diff --git a/.dockerignore b/.dockerignore new file mode 100644 index 0000000..3c3629e --- /dev/null +++ b/.dockerignore @@ -0,0 +1 @@ +node_modules diff --git a/.env.development b/.env.development index 52a3fdf..25ed957 100644 --- a/.env.development +++ b/.env.development @@ -1,6 +1,2 @@ GEN3_COMMONS_NAME=gen3 -NEXT_PUBLIC_GEN3_API=https://localhost:3010 -NEXT_PUBLIC_GEN3_DOMAIN=https://localhost:3010 - -# set these if you want to use different endpoints -#NEXT_PUBLIC_GEN3_GUPPY_API= +NEXT_PUBLIC_GEN3_API=https://prometheus.data-commons.org diff --git a/.env.production b/.env.production index fa20fe4..25ed957 100644 --- a/.env.production +++ b/.env.production @@ -1,3 +1,2 @@ GEN3_COMMONS_NAME=gen3 -NEXT_PUBLIC_GEN3_API=https://localhost/ -NEXT_PUBLIC_GEN3_DOMAIN=https://localhost/ +NEXT_PUBLIC_GEN3_API=https://prometheus.data-commons.org diff --git a/.eslintrc.js b/.eslintrc.js new file mode 100644 index 0000000..edf6734 --- /dev/null +++ b/.eslintrc.js @@ -0,0 +1,55 @@ +module.exports = { + env: { + browser: true, + es2021: true, + node: true, + }, + extends: [ + 'eslint:recommended', + 'plugin:jsx-a11y/recommended', + 'plugin:react/recommended', + 'plugin:react-hooks/recommended', + 'plugin:@typescript-eslint/recommended', + 'plugin:@next/next/recommended', + 'prettier', + ], + parser: '@typescript-eslint/parser', + parserOptions: { + ecmaFeatures: { + jsx: true, + }, + ecmaVersion: 12, + sourceType: 'module', + }, + plugins: ['jsx-a11y', 'react', 'react-hooks', '@typescript-eslint'], + rules: { + 'no-underscore-dangle': 'off', + 'import/prefer-default-export': 'off', + 'linebreak-style': ['error', 'unix'], + '@typescript-eslint/quotes': ['warn', 'single'], + quotes: ['warn', 'single'], + 'jsx-quotes': ['warn', 'prefer-double'], + semi: ['error', 'always'], + 'prefer-destructuring': ['error', { object: true, array: false }], + 'react/jsx-fragments': ['warn', 'element'], + // disable these because we're using React 17+ with the jsx transform + 'react/jsx-uses-react': 'off', + 'react/react-in-jsx-scope': 'off', + }, + overrides: [ + { + files: ['**/*.tsx'], + rules: { + 'react/prop-types': 'off', + }, + }, + ], + settings: { + react: { + version: 'detect', + }, + next: { + rootDir: './', + }, + }, +}; diff --git a/.eslintrc.json b/.eslintrc.json new file mode 100644 index 0000000..bffb357 --- /dev/null +++ b/.eslintrc.json @@ -0,0 +1,3 @@ +{ + "extends": "next/core-web-vitals" +} diff --git a/.github/workflows/ci.yaml b/.github/workflows/ci.yaml index 77d0dc9..642f40d 100644 --- a/.github/workflows/ci.yaml +++ b/.github/workflows/ci.yaml @@ -4,13 +4,16 @@ jobs: build: runs-on: ubuntu-latest steps: - - uses: actions/checkout@v2 - - uses: actions/setup-node@v3 - with: - node-version: 20 - - name: Setup npm - run: npm install -g npm@10.2.4 - - name: Install modules - run: npm ci - - name: Run ESLint - run: npm run lint + - uses: actions/checkout@v2 + - uses: actions/setup-node@v3.4.1 + with: + node-version: 20.11.0 + - name: install npm version + run: npm install -g npm + - name: Get Version + run: npm -v + - name: Install modules + + run: npm ci + - name: Run ESLint + run: npm run lint diff --git a/.npmignore b/.npmignore new file mode 100644 index 0000000..10900e7 --- /dev/null +++ b/.npmignore @@ -0,0 +1,3 @@ +.DS_Store +node_modules +.next/cache/* diff --git a/.nvmrc b/.nvmrc new file mode 100644 index 0000000..209e3ef --- /dev/null +++ b/.nvmrc @@ -0,0 +1 @@ +20 diff --git a/.prettierignore b/.prettierignore new file mode 100644 index 0000000..78960da --- /dev/null +++ b/.prettierignore @@ -0,0 +1,4 @@ +node_modules +.next +public +dist diff --git a/.prettierrc b/.prettierrc new file mode 100644 index 0000000..65a45ac --- /dev/null +++ b/.prettierrc @@ -0,0 +1,6 @@ +{ + "tabWidth": 2, + "useTabs": false, + "trailingComma": "all", + "singleQuote": true +} diff --git a/Dockerfile b/Dockerfile index e5c2456..928e5c0 100644 --- a/Dockerfile +++ b/Dockerfile @@ -3,12 +3,10 @@ # for Macbook silicon M1/m2 uncomment the following lines and comment quay.io/cdis/ubuntu:20.04: #FROM arm64v8/ubuntu:20.04 as build -FROM quay.io/cdis/ubuntu:20.04 as build +FROM quay.io/cdis/ubuntu:20.04 AS build ARG NODE_VERSION=20 -ENV DEBIAN_FRONTEND=noninteractive - ARG BASE_PATH ARG NEXT_PUBLIC_PORTAL_BASENAME ENV NPM_CONFIG_PREFIX=/home/node/.npm-global @@ -24,20 +22,13 @@ RUN apt-get update && apt-get install -y --no-install-recommends \ curl \ git \ gnupg \ - nginx \ - python3 \ - time \ - vim \ && mkdir -p /etc/apt/keyrings \ && curl -fsSL https://deb.nodesource.com/gpgkey/nodesource-repo.gpg.key | gpg --dearmor -o /etc/apt/keyrings/nodesource.gpg \ && echo "deb [signed-by=/etc/apt/keyrings/nodesource.gpg] https://deb.nodesource.com/node_$NODE_VERSION.x nodistro main" | tee /etc/apt/sources.list.d/nodesource.list \ && apt-get update \ && apt-get install -y nodejs \ && apt-get clean \ - && rm -rf /var/src/apt/lists/* \ - && ln -sf /dev/stdout /var/log/nginx/access.log \ - && ln -sf /dev/stderr /var/log/nginx/error.log \ - && npm install -g npm@10.2.4 + && npm install -g npm@10.5.2 RUN addgroup --system --gid 1001 nextjs && adduser --system --uid 1001 nextjs COPY ./package.json ./package-lock.json ./ diff --git a/config/gen3/colors.json b/config/gen3/colors.json index 9ac464a..b339da3 100644 --- a/config/gen3/colors.json +++ b/config/gen3/colors.json @@ -1,9 +1,10 @@ { - "primary": "#345948", - "secondary": "#BF7E06", - "accent": "#8C0404", - "base": "#CCCCCC", - "accentWarm": "#594B04", - "accentCool": "#908719", - "chart": "#0d95A1" + "primary": "#3283C8", + "secondary": "#3283C8", + "accent": "#b75113", + "base": "#c0c0c0", + "accentWarm": "#25869b", + "accentCool": "#1f839b", + "chart": "#0d95A1", + "table": "#c0c0c0" } diff --git a/config/gen3/crosswalk.json b/config/gen3/crosswalk.json new file mode 100644 index 0000000..9363912 --- /dev/null +++ b/config/gen3/crosswalk.json @@ -0,0 +1,38 @@ +{ + "showSubmittedIdInTable": false, + "mapping": { + "source": { + "id": "prom", + "label": "PROMETHEUS", + "description": "PROject for Military Exposures and Toxin History Evaluation in US Service Members" + }, + "external": [ + { + "id": "PROMETHEUS", + "label": "PROMETHEUS", + "dataPath": "crosswalk->subject->https://prometheus.data-commons.org->case_id->value" + }, + { + "id": "GDC", + "label": "GDC", + "dataPath": "crosswalk->subject->https://portal.gdc.cancer.gov->submitter_id->value", + "description": "A repository and computational platform for cancer researchers who need to understand cancer, its clinical progression, and response to therapy." + }, + { + "id": "PDC", + "label": "PDC", + "dataPath": "crosswalk->subject->https://proteomic.datacommons.cancer.gov->case_id->value" + }, + { + "id": "BLOODPAC", + "label": "BLOODPAC", + "dataPath": "crosswalk->subject->https://data.bloodpac.org->subject.subject_id->value" + }, + { + "id": "dbGaP", + "label": "dbGaP", + "dataPath": "crosswalk->subject->https://www.ncbi.nlm.nih.gov->dbgap_subject_id->value" + } + ] + } +} diff --git a/config/gen3/dictionary.json b/config/gen3/dictionary.json new file mode 100644 index 0000000..9e29f7c --- /dev/null +++ b/config/gen3/dictionary.json @@ -0,0 +1,4 @@ +{ +"showGraph": false, +"showDownloads": false +} diff --git a/config/gen3/discovery.json b/config/gen3/discovery.json index e49aaf3..8a0261c 100644 --- a/config/gen3/discovery.json +++ b/config/gen3/discovery.json @@ -1,350 +1,606 @@ { - "tableConfig": { - "selectableRows": true, - "expandableRows": true - }, - "features": { - "advSearchFilters": { - "enabled": true, - "field": "advSearchFilters", - "displayName": "Filters", - "filters": [ + "metadataConfig": [ + { + "label": "Subjects", + "tableConfig": { + "selectableRows": false, + "expandableRows": true + }, + "features": { + "dataLoader": { + "dataFetchFunction": "IndexedAggMDSAllLocal", + "dataFetchArgs": { + "indexKeys": [ + "VPODC-subject-level-metadata", + "APOLLO-subject-level-metadata", + "BloodPAC-subject-level-metadata", + "Proteomic-Data-Commons-subject-level-metadata" + ], + "hasEnoughData": { + "keys": [ + "subject_primary_disease", + "subject_gender", + "subject_race", + "subject_ethnicity" + ], + "limit": 4 + } + } + }, + "aiSearch": false, + "advSearchFilters": { + "enabled": false, + "field": "advSearchFilters", + "displayName": "Filters", + "filters": [ + { + "key": "Research Focus Area" + }, + { + "key": "Administering IC(s)" + }, + { + "key": "Simulated vs. Real Data" + }, + { + "key": "Year Grant Awarded" + }, + { + "key": "Study Description" + } + ] + }, + "pageTitle": { + "enabled": false, + "text": "Study Discovery" + }, + "tagsColumn": { + "enabled": false + }, + "tagsInDescription": { + "enabled": true + }, + "search": { + "searchBar": { + "enabled": true, + "searchableTextFields": [ + "subject_primary_disease", + "subject_cancer_type", + "subject_metastasis", + "subject_gender", + "subject_race", + "subject_ethnicity", + "subject_id", + "commons" + ] + }, + "tagSearchDropdown": { + "enabled": true, + "collapsibleButtonText": "Data