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Imaging Preprocessing Scripts: Added a ScannerID column to files table: Redmine 10939 #2189

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merged 10 commits into from
Sep 28, 2016
Merged

Imaging Preprocessing Scripts: Added a ScannerID column to files table: Redmine 10939 #2189

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f070f69
Imaging Preprocessing Scripts: Added a ScannerCandID column to files …
MounaSafiHarab Sep 14, 2016
be30b3f
adding schema
MounaSafiHarab Sep 14, 2016
47f7370
ScannerID instead of ScannercandID as rightfully suggested by Dave
MounaSafiHarab Sep 15, 2016
fec0f7c
the schema that I ALWAYS have to forget to add
MounaSafiHarab Sep 15, 2016
b306379
renamed constraint to be consistent with the rest in the table and ad…
MounaSafiHarab Sep 16, 2016
38add6c
moved mri_scanner table creation before files to pass Travis
MounaSafiHarab Sep 16, 2016
b36c9a1
trying again to see if I pass Travis
MounaSafiHarab Sep 20, 2016
1382aae
updated the mysql patch as well
MounaSafiHarab Sep 20, 2016
0e9120c
display ScannerID in imaging browser from files table
MounaSafiHarab Sep 22, 2016
5ced65d
changes as per Gregs feedback on not being able to import the ScannerID
MounaSafiHarab Sep 26, 2016
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59 changes: 31 additions & 28 deletions SQL/0000-00-00-schema.sql
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Original file line number Diff line number Diff line change
Expand Up @@ -444,6 +444,33 @@ CREATE TABLE `mri_processing_protocol` (
/*!40101 SET character_set_client = @saved_cs_client */;


--
-- Table structure for table `mri_scanner`
--

DROP TABLE IF EXISTS `mri_scanner`;
CREATE TABLE `mri_scanner` (
`ID` int(11) unsigned NOT NULL auto_increment,
`Manufacturer` varchar(255) default NULL,
`Model` varchar(255) default NULL,
`Serial_number` varchar(255) default NULL,
`Software` varchar(255) default NULL,
`CandID` int(11) default NULL,
PRIMARY KEY (`ID`),
KEY `FK_mri_scanner_1` (`CandID`),
CONSTRAINT `FK_mri_scanner_1` FOREIGN KEY (`CandID`) REFERENCES `candidate` (`CandID`)
) ENGINE=InnoDB DEFAULT CHARSET=utf8;

--
-- Dumping data for table `mri_scanner`
--

LOCK TABLES `mri_scanner` WRITE;
/*!40000 ALTER TABLE `mri_scanner` DISABLE KEYS */;
INSERT INTO `mri_scanner` VALUES (0,NULL,NULL,NULL,NULL,NULL);
/*!40000 ALTER TABLE `mri_scanner` ENABLE KEYS */;
UNLOCK TABLES;

--
-- Table structure for table `files`
--
Expand All @@ -468,18 +495,21 @@ CREATE TABLE `files` (
`ProcessProtocolID` int(11) unsigned,
`Caveat` tinyint(1) default NULL,
`TarchiveSource` int(11) default NULL,
`ScannerID` int(10) unsigned NOT NULL default '0',
PRIMARY KEY (`FileID`),
KEY `file` (`File`),
KEY `sessionid` (`SessionID`),
KEY `outputtype` (`OutputType`),
KEY `filetype_outputtype` (`FileType`,`OutputType`),
KEY `staging_filetype_outputtype` (`PendingStaging`,`FileType`,`OutputType`),
KEY `AcquiIndex` (`AcquisitionProtocolID`,`SessionID`),
KEY `scannerid` (`ScannerID`),
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_FileTypes` FOREIGN KEY (`FileType`) REFERENCES `ImagingFileTypes`(`type`),
CONSTRAINT `FK_files_scannerID` FOREIGN KEY (`ScannerID`) REFERENCES `mri_scanner` (`ID`)
) ENGINE=InnoDB DEFAULT CHARSET=utf8;

DROP TABLE IF EXISTS `files_qcstatus`;
Expand Down Expand Up @@ -706,33 +736,6 @@ INSERT INTO `mri_scan_type` VALUES
/*!40000 ALTER TABLE `mri_scan_type` ENABLE KEYS */;
UNLOCK TABLES;

--
-- Table structure for table `mri_scanner`
--

DROP TABLE IF EXISTS `mri_scanner`;
CREATE TABLE `mri_scanner` (
`ID` int(11) unsigned NOT NULL auto_increment,
`Manufacturer` varchar(255) default NULL,
`Model` varchar(255) default NULL,
`Serial_number` varchar(255) default NULL,
`Software` varchar(255) default NULL,
`CandID` int(11) default NULL,
PRIMARY KEY (`ID`),
KEY `FK_mri_scanner_1` (`CandID`),
CONSTRAINT `FK_mri_scanner_1` FOREIGN KEY (`CandID`) REFERENCES `candidate` (`CandID`)
) ENGINE=InnoDB DEFAULT CHARSET=utf8;

