Merge branch 'main' into react_panel_multiple_views

Author: laemtl

.eslintrc.json

@@ -63,7 +63,7 @@
     "no-case-declarations": "off",
     "no-fallthrough": "off",
     "react/jsx-no-undef": "off",
-    "react/prop-types": "off",
+    "react/prop-types": "error",
     "no-undef": "error",
     "react/jsx-key": "off",
     "no-extra-semi": "off",

.github/workflows/loristest.yml

@@ -11,13 +11,25 @@ jobs:
   build:
     runs-on: ubuntu-latest
     strategy:
+        fail-fast: false
         matrix:
-            testsuite:
-            - static
-            - unit
-            - integration
+            testsuite: ['integration']
             php: ['8.1','8.2']
+            ci_node_index: [0,1,2,3]
 
+            include:
+            # add a variable but do not display it in the job's name 
+            - ci_node_total: 4
+
+            - testsuite: 'static'
+              php: '8.1'
+            - testsuite: 'static'
+              php: '8.2'
+            - testsuite: 'unit'
+              php: '8.1'
+            - testsuite: 'unit'
+              php: '8.2'
+            
     steps:
     - uses: actions/checkout@v2
 
@@ -33,6 +45,7 @@ jobs:
     - name: Cache Composer packages
       id: composer-cache
       run: echo "::set-output name=dir::$(composer config cache-files-dir)"
+
     - name: Composer cache
       uses: actions/cache@v2
       with:
@@ -44,9 +57,15 @@ jobs:
       run: sed -i "s/8.0/${{ matrix.php }}/g" Dockerfile.test.php8
 
     - name: Install package dependencies
-      run: sudo apt-get install -y protobuf-compiler 
-           && cd modules/electrophysiology_browser/jsx/react-series-data-viewer/
-           && protoc protocol-buffers/chunk.proto --js_out=import_style=commonjs,binary:./src/
+      # 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 composer dependencies
       if: steps.composer-cache.outputs.cache-hit != 'true'
@@ -57,3 +76,8 @@ jobs:
 
     - name: Run Test Suite
       run: npm run tests:${{ matrix.testsuite }}
+      env:
+          # Specifies how many jobs you would like to run in parallel,
+          CI_NODE_TOTAL: ${{ matrix.ci_node_total }}
+          # Use the index from matrix as an environment variable
+          CI_NODE_INDEX: ${{ matrix.ci_node_index }}

CHANGELOG.md

@@ -12,12 +12,17 @@ changes in the following format: PR #1234***
 ### Core
 #### Features
 - Added new interface intended to be used for querying module data from PHP (PR #8215) 
+- Added the NOT NULL constraint on Project Name (PR #8295)
+- 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)
 
 #### Updates and Improvements
 - Rename subproject to Cohort (PR #7817)
 - Create new CohortData and CohortController classes to use as data access model 
   and transfer object (PR #7817)
 - BVL Feedback widget only shows notifications for the users sites / projects (PR #7848)
+- Add Date status change value in session table (PR #8350)
 
 #### Bug Fixes
 - placeholder

Makefile

@@ -1,7 +1,9 @@
-.PHONY: clean dev all check checkstatic unittests test phpdev javascript testdata
+.PHONY: clean dev all check checkstatic unittests phpdev jslatest testdata
 
-all: VERSION jsdev
+all: VERSION
 	composer install --no-dev
+	npm ci
+	npm run build
 
 # If anything changes, re-generate the VERSION file
 VERSION: .
@@ -10,7 +12,7 @@ VERSION: .
 phpdev:
 	composer install
 
-jsdev:
+dev: VERSION phpdev
 	npm ci
 	npm run compile
 
@@ -20,8 +22,6 @@ jslatest: clean
 	npm install
 	npm run compile
 
-dev: VERSION phpdev jsdev
-
 clean:
 	rm -f smarty/templates_c/*
 	rm -f VERSION
@@ -52,6 +52,12 @@ check: checkstatic unittests
 testdata:
 	php tools/raisinbread_refresh.php
 
+instrument_manager:
+	target=instrument_manager npm run compile
+
 login:
 	target=login npm run compile
 
