zaliqarosli · zaliqarosli · Mar 28, 2023 · Apr 5, 2023 · Apr 25, 2023 · Apr 25, 2023
diff --git a/.editorconfig b/.editorconfig
@@ -17,3 +17,7 @@ indent_size = 2
 
 [*.md]
 trim_trailing_whitespace = false
+
+[*.yml]
+indent_size = 2
+
diff --git a/.github/ISSUE_TEMPLATE/module_testing.md b/.github/ISSUE_TEMPLATE/module_testing.md
diff --git a/.github/workflows/loristest.yml b/.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

diff --git a/Makefile b/Makefile
@@ -1,4 +1,4 @@
-.PHONY: clean dev all check checkstatic unittests phpdev jslatest testdata
+.PHONY: clean dev all check checkstatic unittests phpdev jslatest testdata fastdev jsdev
 
 all: VERSION
 	composer install --no-dev
@@ -12,8 +12,12 @@ VERSION: .
 phpdev:
 	composer install
 
-dev: VERSION phpdev
+dev: phpdev jsdev fastdev 
+
+jsdev:
 	npm ci
+
+fastdev: VERSION
 	npm run compile
 
 jslatest: clean

diff --git a/README.md b/README.md
@@ -10,7 +10,7 @@ LORIS (Longitudinal Online Research and Imaging System) is a self-hosted web app
 
 * Try the LORIS demo instance at https://demo.loris.ca.
 
-This Readme covers installation of LORIS version <b>24.1</b> on <b>Ubuntu</b>.
+This Readme covers installation of LORIS version <b>25.0</b> on <b>Ubuntu</b>.
 
 ([CentOS Readme also available](docs/wiki/00_SERVER_INSTALL_AND_CONFIGURATION/01_LORIS_Install/CentOS/README.md)).
 

diff --git a/SQL/0000-00-05-ElectrophysiologyTables.sql b/SQL/0000-00-05-ElectrophysiologyTables.sql
@@ -487,7 +487,7 @@ CREATE TABLE `electrophysiology_uploader` (
     `UploadedBy` varchar(255) NOT NULL,
     `UploadDate` DateTime NOT NULL,
     `UploadLocation` varchar(255) NOT NULL,
-    `Status` enum('Not Started', 'Extracted', 'In Progress', 'Complete', 'Failed', 'Archived') DEFAULT 'Not Started',
+    `Status` enum('Not Started', 'Extracted', 'Failed Extraction', 'In Progress', 'Complete', 'Failed', 'Archived') DEFAULT 'Not Started',
     `SessionID` int(10) unsigned,
     `Checksum` varchar(40) DEFAULT NULL,
     `MetaData` TEXT DEFAULT NULL,

diff --git a/SQL/9999-99-99-drop_tables.sql b/SQL/9999-99-99-drop_tables.sql
@@ -1,11 +1,16 @@
 -- 0000-00-05-ElectrophysiologyTables.sql
+DROP TABLE IF EXISTS `physiological_event_parameter_category_level`;
+DROP TABLE IF EXISTS `physiological_event_parameter`;
+DROP TABLE IF EXISTS `physiological_event_archive`;
+DROP TABLE IF EXISTS `physiological_event_file`;
 DROP TABLE IF EXISTS `physiological_coord_system_electrode_rel`;
 DROP TABLE IF EXISTS `physiological_coord_system_point_3d_rel`;
 DROP TABLE IF EXISTS `point_3d`;
 DROP TABLE IF EXISTS `physiological_coord_system`;
 DROP TABLE IF EXISTS `physiological_coord_system_unit`;
 DROP TABLE IF EXISTS `physiological_coord_system_name`;
 DROP TABLE IF EXISTS `physiological_coord_system_type`;
+DROP TABLE IF EXISTS `electrophysiology_uploader`;
 DROP TABLE IF EXISTS `physiological_annotation_rel`;
 DROP TABLE IF EXISTS `physiological_annotation_instance`;
 DROP TABLE IF EXISTS `physiological_annotation_parameter`;
@@ -45,6 +50,7 @@ DROP TABLE IF EXISTS `issues`;
 DROP TABLE IF EXISTS `issues_categories`;
 
 -- 0000-00-02-Permission.sql
+DROP TABLE IF EXISTS `testnames_permissions_rel`;
 DROP TABLE IF EXISTS `user_perm_rel`;
 DROP TABLE IF EXISTS `notification_modules_perm_rel`;
 DROP TABLE IF EXISTS `permissions`;

diff --git a/...es/2021-03-01-publication-add-columns.sql → ....0/2021-03-01-publication-add-columns.sql b/...es/2021-03-01-publication-add-columns.sql → ....0/2021-03-01-publication-add-columns.sql
diff --git a/...es/2021-09-13_fix_project_primary_key.sql → ....0/2021-09-13_fix_project_primary_key.sql b/...es/2021-09-13_fix_project_primary_key.sql → ....0/2021-09-13_fix_project_primary_key.sql
diff --git a/...1-12-01-make_subproject_titles_unique.sql → ...1-12-01-make_subproject_titles_unique.sql b/...1-12-01-make_subproject_titles_unique.sql → ...1-12-01-make_subproject_titles_unique.sql
diff --git a/SQL/New_patches/2022-03-03-AddHEDTags.sql → SQL/Archive/25.0/2022-03-03-AddHEDTags.sql b/SQL/New_patches/2022-03-03-AddHEDTags.sql → SQL/Archive/25.0/2022-03-03-AddHEDTags.sql
@@ -44,6 +44,7 @@ INSERT INTO physiological_event_file (PhysiologicalFileID, FilePath, FileType)
 UPDATE physiological_task_event te
     SET EventFileID=(SELECT EventFileID FROM physiological_event_file WHERE PhysiologicalFileID=te.PhysiologicalFileID)
 ;
+SET FOREIGN_KEY_CHECKS= 1;
 
