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Added a ScannerID column to files table: Redmine 10939 #156

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merged 4 commits into from
Sep 28, 2016
Merged

Added a ScannerID column to files table: Redmine 10939 #156

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e75f35d
Added a ScannerCandID column to files table: Redmine 10939
MounaSafiHarab Sep 14, 2016
2ddc5ac
Populate ScannerID not ScannerCandID
MounaSafiHarab Sep 15, 2016
b19bb30
better way to populate the scannerID in files table
MounaSafiHarab Sep 22, 2016
1de5021
updated DTIPrep files
MounaSafiHarab Sep 22, 2016
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2 changes: 1 addition & 1 deletion uploadNeuroDB/NeuroDB/MRI.pm
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Expand Up @@ -718,7 +718,7 @@ sub register_db {
# build the insert query
my $query = "INSERT INTO files SET ";

foreach my $key ('File', 'SessionID','EchoTime', 'CoordinateSpace', 'OutputType', 'AcquisitionProtocolID', 'FileType', 'InsertedByUserID', 'Caveat', 'SeriesUID', 'TarchiveSource','SourcePipeline','PipelineDate','SourceFileID') {
foreach my $key ('File', 'SessionID','EchoTime', 'CoordinateSpace', 'OutputType', 'AcquisitionProtocolID', 'FileType', 'InsertedByUserID', 'Caveat', 'SeriesUID', 'TarchiveSource','SourcePipeline','PipelineDate','SourceFileID', 'ScannerID') {
# add the key=value pair to the query
$query .= "$key=".$dbh->quote($${fileData{$key}}).", ";
}
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2 changes: 1 addition & 1 deletion uploadNeuroDB/minc_insertion.pl
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Expand Up @@ -378,7 +378,7 @@
## at this point things will appear in the database ############
## Set some file information ###################################
################################################################
$file->setParameter('ScannerID', $scannerID);
$file->setFileData('ScannerID', $scannerID);
$file->setFileData('SessionID', $sessionID);
$file->setFileData('SeriesUID', $file->getParameter('series_instance_uid'));
$file->setFileData('EchoTime', $file->getParameter('echo_time'));
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2 changes: 1 addition & 1 deletion uploadNeuroDB/registerFile.pl
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Expand Up @@ -176,7 +176,7 @@
$file->getParameter('software_versions'),
$centerID,
\$dbh, 0);
$file->setParameter('ScannerID', $scannerID);
$file->setFileData('ScannerID', $scannerID);
print "Set scannerid = $scannerID\n" if $verbose;

# get ids from the headers
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11 changes: 5 additions & 6 deletions uploadNeuroDB/register_processed_data.pl
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Expand Up @@ -168,7 +168,7 @@
print LOG "\nERROR: could not determine scannerID based on sourceFileID $sourceFileID.\n\n";
exit 2;
}
$file->setParameter('ScannerID',$scannerID);
$file->setFileData('ScannerID',$scannerID);
print LOG "\t -> Set ScannerID to $scannerID.\n";


Expand Down Expand Up @@ -302,16 +302,15 @@ sub getSessionID {


=pod
This function gets ScannerID from parameter_file using sourceFileID
This function gets ScannerID from files using sourceFileID
=cut
sub getScannerID {
my ($sourceFileID,$dbh) = @_;

my $scannerID;
my $query = "SELECT pf.Value AS ScannerID " .
"FROM parameter_file AS pf " .
"JOIN parameter_type AS pt ON (pt.ParameterTypeID=pf.ParameterTypeID) " .
"WHERE pt.Name='ScannerID' AND pf.FileID=?";
my $query = "SELECT f.ScannerID AS ScannerID " .
"FROM files AS f " .
"WHERE f.FileID=?";
my $sth = $dbh->prepare($query);
$sth->execute($sourceFileID);
if($sth->rows > 0) {
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