Commons" + }, + "exportToWorkspace": { + "enabled": true, + "manifestFieldName": "__manifest", + "enableDownloadManifest": true, + "downloadManifestButtonText": "Download", + "documentationLinks": { + "gen3Client": "https://gen3.org/resources/user/gen3-client/", + "gen3Workspaces": "https://gen3.org/resources/user/analyze-data/" + } + } + }, + "authorization": { + "enabled": true, + "columnTooltip": "Filter by data access. Accessible indicates you are authorized to access. Not accessible indicates you are not authorized to access.", + "supportedValues": { + "accessible": { + "enabled": true, + "menuText": "Available" + }, + "unaccessible": { + "enabled": false, + "menuText": "Not Accessible" + }, + "pending": { + "enabled": false, + "menuText": "Pending" + }, + "notAvailable": { + "enabled": false, + "menuText": "Not Available" + } + } + } + }, + "aggregations": [ + { + "name": "Subjects", + "field": "gen3MDSGUID", + "type": "count" + } + ], + "tagSelector": { + "title": "Tags by category" + }, + "studyColumns": [ { - "key": "Study Type" + "name": "Cancer Type", + "field": "subject_cancer_type", + "errorIfNotAvailable": false, + "valueIfNotAvailable": "", + "contentType": "string" }, { - "key": "Data Type" + "name": "Primary Disease", + "field": "subject_primary_disease", + "errorIfNotAvailable": false, + "valueIfNotAvailable": "", + "contentType": "string" }, { - "key": "Subject Type" + "name": "Metastasis", + "field": "subject_metastasis", + "errorIfNotAvailable": false, + "valueIfNotAvailable": "", + "contentType": "number" }, { - "key": "Gender" + "name": "Biological Sex", + "field": "subject_gender", + "errorIfNotAvailable": false, + "valueIfNotAvailable": "", + "contentType": "string" }, { - "key": "Age" - } - ] - }, - "tagsColumn": { - "enabled": false - }, - "tagsInDescription": { - "enabled": true - }, - "exportToWorkspace": { - "enabled": true, - "manifestFieldName": "__manifest", - "enableDownloadManifest": true, - "enableDownloadZip": true, - "downloadZipButtonText": "Download Zip", - "downloadManifestButtonText": "Download Manifest", - "documentationLinks": { - "gen3Client": "https://gen3.org/resources/user/gen3-client/", - "gen3Workspaces": "https://gen3.org/resources/user/analyze-data/" - }, - "verifyExternalLogins": true - }, - "pageTitle": { - "enabled": false - }, - "search": { - "searchBar": { - "enabled": true, - "inputSubtitle": "Examples: pain, buprenorphine, intervention", - "searchableTextFields": [ - "study_metadata.minimal_info.study_description", - "institutions", - "investigators_name", - "study_metadata.minimal_info.study_name", - "project_number", - "study_metadata.metadata_location.nih_application_id", - "_hdp_uid", - "dataset_1_title", - "dataset_2_title", - "dataset_3_title", - "dataset_4_title", - "administering_ic", - "research_program", - "doi_identifier", - "doi_resolvable_link" - ] - }, - "tagSearchDropdown": { - "enabled": true, - "collapsibleButtonText": "Data Repository" - } - }, - "authorization": { - "enabled": true, - "columnTooltip": "Filter by data access", - "supportedValues": { - "accessible": { - "enabled": true, - "menuText": "Available" + "name": "Race", + "field": "subject_race", + "errorIfNotAvailable": false, + "valueIfNotAvailable": "", + "contentType": "string" }, - "unaccessible": { - "enabled": false, - "menuText": "Not Accessible" + { + "name": "Ethnicity", + "field": "subject_ethnicity", + "errorIfNotAvailable": false, + "valueIfNotAvailable": "", + "contentType": "string" }, - "pending": { - "enabled": true, - "menuText": "Pending" + { + "name": "ID Number", + "field": "gen3MDSGUID", + "errorIfNotAvailable": false, + "valueIfNotAvailable": "", + "contentType": "string", + "cellRenderFunction": "truncated", + "params": { + "maxLength": 16 + } }, - "notAvailable": { - "enabled": true, - "menuText": "Not Available" + { + "name": "Data Commons", + "field": "commons", + "errorIfNotAvailable": false, + "valueIfNotAvailable": "", + "contentType": "link", + "cellRenderFunction": "withURL", + "params": { + "hrefValueFromField": "commons_url", + "transform": "uppercase" + } + }, + { + "name": "DATA ACCESS METHOD", + "field": "data_access_method", + "errorIfNotAvailable": false, + "valueIfNotAvailable": "API", + "contentType": "string" } - } - } - }, - "aggregations": [ - { - "name": "Studies", - "field": "_hdp_uid", - "type": "count" - } - ], - "tagSelector": { - "showTagCategoryNames": true - }, - "studies": [], - "studyColumns": [ - { - "name": "Project Title", - "field": "study_metadata.minimal_info.study_name", - "errorIfNotAvailable": false, - "valueIfNotAvailable": "n/a" - }, - { - "name": "HEAL Research Focus Area", - "field": "research_focus_area", - "errorIfNotAvailable": false, - "valueIfNotAvailable": "n/a" - }, - { - "name": "HEAL Research Program", - "field": "research_program", - "errorIfNotAvailable": false, - "valueIfNotAvailable": "n/a" - }, - { - "name": "Investigator(s)", - "field": "investigators_name", - "errorIfNotAvailable": false, - "valueIfNotAvailable": "n/a" - } - ], - "studyPreviewField": { - "name": "Summary", - "field": "study_metadata.minimal_info.study_description", - "contentType": "string", - "includeName": false, - "includeIfNotAvailable": true, - "valueIfNotAvailable": "No summary has been provided for this study." - }, - "detailView": { - "headerField": "study_metadata.minimal_info.study_name", - "tabs": [ - { - "tabName": "Summary", - "groups": [ + ], + "studyPreviewField": { + "name": "Description", + "field": "study_description", + "contentType": "string", + "includeName": false, + "includeIfNotAvailable": true, + "valueIfNotAvailable": "No description has been provided for this study." + }, + "simpleDetailsView": { + "showAllAvailableFields": true, + "header": { + "field": "name" + }, + "fieldsToShow": [ { - "header": "Study Description Summary", + "groupWidth": "full", + "includeName": false, "fields": [ { - "type": "block", - "sourceField": "study_metadata.minimal_info.study_description" - } - ] - }, - { - "header": "HEAL Research Initiative/Award Administration", - "fields": [ + "name": "Prometheus ID", + "field": "_unique_id", + "contentType": "string" + }, { - "type": "text", - "label": "Project Number", - "sourceField": "project_number", - "default": "" + "name": "Apollo ID", + "field": "subject_apollo_id", + "contentType": "string" }, { - "type": "text", - "label": "HEAL Research Program", - "sourceField": "research_program", - "default": "Not specified" + "name": "Year born", + "field": "subject_year_of_birth", + "renderer": "yearOfBirthRestricted" }, { - "type": "text", - "label": "Institution(s)", - "sourceField": "institutions" + "name": "Race", + "field": "subject_race", + "contentType": "string" }, { - "type": "text", - "label": "Investigator(s)", - "sourceField": "investigators_name" + "name": "Biological Sex", + "field": "subject_gender", + "contentType": "string" }, { - "type": "text", - "label": "Administering IC(s)", - "sourceField": "administering_ic" + "name": "Ethnicity", + "field": "subject_ethnicity", + "contentType": "string" }, { - "type": "text", - "label": "Year Grant Awarded", - "sourceField": "year_awarded" + "name": "Primary Disease", + "field": "subject_primary_disease", + "contentType": "string" }, { - "type": "link", - "label": "NIH RePORTER Link", - "sourceField": "study_metadata.metadata_location.nih_reporter_link" + "name": "Cancer Type", + "field": "subject_cancer_type", + "contentType": "string" }, { - "type": "text", - "label": "Clinical Trial ID", - "sourceField": "study_metadata.metadata_location.clinical_trials_study_ID" + "name": "Metastasis", + "field": "subject_metastasis", + "contentType": "string" }, { - "type": "link", - "label": "Clinical Trial Link", - "sourceField": "study_metadata.metadata_location.clinical_trials_study_link" + "name": "Cancer Grade", + "field": "subject_cancer_grade", + "contentType": "string" }, { - "type": "text", - "label": "DOI", - "sourceField": "doi_identifier" + "name": "Cancer Stage", + "field": "subject_cancer_stage", + "contentType": "string" }, { - "type": "link", - "label": "DOI Link", - "sourceField": "doi_resolvable_link" - } - ] - }, - { - "header": "Study Characteristics", - "fields": [ + "name": "Type of Exposure", + "field": "subject_type_of_exposure", + "contentType": "string" + }, { - "type": "tags", - "sourceField": "tags" + "name": "Chemical/agents exposed to", + "field": "subject_chemical_agents_of_exposure", + "contentType": "string" } ] } ] }, - { - "tabName": "Data", - "groups": [ + "minimalFieldMapping": { + "tagsListFieldName": "tags", + "authzField": "authz", + "uid": "_unique_id" + }, + "tags": { + "tagCategories": [ { - "fields": [ - { - "type": "accessDescriptor" - } - ] + "name": "ethnicity", + "display": false }, { - "header": "Repository", - "fields": [ - { - "sourceField": "study_metadata.metadata_location.data_repositories[*].repository_study_link", - "type": "linkList", - "label": "" - } - ] + "name": "year_of_birth", + "color": "rgba(129, 