Merge branch 'main' into 2024_10_28_instrument_data_parser

.eslintignore

@@ -2,6 +2,7 @@ node_modules/*
 vendor/*
 project/*
 babel.config.js
+webpack.config.ts
 
 # compiled js ignored since it is run on the jsx directory
 modules/*/js/*

CHANGELOG.md

@@ -167,6 +167,7 @@ the `Data` key instead of `$InstrumentName` (PR #7857)
 - 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)
+- Fix BVL feedback summary in instruments (PR #8889)
 ### Modules
 #### API
 - Ability to use PSCID instead of the CandID in the candidates API (PR #8138)

SQL/0000-00-02-Permission.sql

@@ -105,8 +105,8 @@ INSERT INTO `permissions` VALUES
     (33,'genomic_data_manager','Genomic Files',(SELECT ID FROM modules WHERE Name='genomic_browser'),'Upload','2'),
     (34,'media_write','Candidate Media Files',(SELECT ID FROM modules WHERE Name='media'),'Edit/Upload/Hide','2'),
     (35,'media_read','Candidate Media Files',(SELECT ID FROM modules WHERE Name='media'),'View/Download','2'),
-    (36,'issue_tracker_reporter', 'Create/Edit Own Issues and Comment on All Issues',(SELECT ID FROM modules WHERE Name='issue_tracker'),NULL, 2),
-    (37,'issue_tracker_developer', 'Close/Edit/Re-assign/Comment on All Issues',(SELECT ID FROM modules WHERE Name='issue_tracker'),NULL, 2),
+    (36,'issue_tracker_own_issue', 'See/Edit/Comment and Close on Own Issues',(SELECT ID FROM modules WHERE Name='issue_tracker'),NULL, 2),
+    (37,'issue_tracker_all_issue', 'See/Edit/Comment on all Issues',(SELECT ID FROM modules WHERE Name='issue_tracker'),NULL, 2),
     (38,'imaging_browser_phantom_allsites', 'Phantom Scans - All Sites',(SELECT ID FROM modules WHERE Name='imaging_browser'),'View', 2),
     (39,'imaging_browser_phantom_ownsite', 'Phantom Scans - Own Sites',(SELECT ID FROM modules WHERE Name='imaging_browser'),'View', 2),
     (40,'data_release_view', 'Release Files',(SELECT ID FROM modules WHERE Name='data_release'),'View', 2),
@@ -136,7 +136,11 @@ INSERT INTO `permissions` VALUES
     (64,'dataquery_admin','Admin dataquery queries',(SELECT ID FROM modules WHERE Name='dataquery'),NULL,'2'),
     (65,'schedule_module','Schedule Module - edit and delete the appointment',(SELECT ID FROM modules WHERE Name='schedule_module'),'View/Create/Edit','2'),
     (66,'document_repository_categories','Categories',(SELECT ID FROM modules WHERE Name='document_repository'), 'Edit/Upload/Delete', '2'),
-    (67,'document_repository_hidden','Restricted files',(SELECT ID FROM modules WHERE Name='document_repository'), 'View', '2');
+    (67,'document_repository_hidden','Restricted files',(SELECT ID FROM modules WHERE Name='document_repository'), 'View', '2'),
+    (68,'issue_tracker_site_issue','See/Edit/Comment on Own Site Issues',(SELECT ID FROM modules WHERE Name = 'issue_tracker'),NULL,2),
+    (69,'issue_tracker_close_site_issue','Close Own Site Issues',(SELECT ID FROM modules WHERE Name = 'issue_tracker'),NULL,2),
+    (70,'issue_tracker_close_all_issue','Close all Issues',(SELECT ID FROM modules WHERE Name = 'issue_tracker'),NULL,2);
+
 
 INSERT INTO `user_perm_rel` (userID, permID)
   SELECT u.ID, p.permID

SQL/0000-00-03-ConfigTables.sql

@@ -213,7 +213,6 @@ INSERT INTO Config (ConfigID, Value) SELECT ID, "365" FROM ConfigSettings WHERE
 
