Merge branch 'main' into 2020-02-11-new-schedule

aces · Apr 15, 2024 · 21b2b4d · 21b2b4d
2 parents b352ce0 + 23dbe45
commit 21b2b4d
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -20,6 +20,8 @@ changes in the following format: PR #1234***
 - Fix examiner site display (PR #8967)
 - bvl_feedback updates in real-time (PR #8966)
 - DoB and DoD format respected in candidate parameters (PR #9001)
+- Fix delete file in upload (PR #9181)
+- Fix profile level feedback display in behavioural QC module (PR #9192)
 
 ## LORIS 25.0 (Release Date: ????-??-??)
 ### Core

diff --git a/SQL/0000-00-05-ElectrophysiologyTables.sql b/SQL/0000-00-05-ElectrophysiologyTables.sql
@@ -74,7 +74,8 @@ CREATE TABLE `physiological_split_file` (
 -- information that accompanies the BIDS physiological dataset
 CREATE TABLE `physiological_parameter_file` (
   `PhysiologicalParameterFileID` INT(10) UNSIGNED NOT NULL  AUTO_INCREMENT,
-  `PhysiologicalFileID`          INT(10) UNSIGNED NOT NULL,
+  `PhysiologicalFileID`          INT(10) UNSIGNED DEFAULT NULL,
+  `ProjectID`                    INT(10) UNSIGNED DEFAULT NULL,
   `ParameterTypeID`              INT(10) UNSIGNED NOT NULL,
   `InsertTime`                   TIMESTAMP        NOT NULL  DEFAULT CURRENT_TIMESTAMP,
   `Value`                        TEXT,
@@ -85,7 +86,10 @@ CREATE TABLE `physiological_parameter_file` (
     ON DELETE CASCADE,
   CONSTRAINT `FK_param_type_ParamTypeID`
     FOREIGN KEY (`ParameterTypeID`)
-    REFERENCES `parameter_type` (`ParameterTypeID`)
+    REFERENCES `parameter_type` (`ParameterTypeID`),
+  CONSTRAINT `FK_ppf_project_ID`
+    FOREIGN KEY (`ProjectID`)
+    REFERENCES `Project` (`ProjectID`)
 ) ENGINE=InnoDB DEFAULT CHARSET=utf8;
 
 
@@ -271,7 +275,8 @@ CREATE TABLE IF NOT EXISTS `physiological_coord_system_electrode_rel` (
 -- Create `physiological_event_file` table
 CREATE TABLE `physiological_event_file` (
     `EventFileID` int(10) unsigned NOT NULL AUTO_INCREMENT,
-    `PhysiologicalFileID` int(10) unsigned NOT NULL,
+    `PhysiologicalFileID` int(10) unsigned DEFAULT NULL,
+    `ProjectID` int(10) unsigned DEFAULT NULL,
     `FileType` varchar(20) NOT NULL,
     `FilePath` varchar(255) DEFAULT NULL,
     `LastUpdate` timestamp NOT NULL DEFAULT CURRENT_TIMESTAMP ON UPDATE CURRENT_TIMESTAMP,
@@ -280,7 +285,8 @@ CREATE TABLE `physiological_event_file` (
     KEY `FK_physio_file_ID` (`PhysiologicalFileID`),
     KEY `FK_event_file_type` (`FileType`),
     CONSTRAINT `FK_event_file_type` FOREIGN KEY (`FileType`) REFERENCES `ImagingFileTypes` (`type`),
-    CONSTRAINT `FK_physio_file_ID` FOREIGN KEY (`PhysiologicalFileID`) REFERENCES `physiological_file` (`PhysiologicalFileID`)
+    CONSTRAINT `FK_physio_file_ID` FOREIGN KEY (`PhysiologicalFileID`) REFERENCES `physiological_file` (`PhysiologicalFileID`),
+    CONSTRAINT `FK_pef_project_ID` FOREIGN KEY (`ProjectID`) REFERENCES `Project` (`ProjectID`)
 ) ENGINE=InnoDB DEFAULT CHARSET=utf8
 ;
 
@@ -299,9 +305,10 @@ CREATE TABLE `physiological_task_event` (
   `EventType`                VARCHAR(50)      DEFAULT NULL,
   `TrialType`                VARCHAR(255)     DEFAULT NULL,
   `ResponseTime`             TIME             DEFAULT NULL,
-  `AssembledHED`	     TEXT             DEFAULT NULL,