211, 248, 1)", + "display": false + }, + { + "name": "gender", + "color": "rgba(129, 211, 248, 1)", + "display": false + }, + { + "name": "race", + "color": "rgba(129, 211, 248, 1)", + "display": false + }, + { + "name": "cancer_type", + "color": "rgba(129, 211, 248, 1)", + "display": true + }, + { + "name": "cancer_grade", + "color": "rgba(129, 211, 248, 1)", + "display": true + }, + { + "name": "type_of_exposure", + "color": "rgba(129, 211, 248, 1)", + "display": true + }, + { + "name": "metastasis", + "color": "rgba(129, 211, 248, 1)", + "display": false + }, + { + "name": "primary_disease'", + "color": "rgba(129, 211, 248, 1)", + "display": true } ] + } + }, + { + "label": "Studies", + "tableConfig": { + "selectableRows": false, + "expandableRows": true + }, + "features": { + "dataLoader": { + "dataFetchFunction": "IndexedAggMDSAllLocal", + "dataFetchArgs": { + "indexKeys": [ + "BloodPAC-study-level-metadata", + "VPODC-study-level-metadata", + "APOLLO-study-level-metadata", + "Proteomic-Data-Commons-study-level-metadata" + ] + } + }, + "aiSearch": false, + "advSearchFilters": { + "enabled": false, + "field": "advSearchFilters", + "displayName": "Filters", + "filters": [ + { + "key": "Research Focus Area" + }, + { + "key": "Administering IC(s)" + }, + { + "key": "Simulated vs. Real Data" + }, + { + "key": "Year Grant Awarded" + }, + { + "key": "Study Description" + } + ] + }, + "pageTitle": { + "enabled": false, + "text": "Study Discovery" + }, + "tagsColumn": { + "enabled": false + }, + "tagsInDescription": { + "enabled": true + }, + "search": { + "searchBar": { + "enabled": true, + "searchableTextFields": [ + "short_name", + "full_name", + "study_description", + "study_id", + "commons" + ] + }, + "tagSearchDropdown": { + "enabled": true, + "collapsibleButtonText": "Data Commons" + }, + "exportToWorkspace": { + "enabled": true, + "manifestFieldName": "__manifest", + "enableDownloadManifest": true, + "downloadManifestButtonText": "Download", + "documentationLinks": { + "gen3Client": "https://gen3.org/resources/user/gen3-client/", + "gen3Workspaces": "https://gen3.org/resources/user/analyze-data/" + } + } + }, + "authorization": { + "enabled": true, + "columnTooltip": "Filter by data access. Accessible indicates you are authorized to access. Not accessible indicates you are not authorized to access.", + "supportedValues": { + "accessible": { + "enabled": true, + "menuText": "Available" + }, + "unaccessible": { + "enabled": false, + "menuText": "Not Accessible" + }, + "pending": { + "enabled": false, + "menuText": "Pending" + }, + "notAvailable": { + "enabled": false, + "menuText": "Not Available" + } + } + } + }, + "aggregations": [ + { + "name": "Studies", + "field": "_unique_id", + "type": "count" + } + ], + "tagSelector": { + "title": "Tags by category" + }, + "studyColumns": [ + { + "name": "Study/Project Name", + "field": "short_name", + "errorIfNotAvailable": false, + "valueIfNotAvailable": "n/a", + "width": "157px", + "contentType": "string" + }, + { + "name": "Full Name", + "field": "full_name", + "errorIfNotAvailable": false, + "valueIfNotAvailable": "n/a", + "contentType": "string" + }, + { + "name": "Number of Subjects", + "field": "_subjects_count", + "errorIfNotAvailable": false, + "valueIfNotAvailable": "n/a", + "contentType": "number" + }, + { + "name": "ID Number", + "field": "gen3MDSGUID", + "errorIfNotAvailable": false, + "valueIfNotAvailable": "n/a", + "contentType": "string", + "cellRenderFunction": "truncated" + }, + { + "name": "Data Commons", + "field": "commons", + "errorIfNotAvailable": false, + "valueIfNotAvailable": "n/a", + "contentType": "link", + "cellRenderFunction": "withURL", + "params": { + "hrefValueFromField": "commons_url", + "transform": "uppercase" + } + }, + { + "name": "DATA ACCESS METHOD", + "field": "data_access_method", + "errorIfNotAvailable": false, + "valueIfNotAvailable": "API", + "contentType": "string" + } + ], + "studyPreviewField": { + "name": "Description", + "field": "study_description", + "contentType": "string", + "includeName": false, + "includeIfNotAvailable": true, + "valueIfNotAvailable": "No description has been provided for this study." }, - { - "tabName": "Cite", - "groups": [ + "simpleDetailsView": { + "showAllAvailableFields": false, + "header": { + "field": "name" + }, + "fieldsToShow": [ { - "header": "Citation Requirements", + "groupWidth": "half", + "includeName": false, "fields": [ { - "type": "text", - "label": "Cite the study on the HEAL Data Platform", - "sourceField": "study_metadata.citation.heal_platform_citation" + "name": "Unique ID", + "field": "_unique_id", + "contentType": "string" + }, + { + "name": "Study ID", + "field": "_unique_id", + "contentType": "string" + }, + { + "name": "Study/Project Name:", + "field": "short_name", + "contentType": "text", + "includeName": true, + "includeIfNotAvailable": true, + "valueIfNotAvailable": "N/A" + }, + { + "name": "Full Name", + "field": "full_name", + "contentType": "string" + }, + { + "name": "Number of Subjects", + "field": "_subjects_count", + "contentType": "string", + "includeIfNotAvailable": true }, { - "type": "text", - "label": "Cite the study at the local repository", - "sourceField": "study_metadata.metadata_location.data_repositories[*].repository_citation" + "name": "Study URL", + "field": "study_url", + "contentType": "link", + "includeIfNotAvailable": true + }, + { + "name": "Data Commons", + "field": "commons", + "contentType": "string", + "includeIfNotAvailable": true, + "params": { + "style": "uppercase" + } } ] - } - ] - }, - { - "tabName": "Related Studies", - "groups": [ + }, { - "header": "Related Studies", + "groupWidth": "half", "fields": [ { - "type": "linkList", - "sourceField": "related_studies", - "label": "", - "renderFunction": "linkWithTitle" + "name": "Description", + "field": "study_description", + "contentType": "paragraphs", + "includeName": true, + "includeIfNotAvailable": true, + "valueIfNotAvailable": "No description has been provided for this study." } ] } ] + }, + "minimalFieldMapping": { + "tagsListFieldName": "tags", + "authzField": "authz", + "uid": "_unique_id" + }, + "tags": { + "tagCategories": [ + { + "name": "Cancer Type", + "color": "rgba(129, 211, 248, 1)", + "display": true + }, + { + "name": "Cancer Type", + "color": "rgba(129, 211, 248, 1)", + "display": false + }, + { + "name": "Study Setting", + "color": "rgba(112, 182, 3, 1)", + "display": true + } + ] } - ] - }, - "tagsDisplayName": "Study Filters", - "tagColumnWidth": "500px", - "minimalFieldMapping": { - "authzField": "authz", - "tagsListFieldName": "tags", - "dataAvailabilityField": "data_availability", - "uid": "_hdp_uid" - }, - "tagCategories": [ - { - "name": "Study Type", - "color": "#532565", - "display": false - }, - { - "name": "Data Type", - "color": "#982568", - "display": false - }, - { - "name": "Subject Type", - "color": "#981f32", - "display": false - }, - { - "name": "Gender", - "color": "#bf362e", - "display": false - }, - { - "name": "Age", - "color": "#e07c3e", - "display": false - }, - { - "name": "Research Program", - "color": "#532565", - "display": false - }, - { - "name": "Commons", - "displayName": "Data Resources", - "color": "#981f32", - "display": false - }, - { - "name": "Other", - "color": "#bf362e", - "display": false - }, - { - "name": "Data Repository", - "color": "#bf362e", - "display": true } ] } diff --git a/config/gen3/explorer.json b/config/gen3/explorer.json index afee5ea..fe821a2 100644 --- a/config/gen3/explorer.json +++ b/config/gen3/explorer.json @@ -76,6 +76,12 @@ }, "table": { "enabled": true, + "detailsConfig": { + "panel": "default", + "mode" : "click", + "idField": "submitter_id", + "title": "Details" + }, "fields": [ "submitter_id", "sex", diff --git a/config/gen3/footer.json b/config/gen3/footer.json index 2429d38..ccb53a4 100644 --- a/config/gen3/footer.json +++ b/config/gen3/footer.json @@ -1,4 +1,7 @@ { + "classNames": { + "root": "bg-base-darkest" + }, "footerRightLogos": [ [ { @@ -12,6 +15,12 @@ "width": 170, "height": 60, "description": "Created by CTDS" + }, + { + "logo": "/icons/OCC.png", + "width": 150, + "height": 60, + "description": "OCC" } ] ] diff --git a/config/gen3/landingPage.json b/config/gen3/landingPage.json index 9f1d633..dd161cc 100644 --- a/config/gen3/landingPage.json +++ b/config/gen3/landingPage.json @@ -2,7 +2,7 @@ "body": [ { "title": { - "text": "Gen3 Data Platform", + "text": "Prometheus Data Platform", "level": 2 } }, @@ -10,22 +10,12 @@ "splitarea": { "left": [ { - "text": "The Gen3 Data Platform is a single web interface which allows visitors to discover, access and analyze data. Making data easily findable enables secondary, cross-study analyses, promotes dissemination of research and accelerates new discoveries." + "text": "PROMETHEUS stands for PROject for Military Exposures and Toxin History Evaluation in US Service Members. The PROMETHEUS Data Platform (PDP) is a data mesh to support the PROMETHEUS project.
