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[SQL] General BIDS dataset and file tables #11169

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[SQL] General BIDS dataset and file tables #11169

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47ea3b3
add-bids-tables-patch
MaximeBICMTL Aug 12, 2026
e255e6b
add update time and time default
MaximeBICMTL Aug 13, 2026
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30 changes: 29 additions & 1 deletion SQL/0000-00-00-schema.sql
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Original file line number Diff line number Diff line change
Expand Up @@ -585,6 +585,30 @@ INSERT INTO `mri_scan_type` VALUES
(999,'unknown'),
(1000,'NA');

CREATE TABLE `bids_dataset` (
`ID` INT(10) UNSIGNED NOT NULL AUTO_INCREMENT,
`Path` VARCHAR(255) NOT NULL,
`InsertTime` DATETIME NOT NULL DEFAULT CURRENT_TIMESTAMP,
`UpdateTime` DATETIME NOT NULL DEFAULT CURRENT_TIMESTAMP,
PRIMARY KEY (`ID`),
UNIQUE KEY `bids_dataset_path_unique` (`Path`)
) ENGINE=InnoDB DEFAULT CHARSET=utf8mb4;

CREATE TABLE `bids_file` (
`ID` INT(10) UNSIGNED NOT NULL AUTO_INCREMENT,
`DatasetID` INT(10) UNSIGNED NOT NULL,
`Path` VARCHAR(255) NOT NULL,
`SourcePath` VARCHAR(255) NULL,
`InsertTime` DATETIME NOT NULL DEFAULT CURRENT_TIMESTAMP,
`Blake2bHash` CHAR(128) NOT NULL,
`Derivative` TINYINT(1) NOT NULL,
PRIMARY KEY (`ID`),
UNIQUE KEY `bids_file_dataset_id_path_unique` (`DatasetID`, `Path`),
KEY `bids_file_dataset_id_fk_idx` (`DatasetID`),
CONSTRAINT `bids_file_dataset_id_fk`
FOREIGN KEY (`DatasetID`) REFERENCES `bids_dataset` (`ID`) ON DELETE CASCADE
) ENGINE=InnoDB DEFAULT CHARSET=utf8mb4;

CREATE TABLE `files` (
`FileID` int(10) unsigned NOT NULL auto_increment,
`SessionID` int(10) unsigned NOT NULL,
Expand All @@ -609,6 +633,7 @@ CREATE TABLE `files` (
`ScannerID` int(10) unsigned default NULL,
`AcqOrderPerModality` int(11) default NULL,
`AcquisitionDate` date default NULL,
`BidsInfoID` int(10) unsigned DEFAULT NULL,
PRIMARY KEY (`FileID`),
KEY `file` (`File`),
KEY `sessionid` (`SessionID`),
Expand All @@ -618,14 +643,17 @@ CREATE TABLE `files` (
KEY `scannerid` (`ScannerID`),
KEY `tarchivesource` (`TarchiveSource`),
KEY `FK_files_HrrtArchiveID_1` (`HrrtArchiveID`),
KEY `files_bids_info_id_fk_idx` (`BidsInfoID`),
CONSTRAINT `FK_files_2` FOREIGN KEY (`MriScanTypeID`) REFERENCES `mri_scan_type` (`MriScanTypeID`),
CONSTRAINT `FK_files_1` FOREIGN KEY (`SessionID`) REFERENCES `session` (`ID`),
CONSTRAINT `FK_files_3` FOREIGN KEY (`SourceFileID`) REFERENCES `files` (`FileID`),
CONSTRAINT `FK_files_4` FOREIGN KEY (`ProcessProtocolID`) REFERENCES `mri_processing_protocol` (`ProcessProtocolID`),
CONSTRAINT `FK_files_FileTypes` FOREIGN KEY (`FileType`) REFERENCES `ImagingFileTypes`(`type`),
CONSTRAINT `FK_files_scannerID` FOREIGN KEY (`ScannerID`) REFERENCES `mri_scanner` (`ID`),
CONSTRAINT `FK_files_TarchiveID` FOREIGN KEY (`TarchiveSource`) REFERENCES `tarchive` (`TarchiveID`),
CONSTRAINT `FK_files_HrrtArchiveID` FOREIGN KEY (`HrrtArchiveID`) REFERENCES `hrrt_archive` (`HrrtArchiveID`)
CONSTRAINT `FK_files_HrrtArchiveID` FOREIGN KEY (`HrrtArchiveID`) REFERENCES `hrrt_archive` (`HrrtArchiveID`),
CONSTRAINT `files_bids_info_id_fk`
FOREIGN KEY (`BidsInfoID`) REFERENCES `bids_file` (`ID`) ON DELETE SET NULL
) ENGINE=InnoDB DEFAULT CHARSET=utf8;