 INSERT INTO Config (ConfigID, Value) SELECT ID, "/data/%PROJECTNAME%/data/" FROM ConfigSettings WHERE Name="imagePath";
 INSERT INTO Config (ConfigID, Value) SELECT ID, "%LORISROOT%" FROM ConfigSettings WHERE Name="base";
-INSERT INTO Config (ConfigID, Value) SELECT ID, "%LORISROOT%" FROM ConfigSettings WHERE Name="DownloadPath";
 INSERT INTO Config (ConfigID, Value) SELECT ID, "tools/logs/" FROM ConfigSettings WHERE Name="log";
 INSERT INTO Config (ConfigID, Value) SELECT ID, "/data/%PROJECTNAME%/bin/mri/" FROM ConfigSettings WHERE Name="MRICodePath";
 INSERT INTO Config (ConfigID, Value) SELECT ID, "/data/incoming/" FROM ConfigSettings WHERE Name="MRIUploadIncomingPath";

SQL/9999-99-99-drop_tables.sql

@@ -5,6 +5,7 @@ DROP TABLE IF EXISTS dataquery_shared_queries_rel;
 DROP TABLE IF EXISTS dataquery_run_queries;
 DROP TABLE IF EXISTS dataquery_query_names;
 DROP TABLE IF EXISTS dataquery_queries;
+DROP TABLE IF EXISTS `Login_Summary_Statistics`;
 
 -- 0000-00-05-ElectrophysiologyTables.sql
 DROP TABLE IF EXISTS `physiological_event_parameter_category_level`;

SQL/Login_Summary_Statistics/01_Female Participant.sql

@@ -0,0 +1,9 @@
+SELECT 
+    IFNULL(Project.Name, 'All Projects') as ProjectName, 
+    COUNT(DISTINCT c.CandID) AS count
+    FROM candidate c
+    JOIN Project ON c.RegistrationProjectID = Project.ProjectID
+WHERE Project.showSummaryOnLogin = 1
+    AND c.Sex = 'Female'
+    AND Entity_type = 'Human'
+GROUP BY Project.Name WITH ROLLUP

SQL/Login_Summary_Statistics/02_Male Participant.sql

@@ -0,0 +1,9 @@
+SELECT 
+    IFNULL(Project.Name, 'All Projects') as ProjectName, 
+    COUNT(DISTINCT c.CandID) AS count
+    FROM candidate c
+    JOIN Project ON c.RegistrationProjectID = Project.ProjectID
+WHERE Project.showSummaryOnLogin = 1
+    AND c.Sex = 'Male'
+    AND Entity_type = 'Human'
+GROUP BY Project.Name WITH ROLLUP

SQL/Login_Summary_Statistics/03_Site.sql

@@ -0,0 +1,8 @@
+SELECT 
+    IFNULL(Project.Name, 'All Projects') as ProjectName, 
+    COUNT(DISTINCT psc.CenterID) AS count
+    FROM psc
+    JOIN session s ON s.CenterID = psc.CenterID
+    JOIN Project ON s.ProjectID = Project.ProjectID
+WHERE Project.showSummaryOnLogin = 1
+GROUP BY Project.Name WITH ROLLUP

SQL/Login_Summary_Statistics/04_Visit.sql

@@ -0,0 +1,7 @@
+SELECT 
+    IFNULL(Project.Name, 'All Projects') as ProjectName, 
+    COUNT(s.ID) AS count
+    FROM session s
+    JOIN Project ON (s.ProjectID = Project.ProjectID)
+WHERE Project.showSummaryOnLogin = 1
+GROUP BY Project.Name WITH ROLLUP

SQL/Login_Summary_Statistics/05_Instrument.sql

@@ -0,0 +1,8 @@
+SELECT 
+    IFNULL(Project.Name, 'All Projects') as ProjectName, 
+    COUNT(DISTINCT TestID) AS count
+    FROM flag f
+    JOIN session s ON s.ID = f.SessionID
+    JOIN Project ON s.ProjectID = Project.ProjectID
+WHERE Project.showSummaryOnLogin = 1
+GROUP BY Project.Name WITH ROLLUP;

SQL/Login_Summary_Statistics/06_Scan.sql

@@ -0,0 +1,8 @@
+SELECT 
+    IFNULL(Project.Name, 'All Projects') as ProjectName, 
+    COUNT(FileID) AS count
+    FROM files f
+    JOIN session s ON s.ID = f.SessionID
+    JOIN Project ON s.ProjectID = Project.ProjectID
+WHERE Project.showSummaryOnLogin = 1
+GROUP BY Project.Name WITH ROLLUP;

