#c0c0c0" + "primary": "#2C2C54", + "secondary": "#AAABB8", + "accent": "#474787", + "base": "#ECECEC", + "accentWarm": "#892115", + "accentCool": "#255990", + "chart": "#0d95A1" } diff --git a/config/gen3/explorer.json b/config/gen3/explorer.json index fe821a2..decb552 100644 --- a/config/gen3/explorer.json +++ b/config/gen3/explorer.json @@ -2,75 +2,40 @@ { "tabTitle": "Cases", "charts": { - "covid19_positive": { - "chartType": "fullPie", - "title": "COVID-19 Positive" - }, - "sex": { - "chartType": "fullPie", - "title": "Sex" - }, "race": { "chartType": "fullPie", "title": "Race" + }, + "ethnicity": { + "chartType": "horizontalStacked", + "title": "Ethnicity" + }, + "gender": { + "chartType": "bar", + "title": "Gender" } }, "filters": { "tabs": [ { - "title": "Demographics", - "fields": [ - "sex", - "race", - "ethnicity", - "age_at_index", - "index_event", - "zip", - "covid19_positive", - "project_id" - ] - }, - { - "title": "COVID Tests", - "fields": [ - "measurements.test_name", - "measurements.test_result_text", - "measurements.test_method", - "measurements.test_days_from_index" - ] - }, - { - "title": "Medications", - "fields": [ - "medications.days_to_medication_start", - "medications.days_to_medication_end", - "medications.dose_sequence_number", - "medications.medication_code", - "medications.medication_code_system", - "medications.medication_manufacturer", - "medications.medication_name", - "medications.medication_status", - "medications.medication_type" - ] - }, - { - "title": "Procedures", - "fields": [ - "procedures.breathing_support_type", - "procedures.days_to_procedure_start", - "procedures.days_to_procedure_end", - "procedures.procedure_name" - ] + "title": "Study Selection", + "fields": ["project"] }, { - "title": "Conditions", + "title": "Subjects", "fields": [ - "conditions.condition_name", - "conditions.condition_code_system", - "conditions.condition_code", - "conditions.days_to_condition_start", - "conditions.days_to_condition_end" - ] + "study", + "gender", + "race", + "ethnicity", + "vital_status", + "whatever_lab_result_value" + ], + "fieldsConfig": { + "gender" : { + "type" : "multiselect" + } + } } ] }, @@ -83,70 +48,48 @@ "title": "Details" }, "fields": [ - "submitter_id", - "sex", - "age_at_index", - "index_event", + "project", + "gender", "race", "ethnicity", - "zip", - "covid19_positive", - "measurements.test_name", - "measurements.test_result_text", - "measurements.test_method", - "measurements.test_days_from_index", - "medications.days_to_medication_start", - "medications.days_to_medication_end", - "medications.dose_sequence_number", - "medications.medication_code", - "medications.medication_code_system", - "medications.medication_manufacturer", - "medications.medication_name", - "medications.medication_status", - "medications.medication_type", - "procedures.breathing_support_type", - "procedures.days_to_procedure_start", - "procedures.days_to_procedure_end", - "procedures.procedure_name", - "conditions.condition_name", - "conditions.condition_code_system", - "conditions.condition_code", - "conditions.days_to_condition_start", - "conditions.days_to_condition_end", - "_imaging_studies_count", - "_ct_series_file_count", - "_dx_series_file_count", - "_cr_series_file_count", - "_mr_series_file_count", - "project_id" + "whatever_lab_result_value" ], "columns": { - "measurements.test_name": { - "title": "Test Name", - "type": "array", - "accessorPath": "measurements[*].test_name" - }, - "measurements.test_result_text": { - "title": "Test Results Text", - "type": "array", - "accessorPath": "measurements[*].test_result_text", - "cellRenderFunction": "NegativePositive" - }, - "measurements.test_method": { - "title": "Test Method", - "type": "array", - "accessorPath": "measurements[*].test_method" - }, - "measurements.test_days_from_index": { - "title": "Test Days from Index", - "type": "array", - "accessorPath": "measurements[*].test_days_from_index" + "whatever_lab_result_value": { + "sortable": false } } }, "dropdowns": { "download-table": { - "title": "Download Case Metadata Table" + "title": "Download Table", + "leftIcon": "gen3:download", + "rightIcon": "gen3:chevron-down", + "dropdownItems": [ + { + "enabled": true, + "type": "data-json", + "title": "JSON", + "leftIcon": "datafile", + "rightIcon": "download", + "action": "data-json", + "actionArgs" : { + "filename": "MIDRC_Series_table.json", + "rootPath": "gen3_discovery" + } + }, + { + "enabled": true, + "type": "data-csv", + "title": "CSV", + "leftIcon": "datafile", + "rightIcon": "download", + "action": "data-csv", + "actionArgs" : { + "filename": "data_table.csv" + } + } + ] } }, "buttons": [ @@ -157,7 +100,9 @@ "dropdownId": "download-table", "leftIcon": "datafile", "rightIcon": "download", - "fileName": "MIDRC_Cases_table.json" + "actionArgs": { + "filename": "data_table.json" + } }, { "enabled": true, @@ -166,7 +111,9 @@ "dropdownId": "download-table", "leftIcon": "datafile", "rightIcon": "download", - "fileName": "MIDRC_Cases_table.tsv" + "actionArgs": { + "filename": "data_table.tsv" + } }, { "enabled": true, @@ -175,549 +122,111 @@ "dropdownId": "download-table", "leftIcon": "datafile", "rightIcon": "download", - "fileName": "MIDRC_Cases_table.csv" + "actionArgs": { + "filename": "data_table.csv" + } }, { "enabled": true, "type": "manifest", + "action": "manifest", "title": "Download File Manifest for Cases", "leftIcon": "datafile", "rightIcon": "download", - "fileName": "MIDRC_case_manifest.json" - }, - { - "enabled": false, - "type": "export-to-workspace", - "title": "Export to Workspace", - "leftIcon": "datafile", - "rightIcon": "download" + "fileName": "case_manifest.json", + "actionArgs": { + "resourceIndexType": "file", + "resourceIdField": "object_id", + "referenceIdFieldInResourceIndex": "project_id", + "referenceIdFieldInDataIndex": "project_id", + "fileFields": ["file_name", "file_size", "md5sum", "object_id"] + } } ], - "loginForDownload": true, + "loginForDownload": false, "guppyConfig": { - "dataType": "case", - "nodeCountTitle": "Cases", + "dataType": "subject", + "nodeCountTitle": "Subjects", "fieldMapping": [ { - "field": "project_id", - "name": "Project ID" - }, - { - "field": "submitter_id", - "name": "Case ID" + "field": "_samples_count", + "name": "Samples Count" }, { - "field": "_imaging_studies_count", - "name": "Imaging Studies Count" + "field": "_imaging_files_count", + "name": "Imaging Files Count" }, { - "field": "_ct_series_file_count", - "name": "CT Series Count" + "field": "_unaligned_reads_files_count", + "name": "Unaligned Reads Count" }, { - "field": "_dx_series_file_count", - "name": "DX Series Count" + "field": "_aligned_reads_files_count", + "name": "Aligned Reads Count" }, { - "field": "_cr_series_file_count", - "name": "CR Series Count" - }, - { - "field": "_mr_series_file_count", - "name": "MR Series Count" + "field": "_expression_arrays_count", + "name": "Expression Arrays Count" } ], "manifestMapping": { - "resourceIndexType": "imaging_data_file", + "resourceIndexType": "file", "resourceIdField": "object_id", - "referenceIdFieldInResourceIndex": "_case_id", - "referenceIdFieldInDataIndex": "_case_id" + "referenceIdFieldInResourceIndex": "subject_id", + "referenceIdFieldInDataIndex": "subject_id" }, - "accessibleFieldCheckList": [ - "project_id" - ], - "accessibleValidationField": "project_id" + "accessibleFieldCheckList": ["project"], + "accessibleValidationField": "project" } }, { - "tabTitle": "Measurements", + "tabTitle": "Data Files", "charts": { - "test_method": { - "chartType": "fullPie", - "title": "Test Method" + "file_type": { + "chartType": "stackedBar", + "title": "File Type" }, - "test_result_text": { - "chartType": "fullPie", - "title": "COVID-19 Test Result" - }, - "test_name": { - "chartType": "donut", - "title": "Test Name" + "file_format": { + "chartType": "stackedBar", + "title": "File Format" } }, "filters": { "tabs": [ { - "title": "COVID-19 Tests", - "fields": [ - "test_method", - "test_result_text", - "test_name", - "test_days_from_index", - "project_id" - ] + "title": "File", + "fields": ["subject_id"] } ] }, "table": { "enabled": true, - "fields": [ - "case_ids", - "test_method", - "test_result_text", - "test_name", - "test_days_from_index", - "submitter_id", - "project_id" - ] - }, - "dropdowns": { - "download-table": { - "title": "Download Measurements Metadata Table" - } - }, - "buttons": [ - { - "enabled": true, - "type": "data-json", - "title": "JSON", - "dropdownId": "download-table", - "leftIcon": "datafile", - "rightIcon": "download", - "fileName": "MIDRC_Measurements_table.json" - }, - { - "enabled": true, - "type": "data-tsv", - "title": "TSV", - "dropdownId": "download-table", - "leftIcon": "datafile", - "rightIcon": "download", - "fileName": "MIDRC_Measurements_table.tsv" - }, - { - "enabled": true, - "type": "data-csv", - "title": "CSV", - "dropdownId": "download-table", - "leftIcon": "datafile", - "rightIcon": "download", - "fileName": "MIDRC_Measurements_table.csv" - } - ], - "loginForDownload": true, - "guppyConfig": { - "dataType": "measurement", - "nodeCountTitle": "Measurements", - "fieldMapping": [ - { - "field": "project_id", - "name": "Project ID" - }, - { - "field": "submitter_id", - "name": "Measurement ID" - }, - { - "field": "case_ids", - "name": "Case ID" - } - ], - "accessibleFieldCheckList": [ - "project_id" - ], - "accessibleValidationField": "project_id" - } - }, - { - "tabTitle": "Imaging Studies", - "charts": { - "study_modality": { - "chartType": "fullPie", - "title": "Study Modality" + "detailsConfig": { + "panel": "fileDetails", + "mode": "click", + "idField": "file_name", + "title": "File Details" }, - "sex": { - "chartType": "fullPie", - "title": "Case Sex" - } - }, - "filters": { - "tabs": [ - { - "title": "Study Properties", - "fields": [ - "study_modality", - "study_description", - "age_at_imaging", - "study_year", - "study_year_shifted", - "body_part_examined", - "study_location", - "days_from_study_to_pos_covid_test", - "days_from_study_to_neg_covid_test", - "project_id" - ] - }, - { - "title": "LOINC Properties", - "fields": [ - "loinc_long_common_name", - "loinc_method", - "loinc_system", - "loinc_contrast", - "loinc_code" - ] - }, - { - "title": "Imaging Properties", - "fields": [ - "data_format", - "data_category", - "data_type" - ] - }, - { - "title": "Case Demographics", - "fields": [ - "covid19_positive", - "age_at_index", - "sex", - "race", - "ethnicity", - "zip", - "index_event" - ] - } - ] - }, - "table": { - "enabled": true, - "fields": [ - "submitter_id", - "study_modality", - "study_description", - "body_part_examined", - "age_at_imaging", - "days_to_study", - "study_year", - "study_year_shifted", - "loinc_long_common_name", - "loinc_method", - "loinc_system", - "loinc_contrast", - "loinc_code", - "days_from_study_to_pos_covid_test", - "days_from_study_to_neg_covid_test", - "covid19_positive", - "age_at_index", - "index_event", - "sex", - "race", - "ethnicity", - "zip", - "_ct_series_file_count", - "_dx_series_file_count", - "_cr_series_file_count", - "_mr_series_file_count", - "data_format", - "data_category", - "data_type", - "study_uid", - "case_ids", - "object_id", - "project_id" - ], - "dicomViewerId": "submitter_id", - "linkFields": [ - "submitter_id" - ] - }, - "dropdowns": { - "download-table": { - "title": "Download Imaging Studies Table" - } + "fields": ["subject_id", "file_type", "file_size", "object_id"] }, - "buttons": [ - { - "enabled": true, - "type": "data-json", - "title": "JSON", - "dropdownId": "download-table", - "leftIcon": "datafile", - "rightIcon": "download", - "fileName": "MIDRC_Imaging_Studies_table.json" - }, - { - "enabled": true, - "type": "data-tsv", - "title": "TSV", - "dropdownId": "download-table", - "leftIcon": "datafile", - "rightIcon": "download", - "fileName": "MIDRC_Imaging_Studies_table.tsv" - }, - { - "enabled": true, - "type": "data-csv", - "title": "CSV", - "dropdownId": "download-table", - "leftIcon": "datafile", - "rightIcon": "download", - "fileName": "MIDRC_Imaging_Studies_table.csv" - }, - { - "enabled": true, - "type": "manifest", - "title": "Download File Manifest for Imaging Studies", - "leftIcon": "datafile", - "rightIcon": "download", - "fileName": "MIDRC_imaging_study_manifest.json" - }, - { - "enabled": false, - "type": "export-to-workspace", - "title": "Export to Workspace", - "leftIcon": "datafile", - "rightIcon": "download" - } - ], - "loginForDownload": true, "guppyConfig": { - "dataType": "imaging_study", - "nodeCountTitle": "Imaging Studies", + "dataType": "file", "fieldMapping": [ { - "field": "project_id", - "name": "Project ID" - }, - { - "field": "submitter_id", - "name": "Browse in DICOM viewer" - }, - { - "field": "case_ids", - "name": "Patient ID" - }, - { - "field": "_ct_series_file_count", - "name": "CT Series Count" - }, - { - "field": "_dx_series_file_count", - "name": "DX Series Count" - }, - { - "field": "_cr_series_file_count", - "name": "CR Series Count" - }, - { - "field": "_mr_series_file_count", - "name": "MR Series Count" - }, - { - "field": "loinc_long_common_name", - "name": "Long Common Name (Study description)" - }, - { - "field": "loinc_contrast", - "name": "Contrast" - }, - { - "field": "loinc_code", - "name": "LOINC Code" - }, - { - "field": "loinc_method", - "name": "Method (Modality)" - }, - { - "field": "loinc_system", - "name": "System (Body region)" + "field": "file_id", + "name": "GUID" } ], + "nodeCountTitle": "Files", "manifestMapping": { - "resourceIndexType": "imaging_data_file", - "resourceIdField": "object_id", - "referenceIdFieldInResourceIndex": "_imaging_study_id", - "referenceIdFieldInDataIndex": "_imaging_study_id", - "useFilterForCounts": true - }, - "accessibleFieldCheckList": [ - "project_id" - ], - "accessibleValidationField": "project_id" - } - }, - { - "tabTitle": "Imaging Series", - "charts": { - "sex": { - "chartType": "fullPie", - "title": "Case Sex" - }, - "covid19_positive": { - "chartType": "fullPie", - "title": "Cases that ever had COVID-19" - } - }, - "filters": { - "tabs": [ - { - "title": "Study Properties", - "fields": [ - "study_description", - "age_at_imaging", - "study_year", - "study_year_shifted", - "study_location", - "days_from_study_to_pos_covid_test", - "days_from_study_to_neg_covid_test", - "project_id" - ] - }, - { - "title": "Series Properties", - "fields": [ - "acquisition_type", - "angio_flag", - "contrast_bolus_agent", - "convolution_kernel", - "detector_type", - "diffusion_b_value", - "diffusion_gradient_orientation", - "echo_number", - "echo_time", - "echo_train_length", - "exposure_modulation_type", - "image_type", - "imaged_nucleus", - "imager_pixel_spacing", - "lossy_image_compression", - "manufacturer", - "manufacturer_model_name", - "modality", - "multiframe_images", - "number_of_temporal_positions", - "patient_position", - "pixel_spacing", - "radiopharmaceutical", - "repetition_time", - "scan_options", - "sequence_variant", - "series_description", - "slice_thickness", - "software_version", - "spacing_between_slices", - "spatial_resolution", - "transducer_type", - "view_position", - "data_format", - "data_category", - "data_type" - ] - }, - { - "title": "Case Demographics", - "fields": [ - "covid19_positive", - "age_at_index", - "sex", - "race", - "zip", - "index_event" - ] - } - ] - }, - "table": { - "enabled": true, - "fields": [ - "acquisition_type", - "angio_flag", - "contrast_bolus_agent", - "convolution_kernel", - "detector_type", - "diffusion_b_value", - "diffusion_gradient_orientation", - "echo_number", - "echo_time", - "echo_train_length", - "exposure_modulation_type", - "image_type", - "imaged_nucleus", - "imager_pixel_spacing", - "lossy_image_compression", - "manufacturer", - "manufacturer_model_name", - "modality", - "multiframe_images", - "number_of_temporal_positions", - "patient_position", - "pixel_spacing", - "radiopharmaceutical", - "repetition_time", - "scan_options", - "sequence_variant", - "series_description", - "slice_thickness", - "software_version", - "spacing_between_slices", - "spatial_resolution", - "transducer_type", - "view_position", - "study_description", - "age_at_imaging", - "days_to_study", - "study_year", - "study_year_shifted", - "days_from_study_to_pos_covid_test", - "days_from_study_to_neg_covid_test", - "data_format", - "covid19_positive", - "age_at_index", - "index_event", - "sex", - "race", - "zip", - "data_format", - "data_category", - "data_type", - "series_uid", - "study_uid", - "case_ids", - "object_id", - "submitter_id", - "project_id" - ], - "columns": { - "object_id": { - "title": "Object Id2", - "type": "link", - "accessorPath": "object_id", - "params": { - "baseURL": "/browse/series/" - } - } + "resourceIndexType": "subject", + "resourceIdField": "subject_id", + "referenceIdFieldInResourceIndex": "object_id", + "referenceIdFieldInDataIndex": "object_id" }, - "dicomViewerId": "submitter_id", - "linkFields": [ - "submitter_id" - ] - }, - "dropdowns": { - "download-table": { - "title": "Download Table" - } + "accessibleFieldCheckList": ["subject_id"], + "accessibleValidationField": "subject_id", + "downloadAccessor": "subject_id" }, "buttons": [ { @@ -727,7 +236,9 @@ "dropdownId": "download-table", "leftIcon": "datafile", "rightIcon": "download", - "fileName": "MIDRC_Imaging_Series_table.json" + "actionArgs": { + "filename": "data_table.json" + } }, { "enabled": true, @@ -736,7 +247,9 @@ "dropdownId": "download-table", "leftIcon": "datafile", "rightIcon": "download", - "fileName": "MIDRC_Imaging_Series_table.tsv" + "actionArgs": { + "filename": "data_table.tsv" + } }, { "enabled": true, @@ -745,7 +258,9 @@ "dropdownId": "download-table", "leftIcon": "datafile", "rightIcon": "download", - "fileName": "MIDRC_Imaging_Series_table.csv" + "actionArgs": { + "filename": "data_table.csv" + } }, { "enabled": true, @@ -753,39 +268,11 @@ "title": "Download File Manifest", "leftIcon": "datafile", "rightIcon": "download", - "fileName": "MIDRC_Imaging_Series_manifest.json" - }, - { - "enabled": false, - "type": "export-to-workspace", - "title": "Export to Workspace", - "leftIcon": "datafile", - "rightIcon": "download" + "actionArgs": { + "filename": "data_table_manifest.csv" + } } ], - "loginForDownload": true, - "guppyConfig": { - "dataType": "imaging_data_file", - "nodeCountTitle": "Imaging Series", - "fieldMapping": [ - { - "field": "project_id", - "name": "Project ID" - }, - { - "field": "case_ids", - "name": "Patient ID" - } - ], - "manifestMapping": { - "referenceIdFieldInResourceIndex": "object_id", - "referenceIdFieldInDataIndex": "object_id" - }, - "downloadAccessor": "object_id", - "accessibleFieldCheckList": [ - "project_id" - ], - "accessibleValidationField": "project_id" - } + "loginForDownload": true } ] diff --git a/config/gen3/footer.json b/config/gen3/footer.json index 75bbfc1..4dd0f19 100644 --- a/config/gen3/footer.json +++ b/config/gen3/footer.json @@ -1,6 +1,6 @@ { "classNames": { - "root": "bg-base-darkest", + "root": "bg-base-darker", "layout": "flex items-center justify-end" }, "rightSection": { @@ -9,7 +9,7 @@ "rows": [ { "Icon": { - "logo": "/images/gen3.png", + "logo": "/icons/gen3.png", "width": 132, "height": 60, "description": "Gen3 Logo" @@ -21,25 +21,13 @@ "rows": [ { "Icon": { - "logo": "/images/createdby.png", + "logo": "/icons/createdby.png", "width": 170, "height": 60, "description": "Created by CTDS" } } ] - }, - { - "rows": [ - { - "Icon": { - "logo": "/images/OCC.png", - "width": 150, - "height": 60, - "description": "OCC" - } - } - ] } ] } diff --git a/config/gen3/login.json b/config/gen3/login.json index 141cf68..6f57a90 100644 --- a/config/gen3/login.json +++ b/config/gen3/login.json @@ -11,9 +11,11 @@ ], "bottomContent": [ { - "text": "If you have any questions about access or the registration process, please contact support@gen3.org.", + "text": "If you have any questions about access or the registration process, please contact", + "email": "gen3@datacommons.io", "className": "text-center text-sm" } ], - "image": "images/sideTexture.svg" + "image": "images/gene_side_texture.svg", + "showCredentialsLogin" : true } diff --git a/config/gen3/navigation.json b/config/gen3/navigation.json index df84461..2111f38 100644 --- a/config/gen3/navigation.json +++ b/config/gen3/navigation.json @@ -35,6 +35,12 @@ "href": "/Profile", "name": "Profile", "tooltip": "Create API keys for programmatic data access, and review your authorization privileges to datasets and services." + }, + { + "icon": "gen3:profile", + "href": "/DataLibrary", + "name": "Data Library", + "tooltip": "library of data" } ] }, @@ -45,6 +51,6 @@ "name": "Documentation" } ], - "showLogin": true + "loginButtonVisibility": "visible" } } diff --git a/config/gen3/profile.json b/config/gen3/profile.json index df4c924..ab234cf 100644 --- a/config/gen3/profile.json +++ b/config/gen3/profile.json @@ -1,4 +1,5 @@ { + "hasExternalLogins" : true, "resourceTable": { "serviceColors": { "guppy": { diff --git a/config/gen3/session.json b/config/gen3/session.json index fd92023..07a6273 100644 --- a/config/gen3/session.json +++ b/config/gen3/session.json @@ -2,6 +2,6 @@ "sessionConfig" : { "updateSessionTime": 5, "inactiveTimeLimit": 20, - "logoutInactiveUsers": true + "logoutInactiveUsers": false } } diff --git a/config/gen3/submission.json b/config/gen3/submission.json new file mode 100644 index 0000000..18f6c32 --- /dev/null +++ b/config/gen3/submission.json @@ -0,0 +1,30 @@ +{ + "projectTable": { + "columns": [ + { + "name": "Subjects", + "field": "_subject_count", + "errorIfNotAvailable": false, + "valueIfNotAvailable": "n/a" + }, + { + "name": "Studies", + "field": "_study_count", + "errorIfNotAvailable": false, + "valueIfNotAvailable": "n/a" + }, + { + "name": "Aliquots", + "field": "_aliquot_count", + "errorIfNotAvailable": false, + "valueIfNotAvailable": "n/a" + }, + { + "name": "Files", + "field": "_genotyping_array_count", + "errorIfNotAvailable": false, + "valueIfNotAvailable": "n/a" + } + ] + } +} diff --git a/config/gen3/themeColors.json b/config/gen3/themeColors.json index 26e8e0b..8d96529 100644 --- a/config/gen3/themeColors.json +++ b/config/gen3/themeColors.json @@ -1,39 +1,39 @@ { "primary": { - "max": "#eaf3fa", - "lightest": "#bcd7ed", - "lighter": "#8ebbe1", - "light": "#609fd4", - "DEFAULT": "#3283C8", - "vivid": "#2584d4", - "dark": "#27669b", - "darker": "#1c486e", - "darkest": "#102b41", - "min": "#050d14" + "max": "#eaeaee", + "lightest": "#babac7", + "lighter": "#8b8ba1", + "light": "#5b5b7a", + "DEFAULT": "#2C2C54", + "vivid": "#26265a", + "dark": "#222241", + "darker": "#18182e", + "darkest": "#0e0e1b", + "min": "#040408" }, "primary-contrast": { "max": "#111111", "lightest": "#111111", "lighter": "#111111", - "light": "#111111", - "DEFAULT": "#111111", - "vivid": "#111111", + "light": "#fefefe", + "DEFAULT": "#fefefe", + "vivid": "#fefefe", "dark": "#fefefe", "darker": "#fefefe", "darkest": "#fefefe", "min": "#fefefe" }, "secondary": { - "max": "#eaf3fa", - "lightest": "#bcd7ed", - "lighter": "#8ebbe1", - "light": "#609fd4", - "DEFAULT": "#3283C8", - "vivid": "#2584d4", - "dark": "#27669b", - "darker": "#1c486e", - "darkest": "#102b41", - "min": "#050d14" + "max": "#f7f7f8", + "lightest": "#e3e4e8", + "lighter": "#d0d1d8", + "light": "#bdbec8", + "DEFAULT": "#AAABB8", + "vivid": "#a2a4c0", + "dark": "#84858f", + "darker": "#5e5e65", + "darkest": "#37383c", + "min": "#111112" }, "secondary-contrast": { "max": "#111111", @@ -42,28 +42,28 @@ "light": "#111111", "DEFAULT": "#111111", "vivid": "#111111", - "dark": "#fefefe", + "dark": "#111111", "darker": "#fefefe", "darkest": "#fefefe", "min": "#fefefe" }, "accent": { - "max": "#f8eee7", - "lightest": "#e8c6b2", - "lighter": "#d79f7d", - "light": "#c77848", - "DEFAULT": "#b75113", - "vivid": "#c14f09", - "dark": "#8e3f0f", - "darker": "#652d0a", - "darkest": "#3b1a06", - "min": "#120802" + "max": "#ededf3", + "lightest": "#c3c3d8", + "lighter": "#9a9abd", + "light": "#7070a2", + "DEFAULT": "#474787", + "vivid": "#3d3d91", + "dark": "#373769", + "darker": "#27274a", + "darkest": "#17172c", + "min": "#07070d" }, "accent-contrast": { "max": "#111111", "lightest": "#111111", "lighter": "#111111", - "light": "#111111", + "light": "#fefefe", "DEFAULT": "#fefefe", "vivid": "#fefefe", "dark": "#fefefe", @@ -72,64 +72,64 @@ "min": "#fefefe" }, "accent-warm": { - "max": "#e9f3f5", - "lightest": "#b8d8df", - "lighter": "#87bcc8", - "light": "#56a1b2", - "DEFAULT": "#25869b", - "vivid": "#1b8ca5", - "dark": "#1d6878", - "darker": "#144a55", - "darkest": "#0c2c32", - "min": "#040d0f" + "max": "#f3e9e8", + "lightest": "#d9b7b3", + "lighter": "#be857e", + "light": "#a4534a", + "DEFAULT": "#892115", + "vivid": "#911b0d", + "dark": "#6a1a10", + "darker": "#4b120c", + "darkest": "#2d0b07", + "min": "#0e0302" }, "accent-warm-contrast": { "max": "#111111", "lightest": "#111111", "lighter": "#111111", - "light": "#111111", - "DEFAULT": "#000000", - "vivid": "#111111", + "light": "#fefefe", + "DEFAULT": "#fefefe", + "vivid": "#fefefe", "dark": "#fefefe", "darker": "#fefefe", "darkest": "#fefefe", "min": "#fefefe" }, "accent-cool": { - "max": "#e9f3f5", - "lightest": "#b6d7df", - "lighter": "#84bbc8", - "light": "#519fb2", - "DEFAULT": "#1f839b", - "vivid": "#1689a4", - "dark": "#186678", - "darker": "#114855", - "darkest": "#0a2b32", - "min": "#030d0f" + "max": "#e9eef4", + "lightest": "#b8c9db", + "lighter": "#87a4c2", + "light": "#567ea9", + "DEFAULT": "#255990", + "vivid": "#1c5999", + "dark": "#1d4570", + "darker": "#14314f", + "darkest": "#0c1d2f", + "min": "#04090e" }, "accent-cool-contrast": { "max": "#111111", "lightest": "#111111", "lighter": "#111111", - "light": "#111111", - "DEFAULT": "#000000", - "vivid": "#111111", + "light": "#000000", + "DEFAULT": "#fefefe", + "vivid": "#fefefe", "dark": "#fefefe", "darker": "#fefefe", "darkest": "#fefefe", "min": "#fefefe" }, "base": { - "max": "#f9f9f9", - "lightest": "#ebebeb", - "lighter": "#dcdcdc", - "light": "#cecece", - "DEFAULT": "#c0c0c0", - "vivid": "#c6baba", - "dark": "#959595", - "darker": "#6a6a6a", - "darkest": "#3e3e3e", - "min": "#131313" + "max": "#fdfdfd", + "lightest": "#f9f9f9", + "lighter": "#f5f5f5", + "light": "#f0f0f0", + "DEFAULT": "#ECECEC", + "vivid": "#eeeaea", + "dark": "#b7b7b7", + "darker": "#828282", + "darkest": "#4d4d4d", + "min": "#181818" }, "base-contrast": { "max": "#111111", @@ -139,7 +139,7 @@ "DEFAULT": "#111111", "vivid": "#111111", "dark": "#111111", - "darker": "#fefefe", + "darker": "#111111", "darkest": "#fefefe", "min": "#fefefe" }, @@ -192,18 +192,18 @@ "min": "#fefefe" }, "table": { - "max": "#f9f9f9", - "lightest": "#ebebeb", - "lighter": "#dcdcdc", - "light": "#cecece", - "DEFAULT": "#c0c0c0", - "vivid": "#c6baba", - "dark": "#959595", - "darker": "#6a6a6a", - "darkest": "#3e3e3e", - "min": "#131313" - }, - "tablePallet-contrast": { + "max": "#ffffff", + "lightest": "#ffffff", + "lighter": "#ffffff", + "light": "#ffffff", + "DEFAULT": "#ffffff", + "vivid": "#ffffff", + "dark": "#c6c6c6", + "darker": "#8c8c8c", + "darkest": "#535353", + "min": "#191919" + }, + "table-contrast": { "max": "#111111", "lightest": "#111111", "lighter": "#111111", @@ -211,8 +211,17 @@ "DEFAULT": "#111111", "vivid": "#111111", "dark": "#111111", - "darker": "#fefefe", + "darker": "#111111", "darkest": "#fefefe", "min": "#fefefe" - } + }, + "navigation": { + "footer": "#373A3C", + "topbar_hover": "#FFFFFF", + "light": "#111111", + "DEFAULT": "#111111", + "dark": "#111111", + "darker": "#111111", + "darkest": "#111111", + "min": "#111111"} } diff --git a/config/gen3/themeFonts.json b/config/gen3/themeFonts.json index 1a5a722..f40ccb8 100644 --- a/config/gen3/themeFonts.json +++ b/config/gen3/themeFonts.json @@ -1,5 +1,5 @@ { - "heading": ["Montserrat", "sans-serif"], - "content": ["Noto Sans", "sans-serif"], - "fontFamily": "Montserrat" + "heading": ["Poppins", "sans-serif"], + "content": ["Poppins", "sans-serif"], + "fontFamily": "Poppins" } diff --git a/config/gen3/workspaces.json b/config/gen3/workspaces.json new file mode 100644 index 0000000..0db3279 --- /dev/null +++ b/config/gen3/workspaces.json @@ -0,0 +1,3 @@ +{ + +} diff --git a/config/icons/color.json b/config/icons/color.json new file mode 100644 index 0000000..852e13a --- /dev/null +++ b/config/icons/color.json @@ -0,0 +1,28 @@ +{ + "prefix": "color", + "lastModified": 1724107947, + "icons": { + "analysis": { + "body": "", + "width": 64, + "height": 64 + }, + "discovery": { + "body": "", + "top": -13 + }, + "explorer": { + "body": "", + "left": -30, + "width": 511 + }, + "profile": { + "body": "" + }, + "workspaces": { + "body": "" + } + }, + "width": 512, + "height": 512 +} diff --git a/config/icons/color/analysis.svg b/config/icons/color/analysis.svg new file mode 100644 index 0000000..877872c --- /dev/null +++ b/config/icons/color/analysis.svg @@ -0,0 +1 @@ + diff --git a/config/icons/color/discovery.svg b/config/icons/color/discovery.svg new file mode 100644 index 0000000..2fe223a --- /dev/null +++ b/config/icons/color/discovery.svg @@ -0,0 +1 @@ + diff --git a/config/icons/color/explorer.svg b/config/icons/color/explorer.svg new file mode 100644 index 0000000..7cfe2d0 --- /dev/null +++ b/config/icons/color/explorer.svg @@ -0,0 +1 @@ + diff --git a/config/icons/color/profile.svg b/config/icons/color/profile.svg new file mode 100644 index 0000000..0fb33c8 --- /dev/null +++ b/config/icons/color/profile.svg @@ -0,0 +1 @@ + diff --git a/config/icons/color/workspaces.svg b/config/icons/color/workspaces.svg new file mode 100644 index 0000000..d073469 --- /dev/null +++ b/config/icons/color/workspaces.svg @@ -0,0 +1 @@ + diff --git a/config/icons/dataDictionary.json b/config/icons/dataDictionary.json new file mode 100644 index 0000000..7bf0508 --- /dev/null +++ b/config/icons/dataDictionary.json @@ -0,0 +1,58 @@ +{ + "prefix": "dataDictionary", + "lastModified": 1724107947, + "icons": { + "dictionary-icon-administrative": { + "body": "" + }, + "dictionary-icon-analysis": { + "body": "", + "height": 21 + }, + "dictionary-icon-biospecimen": { + "body": "" + }, + "dictionary-icon-clinical": { + "body": "" + }, + "dictionary-icon-clinical-assessment": { + "body": "" + }, + "dictionary-icon-data-file": { + "body": "" + }, + "dictionary-icon-data-observations": { + "body": "" + }, + "dictionary-icon-default": { + "body": "", + "height": 21 + }, + "dictionary-icon-experimental-methods": { + "body": "" + }, + "dictionary-icon-imaging": { + "body": "" + }, + "dictionary-icon-index-file": { + "body": "" + }, + "dictionary-icon-medical-history": { + "body": "" + }, + "dictionary-icon-metadata": { + "body": "" + }, + "dictionary-icon-notation": { + "body": "" + }, + "dictionary-icon-study-administration": { + "body": "" + }, + "dictionary-icon-subject-characteristics": { + "body": "" + } + }, + "width": 20, + "height": 20 +} diff --git a/config/icons/download.svg b/config/icons/download.svg deleted file mode 100644 index 22a2656..0000000 --- a/config/icons/download.svg +++ /dev/null @@ -1 +0,0 @@ - diff --git a/config/icons/gen3.json b/config/icons/gen3.json index 2f89917..26d4c6a 100644 --- a/config/icons/gen3.json +++ b/config/icons/gen3.json @@ -1,7 +1,12 @@ { "prefix": "gen3", - "lastModified": 1727726759, + "lastModified": 1730144270, "icons": { + "aisearch": { + "body": "", + "width": 682.67, + "height": 682.67 + }, "analysis": { "body": "", "width": 35, @@ -14,11 +19,21 @@ "width": 315.67, "height": 294.22 }, + "chevron-contract": { + "body": "", + "width": 16, + "height": 16 + }, "chevron-down": { "body": "", "width": 58.026, "height": 58.026 }, + "chevron-expand": { + "body": "", + "width": 512, + "height": 512 + }, "comparison": { "body": "", "width": 512, @@ -84,8 +99,13 @@ "dictionary-icon-subject-characteristics": { "body": "" }, + "dot": { + "body": "", + "width": 256, + "height": 256 + }, "download": { - "body": "", + "body": "", "width": 24, "height": 24 }, @@ -104,6 +124,16 @@ "width": 195, "height": 89 }, + "jupyter": { + "body": "", + "width": 44, + "height": 51 + }, + "loginarrowcircle": { + "body": "", + "width": 30, + "height": 30 + }, "logincircle": { "body": "", "width": 24, @@ -114,6 +144,11 @@ "width": 24, "height": 24 }, + "notebook": { + "body": "", + "width": 682.667, + "height": 682.667 + }, "profile": { "body": "", "width": 512.001, @@ -125,9 +160,9 @@ "height": 511.999 }, "upload": { - "body": "", - "width": 512, - "height": 512 + "body": "", + "width": 24, + "height": 24 }, "user": { "body": "", diff --git a/config/icons/gen3/aiSearch.svg b/config/icons/gen3/aiSearch.svg new file mode 100644 index 0000000..593075d --- /dev/null +++ b/config/icons/gen3/aiSearch.svg @@ -0,0 +1,3 @@ + + + diff --git a/config/icons/analysis.svg b/config/icons/gen3/analysis.svg similarity index 100% rename from config/icons/analysis.svg rename to config/icons/gen3/analysis.svg diff --git a/config/icons/bar-chart.svg b/config/icons/gen3/bar-chart.svg similarity index 100% rename from config/icons/bar-chart.svg rename to config/icons/gen3/bar-chart.svg diff --git a/config/icons/gen3/chevron-contract.svg b/config/icons/gen3/chevron-contract.svg new file mode 100644 index 0000000..7b16d84 --- /dev/null +++ b/config/icons/gen3/chevron-contract.svg @@ -0,0 +1 @@ + diff --git a/config/icons/chevron-down.svg b/config/icons/gen3/chevron-down.svg similarity index 100% rename from config/icons/chevron-down.svg rename to config/icons/gen3/chevron-down.svg diff --git a/config/icons/gen3/chevron-expand.svg b/config/icons/gen3/chevron-expand.svg new file mode 100644 index 0000000..3a62aae --- /dev/null +++ b/config/icons/gen3/chevron-expand.svg @@ -0,0 +1 @@ + diff --git a/config/icons/gen3/comparison.svg b/config/icons/gen3/comparison.svg new file mode 100644 index 0000000..114deb8 --- /dev/null +++ b/config/icons/gen3/comparison.svg @@ -0,0 +1 @@ + diff --git a/config/icons/datafile.svg b/config/icons/gen3/datafile.svg similarity index 100% rename from config/icons/datafile.svg rename to config/icons/gen3/datafile.svg diff --git a/config/icons/dictionary.svg b/config/icons/gen3/dictionary.svg similarity index 100% rename from config/icons/dictionary.svg rename to config/icons/gen3/dictionary.svg diff --git a/config/icons/gen3/download.svg b/config/icons/gen3/download.svg new file mode 100644 index 0000000..cab0abb --- /dev/null +++ b/config/icons/gen3/download.svg @@ -0,0 +1 @@ + diff --git a/config/icons/exploration.svg b/config/icons/gen3/exploration.svg similarity index 100% rename from config/icons/exploration.svg rename to config/icons/gen3/exploration.svg diff --git a/config/icons/gen3-dark.svg b/config/icons/gen3/gen3-dark.svg similarity index 100% rename from config/icons/gen3-dark.svg