--
-- Dumping data for table `mri_scanner`
--

LOCK TABLES `mri_scanner` WRITE;
/*!40000 ALTER TABLE `mri_scanner` DISABLE KEYS */;
INSERT INTO `mri_scanner` VALUES (0,NULL,NULL,NULL,NULL,NULL);
/*!40000 ALTER TABLE `mri_scanner` ENABLE KEYS */;
UNLOCK TABLES;

--
-- Table structure for table `notification_spool`
--
Expand Down
5 changes: 5 additions & 0 deletions SQL/Archive/17.0/2016-09-13-AddScannerIDInFiles.sql
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Original file line number Diff line number Diff line change
@@ -0,0 +1,5 @@
-- Add ScannerCandID column to files, back-populate the newly added column from parameter_file table, then add foreign key constraints
ALTER TABLE files ADD `ScannerID` int(10) unsigned NOT NULL default '0';
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set this to NULL (default)

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done in: #2251

CREATE TEMPORARY TABLE ScannerIDs AS SELECT pf.FileID, pf.Value AS ScannerID FROM parameter_file AS pf LEFT JOIN parameter_type AS pt ON pf.ParameterTypeID=pt.ParameterTypeID WHERE pt.Name='ScannerID';
UPDATE files AS f, ScannerIDs AS S SET f.ScannerID=S.ScannerID where f.FileID=S.FileID;
ALTER TABLE files ADD CONSTRAINT `FK_files_scannerID` FOREIGN KEY (`ScannerID`) REFERENCES mri_scanner (`ID`);
8 changes: 4 additions & 4 deletions modules/imaging_browser/php/NDB_Form_imaging_browser.class.inc
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Original file line number Diff line number Diff line change
Expand Up @@ -140,7 +140,7 @@ class NDB_Form_Imaging_Browser extends NDB_Form
}
}
$files = $this->DB->pselect(
"SELECT files.FileID FROM files LEFT JOIN files_qcstatus as sel on (
"SELECT files.FileID, files.ScannerID FROM files LEFT JOIN files_qcstatus as sel on (
files.FileID=sel.FileID)
WHERE SessionID=:SID AND (AcquisitionProtocolID IS NULL
OR AcquisitionProtocolID not in (1, 2, 3, 52))
Expand All @@ -154,7 +154,7 @@ class NDB_Form_Imaging_Browser extends NDB_Form
foreach ($files as $fileRow) {
$FileObj = new MRIFile($fileRow['FileID']);
if (empty($scannerID)) {
$scannerID = $FileObj->getParameter('ScannerID');
$scannerID = $fileRow['ScannerID'];
if (!empty($scannerID)) {
$query = "SELECT
CONCAT_WS(' ', Manufacturer, Model, Serial_number)
Expand Down Expand Up @@ -222,7 +222,7 @@ class NDB_Form_Imaging_Browser extends NDB_Form
'Xstep' => number_format($FileObj->getParameter('xstep'), 2),
'Ystep' => number_format($FileObj->getParameter('ystep'), 2),
'Zstep' => number_format($FileObj->getParameter('zstep'), 2),
'Selected' => $this->_getSelected((int)$FileObj->getParameter('FileID')),
'Selected' => $this->_getSelected((int)$FileObj->getParameter('FileID')),
'QCStatus' => $FileObj->getParameter('QCStatus'),
'QCDate' => $FileObj->getParameter('QCLastChangeTime'),
'Caveat' => $FileObj->getParameter('Caveat'),
Expand Down Expand Up @@ -651,4 +651,4 @@ class NDB_Form_Imaging_Browser extends NDB_Form

}

?>
?>
20 changes: 19 additions & 1 deletion tools/CouchDB_MRI_Importer.php
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Original file line number Diff line number Diff line change
Expand Up @@ -118,7 +118,7 @@ function _addMRIHeaderInfo($FileObj, $scan_type)
$inter_rej = 'IntergradientRejected_'.$type;
$pipeline = 'processing:pipeline';

$header['ScannerID_'.$type] = $FileObj->getParameter('ScannerID');
$header['ScannerID_'.$type] = $this->_getScannerID((int)$FileObj->getParameter('FileID'));
$header['Pipeline_'.$type] = $FileObj->getParameter('Pipeline');
$header['OutputType_'.$type] = $FileObj->getParameter('OutputType');
$header['AcquisitionProtocol_'.$type] = $FileObj->getAcquisitionProtocol();
Expand Down Expand Up @@ -192,6 +192,24 @@ function _getDate($file, $type, $array)
}
}

/**
* Gets the scannerID
*
* @param MRIFile $file file object
*
* @return scannerID
*/
function _getScannerID($FileID){

$scannerID = $this->SQLDB->pselectOne("SELECT ScannerID FROM files ".
"WHERE FileID =:FileID",
array(
'FileID' => $FileID
)
);
return $scannerID;
}

/**
* Gets a rejected parameter according to its type
*
Expand Down