[SQL/imaging] Adding SQL code for the new HRRT PET insertion scripts (a…

…ces#6142)

This updates the SQL schema to include the new PET HRRT archive tables and their link to the already existing imaging tables for Loris-MRI.

See also: aces/Loris-MRI#524, aces/Loris-MRI#480

SQL/0000-00-00-schema.sql

@@ -420,6 +420,42 @@ CREATE TABLE `tarchive_files` (
   CONSTRAINT `tarchive_files_TarchiveSeriesID_fk` FOREIGN KEY (`TarchiveSeriesID`) REFERENCES `tarchive_series` (`TarchiveSeriesID`)
 ) ENGINE=InnoDB DEFAULT CHARSET=utf8;
 
+-- ********************************
+-- HRRT PET archive tables
+-- ********************************
+CREATE TABLE `hrrt_archive` (
+  `HrrtArchiveID`     INT(11)          NOT NULL AUTO_INCREMENT,
+  `SessionID`         INT(10) unsigned          DEFAULT NULL,
+  `EcatFileCount`     INT(11)          NOT NULL DEFAULT '0',
+  `NonEcatFileCount`  INT(11)          NOT NULL DEFAULT '0',
+  `DateAcquired`      DATE                      DEFAULT NULL,
+  `DateArchived`      DATETIME                  DEFAULT NULL,
+  `PatientName`       VARCHAR(50)      NOT NULL DEFAULT '',
+  `CenterName`        VARCHAR(50)      NOT NULL DEFAULT '',
+  `CreatingUser`      VARCHAR(50)      NOT NULL DEFAULT '',
+  `Blake2bArchive`    VARCHAR(255)              DEFAULT NULL,
+  `ArchiveLocation`   VARCHAR(255)              DEFAULT NULL,
+  PRIMARY KEY (`HrrtArchiveID`),
+  KEY `patNam` (`CenterName`(10),`PatientName`(30)),
+  KEY `FK_hrrt_archive_sessionID` (`SessionID`),
+  CONSTRAINT `FK_hrrt_archive_sessionID`
+    FOREIGN KEY (`SessionID`)
+    REFERENCES `session` (`ID`)
+) ENGINE=InnoDB DEFAULT CHARSET=utf8;
+
+CREATE TABLE `hrrt_archive_files` (
+  `HrrtArchiveFileID` INT(11)      NOT NULL AUTO_INCREMENT,
+  `HrrtArchiveID`     INT(11)      NOT NULL DEFAULT '0',
+  `Blake2bHash`       VARCHAR(255) NOT NULL,
+  `FileName`          VARCHAR(255) NOT NULL,
+  PRIMARY KEY (`HrrtArchiveFileID`),
+  KEY `HrrtArchiveID` (`HrrtArchiveID`),
+  CONSTRAINT `hrrt_archive_files_ibfk_1`
+    FOREIGN KEY (`HrrtArchiveID`)
+    REFERENCES  `hrrt_archive` (`HrrtArchiveID`)
+    ON DELETE CASCADE
+) ENGINE=InnoDB DEFAULT CHARSET=utf8;
+
 
 -- ********************************
 -- Imaging tables
@@ -523,6 +559,7 @@ CREATE TABLE `files` (
   `ProcessProtocolID` int(11) unsigned,
   `Caveat` tinyint(1) default NULL,
   `TarchiveSource` int(11) default NULL,
+  `HrrtArchiveID` int(11) default NULL,
   `ScannerID` int(10) unsigned default NULL,
   `AcqOrderPerModality` int(11) default NULL,
   PRIMARY KEY  (`FileID`),
@@ -533,13 +570,15 @@ CREATE TABLE `files` (
   KEY `AcquiIndex` (`AcquisitionProtocolID`,`SessionID`),
   KEY `scannerid` (`ScannerID`),
   KEY `tarchivesource` (`TarchiveSource`),
+  KEY `FK_files_HrrtArchiveID_1` (`HrrtArchiveID`),
   CONSTRAINT `FK_files_2` FOREIGN KEY (`AcquisitionProtocolID`) REFERENCES `mri_scan_type` (`ID`),
   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_TarchiveID` FOREIGN KEY (`TarchiveSource`) REFERENCES `tarchive` (`TarchiveID`),
+  CONSTRAINT `FK_files_HrrtArchiveID` FOREIGN KEY (`HrrtArchiveID`) REFERENCES `hrrt_archive` (`HrrtArchiveID`)
 ) ENGINE=InnoDB DEFAULT CHARSET=utf8;
 
 CREATE TABLE `files_intermediary` (
@@ -663,6 +702,21 @@ CREATE TABLE `mri_upload` (
     FOREIGN KEY (`TarchiveID`) REFERENCES `tarchive` (`TarchiveID`)
 ) ENGINE=InnoDB DEFAULT CHARSET=utf8;
 