The goal of the PROMETHEUS is to discover and study advanced precision technologies that will enable prevention, early detection, and enhanced treatments of cancers potentially arising due to exposures to environmental contaminants and toxin hazards by military service members and veterans.
The vision of PROMETHEUS is to integrate federal scientific platforms with public-private innovators revealing the impact of service-related exposures to environmental contaminants and toxin hazards and developing prevention and early detection approaches and advanced treatments of cancers arising from these exposures." }, { "link": { - "href": "/discovery", - "linkType": "portal", - "text": "Explore Gen3 Data" - } - }, - { - "text": "The Gen3 platform consists of open-source software services that support the emergence of healthy data ecosystems by enabling the interoperation and creation of cloud-based data resources, including data commons and analysis workspaces. Gen3 aims to accelerate and democratize the process of scientific discovery by making it easy to manage, analyze, harmonize, and share large and complex datasets in the cloud." - }, - { - "link": { - "href": "https://gen3.datacommons.io", - "text": "Learn More" + "href": "/Discovery", + "text": "Discover Data" } } ], @@ -41,32 +31,6 @@ }, { "break": "standard" - }, - { - "cardsArea": { - "title": "", - "cards": [ - { - "icon": "MdOutlineSearch", - "bodyText": "Search studies and related datasets for download or analysis in a workspace.", - "btnText": "Discover", - "href": "/Discovery", - "linkType": "portal" - }, - { - "icon": "MdOutlineBarChart", - "bodyText": "Explore Tutorials and Example Analysis.", - "btnText": "Analyze", - "href": "/resource-browser", - "linkType": "portal" - } - ] - } - }, - { - "quoteArea": { - "quote": "Our vision is a world in which researchers have ready access to the data needed and the tools required to make data-driven discoveries that increase our scientific knowledge and improve the quality of life." - } } ] } diff --git a/config/gen3/login.json b/config/gen3/login.json index 8ea514a..141cf68 100644 --- a/config/gen3/login.json +++ b/config/gen3/login.json @@ -1,7 +1,7 @@ { "topContent": [ { - "text": "Gen3 Data Commons", + "text": "Prometheus Data Platform", "className": "text-center text-3xl font-bold" }, { @@ -11,9 +11,9 @@ ], "bottomContent": [ { - "text": "If you have any questions about access or the registration process, please contact gen3@datacommons.io.", + "text": "If you have any questions about access or the registration process, please contact support@gen3.org.", "className": "text-center text-sm" } ], - "image": "images/sideTexture.png" + "image": "images/sideTexture.svg" } diff --git a/config/modals.json b/config/gen3/modals.json similarity index 100% rename from config/modals.json rename to config/gen3/modals.json diff --git a/config/gen3/navigation.json b/config/gen3/navigation.json index f8959b9..ca5b998 100644 --- a/config/gen3/navigation.json +++ b/config/gen3/navigation.json @@ -1,8 +1,12 @@ { - "type": "horizontal", "navigation": { + "classNames": { + "root": "pl-1 mr-6 bg-base-max text-primary opacity-100 hover:opacity-100", + "item": "py-2 px-4 hover:bg-base-lightest hover:text-base-contrast", + "navigationPanel": "bg-base-max text-primary" + }, "logo": { - "src": "/icons/gen3-dark.svg", + "src": "/icons/Prometheus_logo.png", "height": 128, "href": "/" }, @@ -13,36 +17,18 @@ "name": "Discovery", "tooltip": "Use free-text search and tags to rapidly find relevant studies." }, + { + "icon": "gen3:comparison", + "href": "/Crosswalk", + "name": "Crosswalk", + "tooltip": "Match ids across the mesh." + }, { "icon": "gen3:dictionary", "href": "/DataDictionary", "name": "Dictionary", "tooltip": "The Data Dictionary serves to inform the data model and is updated as new data is ingested." }, - { - "icon": "gen3:exploration", - "href": "/Explorer", - "name": "Exploration", - "tooltip": "The Exploration Page enables discovery of the data at the subject level and features a cohort builder." - }, - { - "icon": "gen3:query", - "href": "/Query", - "name": "Query", - "tooltip": "Query the databases using GraphiQL." - }, - { - "icon": "gen3:analysis", - "href": "/resource-browser", - "name": "Analysis", - "tooltip": "Learn how to use Jupyter Notebooks to explore and visualize data available by running a tutorial notebook, or use one of these examples as a launching point for your own custom analysis." - }, - { - "icon": "gen3:workspace", - "href": "/Workspace", - "name": "Workspace", - "tooltip": "Gen3 workspaces are secure data analysis environments in the cloud that can access data from one or more data resources." - }, { "icon": "gen3:profile", "href": "/Profile", @@ -53,11 +39,6 @@ }, "topBar": { "items": [ - { - "rightIcon": "gen3:upload", - "href": "/submission", - "name": "Browse Data" - }, { "href": "https://gen3.org/resources/user/", "name": "Documentation" diff --git a/config/session.json b/config/gen3/session.json similarity index 100% rename from config/session.json rename to config/gen3/session.json diff --git a/config/gen3/siteConfig.json b/config/gen3/siteConfig.json new file mode 100644 index 0000000..e69de29 diff --git a/config/gen3/themeColors.json b/config/gen3/themeColors.json new file mode 100644 index 0000000..26e8e0b --- /dev/null +++ b/config/gen3/themeColors.json @@ -0,0 +1,218 @@ +{ + "primary": { + "max": "#eaf3fa", + "lightest": "#bcd7ed", + "lighter": "#8ebbe1", + "light": "#609fd4", + "DEFAULT": "#3283C8", + "vivid": "#2584d4", + "dark": "#27669b", + "darker": "#1c486e", + "darkest": "#102b41", + "min": "#050d14" + }, + "primary-contrast": { + "max": "#111111", + "lightest": "#111111", + "lighter": "#111111", + "light": "#111111", + "DEFAULT": "#111111", + "vivid": "#111111", + "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" + }, + "secondary-contrast": { + "max": "#111111", + "lightest": "#111111", + "lighter": "#111111", + "light": "#111111", + "DEFAULT": "#111111", + "vivid": "#111111", + "dark": "#fefefe", + "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" + }, + "accent-contrast": { + "max": "#111111", + "lightest": "#111111", + "lighter": "#111111", + "light": "#111111", + "DEFAULT": "#fefefe", + "vivid": "#fefefe", + "dark": "#fefefe", + "darker": "#fefefe", + "darkest": "#fefefe", + "min": "#fefefe" + }, + "accent-warm": { + "max": "#e9f3f5", + "lightest": "#b8d8df", + "lighter": "#87bcc8", + "light": "#56a1b2", + "DEFAULT": "#25869b", + "vivid": "#1b8ca5", + "dark": "#1d6878", + "darker": "#144a55", + "darkest": "#0c2c32", + "min": "#040d0f" + }, + "accent-warm-contrast": { + "max": "#111111", + "lightest": "#111111", + "lighter": "#111111", + "light": "#111111", + "DEFAULT": "#000000", + "vivid": "#111111", + "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" + }, + "accent-cool-contrast": { + "max": "#111111", + "lightest": "#111111", + "lighter": "#111111", + "light": "#111111", + "DEFAULT": "#000000", + "vivid": "#111111", + "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" + }, + "base-contrast": { + "max": "#111111", + "lightest": "#111111", + "lighter": "#111111", + "light": "#111111", + "DEFAULT": "#111111", + "vivid": "#111111", + "dark": "#111111", + "darker": "#fefefe", + "darkest": "#fefefe", + "min": "#fefefe" + }, + "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": { + "max": "#e7f4f6", + "lightest": "#b0dde0", + "lighter": "#7ac5cb", + "light": "#43adb6", + "DEFAULT": "#0d95A1", + "vivid": "#049caa", + "dark": "#0a737d", + "darker": "#075259", + "darkest": "#043034", + "min": "#010f10" + }, + "chart-contrast": { + "max": "#111111", + "lightest": "#111111", + "lighter": "#111111", + "light": "#111111", + "DEFAULT": "#111111", + "vivid": "#111111", + "dark": "#fefefe", + "darker": "#fefefe", + "darkest": "#fefefe", + "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": "#111111", + "lightest": "#111111", + "lighter": "#111111", + "light": "#111111", + "DEFAULT": "#111111", + "vivid": "#111111", + "dark": "#111111", + "darker": "#fefefe", + "darkest": "#fefefe", + "min": "#fefefe" + } +} diff --git a/config/themeFonts.json b/config/gen3/themeFonts.json similarity index 100% rename from config/themeFonts.json rename to config/gen3/themeFonts.json diff --git a/config/icons/comparison.svg b/config/icons/comparison.svg new file mode 100644 index 0000000..114deb8 --- /dev/null +++ b/config/icons/comparison.svg @@ -0,0 +1 @@ + diff --git