Merge remote-tracking branch 'aces/24.0-release' into PUSH_24.0-relea…

…se_INTO_MAIN

.github/workflows/loristest.yml

@@ -29,12 +29,13 @@ 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:
-        path: vendor
-        key: ${{ runner.os }}-php-${{ hashFiles('**/composer.lock') }}
-        restore-keys: |
-          ${{ runner.os }}-php-
+        path: ${{ steps.composer-cache.outputs.dir }}
+        key: ${{ runner.os }}-composer-${{ hashFiles('composer.lock') }}
+        restore-keys: ${{ runner.os }}-composer-
 
     - name: Change PHP Version in Dockerfile
       run: sed -i "s/8.0/${{ matrix.php }}/g" Dockerfile.test.php8

SQL/0000-00-00-schema.sql

@@ -151,7 +151,7 @@ CREATE TABLE `candidate` (
   `EDC` date DEFAULT NULL,
   `Sex` enum('Male','Female','Other') DEFAULT NULL,
   `RegistrationCenterID` integer unsigned NOT NULL DEFAULT '0',
-  `RegistrationProjectID` int(10) unsigned DEFAULT NULL,
+  `RegistrationProjectID` int(10) unsigned NOT NULL,
   `Ethnicity` varchar(255) DEFAULT NULL,
   `Active` enum('Y','N') NOT NULL DEFAULT 'Y',
   `Date_active` date DEFAULT NULL,
@@ -182,7 +182,7 @@ CREATE TABLE `session` (
   `ID` int(10) unsigned NOT NULL AUTO_INCREMENT,
   `CandID` int(6) NOT NULL DEFAULT '0',
   `CenterID` integer unsigned NOT NULL,
-  `ProjectID` int(10) unsigned DEFAULT NULL,
+  `ProjectID` int(10) unsigned NOT NULL,
   `VisitNo` smallint(5) unsigned DEFAULT NULL,
   `Visit_label` varchar(255) NOT NULL,
   `SubprojectID` int(10) unsigned DEFAULT NULL,

SQL/0000-00-03-ConfigTables.sql

@@ -135,7 +135,7 @@ INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType,
 INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'get_dicom_info', 'Full path to get_dicom_info.pl', 1, 0, 'text', ID, 'Full path to get_dicom_info.pl script', 4 FROM ConfigSettings WHERE Name="imaging_pipeline";
 INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'horizontalPics', 'Enable generation of horizontal pictures', 1, 0, 'boolean', ID, 'Horizontal pictures creation', 5 FROM ConfigSettings WHERE Name="imaging_pipeline";
 INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'create_nii', 'Enable creation of NIfTI files', 1, 0, 'boolean', ID, 'NIfTI file creation', 6 FROM ConfigSettings WHERE Name="imaging_pipeline";
-INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'converter', 'If converter is set to dcm2mnc, the c-version of dcm2mnc will be used. If however you want to use any of the various versions of the converter, you will have to specify what it is called and the uploader will try to invoke it', 1, 0, 'text', ID, 'dcm2mnc binary to use when converting', 7 FROM ConfigSettings WHERE Name="imaging_pipeline";
+INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'converter', 'If converter is set to dcm2mnc, the c-version of dcm2mnc will be used. If however you want to use any of the various versions of the converter, you will have to specify what it is called and the uploader will try to invoke it', 1, 0, 'text', ID, 'DICOM converter tool to use (dcm2mnc or dcm2niix)', 7 FROM ConfigSettings WHERE Name="imaging_pipeline";
 INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'tarchiveLibraryDir', 'Location of storing the library of used tarchives. If this is not set, they will not be moved', 1, 0, 'text', ID, 'Path to Tarchives', 8 FROM ConfigSettings WHERE Name="imaging_pipeline";
 INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'lookupCenterNameUsing', 'DICOM field (either PatientName or PatientID) to use to get the patient identifiers and the center name of the DICOM study', 1, 0, 'lookup_center', ID, 'Patient identifiers and center name lookup variable', 9 FROM ConfigSettings WHERE Name="imaging_pipeline";
 INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'createCandidates', 'Enable candidate creation in the imaging pipeline', 1, 0, 'boolean', ID, 'Upload creation of candidates', 10 FROM ConfigSettings WHERE Name="imaging_pipeline";
@@ -147,12 +147,13 @@ INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType,
 INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'QCed2_step', 'DTIPrep protocol step at which a secondary QCed dataset is produced (for example one without motion correction and eddy current correction would be saved at INTERLACE_outputDWIFileNameSuffix step of DTIPrep)', 1, 0, 'text', ID, 'Secondary QCed dataset', 17 FROM ConfigSettings WHERE Name="imaging_pipeline";
 INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'excluded_series_description', 'Series description to be excluded from insertion into the database (typically localizers and scouts)', 1, 1, 'text', ID, 'Series description to exclude from imaging insertion', 18 FROM ConfigSettings WHERE Name="imaging_pipeline";
 INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'ComputeDeepQC', 'Determines whether a call is made from LORIS-MRI to the DeepQC app for automatic QC prediction', 1, 0, 'boolean', ID, 'Compute automatic QC', 18 FROM ConfigSettings WHERE Name="imaging_pipeline";
-INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'MriConfigFile', 'Name of the MRI config file (stored in dicom-archive/.loris_mri/)', 1, 0, 'text', ID, 'Name of the MRI config file', 19 FROM ConfigSettings WHERE Name="imaging_pipeline";
+INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'MriConfigFile', 'Name of the Perl MRI config file (stored in dicom-archive/.loris_mri/)', 1, 0, 'text', ID, 'Name of the Perl MRI config file', 19 FROM ConfigSettings WHERE Name="imaging_pipeline";
 INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'EnvironmentFile', 'Name of the environment file that need to be sourced for the imaging pipeline', 1, 0, 'text', ID, 'Name of the environment file', 20 FROM ConfigSettings WHERE Name="imaging_pipeline";
 INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'compute_snr_modalities', 'Modalities for which the SNR should be computed when running the insertion MRI scripts', 1, 1, 'scan_type', ID, 'Modalities on which SNR should be calculated', 21 FROM ConfigSettings WHERE Name="imaging_pipeline";
 INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'reference_scan_type_for_defacing', 'Scan type to use as a reference for registration when defacing anatomical images (typically a T1W image)', 1, 0, 'scan_type', ID, 'Scan type to use as a reference for defacing (typically a T1W image)', 22 FROM ConfigSettings WHERE Name="imaging_pipeline";
 INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'modalities_to_deface', 'Modalities for which defacing should be run and defaced image inserted in the database', 1, 1, 'scan_type', ID, 'Modalities on which to run the defacing pipeline', 23 FROM ConfigSettings WHERE Name="imaging_pipeline";
 INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'default_bids_vl', 'Default visit label to use when no visit label set in the BIDS dataset', 1, 0, 'text', ID, 'Default visit label for BIDS dataset', 24 FROM ConfigSettings WHERE Name="imaging_pipeline";
+INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'MriPythonConfigFile', 'Name of the Python MRI config file (stored in dicom-archive/.loris_mri/)', 1, 0, 'text', ID, 'Name of the Python MRI config file', 25 FROM ConfigSettings WHERE Name="imaging_pipeline";
 