rename to config/icons/gen3/gen3-dark.svg diff --git a/config/icons/gen3.svg b/config/icons/gen3/gen3.svg similarity index 100% rename from config/icons/gen3.svg rename to config/icons/gen3/gen3.svg diff --git a/config/icons/gen3/jupyter.svg b/config/icons/gen3/jupyter.svg new file mode 100644 index 0000000..d0fa7e4 --- /dev/null +++ b/config/icons/gen3/jupyter.svg @@ -0,0 +1,90 @@ + +Group.svg +Created using Figma 0.90 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/config/icons/gen3/loginArrowCircle.svg b/config/icons/gen3/loginArrowCircle.svg new file mode 100644 index 0000000..1fed0b6 --- /dev/null +++ b/config/icons/gen3/loginArrowCircle.svg @@ -0,0 +1 @@ + diff --git a/config/icons/loginCircle.svg b/config/icons/gen3/loginCircle.svg similarity index 100% rename from config/icons/loginCircle.svg rename to config/icons/gen3/loginCircle.svg diff --git a/config/icons/gen3/not-found.svg b/config/icons/gen3/not-found.svg new file mode 100644 index 0000000..68b0144 --- /dev/null +++ b/config/icons/gen3/not-found.svg @@ -0,0 +1,94 @@ + + + + 404 + Created with Sketch. + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/config/icons/gen3/notebook.svg b/config/icons/gen3/notebook.svg new file mode 100644 index 0000000..db56476 --- /dev/null +++ b/config/icons/gen3/notebook.svg @@ -0,0 +1,92 @@ + + + + diff --git a/config/icons/gen3/open_in_modal.svg b/config/icons/gen3/open_in_modal.svg new file mode 100644 index 0000000..3462c34 --- /dev/null +++ b/config/icons/gen3/open_in_modal.svg @@ -0,0 +1,3 @@ + + + diff --git a/config/icons/profile.svg b/config/icons/gen3/profile.svg similarity index 100% rename from config/icons/profile.svg rename to config/icons/gen3/profile.svg diff --git a/config/icons/query.svg b/config/icons/gen3/query.svg similarity index 100% rename from config/icons/query.svg rename to config/icons/gen3/query.svg diff --git a/config/icons/gen3/upload.svg b/config/icons/gen3/upload.svg new file mode 100755 index 0000000..8859cfc --- /dev/null +++ b/config/icons/gen3/upload.svg @@ -0,0 +1 @@ + diff --git a/config/icons/user.svg b/config/icons/gen3/user.svg similarity index 100% rename from config/icons/user.svg rename to config/icons/gen3/user.svg diff --git a/config/icons/workspace.svg b/config/icons/gen3/workspace.svg similarity index 100% rename from config/icons/workspace.svg rename to config/icons/gen3/workspace.svg diff --git a/config/icons/upload.svg b/config/icons/upload.svg deleted file mode 100755 index c2e2c5f..0000000 --- a/config/icons/upload.svg +++ /dev/null @@ -1,17 +0,0 @@ - - - - - - - - - - - - - - diff --git a/config/icons/workspace.json b/config/icons/workspace.json new file mode 100644 index 0000000..8cd2718 --- /dev/null +++ b/config/icons/workspace.json @@ -0,0 +1,24 @@ +{ + "prefix": "workspace", + "lastModified": 1724107947, + "icons": { + "galaxy": { + "body": "", + "width": 66 + }, + "jupyter": { + "body": "", + "width": 44, + "height": 51 + }, + "rlogo": { + "body": "", + "width": 75 + }, + "rstudio": { + "body": "", + "width": 50 + } + }, + "height": 50 +} diff --git a/config/icons/workspace/galaxy.svg b/config/icons/workspace/galaxy.svg new file mode 100644 index 0000000..3f743b7 --- /dev/null +++ b/config/icons/workspace/galaxy.svg @@ -0,0 +1,19 @@ + + + + Group Copy + Created with Sketch. + + + + + + + + + + + + + + diff --git a/config/icons/workspace/jupyter.svg b/config/icons/workspace/jupyter.svg new file mode 100644 index 0000000..ce0006b --- /dev/null +++ b/config/icons/workspace/jupyter.svg @@ -0,0 +1,90 @@ + +Group.svg +Created using Figma 0.90 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/config/icons/workspace/rlogo.svg b/config/icons/workspace/rlogo.svg new file mode 100644 index 0000000..712b113 --- /dev/null +++ b/config/icons/workspace/rlogo.svg @@ -0,0 +1,17 @@ + + + + + + + + + + + + + + + + + diff --git a/config/icons/workspace/rstudio.svg b/config/icons/workspace/rstudio.svg new file mode 100644 index 0000000..32930f9 --- /dev/null +++ b/config/icons/workspace/rstudio.svg @@ -0,0 +1,12 @@ + + + + RStudio-Logo-flat + Created with Sketch. + + + + + + + diff --git a/config/themeColors.json b/config/themeColors.json deleted file mode 100644 index 1b94621..0000000 --- a/config/themeColors.json +++ /dev/null @@ -1,218 +0,0 @@ -{ - "primary": { - "DEFAULT": "#3283C8", - "vivid": "#2584d4", - "min": "#050d14", - "darkest": "#102b41", - "darker": "#1c486e", - "dark": "#27669b", - "light": "#609fd4", - "lighter": "#8ebbe1", - "lightest": "#bcd7ed", - "max": "#eaf3fa" - }, - "primary-contrast": { - "DEFAULT": "#111111", - "vivid": "#111111", - "min": "#fefefe", - "darkest": "#fefefe", - "darker": "#fefefe", - "dark": "#fefefe", - "light": "#111111", - "lighter": "#111111", - "lightest": "#111111", - "max": "#111111" - }, - "secondary": { - "DEFAULT": "#3283C8", - "vivid": "#2584d4", - "min": "#050d14", - "darkest": "#102b41", - "darker": "#1c486e", - "dark": "#27669b", - "light": "#609fd4", - "lighter": "#8ebbe1", - "lightest": "#bcd7ed", - "max": "#eaf3fa" - }, - "secondary-contrast": { - "DEFAULT": "#111111", - "vivid": "#111111", - "min": "#fefefe", - "darkest": "#fefefe", - "darker": "#fefefe", - "dark": "#fefefe", - "light": "#111111", - "lighter": "#111111", - "lightest": "#111111", - "max": "#111111" - }, - "accent": { - "DEFAULT": "#b75113", - "vivid": "#c14f09", - "min": "#120802", - "darkest": "#3b1a06", - "darker": "#652d0a", - "dark": "#8e3f0f", - "light": "#c77848", - "lighter": "#d79f7d", - "lightest": "#e8c6b2", - "max": "#f8eee7" - }, - "accent-contrast": { - "DEFAULT": "#fefefe", - "vivid": "#fefefe", - "min": "#fefefe", - "darkest": "#fefefe", - "darker": "#fefefe", - "dark": "#fefefe", - "light": "#111111", - "lighter": "#111111", - "lightest": "#111111", - "max": "#111111" - }, - "accent-warm": { - "DEFAULT": "#25869b", - "vivid": "#1b8ca5", - "min": "#040d0f", - "darkest": "#0c2c32", - "darker": "#144a55", - "dark": "#1d6878", - "light": "#56a1b2", - "lighter": "#87bcc8", - "lightest": "#b8d8df", - "max": "#e9f3f5" - }, - "accent-warm-contrast": { - "DEFAULT": "#000000", - "vivid": "#111111", - "min": "#fefefe", - "darkest": "#fefefe", - "darker": "#fefefe", - "dark": "#fefefe", - "light": "#111111", - "lighter": "#111111", - "lightest": "#111111", - "max": "#111111" - }, - "accent-cool": { - "DEFAULT": "#1f839b", - "vivid": "#1689a4", - "min": "#030d0f", - "darkest": "#0a2b32", - "darker": "#114855", - "dark": "#186678", - "light": "#519fb2", - "lighter": "#84bbc8", - "lightest": "#b6d7df", - "max": "#e9f3f5" - }, - "accent-cool-contrast": { - "DEFAULT": "#000000", - "vivid": "#111111", - "min": "#fefefe", - "darkest": "#fefefe", - "darker": "#fefefe", - "dark": "#fefefe", - "light": "#111111", - "lighter": "#111111", - "lightest": "#111111", - "max": "#111111" - }, - "base": { - "DEFAULT": "#c0c0c0", - "vivid": "#c6baba", - "min": "#131313", - "darkest": "#3e3e3e", - "darker": "#6a6a6a", - "dark": "#959595", - "light": "#cecece", - "lighter": "#dcdcdc", - "lightest": "#ebebeb", - "max": "#f9f9f9" - }, - "base-contrast": { - "DEFAULT": "#111111", - "vivid": "#111111", - "min": "#fefefe", - "darkest": "#fefefe", - "darker": "#fefefe", - "dark": "#111111", - "light": "#111111", - "lighter": "#111111", - "lightest": "#111111", - "max": "#111111" - }, - "utility": { - "link": "#155276", - "success": "#318f71", - "warning": "#d9a214", - "error": "#8a0e2a", - "emergency": "#6a0019", - "info": "#1c5e86", - "category1": "#1c5e86", - "category2": "#d1541d", - "category3": "#564990", - "category4": "#4dbc97" - }, - "utility-contrast": { - "link": "#f1f1f1", - "success": "#000000", - "warning": "#1b1b1b", - "error": "#f1f1f1", - "emergency": "#f1f1f1", - "info": "#f1f1f1", - "category1": "#f1f1f1", - "category2": "#000000", - "category3": "#f1f1f1", - "category4": "#1b1b1b" - }, - "chart": { - "DEFAULT": "#0d95A1", - "vivid": "#049caa", - "min": "#010f10", - "darkest": "#043034", - "darker": "#075259", - "dark": "#0a737d", - "light": "#43adb6", - "lighter": "#7ac5cb", - "lightest": "#b0dde0", - "max": "#e7f4f6" - }, - "chart-contrast": { - "DEFAULT": "#111111", - "vivid": "#111111", - "min": "#fefefe", - "darkest": "#fefefe", - "darker": "#fefefe", - "dark": "#fefefe", - "light": "#111111", - "lighter": "#111111", - "lightest": "#111111", - "max": "#111111" - }, - "table": { - "DEFAULT": "#c0c0c0", - "vivid": "#c6baba", - "min": "#131313", - "darkest": "#3e3e3e", - "darker": "#6a6a6a", - "dark": "#959595", - "light": "#cecece", - "lighter": "#dcdcdc", - "lightest": "#ebebeb", - "max": "#f9f9f9" - }, - "tablePallet-contrast": { - "DEFAULT": "#111111", - "vivid": "#111111", - "min": "#fefefe", - "darkest": "#fefefe", - "darker": "#fefefe", - "dark": "#111111", - "light": "#111111", - "lighter": "#111111", - "lightest": "#111111", - "max": "#111111" - } -} diff --git a/next.config.js b/next.config.js index 7395873..b8ea39f 100644 --- a/next.config.js +++ b/next.config.js @@ -17,7 +17,6 @@ const withMDX = require('@next/mdx')({ }, }); - // Next configuration with support for rewrting API to existing common services const nextConfig = { output: 'standalone', @@ -30,18 +29,22 @@ const nextConfig = { transpilePackages: ['@gen3/core', '@gen3/frontend'], webpack: (config) => { config.infrastructureLogging = { - level: "error", + level: 'error', }; return config; }, + experimental: { + esmExternals: true, + instrumentationHook: true, + }, async headers() { return [ { - source: "/(.