a/config/icons/dataDictionary/dictionary_icon_administrative.svg b/config/icons/dataDictionary/dictionary_icon_administrative.svg new file mode 100755 index 0000000..34b2184 --- /dev/null +++ b/config/icons/dataDictionary/dictionary_icon_administrative.svg @@ -0,0 +1,16 @@ + + + + icon-administrative + Created with Sketch. + + + + + + + + + + + diff --git a/config/icons/dataDictionary/dictionary_icon_analysis.svg b/config/icons/dataDictionary/dictionary_icon_analysis.svg new file mode 100755 index 0000000..df8b2ec --- /dev/null +++ b/config/icons/dataDictionary/dictionary_icon_analysis.svg @@ -0,0 +1,13 @@ + + + + icon_analysis + Created with Sketch. + + + + + + + + diff --git a/config/icons/dataDictionary/dictionary_icon_biospecimen.svg b/config/icons/dataDictionary/dictionary_icon_biospecimen.svg new file mode 100755 index 0000000..bdeea3b --- /dev/null +++ b/config/icons/dataDictionary/dictionary_icon_biospecimen.svg @@ -0,0 +1,11 @@ + + + + icon_Biospecimen + Created with Sketch. + + + + + + diff --git a/config/icons/dataDictionary/dictionary_icon_clinical.svg b/config/icons/dataDictionary/dictionary_icon_clinical.svg new file mode 100755 index 0000000..69d2882 --- /dev/null +++ b/config/icons/dataDictionary/dictionary_icon_clinical.svg @@ -0,0 +1,13 @@ + + + + hospital + Created with Sketch. + + + + + + + + diff --git a/config/icons/dataDictionary/dictionary_icon_clinical_assessment.svg b/config/icons/dataDictionary/dictionary_icon_clinical_assessment.svg new file mode 100755 index 0000000..49756c8 --- /dev/null +++ b/config/icons/dataDictionary/dictionary_icon_clinical_assessment.svg @@ -0,0 +1,20 @@ + + + + icon_clinical_assessment + Created with Sketch. + + + + + + + + + + + + + + + diff --git a/config/icons/dataDictionary/dictionary_icon_data_file.svg b/config/icons/dataDictionary/dictionary_icon_data_file.svg new file mode 100755 index 0000000..0284e37 --- /dev/null +++ b/config/icons/dataDictionary/dictionary_icon_data_file.svg @@ -0,0 +1,15 @@ + + + + icon_data_file + Created with Sketch. + + + + + + + + + + diff --git a/config/icons/dataDictionary/dictionary_icon_data_observations.svg b/config/icons/dataDictionary/dictionary_icon_data_observations.svg new file mode 100644 index 0000000..5b80e47 --- /dev/null +++ b/config/icons/dataDictionary/dictionary_icon_data_observations.svg @@ -0,0 +1,14 @@ + + + + Group 22 + Created with Sketch. + + + + + + + + + diff --git a/config/icons/dataDictionary/dictionary_icon_default.svg b/config/icons/dataDictionary/dictionary_icon_default.svg new file mode 100644 index 0000000..90f8248 --- /dev/null +++ b/config/icons/dataDictionary/dictionary_icon_default.svg @@ -0,0 +1,16 @@ + + + + Group 47 + Created with Sketch. + + + + + + + + + + + diff --git a/config/icons/dataDictionary/dictionary_icon_experimental_methods.svg b/config/icons/dataDictionary/dictionary_icon_experimental_methods.svg new file mode 100644 index 0000000..cc0b4fc --- /dev/null +++ b/config/icons/dataDictionary/dictionary_icon_experimental_methods.svg @@ -0,0 +1,11 @@ + + + + Group 23 + Created with Sketch. + + + + + + diff --git a/config/icons/dataDictionary/dictionary_icon_imaging.svg b/config/icons/dataDictionary/dictionary_icon_imaging.svg new file mode 100644 index 0000000..8a96d61 --- /dev/null +++ b/config/icons/dataDictionary/dictionary_icon_imaging.svg @@ -0,0 +1,11 @@ + + + + Group 19 + Created with Sketch. + + + + + + diff --git a/config/icons/dataDictionary/dictionary_icon_index_file.svg b/config/icons/dataDictionary/dictionary_icon_index_file.svg new file mode 100644 index 0000000..dab9dd4 --- /dev/null +++ b/config/icons/dataDictionary/dictionary_icon_index_file.svg @@ -0,0 +1,16 @@ + + + + Group + Created with Sketch. + + + + + + + + + + + diff --git a/config/icons/dataDictionary/dictionary_icon_medical_history.svg b/config/icons/dataDictionary/dictionary_icon_medical_history.svg new file mode 100755 index 0000000..69d2882 --- /dev/null +++ b/config/icons/dataDictionary/dictionary_icon_medical_history.svg @@ -0,0 +1,13 @@ + + + + hospital + Created with Sketch. + + + + + + + + diff --git a/config/icons/dataDictionary/dictionary_icon_metadata.svg b/config/icons/dataDictionary/dictionary_icon_metadata.svg new file mode 100755 index 0000000..5f40962 --- /dev/null +++ b/config/icons/dataDictionary/dictionary_icon_metadata.svg @@ -0,0 +1,16 @@ + + + + icon_metadata + Created with Sketch. + + + + + + + + + + + diff --git a/config/icons/dataDictionary/dictionary_icon_notation.svg b/config/icons/dataDictionary/dictionary_icon_notation.svg new file mode 100755 index 0000000..d546f7d --- /dev/null +++ b/config/icons/dataDictionary/dictionary_icon_notation.svg @@ -0,0 +1,12 @@ + + + + icon_notation + Created with Sketch. + + + + + + + diff --git a/config/icons/dataDictionary/dictionary_icon_study_administration.svg b/config/icons/dataDictionary/dictionary_icon_study_administration.svg new file mode 100644 index 0000000..3fce02a --- /dev/null +++ b/config/icons/dataDictionary/dictionary_icon_study_administration.svg @@ -0,0 +1,16 @@ + + + + Group 21 + Created with Sketch. + + + + + + + + + + + diff --git a/config/icons/dataDictionary/dictionary_icon_subject_characteristics.svg b/config/icons/dataDictionary/dictionary_icon_subject_characteristics.svg new file mode 100644 index 0000000..3da1d98 --- /dev/null +++ b/config/icons/dataDictionary/dictionary_icon_subject_characteristics.svg @@ -0,0 +1,14 @@ + + + + Group 20 + Created with Sketch. + + + + + + + + + diff --git a/config/icons/gen3.json b/config/icons/gen3.json index 95fbc67..45c67db 100644 --- a/config/icons/gen3.json +++ b/config/icons/gen3.json @@ -1,6 +1,6 @@ { "prefix": "gen3", - "lastModified": 1708125912, + "lastModified": 1721757073, "icons": { "analysis": { "body": "", @@ -19,6 +19,11 @@ "width": 58.026, "height": 58.026 }, + "comparison": { + "body": "", + "width": 512, + "height": 512 + }, "datafile": { "body": "", "width": 60, @@ -29,13 +34,65 @@ "width": 489.709, "height": 489.709 }, + "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": "" + }, "download": { "body": "", "width": 24, "height": 24 }, "exploration": { - "body": "" + "body": "", + "width": 512, + "height": 512 }, "gen3": { "body": "", @@ -63,16 +120,21 @@ "height": 511.999 }, "upload": { - "body": "" + "body": "", + "width": 512, + "height": 512 }, "user": { "body": "", - "width": 448 + "width": 448, + "height": 512 }, "workspace": { - "body": "" + "body": "", + "width": 512, + "height": 512 } }, - "width": 512, - "height": 512 + "width": 20, + "height": 20 } diff --git a/config/siteConfig.json b/config/siteConfig.json deleted file mode 100644 index 44fcd28..0000000 --- a/config/siteConfig.json +++ /dev/null @@ -1,3 +0,0 @@ -{ - "commons": "gen3" -} diff --git a/config/themeColors.json b/config/themeColors.json index 8927c01..1b94621 100644 --- a/config/themeColors.json +++ b/config/themeColors.json @@ -1,39 +1,39 @@ { "primary": { - "DEFAULT": "#345948", - "vivid": "#2d6049", - "min": "#050907", - "darkest": "#111d17", - "darker": "#1d3128", - "dark": "#284538", - "light": "#627e71", - "lighter": "#8fa49a", - "lightest": "#bdc9c4", - "max": "#ebeeed" + "DEFAULT": "#3283C8", + "vivid": "#2584d4", + "min": "#050d14", + "darkest": "#102b41", + "darker": "#1c486e", + "dark": "#27669b", + "light": "#609fd4", + "lighter": "#8ebbe1", + "lightest": "#bcd7ed", + "max": "#eaf3fa" }, "primary-contrast": { - "DEFAULT": "#fefefe", - "vivid": "#fefefe", + "DEFAULT": "#111111", + "vivid": "#111111", "min": "#fefefe", "darkest": "#fefefe", "darker": "#fefefe", "dark": "#fefefe", - "light": "#000000", + "light": "#111111", "lighter": "#111111", "lightest": "#111111", "max": "#111111" }, "secondary": { - "DEFAULT": "#BF7E06", - "vivid": "#c58000", - "min": "#130d99", - "darkest": "#3e2902", - "darker": "#694503", - "dark": "#946205", - "light": "#cd9b3e", - "lighter": "#dcb876", - "lightest": "#ead5ae", - "max": "#f9f2e6" + "DEFAULT": "#3283C8", + "vivid": "#2584d4", + "min": "#050d14", + "darkest": "#102b41", + "darker": "#1c486e", + "dark": "#27669b", + "light": "#609fd4", + "lighter": "#8ebbe1", + "lightest": "#bcd7ed", + "max": "#eaf3fa" }, "secondary-contrast": { "DEFAULT": "#111111", @@ -48,16 +48,16 @@ "max": "#111111" }, "accent": { - "DEFAULT": "#8C0404", - "vivid": "#900000", - "min": "#0e6666", - "darkest": "#2d0101", - "darker": "#4d0202", - "dark": "#6d0303", - "light": "#a63c3c", - "lighter": "#c07575", - "lightest": "#daadad", - "max": "#f4e6e6" + "DEFAULT": "#b75113", + "vivid": "#c14f09", + "min": "#120802", + "darkest": "#3b1a06", + "darker": "#652d0a", + "dark": "#8e3f0f", + "light": "#c77848", + "lighter": "#d79f7d", + "lightest": "#e8c6b2", + "max": "#f8eee7" }, "accent-contrast": { "DEFAULT": "#fefefe", @@ -66,49 +66,49 @@ "darkest": "#fefefe", "darker": "#fefefe", "dark": "#fefefe", - "light": "#fefefe", + "light": "#111111", "lighter": "#111111", "lightest": "#111111", "max": "#111111" }, "accent-warm": { - "DEFAULT": "#594B04", - "vivid": "#5d4e00", - "min": "#090766", - "darkest": "#1d1801", - "darker": "#312902", - "dark": "#453a03", - "light": "#7e743c", - "lighter": "#a49c75", - "lightest": "#c9c5ad", - "max": "#eeede6" + "DEFAULT": "#25869b", + "vivid": "#1b8ca5", + "min": "#040d0f", + "darkest": "#0c2c32", + "darker": "#144a55", + "dark": "#1d6878", + "light": "#56a1b2", + "lighter": "#87bcc8", + "lightest": "#b8d8df", + "max": "#e9f3f5" }, "accent-warm-contrast": { - "DEFAULT": "#fefefe", - "vivid": "#fefefe", + "DEFAULT": "#000000", + "vivid": "#111111", "min": "#fefefe", "darkest": "#fefefe", "darker": "#fefefe", "dark": "#fefefe", - "light": "#fefefe", + "light": "#111111", "lighter": "#111111", "lightest": "#111111", "max": "#111111" }, "accent-cool": { - "DEFAULT": "#908719", - "vivid": "#988e11", - "min": "#0e0d02", - "darkest": "#2f2c08", - "darker": "#4f4a0e", - "dark": "#706913", - "light": "#a9a24d", - "lighter": "#c2bd81", - "lightest": "#dbd8b4", - "max": "#f4f3e8" + "DEFAULT": "#1f839b", + "vivid": "#1689a4", + "min": "#030d0f", + "darkest": "#0a2b32", + "darker": "#114855", + "dark": "#186678", + "light": "#519fb2", + "lighter": "#84bbc8", + "lightest": "#b6d7df", + "max": "#e9f3f5" }, "accent-cool-contrast": { - "DEFAULT": "#111111", + "DEFAULT": "#000000", "vivid": "#111111", "min": "#fefefe", "darkest": "#fefefe", @@ -120,16 +120,16 @@ "max": "#111111" }, "base": { - "DEFAULT": "#CCCCCC", - "vivid": "#d1c7c7", - "min": "#141414", - "darkest": "#424242", - "darker": "#707070", - "dark": "#9e9e9e", - "light": "#d7d7d7", - "lighter": "#e3e3e3", - "lightest": "#eeeeee", - "max": "#fafafa" + "DEFAULT": "#c0c0c0", + "vivid": "#c6baba", + "min": "#131313", + "darkest": "#3e3e3e", + "darker": "#6a6a6a", + "dark": "#959595", + "light": "#cecece", + "lighter": "#dcdcdc", + "lightest": "#ebebeb", + "max": "#f9f9f9" }, "base-contrast": { "DEFAULT": "#111111", @@ -190,5 +190,29 @@ "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/package-lock.json b/package-lock.json index 067a46d..b035fd0 100644 --- a/package-lock.json +++ b/package-lock.json @@ -1,23 +1,23 @@ { - "name": "@gen3/commons-portal-app-base", - "version": "0.1.0", + "name": "prometheus-data-platform", + "version": "0.10.32", "lockfileVersion": 3, "requires": true, "packages": { "": { - "name": "@gen3/commons-portal-app-base", - "version": "0.1.0", + "name": "prometheus-data-platform", + "version": "0.10.32", "dependencies": { - "@gen3/frontend": "https://github.com/uc-cdis/gen3-frontend-framework/releases/download/v0.10.0-alpha/gen3-frontend-0.10.23.tgz", + "@gen3/frontend": "https://github.com/uc-cdis/gen3-frontend-framework/releases/download/v0.10.0-alpha/gen3-frontend-0.10.36.tgz", "@mantine/core": "^6.0.21", "@mdx-js/loader": "^3.0.0", "@mdx-js/react": "^3.0.0", - "@next/mdx": "^14.1.0", + "@next/mdx": "^14.2.3", "@types/mdx": "^2.0.11", "cookies-next": "^4.1.1" }, "devDependencies": { - "@gen3/toolsff": "https://github.com/uc-cdis/gen3-frontend-framework/releases/download/v0.10.0-alpha/gen3-toolsff-0.10.23.tgz", + "@gen3/toolsff": "https://github.com/uc-cdis/gen3-frontend-framework/releases/download/v0.10.0-alpha/gen3-toolsff-0.10.36.tgz", "@tailwindcss/aspect-ratio": "^0.4.2", "@tailwindcss/forms": "^0.5.3", "@tailwindcss/line-clamp": "^0.4.2", @@ -25,10 +25,19 @@ 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+ } + }, "node_modules/@floating-ui/core": { "version": "1.6.0", "resolved": "https://registry.npmjs.org/@floating-ui/core/-/core-1.6.0.tgz", @@ -1742,15 +1843,15 @@ "integrity": "sha512-f7iw44q1EjBv3MNcHCGAgrW/QVyweaEouFsJzykPhTOGnZFSwFJRISToXornOmuAy7xUUGiVdqOLiykgZoYB8A==" }, "node_modules/@gen3/core": { - "version": "0.10.23", - "resolved": "https://github.com/uc-cdis/gen3-frontend-framework/releases/download/v0.10.0-alpha/gen3-core-0.10.23.tgz", - "integrity": "sha512-Uinw7D+JdDvl1bvybNKQkq3HzAwuD3+J+8/liz8/ZIT3vlXAqfMV3zxt5HWadaRSsX3hHWC0Dxgcfj4Jsbh7RA==", - "license": "Apache-2.0", + "version": "0.10.36", + "resolved": "https://github.com/uc-cdis/gen3-frontend-framework/releases/download/v0.10.0-alpha/gen3-core-0.10.36.tgz", + "integrity": "sha512-/bo05hZVUnYS/NUBjkK8tUzRrcLI9wwxm3BjTicJA6pbf4/uutYg1kIXCjwkz4eXX3AwhsxkXvMrfWmMPLWEBQ==", "peer": true, "dependencies": { "@reduxjs/toolkit": "1.9.5", "flat": "^6.0.1", "papaparse": "^5.4.1", + "queue": "6.0.2", "react-redux": 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+ "prettier": "^2.7.1", "react": "^18.2.0", "react-dom": "18.2.0", "tailwindcss": "^3.3.7", "ts-jest": "^29.0.3", "ts-node": "^10.9.1", - "typescript": "5.0.2" + "typescript": "5.0.2", + "@typescript-eslint/eslint-plugin": "^7.12.0" }, "peerDependencies": { - "@gen3/core": "https://github.com/uc-cdis/gen3-frontend-framework/releases/download/v0.10.0-alpha/gen3-core-0.10.23.tgz", + "@gen3/core": "https://github.com/uc-cdis/gen3-frontend-framework/releases/download/v0.10.0-alpha/gen3-core-0.10.36.tgz", "react": "^18.2.0", "react-dom": "^18.2.0" } diff --git a/public/icons/OCC.png b/public/icons/OCC.png new file mode 100644 index 0000000..e554252 Binary files /dev/null and b/public/icons/OCC.png differ diff --git a/public/icons/Prometheus_logo.png b/public/icons/Prometheus_logo.png new file mode 100644 index 0000000..6f19760 Binary files /dev/null and b/public/icons/Prometheus_logo.png differ diff --git a/public/images/sideTexture.png b/public/images/sideTexture.png deleted file mode 100644 index 2327f88..0000000 Binary files a/public/images/sideTexture.png and /dev/null differ diff --git a/public/images/sideTexture.svg b/public/images/sideTexture.svg new file mode 100755 index 0000000..eb03d2e --- /dev/null +++ b/public/images/sideTexture.svg @@ -0,0 +1,2676 @@ + + +BG +Created with Sketch. + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/src/lib/CohortBuilder/FileDetailsPanel.tsx b/src/lib/CohortBuilder/FileDetailsPanel.tsx new file mode 100644 index 0000000..11323b5 --- /dev/null +++ b/src/lib/CohortBuilder/FileDetailsPanel.tsx @@ -0,0 +1,171 @@ +/* eslint-disable @typescript-eslint/no-explicit-any */ // TODO remove use of any +import { + Anchor, + Group, + LoadingOverlay, + Stack, + Table, + Text, + CopyButton, + ActionIcon, + Tooltip, + Button, +} from '@mantine/core'; +import { useGeneralGQLQuery, GEN3_FENCE_API } from '@gen3/core'; +import { + ErrorCard, + type TableDetailsPanelProps, + ExplorerTableDetailsPanelFactory, +} from '@gen3/frontend'; +import { + MdContentCopy as IconCopy, + MdCheck as IconCheck, +} from 'react-icons/md'; + +// a definition of the query response +interface QueryResponse { + data?: Record>; +} + +/** + * Checks if the given object is a QueryResponse. + * + * @param {any} obj - The object to be checked. + * @returns {boolean} Returns true if the object is a QueryResponse, false otherwise. + */ +const isQueryResponse = (obj: any): obj is QueryResponse => { + // Considering that the data property can be optional + return ( + typeof obj === 'object' && + (obj.data === undefined || typeof obj.data === 'object') + ); +}; + +/** + * Extracts data from a QueryResponse object based on an index. + * + * @param {QueryResponse} data - The QueryResponse object containing the data. + * @param {string} index - The index to extract the data from. + * @returns {Record} - The extracted data as a key-value pair object. + */ +const extractData = ( + data: QueryResponse, + index: string, +): Record => { + if (data === undefined || data === null) return {}; + if (data.data === undefined || data.data === null) return {}; + + return Array.isArray(data.data[index]) && data.data[index].length > 0 + ? data.data[index][0] + : {}; +}; + +export const FileDetailsPanel = ({ + 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 } + const { data, isLoading, isError } = useGeneralGQLQuery({ + query: `query ($filter: JSON) { + ${index} (filter: $filter, accessibility: all) { + ${tableConfig.fields} + } + }`, + variables: { + filter: { + AND: [ + { + IN: { + [idField ?? 0]: [id], + }, + }, + ], + }, + }, + }); + + // handle misconfiguration + if (!idField) { + return ( + + ); + } + // show data error if graphql fails + if (isError) { + return ; + } + + // process guppy response + const queryData = isQueryResponse(data) ? extractData(data, index) : {}; + + // create the rows for the table + const rows = Object.entries(queryData).map(([field, value]) => ( + + + {field} + + + {/* + if field is one that we want a link for make it an Anchor otherwise + render as text. + */} + {field === 'object_id' ? ( + + {value ? (value as string) : ''} + + ) : ( + {value ? (value as string) : ''} + )} + + + )); + return ( + + + Results for {id} + + + + + + + + {rows} +
