Merge branch 'main' into role_module

.eslintignore

@@ -5,6 +5,8 @@ babel.config.js
 
 # compiled js ignored since it is run on the jsx directory
 modules/*/js/*
+!modules/brainbrowser/js/brainbrowser.config.js
+!modules/brainbrowser/js/brainbrowser.loris.js
 modules/electrophysiology_browser/jsx/react-series-data-viewer/src/protocol-buffers/chunk_pb.js
 htdocs/js/components/*
 

.eslintrc.json

@@ -87,7 +87,8 @@
     "jsdoc/require-param-description": "off",
     "jsdoc/require-returns": "off",
     "jsdoc/require-returns-description": "off",
-    "jsdoc/check-tag-names": "error"
+    "jsdoc/check-tag-names": "error",
+    "jsdoc/check-types": "error"
   },
   "overrides": [
     {
@@ -199,7 +200,8 @@
       "files": [
         "modules/candidate_parameters/**",
         "modules/dqt/**",
-        "modules/configuration/jsx/configuration_helper.js"
+        "modules/configuration/jsx/configuration_helper.js",
+        "modules/brainbrowser/js/brainbrowser.loris.js"
       ],
       "rules": {
         "no-jquery/no-other-utils": "warn",

.github/workflows/loristest.yml

@@ -4,11 +4,207 @@ on:
   - push
   - pull_request
 
-env:
-  EEG_VIS_ENABLED: 'true'
 