CREATE TABLE `files_intermediary` (
Expand Down
24 changes: 21 additions & 3 deletions SQL/0000-00-05-ElectrophysiologyTables.sql
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Original file line number Diff line number Diff line change
Expand Up @@ -7,7 +7,14 @@ CREATE TABLE `meg_ctf_head_shape_file` (
`ID` INT(10) UNSIGNED NOT NULL AUTO_INCREMENT,
`Path` VARCHAR(255) NOT NULL,
`Blake2bHash` VARCHAR(128) NOT NULL,
PRIMARY KEY (`ID`)
`BidsInfoID` INT(10) UNSIGNED DEFAULT NULL,
`InsertTime` DATETIME NOT NULL DEFAULT CURRENT_TIMESTAMP,
PRIMARY KEY (`ID`),
KEY `meg_ctf_head_shape_file_bids_info_id_fk_idx` (`BidsInfoID`),
CONSTRAINT `meg_ctf_head_shape_file_bids_info_id_fk`
FOREIGN KEY (`BidsInfoID`)
REFERENCES `bids_file` (`ID`)
ON DELETE SET NULL
) ENGINE=InnoDB DEFAULT CHARSET=utf8;

-- Create a meg_ctf_head_shape_point table
Expand Down Expand Up @@ -57,7 +64,9 @@ CREATE TABLE `physiological_file` (
`Index` INT(5) DEFAULT NULL,
`ParentID` INT(10) unsigned DEFAULT NULL,
`HeadShapeFileID` INT(10) unsigned DEFAULT NULL,
`BidsInfoID` INT(10) unsigned DEFAULT NULL,
PRIMARY KEY (`PhysiologicalFileID`),
KEY `physiological_file_bids_info_id_fk_idx` (`BidsInfoID`),
CONSTRAINT `FK_session_ID`
FOREIGN KEY (`SessionID`)
REFERENCES `session` (`ID`),
Expand All @@ -73,9 +82,14 @@ CREATE TABLE `physiological_file` (
CONSTRAINT `FK_ParentID`
FOREIGN KEY (`ParentID`)
REFERENCES `physiological_file` (`PhysiologicalFileID`),
CONSTRAINT `FK_head_shape_HeadShapeFileID`
CONSTRAINT `physiological_file_head_shape_file_id_fk`
FOREIGN KEY (`HeadShapeFileID`)
REFERENCES `meg_ctf_head_shape_file` (`ID`)
ON DELETE SET NULL,
CONSTRAINT `physiological_file_bids_info_id_fk`
FOREIGN KEY (`BidsInfoID`)
REFERENCES `bids_file` (`ID`)
ON DELETE SET NULL
) ENGINE=InnoDB DEFAULT CHARSET=utf8;


Expand Down Expand Up @@ -307,12 +321,16 @@ CREATE TABLE `physiological_event_file` (
`FilePath` varchar(255) DEFAULT NULL,
`LastUpdate` timestamp NOT NULL DEFAULT CURRENT_TIMESTAMP ON UPDATE CURRENT_TIMESTAMP,
`LastWritten` timestamp NOT NULL DEFAULT CURRENT_TIMESTAMP,
`BidsInfoID` int(10) unsigned DEFAULT NULL,
PRIMARY KEY (`EventFileID`),
KEY `FK_physio_file_ID` (`PhysiologicalFileID`),
KEY `FK_event_file_type` (`FileType`),
KEY `physiological_event_file_bids_info_id_fk_idx` (`BidsInfoID`),
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_pef_project_ID` FOREIGN KEY (`ProjectID`) REFERENCES `Project` (`ProjectID`)
CONSTRAINT `FK_pef_project_ID` FOREIGN KEY (`ProjectID`) REFERENCES `Project` (`ProjectID`),
CONSTRAINT `physiological_event_file_bids_info_id_fk`
FOREIGN KEY (`BidsInfoID`) REFERENCES `bids_file` (`ID`) ON DELETE SET NULL
) ENGINE=InnoDB DEFAULT CHARSET=utf8
;

Expand Down
85 changes: 85 additions & 0 deletions SQL/New_patches/2026-08-12-bids-dataset-tables.sql
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Original file line number Diff line number Diff line change
@@ -0,0 +1,85 @@
CREATE TABLE `bids_dataset` (
`ID` INT(10) UNSIGNED NOT NULL AUTO_INCREMENT,
`Path` VARCHAR(255) NOT NULL,
`InsertTime` DATETIME NOT NULL DEFAULT CURRENT_TIMESTAMP,
`UpdateTime` DATETIME NOT NULL DEFAULT CURRENT_TIMESTAMP,
PRIMARY KEY (`ID`),
UNIQUE KEY `bids_dataset_path_unique` (`Path`)
) ENGINE=InnoDB DEFAULT CHARSET=utf8mb4;