   PRIMARY KEY (`PhysiologicalTaskEventID`),
   KEY `FK_event_file` (`EventFileID`),
+  INDEX idx_pte_EventValue (`EventValue`),
+  INDEX idx_pte_TrialType (`TrialType`),
   CONSTRAINT `FK_phys_file_FileID_4`
     FOREIGN KEY (`PhysiologicalFileID`)
     REFERENCES `physiological_file` (`PhysiologicalFileID`)
@@ -382,105 +389,6 @@ CREATE TABLE `physiological_archive` (
     ON DELETE CASCADE
 ) ENGINE=InnoDB DEFAULT CHARSET=utf8;
 
--- SQL tables for BIDS derivative file structure
--- Create physiological_annotation_file_type table
-CREATE TABLE `physiological_annotation_file_type` (
-    `FileType`        VARCHAR(20)   NOT NULL UNIQUE,
-    `Description`     VARCHAR(255),
-    PRIMARY KEY (`FileType`)
-) ENGINE=InnoDB DEFAULT CHARSET=utf8;
-
--- Create physiological_annotation_file table
-CREATE TABLE `physiological_annotation_file` (
-    `AnnotationFileID`    INT(10)      UNSIGNED NOT NULL AUTO_INCREMENT,
-    `PhysiologicalFileID` INT(10)      UNSIGNED NOT NULL,
-    `FileType`            VARCHAR(20)  NOT NULL,
-    `FilePath`            VARCHAR(255),
-    `LastUpdate`          TIMESTAMP    NOT NULL DEFAULT CURRENT_TIMESTAMP ON UPDATE CURRENT_TIMESTAMP,
-    `LastWritten`         TIMESTAMP    NOT NULL DEFAULT CURRENT_TIMESTAMP,
-    PRIMARY KEY (`AnnotationFileID`),
-    CONSTRAINT `FK_phys_file_ID`
-        FOREIGN KEY (`PhysiologicalFileID`)
-        REFERENCES `physiological_file` (`PhysiologicalFileID`),
-    CONSTRAINT `FK_annotation_file_type`
-        FOREIGN KEY (`FileType`)
-        REFERENCES `physiological_annotation_file_type` (`FileType`)
-) ENGINE=InnoDB DEFAULT CHARSET=utf8;
-
--- Create annotation_archive which will store archives of all the annotation files for
--- Front-end download
-CREATE TABLE `physiological_annotation_archive` (
-  `AnnotationArchiveID` INT(10) UNSIGNED NOT NULL   AUTO_INCREMENT,
-  `PhysiologicalFileID` INT(10) UNSIGNED NOT NULL,
-  `Blake2bHash`         VARCHAR(128)     NOT NULL,
-  `FilePath`            VARCHAR(255)     NOT NULL,
-  PRIMARY KEY (`AnnotationArchiveID`),
-  CONSTRAINT `FK_physiological_file_ID`
-    FOREIGN KEY (`PhysiologicalFileID`)
-    REFERENCES `physiological_file` (`PhysiologicalFileID`)
-    ON DELETE CASCADE
-) ENGINE=InnoDB DEFAULT CHARSET=utf8;
-
--- Create annotation_parameter table
--- Note: This corresponds with the JSON annotation files
-CREATE TABLE `physiological_annotation_parameter` (
-    `AnnotationParameterID` INT(10)      UNSIGNED NOT NULL AUTO_INCREMENT,
-    `AnnotationFileID`      INT(10)      UNSIGNED NOT NULL,
-    `Description`           TEXT         DEFAULT NULL,
-    `Sources`               VARCHAR(255),
-    `Author`                VARCHAR(255),
-    PRIMARY KEY (`AnnotationParameterID`),
-    CONSTRAINT `FK_annotation_file_ID`
-        FOREIGN KEY (`AnnotationFileID`)
-        REFERENCES `physiological_annotation_file` (`AnnotationFileID`)
-) ENGINE=InnoDB DEFAULT CHARSET=utf8;
-
--- Create an annotation_label_type table
-CREATE TABLE `physiological_annotation_label` (
-  `AnnotationLabelID`    INT(5)       UNSIGNED NOT NULL AUTO_INCREMENT,
-  `AnnotationFileID`     INT(10)      UNSIGNED DEFAULT NULL,
-  `LabelName`            VARCHAR(255) NOT NULL,
-  `LabelDescription`     TEXT         DEFAULT NULL,
-  PRIMARY KEY (`AnnotationLabelID`)