 jobs:
-  build:
+  buildjs:
+    env:
+      EEG_VIS_ENABLED: 'true'
+    runs-on: ubuntu-latest
+    steps: 
+      - uses: actions/checkout@v2
+
+      - name: Install EEG package dependencies
+      # We only need to install protobuf-compiler
+      # Other deps were added to fix an apt dependency issue introduced by a new github Ubuntu image
+      # (see https://github.com/actions/runner-images/blob/releases/ubuntu22/20230305/images/linux/Ubuntu2204-Readme.md)
+      # that updated the list of installed apt packages/apt repositories. That issue may disappear in future Ubuntu images.
+        run: |
+          sudo apt install -y imagemagick-6-common libmagickcore-6.q16-6 libmagickwand-6.q16-6 \
+             libprotobuf-dev libprotobuf23 libprotoc23 protobuf-compiler
+          cd modules/electrophysiology_browser/jsx/react-series-data-viewer/
+          protoc protocol-buffers/chunk.proto --js_out=import_style=commonjs,binary:./src/
+
+      - name: Install npm modules
+        run: npm ci
+
+      - name: Compile LORIS javascript
+        run: npm run compile
+
+      - name: Create LORIS JS tarball
+        run: tar cfvz lorisjs.tar.gz htdocs/js/components/ modules/*/js/*
+
+      - name: Create node_modules tarball
+        run: tar cfvz node_modules.tar.gz node_modules
+
+      - uses: actions/upload-artifact@v3
+        name: Upload node_modules artifact
+        with:
+          name: node_modules
+          path: node_modules.tar.gz
+
+      - uses: actions/upload-artifact@v3
+        name: Upload lorisjs.tar.gz artifact
+        with:
+          name: lorisjs
+          path: lorisjs.tar.gz
+
+  buildphp:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        php: ['8.1', '8.2']
+    steps:
+      - uses: actions/checkout@v2
+
+      - name: Setup PHP
+        uses: shivammathur/setup-php@v2
+        with:
+          php-version: ${{ matrix.php }}
+          extensions: zip, php-ast
+
+      - name: Validate composer.json and composer.lock
+        run: composer validate
+
+      - name: Cache Composer packages
+        id: composer-cache
+        run: echo "::set-output name=dir::$(composer config cache-files-dir)"
+
+      - name: Composer cache
+        uses: actions/cache@v2
+        with:
+          path: ${{ steps.composer-cache.outputs.dir }}
+          key: ${{ runner.os }}-composer-${{ hashFiles('composer.lock') }}
+          restore-keys: ${{ runner.os }}-composer-
+
+      - name: Install composer dependencies
+        if: steps.composer-cache.outputs.cache-hit != 'true'
+        run: composer install --prefer-dist --no-progress --no-suggest
+
+      - name: Create vendor tarball
+        run: tar cfvz vendor-php${{matrix.php}}.tar.gz vendor
+
+      - uses: actions/upload-artifact@v3
+        name: Upload vendor-php${{matrix.php}}.tar.gz artifact
+        with:
+          name: vendor-php${{matrix.php}}
+          path: vendor-php${{matrix.php}}.tar.gz
+
+  api:
+    runs-on: ubuntu-latest
+    needs:
+      - buildjs
+      - buildphp 
+
+    env:
+      DB_DATABASE: LorisTest
+      DB_USER: SQLTestUser
+      DB_PASSWORD: TestPassword
+      LORIS_DB_CONFIG: project/config.xml
+      DOCKER_WEB_SERVER: http://localhost:8000/
+    strategy:
+      fail-fast: false
+      matrix:
+        php: ['8.1', '8.2']
+        apiversion: ['v0.0.3', 'v0.0.4-dev']
+    steps:
+    - uses: actions/checkout@v2
+
+    - uses: actions/download-artifact@v3
+      name: Download node_modules artifact
+      with:
+        name: node_modules
+        path: .
+
+    - uses: actions/download-artifact@v3
+      name: Download compiled LORIS javascript artifact
+      with:
+        name: lorisjs
+        path: .
+
+    - uses: actions/download-artifact@v3
+      name: Download PHP dependencies artifact
+      with:
+        name: vendor-php${{matrix.php}}
+        path: .
+
+
+    - name: Extract node_modules
+      run: tar xfvz node_modules.tar.gz
+
+    - name: Extract compiled JS
+      run: tar xfvz lorisjs.tar.gz
+
+    - name: Extract composer vendor directory
+      run: tar xfvz vendor-php${{matrix.php}}.tar.gz
+
+    - name: Generate VERSION file
+      run: make VERSION
+
+    - name: Setup project/ directory
+      run: |
+        mkdir -p project/instruments
+        cp test/config.xml project/config.xml
+        cp test/test_instrument/NDB_BVL_Instrument_testtest.class.inc project/instruments/
+        cp -r raisinbread/instruments/* project/instruments/
+        sed -i 's/<sandbox>1<\/sandbox>/<sandbox>0<\/sandbox>/g' project/config.xml
+        sed -i 's/<adminUser>SQLTestUser<\/adminUser>/<adminUser>root<\/adminUser>/g' project/config.xml
+        sed -i 's/<adminPassword>TestPassword<\/adminPassword>/<adminPassword>root<\/adminPassword>/g' project/config.xml
+        sed -i 's/<host>db<\/host>/<host>localhost<\/host>/g' project/config.xml
+        cat project/config.xml
+
+    - name: Set up MySQL
+      run: |
+        sudo /etc/init.d/mysql start
+        mysql -e 'CREATE DATABASE ${{ env.DB_DATABASE }};' -uroot -proot
+        mysql -e "CREATE USER '${{env.DB_USER}}'@'localhost' IDENTIFIED BY '${{env.DB_PASSWORD}}'" -uroot -proot
+        mysql -e "GRANT UPDATE,INSERT,SELECT,DELETE,CREATE TEMPORARY TABLES ON ${{env.DB_DATABASE}}.* TO '${{env.DB_USER}}'@'localhost'" -uroot -proot
+
+    - name: Source default schema and Raisinbread
+      run: |
+        mysql ${{ env.DB_DATABASE}} -uroot -proot < SQL/0000-00-00-schema.sql
+        mysql ${{ env.DB_DATABASE}} -uroot -proot < SQL/0000-00-01-Modules.sql
+        mysql ${{ env.DB_DATABASE}} -uroot -proot < SQL/0000-00-02-Permission.sql
+        mysql ${{ env.DB_DATABASE}} -uroot -proot < SQL/0000-00-03-ConfigTables.sql
+        mysql ${{ env.DB_DATABASE}} -uroot -proot < SQL/0000-00-04-Help.sql
+        mysql ${{ env.DB_DATABASE}} -uroot -proot < SQL/0000-00-05-ElectrophysiologyTables.sql
+        find raisinbread/instruments/instrument_sql -name *.sql -exec sh -c "echo Sourcing {}; mysql ${{ env.DB_DATABASE}} -uroot -proot < {}" \;
+        find raisinbread/RB_files/ -name *.sql -exec sh -c "echo Sourcing {}; mysql ${{ env.DB_DATABASE}} -uroot -proot < {}" \;
+
+    - name: Source instrument schemas
+      run: |
+        find raisinbread/instruments/instrument_sql -name 0000-*.sql -exec sh -c "echo Sourcing {}; mysql ${{ env.DB_DATABASE}} -uroot -proot < {}" \;
+        echo Sourcing test/test_instrument/testtest.sql
+        mysql ${{ env.DB_DATABASE}} -uroot -proot < test/test_instrument/testtest.sql
+ 
+    - name: Set LORIS base path
+      run: |
+        echo UPDATE Config SET VALUE=\'`pwd`/\' WHERE ConfigID IN \(SELECT ID FROM ConfigSettings WHERE Name=\'base\'\)
+        echo UPDATE Config SET VALUE=\'`pwd`/\' WHERE ConfigID IN \(SELECT ID FROM ConfigSettings WHERE Name=\'base\'\) | mysql ${{env.DB_DATABASE}} -uroot -proot
+
+    - name: Setup PHP
+      uses: shivammathur/setup-php@v2
+      with:
+        php-version: ${{ matrix.php }}
+        extensions: zip, php-ast
+
+    - name: Start PHP Web Server
+      run: php -S localhost:8000 -t htdocs/ htdocs/router.php 2>error_log &
+
+    - name: Test server
+      run: |
+           sleep 1
+           curl -v http://localhost:8000
+
+
+    - name: Run Test Suite
+      run: |
+          vendor/bin/phpunit --configuration test/phpunit.xml --testsuite LorisAPITests --group api-${{ matrix.apiversion }}
+
+    - name: Print Error Logs
+      if: always()
+      run: cat error_log
+
+  docker:
     runs-on: ubuntu-latest
     strategy:
         fail-fast: false