*)?", // Matches all pages + source: '/(.*)?', // Matches all pages headers: [ { - key: "X-Frame-Options", - value: "SAMEORIGIN", + key: 'X-Frame-Options', + value: 'SAMEORIGIN', }, ], }, diff --git a/package-lock.json b/package-lock.json index 7283c14..a553c9a 100644 --- a/package-lock.json +++ b/package-lock.json @@ -1,39 +1,40 @@ { - "name": "prometheus-data-platform", - "version": "0.10.32", + "name": "@gen3/commons-portal-app-base", + "version": "0.10.55", "lockfileVersion": 3, "requires": true, "packages": { "": { - "name": "prometheus-data-platform", - "version": "0.10.32", + "name": "@gen3/commons-portal-app-base", + "version": "0.10.55", "dependencies": { - "@axe-core/react": "^4.10.0", "@fontsource/montserrat": "^5.0.19", "@fontsource/poppins": "^5.0.15", "@fontsource/source-sans-pro": "^5.0.8", - "@gen3/core": "^0.10.47", - "@gen3/frontend": "^0.10.47", + "@gen3/core": "^0.10.55", + "@gen3/frontend": "^0.10.55", "@grafana/faro-react": "^1.9.1", "@grafana/faro-web-sdk": "^1.9.1", "@grafana/faro-web-tracing": "^1.9.1", - "@mantine/core": "^7.12.1", - "@mantine/form": "^7.12.1", - "@mantine/hooks": "^7.12.1", - "@mantine/modals": "^7.12.1", - "@mantine/notifications": "^7.12.1", + "@mantine/core": "^7.13.3", + "@mantine/dates": "^7.13.3", + "@mantine/form": "^7.13.3", + "@mantine/hooks": "^7.13.3", + "@mantine/modals": "^7.13.3", + "@mantine/notifications": "^7.13.3", "@mdx-js/loader": "^3.0.0", "@mdx-js/react": "^3.0.0", - "@next/mdx": "^14.2.8", + "@next/mdx": "^14.2.15", "cookies-next": "^4.1.1", - "mantine-react-table": "^2.0.0-beta.6", + "idb": "^8.0.0", + "jsonpath-plus": "^10.2.0", "react": "^18.2.0", - "react-dom": "^18.2.0", - "sharp": "^0.33.5", + "react-dom": "18.2.0", "swr": "^2.2.5" }, "devDependencies": { - "@gen3/toolsff": "^0.10.47", + "@axe-core/react": "^4.10.0", + "@gen3/toolsff": "^0.10.55", "@tailwindcss/aspect-ratio": "^0.4.2", "@tailwindcss/forms": "^0.5.3", "@tailwindcss/line-clamp": "^0.4.2", @@ -42,14 +43,15 @@ "@types/mdx": "^2.0.11", "@types/react": "^18.2.21", "@types/react-dom": "^18.2.7", + "@typescript-eslint/eslint-plugin": "^7.12.0", "eslint": "8.57.0", - "eslint-config-next": "14.2.8", + "eslint-config-next": "14.2.3", "eslint-config-prettier": "^8.8.0", "eslint-plugin-import": "^2.27.5", "eslint-plugin-jsx-a11y": "^6.6.1", "eslint-plugin-react": "^7.30.1", "eslint-plugin-react-hooks": "^4.6.0", - "next": "^14.2.8", + "next": "^14.2.15", "postcss": "^8.4.29", "postcss-import": "^16.1.0", "postcss-loader": "^7.3.2", @@ -57,19 +59,16 @@ "postcss-preset-env": "^8.4.2", "postcss-preset-mantine": "^1.17.0", "prettier": "^2.7.1", + "react": "^18.2.0", + "react-dom": "18.2.0", "tailwindcss": "^3.4.10", "ts-jest": "^29.1.2", "ts-node": "^10.9.1", - "typescript": "5.6.2" + "typescript": "^5.6.2" }, "engines": { "node": ">=20.11.0", "npm": ">=10.2.3" - }, - "peerDependencies": { - "@gen3/core": "^0.10.47", - "react": "^18.2.0", - "react-dom": "^18.2.0" } }, "node_modules/@alloc/quick-lru": { @@ -102,6 +101,7 @@ "resolved": "https://registry.npmjs.org/@antfu/install-pkg/-/install-pkg-0.4.1.tgz", "integrity": "sha512-T7yB5QNG29afhWVkVq7XeIMBa5U/vs9mX69YqayXypPRmYzUmzwnYltplHmPtZ4HPCn+sQKeXW8I47wCbuBOjw==", "dev": true, + "license": "MIT", "dependencies": { "package-manager-detector": "^0.2.0", "tinyexec": "^0.3.0" @@ -115,6 +115,7 @@ "resolved": "https://registry.npmjs.org/@antfu/utils/-/utils-0.7.10.tgz", "integrity": "sha512-+562v9k4aI80m1+VuMHehNJWLOFjBnXn3tdOitzD0il5b7smkSBal4+a3oKiQTbrwMmN/TBUMDvbdoWDehgOww==", "dev": true, + "license": "MIT", "funding": { "url": "https://github.com/sponsors/antfu" } @@ -123,7 +124,27 @@ "version": "4.10.0", "resolved": "https://registry.npmjs.org/@axe-core/react/-/react-4.10.0.tgz", "integrity": "sha512-gpFj1+G0zabbd0ZDum1N5FPJtUOfPIfslXNH58WuR7opSK0WTwPJ49ZlYr/Wg2fA4VGI5lfkG5fAZSG9p8ecKw==", + "dev": true, + "license": "MPL-2.0", + "dependencies": { + "axe-core": "~4.10.0", + "requestidlecallback": "^0.3.0" + } + }, + "node_modules/@axe-core/react/node_modules/axe-core": { + "version": "4.10.0", + "resolved": "https://registry.npmjs.org/axe-core/-/axe-core-4.10.0.tgz", + "integrity": "sha512-Mr2ZakwQ7XUAjp7pAwQWRhhK8mQQ6JAaNWSjmjxil0R8BPioMtQsTLOolGYkji1rcL++3dCqZA3zWqpT+9Ew6g==", + "dev": true, "license": "MPL-2.0", + "engines": { + "node": ">=4" + } + }, + "node_modules/@babel/code-frame": { + "version": "7.23.5", + "resolved": "https://registry.npmjs.org/@babel/code-frame/-/code-frame-7.23.5.tgz", + "integrity": "sha512-CgH3s1a96LipHCmSUmYFPwY7MNx8C3avkq7i4Wl3cfa662ldtUe4VM1TPXX70pfmrlWTb6jLqTYrZyT2ZTJBgA==", "dependencies": { "axe-core": "~4.10.0", "requestidlecallback": "^0.3.0" @@ -243,9 +264,9 @@ } }, "node_modules/@babel/helper-module-imports": { - "version": "7.24.7", - "resolved": "https://registry.npmjs.org/@babel/helper-module-imports/-/helper-module-imports-7.24.7.tgz", - "integrity": "sha512-8AyH3C+74cgCVVXow/myrynrAGv+nTVg5vKu2nZph9x7RcRwzmh0VFallJuFTZ9mx6u4eSdXZfcOzSqTUm0HCA==", + "version": "7.22.15", + "resolved": "https://registry.npmjs.org/@babel/helper-module-imports/-/helper-module-imports-7.22.15.tgz", + "integrity": "sha512-0pYVBnDKZO2fnSPCrgM/6WMc7eS20Fbok+0r88fp+YtWVLZrp4CkafFGIp+W0VKw4a22sgebPT99y+FDNMdP4w==", "dev": true, "peer": true, "dependencies": { @@ -300,9 +321,9 @@ } }, 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"sha512-FjoyLe754PMiYsFaN5C94ttGiOmBNYTf6pLr4xXHAT5uctHb092PBszndLDR5XA/jghQvn4n7JMHl7dmTgbm9w==", + "license": "MIT", "dependencies": { "regenerator-runtime": "^0.14.0" }, @@ -656,9 +678,9 @@ } }, "node_modules/@babel/types": { - "version": "7.25.6", - "resolved": "https://registry.npmjs.org/@babel/types/-/types-7.25.6.tgz", - "integrity": "sha512-/l42B1qxpG6RdfYf343Uw1vmDjeNhneUXtzhojE7pDgfpEypmRhI6j1kr17XCVv4Cgl9HdAiQY2x0GwKm7rWCw==", + "version": "7.23.9", + "resolved": "https://registry.npmjs.org/@babel/types/-/types-7.23.9.tgz", + "integrity": "sha512-dQjSq/7HaSjRM43FFGnv5keM2HsxpmyV1PfaSVm0nzzjwwTmjOe6J4bC8e3+pTEIgHaHj+1ZlLThRJ2auc/w1Q==", "dev": true, "peer": true, "dependencies": { @@ -693,6 +715,7 @@ "version": "6.0.0", "resolved": "https://registry.npmjs.org/@codemirror/language/-/language-6.0.0.tgz", "integrity": "sha512-rtjk5ifyMzOna1c7PBu7J1VCt0PvA5wy3o8eMVnxMKb7z8KA7JFecvD04dSn14vj/bBaAbqRsGed5OjtofEnLA==", + "license": "MIT", "peer": true, "dependencies": { "@codemirror/state": "^6.0.0", @@ -707,12 +730,14 @@ "version": "6.4.1", "resolved": "https://registry.npmjs.org/@codemirror/state/-/state-6.4.1.tgz", "integrity": "sha512-QkEyUiLhsJoZkbumGZlswmAhA7CBU02Wrz7zvH4SrcifbsqwlXShVXg65f3v/ts57W3dqyamEriMhij1Z3Zz4A==", + "license": "MIT", "peer": true }, "node_modules/@codemirror/view": { - "version": "6.34.1", - "resolved": "https://registry.npmjs.org/@codemirror/view/-/view-6.34.1.tgz", - "integrity": "sha512-t1zK/l9UiRqwUNPm+pdIT0qzJlzuVckbTEMVNFhfWkGiBQClstzg+78vedCvLSX0xJEZ6lwZbPpnljL7L6iwMQ==", + "version": "6.33.0", + "resolved": "https://registry.npmjs.org/@codemirror/view/-/view-6.33.0.tgz", + "integrity": "sha512-AroaR3BvnjRW8fiZBalAaK+ZzB5usGgI014YKElYZvQdNH5ZIidHlO+cyf/2rWzyBFRkvG6VhiXeAEbC53P2YQ==", + "license": "MIT", "peer": true, "dependencies": { "@codemirror/state": "^6.4.0", @@ -1455,29 +1480,21 @@ "postcss": "^8.4" } }, - "node_modules/@emnapi/runtime": { - "version": "1.2.0", - "resolved": 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"~0.2.3", "fd-slicer": "~1.1.0" @@ -29814,6 +30361,7 @@ "version": "5.6.0", "resolved": "https://registry.npmjs.org/zrender/-/zrender-5.6.0.tgz", "integrity": "sha512-uzgraf4njmmHAbEUxMJ8Oxg+P3fT04O+9p7gY+wJRVxo8Ge+KmYv0WJev945EH4wFuc4OY2NLXz46FZrWS9xJg==", + "license": "BSD-3-Clause", "dependencies": { "tslib": "2.3.0" } @@ -29821,7 +30369,8 @@ "node_modules/zrender/node_modules/tslib": { "version": "2.3.0", "resolved": "https://registry.npmjs.org/tslib/-/tslib-2.3.0.tgz", - "integrity": "sha512-N82ooyxVNm6h1riLCoyS9e3fuJ3AMG2zIZs2Gd1ATcSFjSA23Q0fzjjZeh0jbJvWVDZ0cJT8yaNNaaXHzueNjg==" + "integrity": "sha512-N82ooyxVNm6h1riLCoyS9e3fuJ3AMG2zIZs2Gd1ATcSFjSA23Q0fzjjZeh0jbJvWVDZ0cJT8yaNNaaXHzueNjg==", + "license": "0BSD" }, "node_modules/zwitch": { "version": "2.0.4", diff --git a/package.json b/package.json index f8f0ce3..9d0d3cf 100644 --- a/package.json +++ b/package.json @@ -1,6 +1,6 @@ { - "name": "prometheus-data-platform", - "version": "0.10.32", + "name": "@gen3/commons-portal-app-base", + "version": "0.10.55", "private": "true", "engines": { "npm": ">=10.2.3", @@ -18,32 +18,33 @@ "getDRSToHostname": "node ./node_modules/@gen3/toolsff/dist/getDRSToHostname.esm.js --out=config/" }, "dependencies": { - "@axe-core/react": "^4.10.0", "@fontsource/montserrat": "^5.0.19", "@fontsource/poppins": "^5.0.15", "@fontsource/source-sans-pro": "^5.0.8", - "@gen3/core": "^0.10.47", - "@gen3/frontend": "^0.10.47", + "jsonpath-plus": "^10.2.0", + "@gen3/core": "^0.10.55", + "@gen3/frontend": "^0.10.55", "@grafana/faro-react": "^1.9.1", "@grafana/faro-web-sdk": "^1.9.1", "@grafana/faro-web-tracing": "^1.9.1", - "@mantine/core": "^7.12.1", - "@mantine/form": "^7.12.1", - "@mantine/hooks": "^7.12.1", - "@mantine/modals": "^7.12.1", - "@mantine/notifications": "^7.12.1", + "idb": "^8.0.0", + "@mantine/core": "^7.13.3", + "@mantine/form": "^7.13.3", + "@mantine/hooks": "^7.13.3", + "@mantine/modals": "^7.13.3", + "@mantine/dates": "^7.13.3", + "@mantine/notifications": "^7.13.3", "@mdx-js/loader": "^3.0.0", "@mdx-js/react": "^3.0.0", - "@next/mdx": "^14.2.8", + "@next/mdx": "^14.2.15", "cookies-next": "^4.1.1", - "mantine-react-table": "^2.0.0-beta.6", "react": "^18.2.0", - "react-dom": "^18.2.0", - "sharp": "^0.33.5", + "react-dom": "18.2.0", "swr": "^2.2.5" }, "devDependencies": { - "@gen3/toolsff": "^0.10.47", + "@axe-core/react": "^4.10.0", + "@gen3/toolsff": "^0.10.55", "@tailwindcss/aspect-ratio": "^0.4.2", "@tailwindcss/forms": "^0.5.3", "@tailwindcss/line-clamp": "^0.4.2", @@ -52,14 +53,16 @@ "@types/mdx": "^2.0.11", "@types/react": "^18.2.21", "@types/react-dom": "^18.2.7", + "@types/mdx": "^2.0.11", + "@typescript-eslint/eslint-plugin": "^7.12.0", "eslint": "8.57.0", - "eslint-config-next": "14.2.8", + "eslint-config-next": "14.2.3", "eslint-config-prettier": "^8.8.0", "eslint-plugin-import": "^2.27.5", "eslint-plugin-jsx-a11y": "^6.6.1", "eslint-plugin-react": "^7.30.1", "eslint-plugin-react-hooks": "^4.6.0", - "next": "^14.2.8", + "next": "^14.2.15", "postcss": "^8.4.29", "postcss-import": "^16.1.0", "postcss-loader": "^7.3.2", @@ -67,14 +70,11 @@ "postcss-preset-env": "^8.4.2", "postcss-preset-mantine": "^1.17.0", "prettier": "^2.7.1", + "react": "^18.2.0", + "react-dom": "18.2.0", "tailwindcss": "^3.4.10", "ts-jest": "^29.1.2", "ts-node": "^10.9.1", - "typescript": "5.6.2" - }, - "peerDependencies": { - "@gen3/core": "^0.10.47", - "react": "^18.2.0", - "react-dom": "^18.2.0" + "typescript": "^5.6.2" } } diff --git a/src/lib/CohortBuilder/CustomCellRenderers.tsx b/src/lib/CohortBuilder/CustomCellRenderers.tsx index 01e3c9b..0258645 100644 --- a/src/lib/CohortBuilder/CustomCellRenderers.tsx +++ b/src/lib/CohortBuilder/CustomCellRenderers.tsx @@ -3,26 +3,26 @@ import { type CellRendererFunctionProps, } from '@gen3/frontend'; import { ActionIcon } from '@mantine/core'; -import React from 'react'; +import React from 'react'; import { FaExternalLinkAlt } from 'react-icons/fa'; - -const RenderDiacomLink = ({ cell }: CellRendererFunctionProps) => { - if (cell.getValue() === undefined || cell.getValue() === '') { +const RenderDicomLink = ({ cell }: CellRendererFunctionProps) => { + if (!cell?.getValue() || cell?.getValue() === '') { return ; } else return ( - - - - - + + + + + ); }; export const registerCohortTableCustomCellRenderers = () => { ExplorerTableCellRendererFactory().registerRenderer( - 'link', 'DiacomLink' , - RenderDiacomLink, + 'link', + 'DicomLink', + RenderDicomLink, ); }; diff --git a/src/lib/CohortBuilder/FileDetailsPanel.tsx b/src/lib/CohortBuilder/FileDetailsPanel.tsx index 43cb336..0721c01 100644 --- a/src/lib/CohortBuilder/FileDetailsPanel.tsx +++ b/src/lib/CohortBuilder/FileDetailsPanel.tsx @@ -1,4 +1,3 @@ -/* eslint-disable @typescript-eslint/no-explicit-any */ // TODO remove use of any import { Anchor, Group, @@ -51,7 +50,7 @@ const isQueryResponse = (obj: any): obj is QueryResponse => { const extractData = ( data: QueryResponse, index: string, -): Record => { +): Record => { if (data === undefined || data === null) return {}; if (data.data === undefined || data.data === null) return {}; @@ -61,11 +60,11 @@ const extractData = ( }; export const FileDetailsPanel = ({ - id, - index, - tableConfig, - onClose, - }: TableDetailsPanelProps) => { + id, + index, + tableConfig, + onClose, +}: TableDetailsPanelProps) => { // get the idField from the configuration const idField = tableConfig.detailsConfig?.idField; // call the general Guppy GQL which takes an object { query: string, variables: object } @@ -104,11 +103,11 @@ export const FileDetailsPanel = ({ // create the rows for the table const rows = Object.entries(queryData).map(([field, value]) => ( - - - {field} - - + + + {field} + + {/* if field is one that we want a link for make it an Anchor otherwise render as text. @@ -125,23 +124,23 @@ export const FileDetailsPanel = ({ ) : ( {value ? (value as string) : ''} )} - - + + )); return ( - Results for {id} - - - - Field - Value - - + Results for {id} +
+ + + + + + {rows}
FieldValue
- + {({ copied, copy }) => ( { + const modals = await ContentSource.get( + `config/${GEN3_COMMONS_NAME}/modals.json`, + ); + const session = await ContentSource.get( + `config/${GEN3_COMMONS_NAME}/session.json`, + ); + + const fonts = await ContentSource.get( + `config/${GEN3_COMMONS_NAME}/themeFonts.json`, + ); + + const themeColors = await ContentSource.get( + `config/${GEN3_COMMONS_NAME}/themeColors.json`, + ); + + const colors = Object.fromEntries( + Object.entries(themeColors).map(([key, values]) => [ + key, + Object.values(values) as TenStringArray, + ]), + ); + + const icons = await ContentSource.getAll(`config/icons/`, '\\.json'); + return { + modalsConfig: modals, + sessionConfig: session, + themeFonts: fonts as Fonts, + colors: colors, + icons: icons as RegisteredIcons[], + }; +}; diff --git a/src/lib/plugins/index.js b/src/lib/plugins/index.js index 222c6c3..2d8f48e 100644 --- a/src/lib/plugins/index.js +++ b/src/lib/plugins/index.js @@ -17,7 +17,7 @@ function main() { const plugins = JSON.parse( fs .readFileSync(path.join(process.cwd(), 'config', 'plugins.json')) - .toString('utf8'), + .toString('utf-8'), ); const imports = plugins .map( diff --git a/src/pages/AISearch.tsx b/src/pages/AISearch.tsx new file mode 100644 index 0000000..5dacef7 --- /dev/null +++ b/src/pages/AISearch.tsx @@ -0,0 +1,9 @@ +import { + AiSearchPage, + AISearchPageGetServerSideProps as getServerSideProps, +} from '@gen3/frontend'; + + +export default AiSearchPage; + +export { getServerSideProps }; diff --git a/src/pages/Analysis.tsx b/src/pages/Analysis.tsx new file mode 100644 index 0000000..21e809d --- /dev/null +++ b/src/pages/Analysis.tsx @@ -0,0 +1,7 @@ +import { + AnalysisPage, + AnalysisPageGetServerSideProps as getServerSideProps, + } from '@gen3/frontend'; + export default AnalysisPage; + + export { getServerSideProps }; diff --git a/src/pages/DataLibrary.tsx b/src/pages/DataLibrary.tsx new file mode 100644 index 0000000..23c665c --- /dev/null +++ b/src/pages/DataLibrary.tsx @@ -0,0 +1,8 @@ +import { + DataLibraryPage, + DataLibraryPageGetServerSideProps as getServerSideProps, +} from '@gen3/frontend'; + +export default DataLibraryPage; + +export { getServerSideProps }; diff --git a/src/pages/Explorer.tsx b/src/pages/Explorer.tsx index 9923b56..631cff0 100644 --- a/src/pages/Explorer.tsx +++ b/src/pages/Explorer.tsx @@ -3,9 +3,7 @@ import { ExplorerPageGetServerSideProps as getServerSideProps, } from '@gen3/frontend'; -import { registerCohortTableCustomCellRenderers -} from '@/lib/CohortBuilder/CustomCellRenderers'; - +import { registerCohortTableCustomCellRenderers } from '@/lib/CohortBuilder/CustomCellRenderers'; import { registerCustomExplorerDetailsPanels } from '@/lib/CohortBuilder/FileDetailsPanel'; registerCohortTableCustomCellRenderers(); diff --git a/src/pages/NotebookLite.tsx b/src/pages/NotebookLite.tsx new file mode 100644 index 0000000..6c163d2 --- /dev/null +++ b/src/pages/NotebookLite.tsx @@ -0,0 +1,7 @@ +import { + NotebookLitePage, + NotebookLitePageGetStaticProps as getStaticProps, +} from '@gen3/frontend'; + +export default NotebookLitePage; +export { getStaticProps }; diff --git a/src/pages/SamplePage.tsx b/src/pages/SamplePage.tsx new file mode 100644 index 0000000..9b652e1 --- /dev/null +++ b/src/pages/SamplePage.tsx @@ -0,0 +1,46 @@ +import React from 'react'; +import { Center, Text, Paper } from '@mantine/core'; +import { + NavPageLayout, + NavPageLayoutProps, + getNavPageLayoutPropsFromConfig, +} from '@gen3/frontend'; +import { GetServerSideProps } from 'next'; + +const SamplePage = ({ headerProps, footerProps }: NavPageLayoutProps) => { + return ( + +