+CREATE TABLE `mri_upload_rel` (
+  `UploadRelID`   INT(10) UNSIGNED NOT NULL AUTO_INCREMENT,
+  `UploadID`      INT(10) UNSIGNED NOT NULL,
+  `HrrtArchiveID` INT(11) DEFAULT NULL,
+  PRIMARY KEY (`UploadRelID`),
+  KEY `FK_mriuploadrel_UploadID` (`UploadID`),
+  KEY `FK_mriuploadrel_HrrtArchiveID` (`HrrtArchiveID`),
+  CONSTRAINT `FK_mriuploadrel_UploadID`
+    FOREIGN KEY (`UploadID`)
+    REFERENCES `mri_upload` (`UploadID`),
+  CONSTRAINT `FK_mriuploadrel_HrrtArchiveID`
+    FOREIGN KEY (`HrrtArchiveID`)
+    REFERENCES `hrrt_archive` (`HrrtArchiveID`)
+) ENGINE=InnoDB DEFAULT CHARSET=utf8;
+
 CREATE TABLE `mri_protocol_checks_group` (
     `MriProtocolChecksGroupID`   INT(4) UNSIGNED NOT NULL AUTO_INCREMENT,
     `Name`                       VARCHAR(255)    NOT NULL UNIQUE,
@@ -945,7 +999,8 @@ INSERT INTO `notification_types` (Type,private,Description) VALUES
     ('tarchive validation',1,'Validation of the dicoms After uploading'),
     ('mri upload runner',1,'Validation of DICOMS before uploading'),
     ('mri upload processing class',1,'Validation and execution of DicomTar.pl and TarchiveLoader'),
-    ('imaging non minc file insertion', 1, 'Insertion of a non-MINC file into the MRI tables (files/parameter_file)');
+    ('imaging non minc file insertion', 1, 'Insertion of a non-MINC file into the MRI tables (files/parameter_file)'),
+    ('hrrt pet new series', 0, 'New HRRT PET studies inserted into the database');
 
 CREATE TABLE `notification_spool` (
   `NotificationID` int(11) NOT NULL auto_increment,

SQL/New_patches/2020-03-09-SQL_patch_for_HRRT_PET_images_insertion.sql

@@ -0,0 +1,68 @@
+-- Create the hrrt_archive and hrrt_archive_files tables
+CREATE TABLE `hrrt_archive` (
+  `HrrtArchiveID`     INT(11)          NOT NULL AUTO_INCREMENT,
+  `SessionID`         INT(10) unsigned          DEFAULT NULL,
+  `EcatFileCount`     INT(11)          NOT NULL DEFAULT '0',
+  `NonEcatFileCount`  INT(11)          NOT NULL DEFAULT '0',
+  `DateAcquired`      DATE                      DEFAULT NULL,
+  `DateArchived`      DATETIME                  DEFAULT NULL,
+  `PatientName`       VARCHAR(50)      NOT NULL DEFAULT '',
+  `CenterName`        VARCHAR(50)      NOT NULL DEFAULT '',
+  `CreatingUser`      VARCHAR(50)      NOT NULL DEFAULT '',
+  `Blake2bArchive`    VARCHAR(255)              DEFAULT NULL,
+  `ArchiveLocation`   VARCHAR(255)              DEFAULT NULL,
+  PRIMARY KEY (`HrrtArchiveID`),
+  KEY `patNam` (`CenterName`(10),`PatientName`(30)),
+  KEY `FK_hrrt_archive_sessionID` (`SessionID`),
+  CONSTRAINT `FK_hrrt_archive_sessionID`
+    FOREIGN KEY (`SessionID`)
+    REFERENCES `session` (`ID`)
+) ENGINE=InnoDB DEFAULT CHARSET=utf8;
+
+
+CREATE TABLE `hrrt_archive_files` (
+  `HrrtArchiveFileID` INT(11)      NOT NULL AUTO_INCREMENT,
+  `HrrtArchiveID`     INT(11)      NOT NULL DEFAULT '0',
+  `Blake2bHash`       VARCHAR(255) NOT NULL,
+  `FileName`          VARCHAR(255) NOT NULL,
+  PRIMARY KEY (`HrrtArchiveFileID`),
+  KEY `HrrtArchiveID` (`HrrtArchiveID`),
+  CONSTRAINT `hrrt_archive_files_ibfk_1`
+    FOREIGN KEY (`HrrtArchiveID`)
+    REFERENCES  `hrrt_archive` (`HrrtArchiveID`)
+    ON DELETE CASCADE
+) ENGINE=InnoDB DEFAULT CHARSET=utf8;
+
+
+
+-- Create the mri_upload_rel table
+CREATE TABLE `mri_upload_rel` (
+  `UploadRelID`   INT(10) UNSIGNED NOT NULL AUTO_INCREMENT,
+  `UploadID`      INT(10) UNSIGNED NOT NULL,
+  `HrrtArchiveID` INT(11) DEFAULT NULL,
+  PRIMARY KEY (`UploadRelID`),
+  KEY `FK_mriuploadrel_UploadID` (`UploadID`),
+  KEY `FK_mriuploadrel_HrrtArchiveID` (`HrrtArchiveID`),
+  CONSTRAINT `FK_mriuploadrel_UploadID`
+    FOREIGN KEY (`UploadID`)
+    REFERENCES `mri_upload` (`UploadID`),
+  CONSTRAINT `FK_mriuploadrel_HrrtArchiveID`
+    FOREIGN KEY (`HrrtArchiveID`)
+    REFERENCES `hrrt_archive` (`HrrtArchiveID`)
+) ENGINE=InnoDB DEFAULT CHARSET=utf8;
+
+
+-- Insert into notification type 'hrrt pet new series'
+INSERT INTO notification_types SET
+  Type        = 'hrrt pet new series',
+  private     = 0,
+  Description = 'New HRRT PET studies inserted into the database';
+
+
+-- Alter files table to add a HrrtArchiveID field that links HRRT MINC files
+-- to hrrt_archive tables
+ALTER TABLE files
+  ADD COLUMN `HrrtArchiveID` INT(11) DEFAULT NULL,
+  ADD KEY `FK_files_HrrtArchiveID_1` (`HrrtArchiveID`),
+  ADD CONSTRAINT `FK_files_HrrtArchiveID`
+    FOREIGN KEY (`HrrtArchiveID`) REFERENCES `hrrt_archive` (`HrrtArchiveID`);