CHANGELOG.md

@@ -17,8 +17,12 @@ changes in the following format: PR #1234***
 - Migrated instrument permissions from config.xml to database and added the ability
   to manage instrument permissions in the frontend from the `instrument_manager`
   module. (PR #8302)
+- new postinstall script that automatically installs /project and eeg-browser additional npm dependencies 
+  when `make` or `npm ci` is executed (PR #8244)
+
 
 #### Updates and Improvements
+- Upgrade react to version 18 (PR #8188)
 - Rename subproject to Cohort (PR #7817, applied changes in LORIS-MRI PR #882)
 - Create new CohortData and CohortController classes to use as data access model 
   and transfer object (PR #7817)
@@ -27,41 +31,77 @@ changes in the following format: PR #1234***
 - Fixed the Candidate Age at Death field label and Data Dictionary item for LINST instruments (PR #8362)
 - Allow clearing a previously entered consent status in candidate parameters (PR #7772)
 - Add code sanitizer before dangerouslySetInnerHTML is used in login to protect against XSS attacks (PR #7491)
+- npm package freeze with versionning of `package-lock.json` and switch from `npm install` to `npm ci` (PR #8224)
+- New imaging config to set:
+  - createVisit
+  - a default project (default_project) used if createVisit or createCandidate is set to true, or for phantom scans
+  - a default cohort (default_cohort) used if createVisit is set to true (PR #8384)
+- Help and help editor reactification (PR #8309)
 