SQL/Login_Summary_Statistics/07_EEG Recording.sql

@@ -0,0 +1,17 @@
+SELECT
+   IFNULL(Project.Name, 'All Projects') as ProjectName,
+   COUNT(PhysiologicalFileID) AS count
+FROM physiological_parameter_file ppf
+LEFT JOIN physiological_file USING (PhysiologicalFileID)
+LEFT JOIN physiological_output_type USING (PhysiologicalOutputTypeID)
+LEFT JOIN Project ON ppf.ProjectID = Project.ProjectID
+WHERE (
+   ParameterTypeID = (
+       SELECT ParameterTypeID
+       FROM parameter_type
+       WHERE Name = 'RecordingDuration'
+   )
+) 
+-- AND OutputTypeName = 'raw'
+AND Project.showSummaryOnLogin = 1
+GROUP BY Project.Name WITH ROLLUP

SQL/New_patches/2024-10-08-issuetracker-watch-all.sql

@@ -0,0 +1,5 @@
+INSERT INTO notification_modules (module_name, operation_type, as_admin, template_file, description) VALUES
+    ('issue_tracker', 'create/edit', 'N', 'issue_change.tpl', 'Notify for all issues created or edited');
+
+INSERT INTO notification_modules_services_rel (module_id, service_id) VALUES
+    ((SELECT id FROM notification_modules WHERE module_name='issue_tracker' AND operation_type='create/edit'), (SELECT id FROM notification_services WHERE service='email_text'));

SQL/New_patches/2024-12-18-Login_statistics.sql

@@ -0,0 +1,13 @@
+CREATE TABLE Login_Summary_Statistics (
+    Title VARCHAR(255),
+    Project VARCHAR(255),
+    Value INT,
+    QueryOrder INT,
+     PRIMARY KEY (Title, Project)
+);
+
+ALTER TABLE dataquery_study_queries_rel
+MODIFY COLUMN PinType enum('topquery','dashboard', 'loginpage') DEFAULT NULL;
+
+ALTER TABLE Project
+ADD COLUMN showSummaryOnLogin BOOLEAN DEFAULT TRUE;

SQL/New_patches/2025-02-07_update_add_issue_tracker_permissions.sql

@@ -0,0 +1,9 @@
+UPDATE permissions SET code = 'issue_tracker_own_issue', description = 'See/Edit/Comment and Close on Own Issues' 
+WHERE code = 'issue_tracker_reporter';
+UPDATE permissions SET code = 'issue_tracker_all_issue', description = 'See/Edit/Comment on all Issues' 
+WHERE code = 'issue_tracker_developer';
+
+INSERT INTO permissions (code, description, moduleID, categoryID) VALUES
+('issue_tracker_site_issue','See/Edit/Comment on Own Site Issues',(SELECT ID FROM modules WHERE Name = 'issue_tracker'),2),
+('issue_tracker_close_site_issue','Close Own Site Issues',(SELECT ID FROM modules WHERE Name = 'issue_tracker'),2),
+('issue_tracker_close_all_issue','Close all Issues',(SELECT ID FROM modules WHERE Name = 'issue_tracker'),2);

SQL/New_patches/2025_02_03_permissions_Modifies_issue_tracker_reporter_description.sql

@@ -0,0 +1,3 @@
+UPDATE permissions
+    SET description = 'Create/Edit/Close Own Issues and Comment on All Issues'
+    WHERE code = 'issue_tracker_reporter';