CREATE TABLE `bids_file` (
`ID` INT(10) UNSIGNED NOT NULL AUTO_INCREMENT,
`DatasetID` INT(10) UNSIGNED NOT NULL,
`Path` VARCHAR(255) NOT NULL,
`SourcePath` VARCHAR(255) NULL,
`InsertTime` DATETIME NOT NULL DEFAULT CURRENT_TIMESTAMP,
`Blake2bHash` CHAR(128) NOT NULL,
`Derivative` TINYINT(1) NOT NULL,
PRIMARY KEY (`ID`),
UNIQUE KEY `bids_file_dataset_id_path_unique` (`DatasetID`, `Path`),
KEY `bids_file_dataset_id_fk_idx` (`DatasetID`),
CONSTRAINT `bids_file_dataset_id_fk`
FOREIGN KEY (`DatasetID`) REFERENCES `bids_dataset` (`ID`) ON DELETE CASCADE
) ENGINE=InnoDB DEFAULT CHARSET=utf8mb4;

ALTER TABLE `files`
ADD COLUMN `BidsInfoID` INT(10) UNSIGNED NULL,
ADD KEY `files_bids_info_id_fk_idx` (`BidsInfoID`),
ADD CONSTRAINT `files_bids_info_id_fk`
FOREIGN KEY (`BidsInfoID`) REFERENCES `bids_file` (`ID`) ON DELETE SET NULL;

ALTER TABLE `physiological_file`
ADD COLUMN `BidsInfoID` INT(10) UNSIGNED NULL,
ADD KEY `physiological_file_bids_info_id_fk_idx` (`BidsInfoID`),
ADD CONSTRAINT `physiological_file_bids_info_id_fk`
FOREIGN KEY (`BidsInfoID`) REFERENCES `bids_file` (`ID`) ON DELETE SET NULL;

ALTER TABLE `physiological_event_file`
ADD COLUMN `BidsInfoID` INT(10) UNSIGNED NULL,
ADD KEY `physiological_event_file_bids_info_id_fk_idx` (`BidsInfoID`),
ADD CONSTRAINT `physiological_event_file_bids_info_id_fk`
FOREIGN KEY (`BidsInfoID`) REFERENCES `bids_file` (`ID`) ON DELETE SET NULL;

ALTER TABLE `meg_ctf_head_shape_file`
ADD COLUMN `BidsInfoID` INT(10) UNSIGNED NULL,
ADD COLUMN `InsertTime` DATETIME NOT NULL DEFAULT CURRENT_TIMESTAMP,
ADD KEY `meg_ctf_head_shape_file_bids_info_id_fk_idx` (`BidsInfoID`),
ADD CONSTRAINT `meg_ctf_head_shape_file_bids_info_id_fk`
FOREIGN KEY (`BidsInfoID`) REFERENCES `bids_file` (`ID`) ON DELETE SET NULL;

ALTER TABLE `physiological_file`
DROP FOREIGN KEY `physiological_file_head_shape_file_id_fk`,
ADD CONSTRAINT `physiological_file_head_shape_file_id_fk`
FOREIGN KEY (`HeadShapeFileID`) REFERENCES `meg_ctf_head_shape_file` (`ID`) ON DELETE SET NULL;

/* Revert patch

ALTER TABLE `physiological_file`
DROP FOREIGN KEY `physiological_file_head_shape_file_id_fk`,
ADD CONSTRAINT `physiological_file_head_shape_file_id_fk`
FOREIGN KEY (`HeadShapeFileID`) REFERENCES `meg_ctf_head_shape_file` (`ID`);

ALTER TABLE `meg_ctf_head_shape_file`
DROP FOREIGN KEY `meg_ctf_head_shape_file_bids_info_id_fk`,
DROP KEY `meg_ctf_head_shape_file_bids_info_id_fk_idx`,
DROP COLUMN `InsertTime`,
DROP COLUMN `BidsInfoID`;

ALTER TABLE `physiological_event_file`
DROP FOREIGN KEY `physiological_event_file_bids_info_id_fk`,
DROP KEY `physiological_event_file_bids_info_id_fk_idx`,
DROP COLUMN `BidsInfoID`;

ALTER TABLE `physiological_file`
DROP FOREIGN KEY `physiological_file_bids_info_id_fk`,
DROP KEY `physiological_file_bids_info_id_fk_idx`,
DROP COLUMN `BidsInfoID`;

ALTER TABLE `files`
DROP FOREIGN KEY `files_bids_info_id_fk`,
DROP KEY `files_bids_info_id_fk_idx`,
DROP COLUMN `BidsInfoID`;

DROP TABLE `bids_file`;

DROP TABLE `bids_dataset`; */
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