 -- MINC to BIDS converter settings
 INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, Label, OrderNumber) VALUES ('minc2bids', 'Settings related to converting MINC to BIDS LORIS-MRI tool script', 1, 0,  'MINC to BIDS Converter Tool Options', 13);
@@ -165,6 +166,12 @@ INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, Label, Or
 INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'database_log_level', 'Verbosity of database logging', 1, 0, 'log_level', ID, 'Database Log Level', 3 FROM ConfigSettings WHERE Name='logs';
 INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'request_log_level', 'Verbosity of HTTP request logs', 1, 0, 'log_level', ID, 'HTTP Request Log Level', 3 FROM ConfigSettings WHERE Name='logs';
 INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'exception_log_level', 'Verbosity of PHP exception logging', 1, 0, 'log_level', ID, 'Exception Log Level', 3 FROM ConfigSettings WHERE Name='logs';
+
+INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, Label, OrderNumber) VALUES ('aws', 'Settings related to AWS services', 1, 0, 'AWS Settings', 13);
+INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'AWS_S3_Endpoint', 'Endpoint to use for accessing files stored in S3. Endpoint or region are required for S3 support.', 1, 0, 'text', ID, 'AWS S3 Endpoint', 3 FROM ConfigSettings WHERE Name='aws';
+INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'AWS_S3_Region', 'AWS Region to use for accessing files stored in S3. Endpoint or region are required for S3 support.', 1, 0, 'text', ID, 'AWS S3 Region', 3 FROM ConfigSettings WHERE Name='aws';
+INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'AWS_S3_Default_Bucket', 'Default bucket for LORIS to use for accessing files in S3.', 1, 0, 'text', ID, 'AWS S3 Default Bucket', 3 FROM ConfigSettings WHERE Name='aws';
+
 --
 -- Filling Config table with default values
 --
@@ -256,6 +263,7 @@ INSERT INTO Config (ConfigID, Value) SELECT ID, "scout" FROM ConfigSettings cs W
 INSERT INTO Config (ConfigID, Value) SELECT ID, "/issue_tracker" FROM ConfigSettings WHERE Name="issue_tracker_url";
 INSERT INTO Config (ConfigID, Value) SELECT ID, 0 FROM ConfigSettings cs WHERE cs.Name="ComputeDeepQC";
 INSERT INTO Config (ConfigID, Value) SELECT ID, 'prod' FROM ConfigSettings cs WHERE cs.Name="mriConfigFile";
+INSERT INTO Config (ConfigID, Value) SELECT ID, 'database_config.py' FROM ConfigSettings cs WHERE cs.Name="mriPythonConfigFile";
 INSERT INTO Config (ConfigID, Value) SELECT ID, 'environment' FROM ConfigSettings cs WHERE cs.Name="EnvironmentFile";
 INSERT INTO Config (ConfigID, Value) SELECT ID, 'flair' FROM ConfigSettings WHERE Name="compute_snr_modalities";
 INSERT INTO Config (ConfigID, Value) SELECT ID, 't1'    FROM ConfigSettings WHERE Name="compute_snr_modalities";