-) ENGINE=InnoDB DEFAULT CHARSET=utf8;
-
--- Create annotation_tsv table
--- Note: This corresponds with the .tsv annotation files
-CREATE TABLE `physiological_annotation_instance` (
-    `AnnotationInstanceID`  INT(10)         UNSIGNED NOT NULL AUTO_INCREMENT,
-    `AnnotationFileID`      INT(10)         UNSIGNED NOT NULL,
-    `AnnotationParameterID` INT(10)         UNSIGNED NOT NULL,
-    `Onset`                 DECIMAL(10, 4),
-    `Duration`              DECIMAL(10, 4)  DEFAULT 0,
-    `AnnotationLabelID`     INT(5)          UNSIGNED NOT NULL,
-    `Channels`              TEXT,
-    `AbsoluteTime`          TIMESTAMP,
-    `Description`           VARCHAR(255),
-    PRIMARY KEY (`AnnotationInstanceID`),
-    CONSTRAINT `FK_annotation_parameter_ID`
-        FOREIGN KEY (`AnnotationParameterID`)
-        REFERENCES `physiological_annotation_parameter` (`AnnotationParameterID`),
-    CONSTRAINT `FK_annotation_file`
-        FOREIGN KEY (`AnnotationFileID`)
-        REFERENCES `physiological_annotation_file` (`AnnotationFileID`),
-    CONSTRAINT `FK_annotation_label_ID`
-        FOREIGN KEY (`AnnotationLabelID`)
-        REFERENCES `physiological_annotation_label` (`AnnotationLabelID`)
-) ENGINE=InnoDB DEFAULT CHARSET=utf8;
-
--- Create physiological_annotation_rel table
-CREATE TABLE `physiological_annotation_rel` (
-    `AnnotationTSV`  INT(10)    UNSIGNED NOT NULL,
-    `AnnotationJSON` INT(10)    UNSIGNED NOT NULL,
-    PRIMARY KEY (`AnnotationTSV`, `AnnotationJSON`),
-    CONSTRAINT `FK_AnnotationTSV`
-        FOREIGN KEY (`AnnotationTSV`)
-        REFERENCES `physiological_annotation_file` (`AnnotationFileID`),
-    CONSTRAINT `FK_AnnotationJSON`
-        FOREIGN KEY (`AnnotationJSON`)
-        REFERENCES `physiological_annotation_file` (`AnnotationFileID`)
-) ENGINE=InnoDB DEFAULT CHARSET=utf8;
-
 -- Create EEG upload table
 CREATE TABLE `electrophysiology_uploader` (
     `UploadID` int(10) unsigned NOT NULL AUTO_INCREMENT,
@@ -635,38 +543,83 @@ INSERT INTO ImagingFileTypes
   ('cnt',  'Neuroscan CNT data format (EEG)'),
   ('archive', 'Archive file');
 
--- Insert into annotation_file_type
-INSERT INTO physiological_annotation_file_type
-    (FileType, Description)
-    VALUES
-    ('tsv',  'TSV File Type, contains information about each annotation'),
-    ('json', 'JSON File Type, metadata for annotations');
-
--- Insert into annotation_label_type
-INSERT INTO physiological_annotation_label
-    (AnnotationLabelID, LabelName, LabelDescription)
-    VALUES
-    (1,  'artifact',            'artifactual data'),
-    (2,  'motion',              'motion related artifact'),
-    (3,  'flux_jump',           'artifactual data due to flux jump'),
-    (4,  'line_noise',          'artifactual data due to line noise (e.g., 50Hz)'),
-    (5,  'muscle',              'artifactual data due to muscle activity'),
-    (6,  'epilepsy_interictal', 'period deemed interictal'),
-    (7,  'epilepsy_preictal',   'onset of preictal state prior to onset of epilepsy'),
-    (8,  'epilepsy_seizure',    'onset of epilepsy'),
-    (9,  'epilepsy_postictal',  'postictal seizure period'),
-    (10, 'epileptiform',        'unspecified epileptiform activity'),
-    (11, 'epileptiform_single', 'a single epileptiform graphoelement (including possible slow wave)'),