+mri_violations:
+	target=mri_violations npm run compile
+

SQL/0000-00-00-schema.sql

@@ -4,7 +4,7 @@
 
 CREATE TABLE `Project` (
     `ProjectID` INT(10) unsigned NOT NULL AUTO_INCREMENT,
-    `Name` VARCHAR(255) NULL,
+    `Name` VARCHAR(255) NOT NULL,
     `Alias` char(4) NOT NULL,
     `recruitmentTarget` INT(6) Default NULL,
     PRIMARY KEY (`ProjectID`),
@@ -195,6 +195,7 @@ CREATE TABLE `session` (
   `Date_screening` date DEFAULT NULL,
   `Visit` enum('Pass','Failure','Withdrawal','In Progress') DEFAULT NULL,
   `Date_visit` date DEFAULT NULL,
+  `Date_status_change` date DEFAULT NULL,
   `Approval` enum('In Progress','Pass','Failure') DEFAULT NULL,
   `Date_approval` date DEFAULT NULL,
   `Active` enum('Y','N') NOT NULL DEFAULT 'Y',
@@ -281,12 +282,10 @@ CREATE TABLE `flag` (
   `Administration` enum('None','Partial','All') default NULL,
   `Validity` enum('Questionable','Invalid','Valid') default NULL,
   `Exclusion` enum('Fail','Pass') default NULL,
-  `Flag_status` enum('P','Y','N','F') default NULL,
   `UserID` varchar(255) default NULL,
   `Testdate` timestamp NOT NULL default CURRENT_TIMESTAMP on update CURRENT_TIMESTAMP,
   `Data` TEXT default NULL,
   PRIMARY KEY  (`CommentID`),
-  KEY `Status` (`Flag_status`),
   KEY `flag_ID` (`ID`),
   KEY `flag_SessionID` (`SessionID`),
   KEY `flag_Test_name` (`Test_name`),
@@ -980,7 +979,8 @@ CREATE TABLE `violations_resolved` (
   `User` varchar(255) DEFAULT NULL,
   `ChangeDate` datetime DEFAULT NULL,
   `Resolved` enum('unresolved', 'reran', 'emailed', 'inserted', 'rejected', 'inserted_flag', 'other') DEFAULT 'unresolved',
-  PRIMARY KEY (`ID`)
+  PRIMARY KEY (`ID`),
+  KEY `i_violations_resolved_extid_type` (`ExtID`,`TypeTable`)
 ) ENGINE=InnoDB DEFAULT CHARSET=utf8;
 
 CREATE TABLE `mri_protocol_violated_scans` (
@@ -1283,7 +1283,6 @@ CREATE TABLE `participant_accounts` (
   `ID` int(10) unsigned NOT NULL AUTO_INCREMENT,
   `SessionID` int(6) DEFAULT NULL,
   `Test_name` varchar(255) DEFAULT NULL,
-  `Email` varchar(255) DEFAULT NULL,
   `Status` enum('Created','Sent','In Progress','Complete') DEFAULT NULL,
   `OneTimePassword` varchar(16) DEFAULT NULL,
   `CommentID` varchar(255) DEFAULT NULL,

SQL/0000-00-02-Permission.sql

@@ -152,3 +152,11 @@ CREATE TABLE `notification_modules_perm_rel` (
 INSERT INTO notification_modules_perm_rel SELECT nm.id, p.permID FROM notification_modules nm JOIN permissions p WHERE nm.module_name='media' AND (p.code='media_write' OR p.code='media_read');
 INSERT INTO notification_modules_perm_rel SELECT nm.id, p.permID FROM notification_modules nm JOIN permissions p WHERE nm.module_name='document_repository' AND (p.code='document_repository_view' OR p.code='document_repository_delete');
 INSERT INTO notification_modules_perm_rel SELECT nm.id, p.permID FROM notification_modules nm JOIN permissions p WHERE nm.module_name='publication' AND (p.code='publication_view' OR p.code='publication_propose' OR p.code='publication_approve');
+
+CREATE TABLE `testnames_permissions_rel` (
+    `TestID` int(10) unsigned NOT NULL,
+    `permID` int(10) unsigned NOT NULL,
+    PRIMARY KEY  (`TestID`,`permID`),
+    CONSTRAINT `FK_testnames_permissions_rel_test` FOREIGN KEY (`TestID`) REFERENCES `test_names` (`ID`),
+    CONSTRAINT `FK_testnames_permissions_rel_perm` FOREIGN KEY (`permID`) REFERENCES `permissions` (`permID`)
+) ENGINE=InnoDB DEFAULT CHARSET=utf8;