SQL/Archive/24.0/2019-07-01_fix_project_in_session.sql

@@ -0,0 +1,12 @@
+-- Populate new session field with pre recorded candidate project
+ALTER TABLE candidate DROP FOREIGN KEY `FK_candidate_RegistrationProjectID`;
+ALTER TABLE candidate CHANGE `RegistrationProjectID` `RegistrationProjectID` int(10) unsigned NOT NULL;
+ALTER TABLE candidate ADD CONSTRAINT `FK_candidate_RegistrationProjectID` FOREIGN KEY (`RegistrationProjectID`) REFERENCES `Project` (`ProjectID`) ON UPDATE CASCADE;
+
+UPDATE session s JOIN candidate c ON s.CandID=c.CandID SET ProjectID=c.RegistrationProjectID WHERE ProjectID IS NULL;
+
+ALTER TABLE `session` DROP FOREIGN KEY `FK_session_ProjectID`;
+ALTER TABLE `session` CHANGE `ProjectID` `ProjectID` int(10) unsigned NOT NULL;
+ALTER TABLE `session` ADD CONSTRAINT `FK_session_ProjectID` FOREIGN KEY (`ProjectID`) REFERENCES `Project` (`ProjectID`);
+
+

SQL/Archive/24.0/2022-01-04-add_config_for_python_config_file.sql

@@ -0,0 +1,6 @@
+
+UPDATE ConfigSettings SET Description='Name of the Perl MRI config file (stored in dicom-archive/.loris_mri/)', Label='Name of the Perl MRI config file' WHERE Name="MriConfigFile";
+UPDATE ConfigSettings SET Label='DICOM converter tool to use (dcm2mnc or dcm2niix)' WHERE Name="converter";
+INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'MriPythonConfigFile', 'Name of the Python MRI config file (stored in dicom-archive/.loris_mri/)', 1, 0, 'text', ID, 'Name of the Python MRI config file', 25 FROM ConfigSettings WHERE Name="imaging_pipeline";
+
+INSERT INTO Config (ConfigID, Value) SELECT ID, 'database_config.py' FROM ConfigSettings cs WHERE cs.Name="mriPythonConfigFile";

SQL/Archive/24.0/2022-01-26-S3Support.sql

@@ -0,0 +1,6 @@
+INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, Label, OrderNumber) VALUES ('aws', 'Settings related to AWS services', 1, 0, 'AWS Settings', 13);
+INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'AWS_S3_Endpoint', 'Endpoint to use for accessing files stored in S3. Endpoint or region are required for S3 support.', 1, 0, 'text', ID, 'AWS S3 Endpoint', 3 FROM ConfigSettings WHERE Name='aws';
+INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'AWS_S3_Region', 'AWS Region to use for accessing files stored in S3. Endpoint or region are required for S3 support.', 1, 0, 'text', ID, 'AWS S3 Region', 3 FROM ConfigSettings WHERE Name='aws';
+INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'AWS_S3_Default_Bucket', 'Default bucket for LORIS to use for accessing files in S3.', 1, 0, 'text', ID, 'AWS S3 Default Bucket', 3 FROM ConfigSettings WHERE Name='aws';
+
+

SQL/Archive/24.0/Cleanup/2022-02-03-remove_CenterName_from_mri_protocol.sql

@@ -0,0 +1,3 @@
+-- Drop the Center_name table (CenterID will be replacing it)
+-- Before droping the column, ensure the relevant data have been ported into the CenterID column
+ALTER TABLE mri_protocol DROP COLUMN `Center_name`;

SQL/Archive/24.0/Cleanup/2022-02-03-remove_password_expiry_from_users.sql

@@ -0,0 +1 @@
+ALTER TABLE users DROP COLUMN Password_expiry;