-    (12, 'epileptiform_run',    'a run of one or more epileptiform graphoelements'),
-    (13, 'eye_blink',           'Eye blink'),
-    (14, 'eye_movement',        'Smooth Pursuit / Saccadic eye movement'),
-    (15, 'eye_fixation',        'Fixation onset'),
-    (16, 'sleep_N1',            'sleep stage N1'),
-    (17, 'sleep_N2',            'sleep stage N2'),
-    (18, 'sleep_N3',            'sleep stage N3'),
-    (19, 'sleep_REM',           'REM sleep'),
-    (20, 'sleep_wake',          'sleep stage awake'),
-    (21, 'sleep_spindle',       'sleep spindle'),
-    (22, 'sleep_k-complex',     'sleep K-complex'),
-    (23, 'scorelabeled',        'a global label indicating that the EEG has been annotated with SCORE.');
+-- Create `hed_schema` table
+CREATE TABLE `hed_schema` (
+  `ID` int(10) unsigned NOT NULL AUTO_INCREMENT,
+  `Name` varchar(255) NOT NULL,
+  `Version` varchar(255) NOT NULL,
+  `Description` text NULL,
+  `URL` varchar(255) NOT NULL UNIQUE,
+  PRIMARY KEY (`ID`)
+) ENGINE=InnoDB DEFAULT CHARSET=utf8;
+
+-- Create `hed_schema_nodes` table
+CREATE TABLE `hed_schema_nodes` (
+  `ID` int(10) unsigned NOT NULL AUTO_INCREMENT,
+  `ParentID` int(10) unsigned NULL,
+  `SchemaID` int(10) unsigned NOT NULL,
+  `Name` varchar(255) NOT NULL,
+  `LongName` varchar(255) NOT NULL,
+  `Description` text NOT NULL,
+  PRIMARY KEY (`ID`),
+  CONSTRAINT `FK_hed_parent_node`
+      FOREIGN KEY (`ParentID`)
+          REFERENCES `hed_schema_nodes` (`ID`),
+  CONSTRAINT `FK_hed_schema` FOREIGN KEY (`SchemaID`) REFERENCES `hed_schema` (`ID`) ON DELETE CASCADE ON UPDATE CASCADE
+) ENGINE=InnoDB DEFAULT CHARSET=utf8;
+
+-- Create `physiological_task_event_hed_rel` table
+CREATE TABLE `physiological_task_event_hed_rel` (
+  `ID` int(10) unsigned NOT NULL AUTO_INCREMENT,
+  `PhysiologicalTaskEventID` int(10) unsigned NOT NULL,
+  `HEDTagID` int(10) unsigned NULL,     -- Reference to hed_schema_nodes.ID. Can be null to only add parentheses
+  `TagValue` text NULL,                 -- For value tags
+  `HasPairing` boolean DEFAULT FALSE,   -- Is grouped with #AdditionalMembers# members
+  `PairRelID` int(10) unsigned NULL,    -- The `ID` of right side of the pair
+  `AdditionalMembers` int(10) unsigned DEFAULT 0, -- Number of additional members to encapsulate
+  PRIMARY KEY (`ID`),
+  CONSTRAINT `FK_physiological_task_event_hed_rel_pair` FOREIGN KEY (`PairRelID`)
+      REFERENCES `physiological_task_event_hed_rel` (`ID`) ON DELETE CASCADE ON UPDATE CASCADE,
+  KEY `FK_physiological_task_event_hed_rel_2` (`HEDTagID`),
+  CONSTRAINT `FK_physiological_task_event_hed_rel_2` FOREIGN KEY (`HEDTagID`)
+      REFERENCES `hed_schema_nodes` (`ID`) ON DELETE CASCADE ON UPDATE CASCADE,
+  CONSTRAINT `FK_physiological_task_event_hed_rel_1` FOREIGN KEY (`PhysiologicalTaskEventID`)
+        REFERENCES `physiological_task_event` (`PhysiologicalTaskEventID`) ON DELETE CASCADE ON UPDATE CASCADE
+) ENGINE=InnoDB DEFAULT CHARSET=utf8;
 
+-- Create `bids_event_dataset_mapping` table
+CREATE TABLE `bids_event_dataset_mapping` (
+  `ID` int(10) unsigned NOT NULL AUTO_INCREMENT,
+  `ProjectID` int(10) unsigned NOT NULL,
+  `PropertyName` varchar(50) NOT NULL,
+  `PropertyValue` varchar(255) NOT NULL,