+
+ + This is a example custom page in Gen3 + + You can add your own content here, and add a link to this page in + the navigation bar by editing the config file in navigation.json + + +
+
+
+ ); +}; + +// TODO: replace this with a custom getServerSideProps function +export const getServerSideProps: GetServerSideProps< + NavPageLayoutProps +> = async () => { + return { + props: { + ...(await getNavPageLayoutPropsFromConfig()), + }, + }; +}; + +export default SamplePage; diff --git a/src/pages/Workspace.tsx b/src/pages/Workspace.tsx index e4578be..96f172e 100644 --- a/src/pages/Workspace.tsx +++ b/src/pages/Workspace.tsx @@ -1,7 +1,7 @@ import { - WorkspacesPage, - WorkspacesPageGetServerSideProps as getServerSideProps, + WorkspacePage, + WorkspacePageGetServerSideProps as getServerSideProps, } from '@gen3/frontend'; -export default WorkspacesPage; +export default WorkspacePage; export { getServerSideProps }; diff --git a/src/pages/_app.tsx b/src/pages/_app.tsx index 006745d..9b45c99 100644 --- a/src/pages/_app.tsx +++ b/src/pages/_app.tsx @@ -1,37 +1,46 @@ -import App, {AppProps, AppContext, AppInitialProps} from 'next/app'; -import React, {useEffect, useRef } from 'react'; +import App, { AppProps, AppContext, AppInitialProps } from 'next/app'; +import React, { useEffect, useRef } from 'react'; + import { Faro, FaroErrorBoundary, withFaroProfiler } from '@grafana/faro-react'; + +import { initGrafanaFaro } from '../lib/Grafana/grafana'; + import { Gen3Provider, TenStringArray, type ModalsConfig, - ContentSource, RegisteredIcons, Fonts, SessionConfiguration, + // registerCohortDiscoveryApp, + registerCohortDiversityApp, + registerCohortBuilderDefaultPreviewRenderers, + registerExplorerDefaultCellRenderers, } from '@gen3/frontend'; + +import { registerCohortTableCustomCellRenderers } from '@/lib/CohortBuilder/CustomCellRenderers'; +import { registerCustomExplorerDetailsPanels } from '@/lib/CohortBuilder/FileDetailsPanel'; + import '../styles/globals.css'; -import 'graphiql/graphiql.css'; -import '@graphiql/react/dist/style.css'; import '@fontsource/montserrat'; import '@fontsource/source-sans-pro'; import '@fontsource/poppins'; -import {GEN3_COMMONS_NAME, setDRSHostnames} from '@gen3/core'; -import drsHostnames from '../../config/drsHostnames.json'; -import { initGrafanaFaro } from '../lib/Grafana/grafana'; +import { setDRSHostnames } from '@gen3/core'; +import drsHostnames from '../../config/drsHostnames.json'; +import { loadContent } from '../lib/content/loadContent'; if (typeof window !== 'undefined' && process.env.NODE_ENV !== 'production') { - // eslint-disable-next-line @typescript-eslint/no-var-requires + // eslint-disable-next-line @typescript-eslint/no-var-requires, @typescript-eslint/no-require-imports const ReactDOM = require('react-dom'); - // eslint-disable-next-line @typescript-eslint/no-var-requires + // eslint-disable-next-line @typescript-eslint/no-var-requires, @typescript-eslint/no-require-imports const axe = require('@axe-core/react'); axe(React, ReactDOM, 1000); } interface Gen3AppProps { colors: Record; - icons: RegisteredIcons; + icons: Array; themeFonts: Fonts; modalsConfig: ModalsConfig; sessionConfig: SessionConfiguration; @@ -53,12 +62,19 @@ const Gen3App = ({ const faroRef = useRef(null); useEffect(() => { + // one time init // if ( // process.env.NEXT_PUBLIC_FARO_COLLECTOR_URL && // process.env.NEXT_PUBLIC_FARO_APP_ENVIRONMENT != "local" && // !faroRef.current // ) { - faroRef.current = initGrafanaFaro(); + if (!faroRef.current) faroRef.current = initGrafanaFaro(); + // registerCohortDiscoveryApp(); + registerCohortDiversityApp(); + registerExplorerDefaultCellRenderers(); + registerCohortBuilderDefaultPreviewRenderers(); + registerCohortTableCustomCellRenderers(); + registerCustomExplorerDetailsPanels(); // } }, []); @@ -84,41 +100,13 @@ Gen3App.getInitialProps = async ( const ctx = await App.getInitialProps(context); try { - const modals = await ContentSource.get( - `config/${GEN3_COMMONS_NAME}/modals.json`, - ); - const session = await ContentSource.get( - `config/${GEN3_COMMONS_NAME}/session.json`, - ); - - const fonts = await ContentSource.get( - `config/${GEN3_COMMONS_NAME}/themeFonts.json`, - ); - - const themeColors = await ContentSource.get( - `config/${GEN3_COMMONS_NAME}/themeColors.json`, - ); - - const colors = Object.fromEntries( - Object.entries(themeColors).map(([key, values]) => [ - key, - Object.values(values) as TenStringArray, - ]), - ); - - const icons = await ContentSource.get('config/icons/gen3.json'); + const res = await loadContent(); return { ...ctx, - modalsConfig: modals, - sessionConfig: session, - themeFonts: fonts as Fonts, - colors: colors, - icons: icons as RegisteredIcons, + ...res, }; - } catch (error: unknown) { - if (error instanceof Error) { - console.error('Provider Wrapper error loading config', error.toString()); - } else console.error('Provider wrapper: unknown error'); + } catch (error: any) { + console.error('Provider Wrapper error loading config', error.toString()); } // return default return { @@ -129,13 +117,15 @@ Gen3App.getInitialProps = async ( content: ['Poppins', 'sans-serif'], fontFamily: 'Poppins', }, - icons: { - prefix: 'gen3', - lastModified: 0, - icons: {}, - width: 0, - height: 0, - }, + icons: [ + { + prefix: 'gen3', + lastModified: 0, + icons: {}, + width: 0, + height: 0, + }, + ], modalsConfig: {}, sessionConfig: {}, }; diff --git a/src/pages/_document.tsx b/src/pages/_document.tsx index e1e9cbb..53ff867 100644 --- a/src/pages/_document.tsx +++ b/src/pages/_document.tsx @@ -1,12 +1,15 @@ -import { Html, Head, Main, NextScript } from 'next/document'; +import { Head, Html, Main, NextScript } from 'next/document'; +import { ColorSchemeScript } from '@mantine/core'; export default function Document() { return ( - + + + -
- +
+ ); diff --git a/src/pages/app/[appName].tsx b/src/pages/app/[appName].tsx new file mode 100644 index 0000000..6ac5ce6 --- /dev/null +++ b/src/pages/app/[appName].tsx @@ -0,0 +1,78 @@ +import React from 'react'; +import { + useCoreSelector, + selectGen3AppByName, + GEN3_COMMONS_NAME, +} from '@gen3/core'; +import { GetServerSideProps } from 'next'; +import { NextRouter, useRouter } from 'next/dist/client/router'; + +import { + NavPageLayout, + NavPageLayoutProps, + getNavPageLayoutPropsFromConfig, + ContentSource, +} from '@gen3/frontend'; + +interface AppConfig extends NavPageLayoutProps { + config?: object; +} + +const AppsPage = ({ headerProps, footerProps, config }: AppConfig) => { + const router = useRouter(); + const appName = getAppName(router); + + const GdcApp = useCoreSelector( + () => selectGen3AppByName(appName), // TODO update ById to ByName + ) as React.ElementType; + + return ( + + {GdcApp && } + + ); +}; + +const getAppName = (router: NextRouter): string => { + const { appName } = router.query; + if (typeof appName === 'string') return appName; + else if (typeof appName === 'object') return appName[0]; + + return 'UNKNOWN_APP_ID'; +}; + +export const getServerSideProps: GetServerSideProps< + NavPageLayoutProps +> = async (context) => { + const appName = context.query.appName as string; + + try { + const config: any = await ContentSource.get( + `config/${GEN3_COMMONS_NAME}/apps/${appName}.json`, + ); + + return { + props: { + ...(await getNavPageLayoutPropsFromConfig()), + config: config, + }, + }; + } catch (err) { + console.error(err); + return { + props: { + ...(await getNavPageLayoutPropsFromConfig()), + config: undefined, + }, + }; + } +}; + +export default AppsPage; diff --git a/src/pages/no-workspace-access.tsx b/src/pages/no-workspace-access.tsx new file mode 100644 index 0000000..b9c9aa9 --- /dev/null +++ b/src/pages/no-workspace-access.tsx @@ -0,0 +1,7 @@ +import { + WorkspaceNoAccessPage, + WorkspaceNoAccessPageServerSideProps as getServerSideProps, +} from '@gen3/frontend'; +export default WorkspaceNoAccessPage; + +export { getServerSideProps }; diff --git a/src/styles/globals.css b/src/styles/globals.css index fd79e06..94981ea 100644 --- a/src/styles/globals.css +++ b/src/styles/globals.css @@ -7,6 +7,9 @@ @import "tailwindcss/utilities"; @import '@gen3/frontend/dist/styles.css'; +@import 'graphiql/graphiql.css'; +@import '@graphiql/react/dist/style.css'; + @layer base { html { @apply font-heading;