SQL/New_patches/2025_02_05_change_candid_fk_to_id.sql

@@ -0,0 +1,88 @@
+-- Change FKs from CandID to CandidateID which is now candidate.ID
+ALTER TABLE CNV DROP constraint CNV_ibfk_3;
+UPDATE CNV SET CandID=(SELECT ID from candidate c WHERE c.CandID=CNV.CandID);
+ALTER TABLE CNV CHANGE CandID CandidateID int(10) unsigned DEFAULT NULL;
+ALTER TABLE CNV ADD CONSTRAINT CNV_ibfk_3 FOREIGN KEY (CandidateID) REFERENCES candidate(ID);
+
+ALTER TABLE candidate_consent_rel DROP CONSTRAINT `FK_candidate_consent_rel_CandidateID`;
+UPDATE candidate_consent_rel SET CandidateID=(SELECT ID from candidate c WHERE c.CandID=candidate_consent_rel.CandidateID);
+ALTER TABLE candidate_consent_rel CHANGE CandidateID CandidateID int(10) unsigned NOT NULL;
+ALTER TABLE candidate_consent_rel ADD CONSTRAINT FK_candidate_consent_rel_CandidateID FOREIGN KEY (CandidateID) REFERENCES candidate(ID) ON DELETE RESTRICT ON UPDATE RESTRICT;
+
+ALTER TABLE participant_status DROP CONSTRAINT `fk_participant_status_3`;
+UPDATE participant_status SET CandID=(SELECT ID from candidate c WHERE c.CandID=participant_status.CandID);
+ALTER TABLE participant_status CHANGE CandID CandidateID int(10) unsigned NOT NULL;
+ALTER TABLE participant_status ADD CONSTRAINT FK_participant_status_3 FOREIGN KEY (CandidateID) REFERENCES candidate(ID) ON DELETE CASCADE ON UPDATE CASCADE;
+
+ALTER TABLE dataquery_run_results DROP CONSTRAINT `dataquery_run_results_ibfk_1`;
+UPDATE dataquery_run_results SET CandID=(SELECT ID from candidate c WHERE c.CandID=dataquery_run_results.CandID);
+ALTER TABLE dataquery_run_results CHANGE CandID CandidateID int(10) unsigned NOT NULL;
+ALTER TABLE dataquery_run_results ADD CONSTRAINT dataquery_run_results_ibfk_1 FOREIGN KEY (CandidateID) REFERENCES candidate(ID);
+
+ALTER TABLE issues DROP CONSTRAINT `fk_issues_3`;
+UPDATE issues SET CandID=(SELECT ID from candidate c WHERE c.CandID=issues.CandID);
+ALTER TABLE issues CHANGE CandID CandidateID int(10) unsigned DEFAULT NULL;
+ALTER TABLE issues ADD CONSTRAINT fk_issues_3 FOREIGN KEY (CandidateID) REFERENCES candidate(ID);
+
+ALTER TABLE session DROP CONSTRAINT `fk_session_1`;
+UPDATE session SET CandID=(SELECT ID from candidate c WHERE c.CandID=session.CandID);
+ALTER TABLE session CHANGE CandID CandidateID int(10) unsigned NOT NULL;
+ALTER TABLE session ADD CONSTRAINT fk_session_1 FOREIGN KEY (CandidateID) REFERENCES candidate(ID);
+
+ALTER TABLE genomic_candidate_files_rel DROP CONSTRAINT `genomic_candidate_files_rel_ibfk_1`;
+UPDATE genomic_candidate_files_rel SET CandID=(SELECT ID from candidate c WHERE c.CandID=genomic_candidate_files_rel.CandID);
+ALTER TABLE genomic_candidate_files_rel CHANGE CandID CandidateID int(10) unsigned NOT NULL;
+ALTER TABLE genomic_candidate_files_rel ADD CONSTRAINT genomic_candidate_files_rel_ibfk_1 FOREIGN KEY (CandidateID) REFERENCES candidate(ID);
+
+ALTER TABLE mri_scanner DROP CONSTRAINT `FK_mri_scanner_1`;
+UPDATE mri_scanner SET CandID=(SELECT ID from candidate c WHERE c.CandID=mri_scanner.CandID);
+ALTER TABLE mri_scanner CHANGE CandID CandidateID int(10) unsigned DEFAULT NULL;
+ALTER TABLE mri_scanner ADD CONSTRAINT FK_mri_scanner_1 FOREIGN KEY (CandidateID) REFERENCES candidate(ID);
+
+ALTER TABLE genomic_sample_candidate_rel DROP CONSTRAINT `genomic_sample_candidate_rel_ibfk_1`;
+UPDATE genomic_sample_candidate_rel SET CandID=(SELECT ID from candidate c WHERE c.CandID=genomic_sample_candidate_rel.CandID);
+ALTER TABLE genomic_sample_candidate_rel CHANGE CandID CandidateID int(10) unsigned NOT NULL;
