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HED Tag Support + HED Tag Manager (Rebased with aces#9032 CI fixes)
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@jeffersoncasimir
jeffersoncasimir committed Jan 31, 2024
1 parent 2d6ce08 commit ff13fe7
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Showing 18 changed files with 4,136 additions and 123 deletions.
95 changes: 91 additions & 4 deletions SQL/0000-00-05-ElectrophysiologyTables.sql
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Original file line number Diff line number Diff line change
Expand Up @@ -75,6 +75,7 @@ CREATE TABLE `physiological_split_file` (
CREATE TABLE `physiological_parameter_file` (
`PhysiologicalParameterFileID` INT(10) UNSIGNED NOT NULL AUTO_INCREMENT,
`PhysiologicalFileID` INT(10) UNSIGNED NOT NULL,
`ProjectID` INT(10) UNSIGNED NOT NULL,
`ParameterTypeID` INT(10) UNSIGNED NOT NULL,
`InsertTime` TIMESTAMP NOT NULL DEFAULT CURRENT_TIMESTAMP,
`Value` TEXT,
Expand All @@ -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;


Expand Down Expand Up @@ -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 NOT NULL,
`FileType` varchar(20) NOT NULL,
`FilePath` varchar(255) DEFAULT NULL,
`LastUpdate` timestamp NOT NULL DEFAULT CURRENT_TIMESTAMP ON UPDATE CURRENT_TIMESTAMP,
Expand All @@ -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
;

Expand All @@ -299,9 +305,9 @@ 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`),
CONSTRAINT `FK_phys_file_FileID_4`
FOREIGN KEY (`PhysiologicalFileID`)
REFERENCES `physiological_file` (`PhysiologicalFileID`)
Expand Down Expand Up @@ -535,3 +541,84 @@ INSERT INTO ImagingFileTypes
('edf', 'European data format (EEG)'),
('cnt', 'Neuroscan CNT data format (EEG)'),
('archive', 'Archive file');

-- 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;
109 changes: 109 additions & 0 deletions SQL/New_patches/2024-01-30-HED-Tag-Support.sql
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Original file line number Diff line number Diff line change
@@ -0,0 +1,109 @@
-- Remove unused column
ALTER TABLE `physiological_task_event` DROP COLUMN `AssembledHED`;

-- Add index for performance improvement
ALTER TABLE `physiological_task_event` ADD INDEX idx_pte_EventValue (`EventValue`);

-- 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`);

-- Add ProjectID and make PhysiologicalFileID DEFAULT NULL
ALTER TABLE `physiological_parameter_file`
CHANGE `PhysiologicalFileID` `PhysiologicalFileID` int(10) unsigned DEFAULT NULL,
ADD COLUMN `ProjectID` int(10) unsigned DEFAULT NULL AFTER `PhysiologicalFileID`,
ADD KEY `FK_physiological_parameter_file_project_id` (`ProjectID`),
ADD CONSTRAINT `FK_physiological_parameter_file_project_id`
FOREIGN KEY (`ProjectID`) REFERENCES `Project` (`ProjectID`);

-- 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;






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