FieldValue
+ + + {({ copied, copy }) => ( + + + {copied ? : } + + + )} + + + +
+ ); +}; + +export const registerCustomExplorerDetailsPanels = () => { + ExplorerTableDetailsPanelFactory().registerRendererCatalog({ + // NOTE: The catalog name must be tableDetails + tableDetails: { fileDetails: FileDetailsPanel }, // TODO: add simpler registration function that ensures the catalog name is tableDetails + }); +}; diff --git a/src/lib/Discovery/CustomCellRenderers.tsx b/src/lib/Discovery/CustomCellRenderers.tsx index 312297d..4a30224 100644 --- a/src/lib/Discovery/CustomCellRenderers.tsx +++ b/src/lib/Discovery/CustomCellRenderers.tsx @@ -11,55 +11,56 @@ import { import { isArray } from 'lodash'; import { JSONObject } from '@gen3/core'; import { toString } from 'lodash'; +import { FilemapPopup, FilemapInline } from '@/lib/Discovery/Filemap'; /** - * Custom cell renderer for the linked study column + * Custom cell renderer for the linked study column for HEAL * @param cell */ export const LinkedStudyCell = ({ - value: cellValue, - }: CellRenderFunctionProps) => { + value: cellValue, +}: CellRenderFunctionProps) => { const value = cellValue as boolean; return value ? ( - } - color="green" - > - Linked - + } + color="green" + > + Linked + ) : ( - } color="primary"> - Not Linked - + } color="primary"> + Not Linked + ); }; const WrappedStringCell = ( - { value }: CellRenderFunctionProps, - // eslint-disable-next-line @typescript-eslint/no-unused-vars - params?: JSONObject, + { value }: CellRenderFunctionProps, + // eslint-disable-next-line @typescript-eslint/no-unused-vars + params?: JSONObject, ) => { if (value === undefined || value === null || toString(value) === '') { return ( - - {`${ - params && params?.valueIfNotAvailable - ? params?.valueIfNotAvailable - : '' - }`}{' '} - + + {`${ + params && params?.valueIfNotAvailable + ? params?.valueIfNotAvailable + : '' + }`}{' '} + ); } const content = value as string | string[]; return ( -
+
{isArray(content) ? content.join(', ') : content} -
+
); }; @@ -70,10 +71,14 @@ const WrappedStringCell = ( export const registerDiscoveryCustomCellRenderers = () => { DiscoveryCellRendererFactory.registerCellRendererCatalog({ string: { - sampleString: WrappedStringCell, + default: WrappedStringCell, }, boolean: { LinkedStudyCell, }, + manifest: { + default: FilemapPopup, + inline: FilemapInline, + } }); }; diff --git a/src/lib/Discovery/CustomRowRenderers.tsx b/src/lib/Discovery/CustomRowRenderers.tsx index 6030dd9..dcf0101 100644 --- a/src/lib/Discovery/CustomRowRenderers.tsx +++ b/src/lib/Discovery/CustomRowRenderers.tsx @@ -7,77 +7,69 @@ import { RowRenderFunctionParams, DiscoveryRowRendererFactory, useDiscoveryContext, - getTagColor, + getTagInfo, + TagData, } from '@gen3/frontend'; -// TODO: This is a hack to get around the fact that the data is not typed -interface TagData { - name: string; - category: string; -} +const DetailsWithTagsRowRenderer = ( + { row }: RowRenderFunctionParams, + studyPreviewConfig?: StudyDetailsField, +): ReactElement => { + const { discoveryConfig: config } = useDiscoveryContext(); -const DetailsWithTagsRowRenderer = - ( - { row } : RowRenderFunctionParams, - studyPreviewConfig?: StudyDetailsField, - ): ReactElement => { - const { discoveryConfig: config, setStudyDetails } = useDiscoveryContext(); + if (!studyPreviewConfig) { + return ; + } + const value = + JSONPath({ + json: row.original, + path: studyPreviewConfig.field, + }) ?? + config?.studyPreviewField?.valueIfNotAvailable ?? + ''; - if (!studyPreviewConfig) { - return ; - } - const value = - JSONPath({ - json: row.original, - path: studyPreviewConfig.field, - }) ?? - config?.studyPreviewField?.valueIfNotAvailable ?? - ''; + return ( + +
+ + {value} + - return ( - { - setStudyDetails(() => { - return { ...row.original }; - }); - }} - > -
- - {value} - +
+ {row.original?.tags.map((tagInfo: TagData) => { + const { color, display, label } = getTagInfo(tagInfo, config.tags); -
- {row.original?.tags.map(({ name, category }: TagData) => { - const color = getTagColor(category, config.tagCategories); - return ( - - {name} - - ); - })} -
-
- - ); - }; + if (tagInfo.name === '') return null; // no tag + if (!display) return null; + return ( + + {label} + + ); + })} +
+
+
+ ); +}; export default DetailsWithTagsRowRenderer; diff --git a/src/lib/Discovery/Filemap.tsx b/src/lib/Discovery/Filemap.tsx new file mode 100644 index 0000000..8c859c2 --- /dev/null +++ b/src/lib/Discovery/Filemap.tsx @@ -0,0 +1,183 @@ +import { + CellRenderFunctionProps, + ReactECharts, + ReactEChartsProps, +} from '@gen3/frontend'; +import { Button, Popover, Text } from '@mantine/core'; +import { isArray } from 'lodash'; +import { useDeepCompareMemo } from 'use-deep-compare'; +import { useDisclosure } from '@mantine/hooks'; + +/** + * Represents a manifest item. + * @interface ManifestItem + */ +interface ManifestItem { + md5sum: string; + file_name: string; + file_size?: number; + object_id: string; + commons_name?: string; +} + +/** + * Interface representing the data structure for Bar Chart. + * + * @interface + * @name BarChartData + * @property {number} value - The numerical value associated with the bar. + * @property {string} name - The name or label associated with the bar. + */ +interface BarChartData { + value: number; + name: string; +} + +/** + * Counts the number of occurrences of file types in the given data array and returns an array of objects + * representing the file type and its percentage value within the total count. + * + * @param {Array} data - The array of data containing ManifestItem objects. + * @returns {Array} - The array of objects representing file types and their percentages. + */ +const countTypes = (data: Array): BarChartData[] => { + const counts: Record = {}; + data.forEach((item: ManifestItem) => { + const filetype = item.file_name.split('.').pop(); + if (!filetype) return; + counts[filetype] = counts[filetype] ? counts[filetype] + 1 : 1; + }); + const total = Object.values(counts).reduce((acc, val) => acc + val, 0); + return Object.entries(counts).map(([name, value]) => ({ + name, + value: Number(((value / total) * 100).toFixed(2)), + })); +}; + +/** + * Converts an array of manifest items into a chart definition for React ECharts. + * + * @param {Array} data - The array of manifest items to convert. + * @returns {ReactEChartsProps['option'] | undefined} - The chart definition or undefined if the data is invalid or empty. + */ +const useProcessManifestToChart = ( + values: Array, + showLabel = true, + showToolip = false, +): ReactEChartsProps['option'] | undefined => { + const chartDefinition = useDeepCompareMemo((): + | ReactEChartsProps['option'] + | undefined => { + if ( + values === undefined || + values === null || + !isArray(values) || + values.length === 0 + ) { + return undefined; + } + + const data = countTypes(values); + + return { + grid: { + left: 2, + top: 2, + right: 2, + bottom: 2, + }, + tooltip: { + trigger: 'item', + show: showToolip, + formatter: '{a} - {c}%', + position: 'right', + z: 100, + }, + xAxis: { + type: 'value', + show: false, + }, + yAxis: { + type: 'category', + data: data.map((d) => d.name), + show: false, + }, + series: data.map((d) => ({ + type: 'bar', + stack: 'total', + barWidth: 40, + name: d.name, + data: [d.value], + label: { + show: showLabel, + position: 'top', + minMargin: 8, + formatter: '{a} - {c}%', + }, + labelLine: { + show: true, + }, + labelLayout: () => { + return { + y: '35%', + moveOverlap: 'shiftX', + }; + }, + })), + }; + }, [values]); + + return chartDefinition; +}; + +/** + * Represents a Filemap popup component. + * + * @component + * @param {Object} value - An object containing the __manifest value to render. + * @returns {JSX.Element} - The rendered JSX element. + */ +export const FilemapPopup = ({ value }: CellRenderFunctionProps) => { + const [opened, { close, open }] = useDisclosure(false); + const chartDefinition = useProcessManifestToChart(value[0]); + + if (!chartDefinition) { + return n/a; + } + return ( + + + + + +