+ALTER TABLE genomic_sample_candidate_rel ADD CONSTRAINT `genomic_sample_candidate_rel_ibfk_1` FOREIGN KEY (CandidateID) REFERENCES `candidate`(`ID`);
+
+ALTER TABLE SNP_candidate_rel DROP CONSTRAINT `fk_SNP_candidate_rel_2`;
+UPDATE SNP_candidate_rel SET CandID=(SELECT ID from candidate c WHERE c.CandID=SNP_candidate_rel.CandID);
+ALTER TABLE SNP_candidate_rel CHANGE CandID CandidateID int(10) unsigned NOT NULL;
+ALTER TABLE SNP_candidate_rel ADD CONSTRAINT `fk_SNP_candidate_rel_2` FOREIGN KEY (CandidateID) REFERENCES candidate(ID) ON DELETE NO ACTION ON UPDATE NO ACTION;
+
+ALTER TABLE parameter_candidate DROP CONSTRAINT `FK_parameter_candidate_2`;
+UPDATE parameter_candidate SET CandID=(SELECT ID from candidate c WHERE c.CandID=parameter_candidate.CandID);
+ALTER TABLE parameter_candidate CHANGE CandID CandidateID int(10) unsigned NOT NULL;
+ALTER TABLE parameter_candidate ADD CONSTRAINT FK_parameter_candidate_2 FOREIGN KEY (CandidateID) REFERENCES candidate(ID);
+
+ALTER TABLE candidate_diagnosis_evolution_rel DROP CONSTRAINT `PK_candidate_diagnosis_evolution_rel`;
+ALTER TABLE candidate_diagnosis_evolution_rel DROP CONSTRAINT `FK_candidate_diagnosis_evolution_rel_CandID`;
+UPDATE candidate_diagnosis_evolution_rel SET CandID=(SELECT ID from candidate c WHERE c.CandID=candidate_diagnosis_evolution_rel.CandID);
+ALTER TABLE candidate_diagnosis_evolution_rel CHANGE CandID CandidateID int(10) unsigned NOT NULL;
+ALTER TABLE candidate_diagnosis_evolution_rel ADD CONSTRAINT PK_candidate_diagnosis_evolution_rel PRIMARY KEY (CandidateID, DxEvolutionID);
+ALTER TABLE candidate_diagnosis_evolution_rel ADD CONSTRAINT FK_candidate_diagnosis_evolution_rel_CandID FOREIGN KEY (CandidateID) REFERENCES candidate(ID) ON DELETE RESTRICT ON UPDATE RESTRICT;
+
+
+-- Changes references to candidate.CandID that were NOT FK. Add FK
+UPDATE feedback_bvl_thread SET CandID=(SELECT ID from candidate c WHERE c.CandID=feedback_bvl_thread.CandID);
+ALTER TABLE feedback_bvl_thread CHANGE CandID CandidateID int(10) unsigned DEFAULT NULL;
+ALTER TABLE feedback_bvl_thread ADD CONSTRAINT FK_feedback_bvl_thread_candidate_1 FOREIGN KEY (CandidateID) REFERENCES candidate(ID);
+
+UPDATE mri_violations_log SET CandID=(SELECT ID from candidate c WHERE c.CandID=mri_violations_log.CandID);
+ALTER TABLE mri_violations_log CHANGE CandID CandidateID int(10) unsigned DEFAULT NULL;
+ALTER TABLE mri_violations_log ADD CONSTRAINT FK_mri_violations_log_candidate_1 FOREIGN KEY (CandidateID) REFERENCES candidate(ID);
+
+UPDATE mri_protocol_violated_scans SET CandID=(SELECT ID from candidate c WHERE c.CandID=mri_protocol_violated_scans.CandID);
+ALTER TABLE mri_protocol_violated_scans CHANGE CandID CandidateID int(10) unsigned;
+ALTER TABLE mri_protocol_violated_scans ADD CONSTRAINT FK_mri_protocol_violated_scans_candidate_1 FOREIGN KEY (CandidateID) REFERENCES candidate(ID);
+
+UPDATE participant_status_history SET CandID=(SELECT ID from candidate c WHERE c.CandID=participant_status_history.CandID);
+ALTER TABLE participant_status_history CHANGE CandID CandidateID int(10) unsigned NOT NULL;
+ALTER TABLE participant_status_history ADD CONSTRAINT FK_participant_status_history_candidate_1 FOREIGN KEY (CandidateID) REFERENCES candidate(ID);
+
+UPDATE family SET CandID=(SELECT ID from candidate c WHERE c.CandID=family.CandID);
+ALTER TABLE family CHANGE CandID CandidateID int(10) unsigned NOT NULL;
+ALTER TABLE family ADD CONSTRAINT FK_family_candidate_1 FOREIGN KEY (CandidateID) REFERENCES candidate(ID);
+
+
+-- Change candidate's PK to ID
+ALTER TABLE candidate DROP PRIMARY KEY, ADD PRIMARY KEY(ID);