 #### Bug Fixes
-- placeholder
+- Fix a Fatal error on the Genomic Browser tabs (PR #8468)
 
 ### Modules
 
 #### API
 - Modified in v0.0.4-dev the candidate instrument data format returned by a GET request or
 provided as the body of a PUT/PATCH request. The values of all fields are now defined by
 the `Data` key instead of `$InstrumentName` (PR #7857)
+- Fix Candidate endpoint error:
+The candidates/{CanID} endpoint throws a fatal error if a missing but valid (format pass validation) CanID is provided (PR #8417)
+
+
 #### Candidate Parameters
 - Added date restriction for consent withdrawal so that withdrawal date cannot be earlier
 than the given consent response date (PR #8298)
+
 #### EEG Browser
 - Visualization:
   - Electrode 2D montage: detect if the coordinate space is in the ALS orientation to convert to RAS (nose up)
   - Use the optimal signal sampling that fulfills number of chunk displayed < MAX_VIEWED_CHUNKS
-  - Fixes UI panels open/close glitches
+  - Fixes UI panels open/close glitches (PR #8238)
+  - Upgrade codebase to Typescript 4.0 syntax (PR #8211)
+  - New config (GUI/useEEGBrowserVisualizationComponents) to enable the EEG visualization (PR #8263)
+  - Annotations: HED tags support (PR #8236)
 - Added a SQL table to save any additional task events property data imported through BIDS files (PR #8237)
   - Added method to extract from BIDS files in LORIS-MRI (LORIS-MRI PR #873)
 - Added SQL tables to save coordinate system data imported through BIDS files (PR #8242)
   - Added method to extract from BIDS files in LORIS-MRI (LORIS-MRI PR #885)
+- Fix a few issues with EEGLAB set/fdt files:
+  - Download link broken
+  - Incorrect placement, it should be logically after the .set file (PR #8323)
+- Download All files fails when no annotations exists (PR #8323)
+- Clean dependency tree and fix security issues (PR #8486)
+
 #### Instrument Builder
 - Fixed display order of select options that were previously ordered alphabetically.
 Now the options correctly display in order of how they are defined in the instrument. (PR #8361)
+
 #### Instruments
 - Added `postMortem` functionality for LINST instruments, fixing display of 'Candidate Age at Death' when `postMortem` is set to true (PR #8362)
 - Added/modified documentation for configuring 'Candidate Age at Death' field display in instruments (PR #8362)
 
 #### Issue Tracker
-
 - Modified username (i.e. user ID) to full names throughout the main table, edit form and history sections (PR #8451)
 
+#### EEG uploader
+- New module (PR #8409)
+
+#### Dashboard
+- Reactification (PR #8476)
+
+#### MRI violation
+- Reactification (PR #7473)
+- Fixes links to BrainBrowser from the MRI violations module (PR #8392)
+- Remove MRI violation module tabs (PR #8399)
+- Fix multiple rows for file protocol violations not resolvable (PR #8661)
+- Fix hashing algorithm for `violations_resolved` table's `hash` column (PR #8664)
+
+#### Statistics
+- Reactification (PR #8476)
+
 ### Tools
-- placeholder
+- Fix CouchDB_MRI_Importer.php script for PHP > 8.0 (PR #8369) 
 
 ### Clean Up
 - Fixed inconsistency in candidate consent data and history in Raisinbread (PR #8297)
@@ -72,11 +112,14 @@ SQL schema, and automated testing (PR #8313)
 - API: Modified in v0.0.4-dev the candidate instrument data format returned by a GET request or
 provided as the body of a PUT/PATCH request. The values of all fields are now defined by
 the `Data` key instead of `$InstrumentName` (PR #7857)
-
+- Run the script `tools/single_use/update_violations_resolved_hashes.sql.php` to update hashes
+  for the `violations_resolved` table according to the new hashing nomenclature. Not doing so 
+  will result in duplication of data in the `violations_resolved` table when users update
+  a resolution status for a violation.
 
 ### Notes For Developers
-- placeholder
-
+- Require jsodc comments to have correct `@return` and `@param` values in javascript (PR #8266)
+- Disable ESLint on build (prod instances) (PR #8229)
 
 
 
@@ -105,6 +148,7 @@ the `Data` key instead of `$InstrumentName` (PR #7857)
 - Add psr/log to composer (PR #8109)
 - Fixed broken DB calls in `assign_missing_instruments` and `instruments` (PR #8162)
 - Add support for PHP 8.1 (PR #7989)
+- Fix Project tab of Configuration module to give correct errors, and prevent saving without Alias (PR #8349)
 ### Modules
 #### API
 - Ability to use PSCID instead of the CandID in the candidates API (PR #8138)