+ +
+
+
+ ); +}; + +/** + * Render a chart component based on the provided value. + * + * @param {object} value - An object or array containing the value for the chart component. + * @returns {JSX.Element} - The rendered chart component. + */ +export const FilemapInline = ({ value }: CellRenderFunctionProps) => { + const chartDefinition = useProcessManifestToChart(value[0], false, true); + + if (!chartDefinition) { + return n/a; + } + return ( +
+ +
+ ); +}; diff --git a/src/lib/plugins/index.js b/src/lib/plugins/index.js index c9426cb..2d8f48e 100644 --- a/src/lib/plugins/index.js +++ b/src/lib/plugins/index.js @@ -5,32 +5,37 @@ const fs = require('fs'); // eslint-disable-next-line @typescript-eslint/no-var-requires const path = require('path'); -if (!fs.existsSync(path.join(process.cwd(), 'config', 'plugins.json'))) { - console.log('No plugins to generate.'); - return; -} -console.log('Generating plugins...'); +function main() { + if (!fs.existsSync(path.join(process.cwd(), 'config', 'plugins.json'))) { + console.log('No plugins to generate.'); + return; + } -const plugins = JSON.parse( - fs - .readFileSync(path.join(process.cwd(), 'config', 'plugins.json')) - .toString('utf-8'), -); -const imports = plugins - .map( - (plugin) => - `import { registerApp as registerApp${plugin.name} } from "${plugin.module}";`, - ) - .join('\n'); -const register = plugins - .map((plugin) => `registerApp${plugin.name}();`) - .join('\n'); -fs.writeFileSync( - path.join(process.cwd(), 'config', 'registerSitePlugins.js'), - `${imports} + console.log('Generating plugins...'); + + const plugins = JSON.parse( + fs + .readFileSync(path.join(process.cwd(), 'config', 'plugins.json')) + .toString('utf-8'), + ); + const imports = plugins + .map( + (plugin) => + `import { registerApp as registerApp${plugin.name} } from "${plugin.module}";`, + ) + .join('\n'); + const register = plugins + .map((plugin) => `registerApp${plugin.name}();`) + .join('\n'); + fs.writeFileSync( + path.join(process.cwd(), 'config', 'registerSitePlugins.js'), + `${imports} export const registerSitePlugins = () => { ${register} }; `, -); + ); +}; + +main(); 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/Crosswalk.tsx b/src/pages/Crosswalk.tsx new file mode 100644 index 0000000..6474055 --- /dev/null +++ b/src/pages/Crosswalk.tsx @@ -0,0 +1,7 @@ +import { + CrosswalkPage, + CrosswalkPageGetServerSideProps as getServerSideProps, +} from '@gen3/frontend'; +export default CrosswalkPage; + +export { getServerSideProps }; diff --git a/src/pages/DataDictionary.tsx b/src/pages/DataDictionary.tsx index 274b3b1..0302c07 100644 --- a/src/pages/DataDictionary.tsx +++ b/src/pages/DataDictionary.tsx @@ -1,7 +1,7 @@ import { - DataDictionaryPage, - DataDictionaryPageGetServerSideProps as getServerSideProps, + DictionaryPage, + DictionaryPageGetServerSideProps as getServerSideProps, } from '@gen3/frontend'; -export default DataDictionaryPage; +export default DictionaryPage; export { getServerSideProps }; diff --git a/src/pages/Explorer.tsx b/src/pages/Explorer.tsx index 8322e2c..9923b56 100644 --- a/src/pages/Explorer.tsx +++ b/src/pages/Explorer.tsx @@ -3,9 +3,13 @@ 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(); +registerCustomExplorerDetailsPanels(); export default ExplorerPage; diff --git a/src/pages/SamplePage.tsx b/src/pages/SamplePage.tsx index 7fe48bb..1124364 100644 --- a/src/pages/SamplePage.tsx +++ b/src/pages/SamplePage.tsx @@ -26,7 +26,7 @@ const SamplePage = ({ headerProps, footerProps }: NavPageLayoutProps) => { export const getServerSideProps: GetServerSideProps< NavPageLayoutProps -> = async (_context) => { +> = async () => { return { props: { ...(await getNavPageLayoutPropsFromConfig()), diff --git a/src/pages/Submission.tsx b/src/pages/Submission.tsx new file mode 100644 index 0000000..f6e0969 --- /dev/null +++ b/src/pages/Submission.tsx @@ -0,0 +1,7 @@ +import { + SubmissionPage, + SubmissionPageGetServerSideProps as getServerSideProps, +} from '@gen3/frontend'; +export default SubmissionPage; + +export { getServerSideProps }; diff --git a/src/pages/Workspaces.tsx b/src/pages/Workspace.tsx similarity index 100% rename from src/pages/Workspaces.tsx rename to src/pages/Workspace.tsx diff --git a/src/pages/_app.tsx b/src/pages/_app.tsx index 85551da..6b1c2ed 100644 --- a/src/pages/_app.tsx +++ b/src/pages/_app.tsx @@ -1,32 +1,39 @@ -import type { AppProps } from 'next/app'; +import App, { AppProps, AppContext, AppInitialProps } from 'next/app'; import { useEffect } from 'react'; -import { Gen3Provider, TenStringArray, type ModalsConfig } from '@gen3/frontend'; -import themeColors from '../../config/themeColors.json'; -import themeFonts from '../../config/themeFonts.json'; -import icons from '../../config/icons/gen3.json'; +import { + Gen3Provider, + TenStringArray, + type ModalsConfig, + ContentSource, + RegisteredIcons, + Fonts, + SessionConfiguration, +} from '@gen3/frontend'; import '../styles/globals.css'; import 'graphiql/graphiql.css'; import '@graphiql/react/dist/style.css'; -import { setDRSHostnames } from '@gen3/core'; - - -// TODO: This can be done in a better way using newer NextJS features -import sessionConfig from '../../config/session.json'; -import modalsConfig from '../../config/modals.json'; +import { GEN3_COMMONS_NAME, setDRSHostnames } from '@gen3/core'; import drsHostnames from '../../config/drsHostnames.json'; -const colors = Object.fromEntries( - Object.entries(themeColors).map(([key, values]) => [ - key, - Object.values(values) as TenStringArray, - ]), -); - -export default function App({ Component, pageProps }: AppProps) { +interface Gen3AppProps { + colors: Record; + icons: RegisteredIcons; + themeFonts: Fonts; + modalsConfig: ModalsConfig; + sessionConfig: SessionConfiguration; +} +const Gen3App = ({ + Component, + pageProps, + colors, + icons, + themeFonts, + sessionConfig, + modalsConfig, +}: AppProps & Gen3AppProps) => { useEffect(() => { setDRSHostnames(drsHostnames); - }, []); return ( @@ -34,10 +41,75 @@ export default function App({ Component, pageProps }: AppProps) { colors={colors} icons={icons} fonts={themeFonts} - sessionConfig={sessionConfig.sessionConfig} - modalsConfig={modalsConfig as ModalsConfig} + sessionConfig={sessionConfig} + modalsConfig={modalsConfig} > ); -} +}; + +// TODO: replace with page router +Gen3App.getInitialProps = async ( + context: AppContext, +): Promise => { + 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/${GEN3_COMMONS_NAME}/themeColors.json`, + ); + + const colors = Object.fromEntries( + Object.entries(themeColors).map(([key, values]) => [ + key, + Object.values(values) as TenStringArray, + ]), + ); + + const icons = await ContentSource.get('config/icons/gen3.json'); + return { + ...ctx, + modalsConfig: modals, + sessionConfig: session, + themeFonts: fonts as Fonts, + colors: colors, + icons: icons as RegisteredIcons, + }; + } catch (error: unknown) { + if (error instanceof Error) { + console.error('Provider Wrapper error loading config', error.toString()); + } else console.error('Provider wrapper: unknown error'); + } + // return default + return { + ...ctx, + colors: {}, + themeFonts: { + heading: ['Poppins', 'sans-serif'], + content: ['Poppins', 'sans-serif'], + fontFamily: 'Poppins', + }, + icons: { + prefix: 'gen3', + lastModified: 0, + icons: {}, + width: 0, + height: 0, + }, + modalsConfig: {}, + sessionConfig: {}, + }; +}; +export default Gen3App; diff --git a/tailwind.config.js b/tailwind.config.js index f49e613..142084b 100644 --- a/tailwind.config.js +++ b/tailwind.config.js @@ -2,12 +2,13 @@ /* eslint-disable @typescript-eslint/no-var-requires */ const plugin = require('tailwindcss/plugin'); -const themeColors = require('./config/themeColors.json'); -const themeFonts = require('./config/themeFonts.json'); +/* eslint-disable @typescript-eslint/no-var-requires */ +const { GEN3_COMMONS_NAME } = require('@gen3/core'); +const themeColors = require(`./config/${GEN3_COMMONS_NAME}/themeColors.json`); +const themeFonts = require(`./config/${GEN3_COMMONS_NAME}/themeFonts.json`); module.exports = { presets: [require('@gen3/frontend/tailwind')], - // important: '#__next', // Uncommenting this affects tailwind styling in Modals content: [ './src/pages/**/*.{js,ts,jsx,tsx}', './src/components/**/*.{js,ts,jsx,tsx}',