+  `HEDTagID` int(10) unsigned NULL,     -- Reference to hed_schema_nodes.ID. Can be null to only add parentheses
+  `TagValue` text NULL,                 -- For value tags
+  `Description` TEXT NULL,              -- Level Description
+  `HasPairing` BOOLEAN DEFAULT FALSE,   -- Is grouped with #AdditionalMembers# members
+  `PairRelID` int(10) unsigned NULL,    -- The `ID` of right side of the pair
+  `AdditionalMembers` int(10) unsigned DEFAULT 0, -- Number of additional members to encapsulate
+  PRIMARY KEY (`ID`),
+  INDEX idx_event_dataset_PropertyName_PropertyValue (`PropertyName`, `PropertyValue`),
+  CONSTRAINT `FK_project_id` FOREIGN KEY (`ProjectID`) REFERENCES `Project` (`ProjectID`) ON DELETE CASCADE ON UPDATE CASCADE,
+  CONSTRAINT `FK_dataset_hed_tag_id` FOREIGN KEY (`HEDTagID`) REFERENCES `hed_schema_nodes` (`ID`) ON DELETE CASCADE ON UPDATE CASCADE
+) ENGINE=InnoDB DEFAULT CHARSET=utf8;
+
+
+-- Create `bids_event_file_mapping` table
+CREATE TABLE `bids_event_file_mapping` (
+ `ID` int(10) unsigned NOT NULL AUTO_INCREMENT,
+ `EventFileID` int(10) unsigned NOT NULL,
+ `PropertyName` varchar(50) NOT NULL,
+ `PropertyValue` varchar(255) NOT NULL,
+ `HEDTagID` int(10) unsigned NULL,     -- Reference to hed_schema_nodes.ID. Can be null to only add parentheses
+ `TagValue` text NULL,                 -- For value tags
+ `Description` TEXT NULL,              -- Level Description
+ `HasPairing` BOOLEAN DEFAULT FALSE,   -- Is grouped with #AdditionalMembers# members
+ `PairRelID` int(10) unsigned NULL,    -- The `ID` of right side of the pair
+ `AdditionalMembers` int(10) unsigned DEFAULT 0, -- Number of additional members to encapsulate
+ PRIMARY KEY (`ID`),
+ INDEX idx_event_file_PropertyName_PropertyValue (`PropertyName`, `PropertyValue`),
+ CONSTRAINT `FK_event_mapping_file_id` FOREIGN KEY (`EventFileID`) REFERENCES `physiological_event_file` (`EventFileID`) ON DELETE CASCADE ON UPDATE CASCADE,
+ CONSTRAINT `FK_file_hed_tag_id` FOREIGN KEY (`HEDTagID`) REFERENCES `hed_schema_nodes` (`ID`) ON DELETE CASCADE ON UPDATE CASCADE
+) ENGINE=InnoDB DEFAULT CHARSET=utf8;
diff --git a/SQL/New_patches/2024-01-29-Physiological-Events-Replace-Annotations.sql b/SQL/New_patches/2024-01-29-Physiological-Events-Replace-Annotations.sql
@@ -0,0 +1,17 @@
+-- Dropping all tables regarding annotations
+DROP TABLE physiological_annotation_archive;
+DROP TABLE physiological_annotation_rel;
+DROP TABLE physiological_annotation_instance;
+DROP TABLE physiological_annotation_parameter;
+DROP TABLE physiological_annotation_label;
+DROP TABLE physiological_annotation_file;
+DROP TABLE physiological_annotation_file_type;
+
+-- Event files are always associated to Projects, sometimes exclusively (dataset-scope events.json files)
+-- Add ProjectID and make PhysiologicalFileID DEFAULT NULL (ProjectID should ideally not be NULLable)
+ALTER TABLE `physiological_event_file`
+  CHANGE `PhysiologicalFileID` `PhysiologicalFileID` int(10) unsigned DEFAULT NULL,
+  ADD COLUMN `ProjectID` int(10) unsigned DEFAULT NULL AFTER `PhysiologicalFileID`,
+  ADD KEY `FK_physiological_event_file_project_id` (`ProjectID`),
+  ADD CONSTRAINT `FK_physiological_event_file_project_id`
+    FOREIGN KEY (`ProjectID`) REFERENCES `Project` (`ProjectID`);