 -- Delete FilePath column in `physiological_task_event` table
 ALTER TABLE physiological_task_event

diff --git a/...022-11-22-eeg-additional-events-table.sql → ...022-11-22-eeg-additional-events-table.sql b/...022-11-22-eeg-additional-events-table.sql → ...022-11-22-eeg-additional-events-table.sql
diff --git a/...hes/2022-11-24-electrode-coord-system.sql → ...5.0/2022-11-24-electrode-coord-system.sql b/...hes/2022-11-24-electrode-coord-system.sql → ...5.0/2022-11-24-electrode-coord-system.sql
diff --git a/...atches/2022-12-01-subprojects_no_more.sql → ...e/25.0/2022-12-01-subprojects_no_more.sql b/...atches/2022-12-01-subprojects_no_more.sql → ...e/25.0/2022-12-01-subprojects_no_more.sql
diff --git a/SQL/New_patches/2022-12-05-AddVizConfig.sql → SQL/Archive/25.0/2022-12-05-AddVizConfig.sql b/SQL/New_patches/2022-12-05-AddVizConfig.sql → SQL/Archive/25.0/2022-12-05-AddVizConfig.sql
diff --git a/...ches/2022-12-20-instrumentpermissions.sql → ...25.0/2022-12-20-instrumentpermissions.sql b/...ches/2022-12-20-instrumentpermissions.sql → ...25.0/2022-12-20-instrumentpermissions.sql
diff --git a/...ches/2022-12-20-project-name-not-null.sql → ...25.0/2022-12-20-project-name-not-null.sql b/...ches/2022-12-20-project-name-not-null.sql → ...25.0/2022-12-20-project-name-not-null.sql
diff --git a/...0119_add_index_on_violations_resolved.sql → ...1-19_add_index_on_violations_resolved.sql b/...0119_add_index_on_violations_resolved.sql → ...1-19_add_index_on_violations_resolved.sql
diff --git a/...ches/2023-01-31-add-date-stage-change.sql → ...25.0/2023-01-31-add-date-stage-change.sql b/...ches/2023-01-31-add-date-stage-change.sql → ...25.0/2023-01-31-add-date-stage-change.sql
diff --git a/...patches/2023-02-17-imaging-new-config.sql → ...ve/25.0/2023-02-17-imaging-new-config.sql b/...patches/2023-02-17-imaging-new-config.sql → ...ve/25.0/2023-02-17-imaging-new-config.sql
diff --git a/...2023-02-24-electrophysiology_uploader.sql → ...2023-02-24-electrophysiology_uploader.sql b/...2023-02-24-electrophysiology_uploader.sql → ...2023-02-24-electrophysiology_uploader.sql
diff --git a/...te_max_days_inactive_config_for_users.sql → ...te_max_days_inactive_config_for_users.sql b/...te_max_days_inactive_config_for_users.sql → ...te_max_days_inactive_config_for_users.sql
diff --git a/...and_echo_number_to_MRICandidateErrors.sql → ...and_echo_number_to_MRICandidateErrors.sql b/...and_echo_number_to_MRICandidateErrors.sql → ...and_echo_number_to_MRICandidateErrors.sql
diff --git a/SQL/Cleanup_patches/2021-11-17-noextlibs.sql → ...ive/25.0/Cleanup/2021-11-17-noextlibs.sql b/SQL/Cleanup_patches/2021-11-17-noextlibs.sql → ...ive/25.0/Cleanup/2021-11-17-noextlibs.sql
diff --git a/...p_patches/2022-12-15-Drop_Flag_status.sql → ...0/Cleanup/2022-12-15-Drop_Flag_status.sql b/...p_patches/2022-12-15-Drop_Flag_status.sql → ...0/Cleanup/2022-12-15-Drop_Flag_status.sql
diff --git a/...anup_patches/2023-02-21-unusedconfigs.sql → ...25.0/Cleanup/2023-02-21-unusedconfigs.sql b/...anup_patches/2023-02-21-unusedconfigs.sql → ...25.0/Cleanup/2023-02-21-unusedconfigs.sql
diff --git a/SQL/Archive/25.0/Cleanup/2023-07-10-remove_quality_control_from_projects.sql b/SQL/Archive/25.0/Cleanup/2023-07-10-remove_quality_control_from_projects.sql
@@ -0,0 +1,2 @@
+DELETE FROM permissions WHERE code='quality_control';
+
-Original file line number
+Diff line change
@@ Expand Up / @@ -17,3 +17,7 @@ indent_size = 2 @@
     [*.md]
     trim_trailing_whitespace = false
+    [*.yml]
+    indent_size = 2
Original file line number	Diff line number	Diff line change
		@@ -0,0 +1,2 @@
		DELETE FROM permissions WHERE code='quality_control';