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Fix various little bugs preventing the insertion of a MINC file without DICOMs #1289

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Merged
merged 2 commits into from
May 27, 2025
Merged

Fix various little bugs preventing the insertion of a MINC file without DICOMs #1289

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f0fa3ad
fix bug
cmadjar May 22, 2025
9c51c90
more bug fix
cmadjar May 22, 2025
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14 changes: 8 additions & 6 deletions uploadNeuroDB/minc_insertion.pl
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Original file line number Diff line number Diff line change
Expand Up @@ -355,9 +355,6 @@ =head2 Methods
$is_valid = $array[0];
$ArchiveLocation = $array[1];

# create the studyInfo object
%studyInfo = $utility->createTarchiveArray($ArchiveLocation);

} elsif ($tarchive) {
my $mriUploadOB = NeuroDB::objectBroker::MriUploadOB->new(db => $db);
my $mriUploadsRef = $mriUploadOB->getWithTarchive(GET_COLUMNS, $tarchive);
Expand All @@ -383,6 +380,8 @@ =head2 Methods
my %row = %{ $mriUploadsRef->[0] };
$is_valid = $row{'isTarchiveValidated'};
$upload_id = $row{'UploadID'};
$ArchiveLocation = $tarchive;
$ArchiveLocation =~ s/$tarchiveLibraryDir//;
}

} elsif ($hrrt) {
Expand All @@ -403,7 +402,7 @@ =head2 Methods
$is_valid = 1; # if it is HRRT datasets, mark study as valid
}

if (($is_valid == 0) && ($force==0)) {
if (!$is_valid && !$force) {
$message = "\n ERROR: The validation has failed. ".
"Either run the validation again and fix ".
"the problem. Or use -force to force the ".
Expand All @@ -419,8 +418,11 @@ =head2 Methods

## Construct the tarchiveinfo Array and the MINC file object

# Create the study info array
%studyInfo = $utility->createTarchiveArray($ArchiveLocation, $hrrt);
# Create the study info array if ArchiveLocation is defined, otherwise, will populate
# with MINC file header later on
if (defined $ArchiveLocation) {
%studyInfo = $utility->createTarchiveArray($ArchiveLocation, $hrrt);
}

# Create the MINC file object and maps DICOM fields
my $file = $utility->loadAndCreateObjectFile($minc, $upload_id);
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