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Fix various little bugs preventing the insertion of a MINC file without DICOMs #1288

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Fix various little bugs preventing the insertion of a MINC file without DICOMs #1288

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f0fa3ad
fix bug
cmadjar May 22, 2025
9c51c90
more bug fix
cmadjar May 22, 2025
9ef65aa
more bug fix
cmadjar May 22, 2025
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119 changes: 72 additions & 47 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);
Expand Down Expand Up @@ -477,11 +479,13 @@ =head2 Methods
$utility->writeErrorLog(
$message, $NeuroDB::ExitCodes::INVALID_ARG, $logfile
);
$notifier->spool(
'tarchive validation', $message, 0,
'minc_insertion.pl', $upload_id, 'Y',
$notify_notsummary
);
if (defined $upload_id) {
$notifier->spool(
'tarchive validation', $message, 0,
'minc_insertion.pl', $upload_id, 'Y',
$notify_notsummary
);
}
exit $NeuroDB::ExitCodes::INVALID_ARG;
}
}
Expand Down Expand Up @@ -555,9 +559,14 @@ =head2 Methods
}
$mriCandidateErrorsOB->insert(\%newMriCandidateErrors) unless defined $already_inserted;

$notifier->spool('tarchive validation', $message, 0,
'minc_insertion.pl', $upload_id, 'Y',
$notify_notsummary);
if (defined $upload_id) {
$notifier->spool(
'tarchive validation', $message, 0,
'minc_insertion.pl', $upload_id, 'Y',
$notify_notsummary
);
}


exit $NeuroDB::ExitCodes::CANDIDATE_MISMATCH;
}
Expand All @@ -580,11 +589,14 @@ =head2 Methods
if (!$sessionRef) {
print STDERR $errMsg if $verbose;
print LOG $errMsg;
$notifier->spool(
'tarchive validation', "$errMsg. Minc insertion failed.", 0,
'minc_insertion.pl', $upload_id, 'Y',
$notify_notsummary
);
if (defined $upload_id) {
$notifier->spool(
'tarchive validation', "$errMsg. Minc insertion failed.", 0,
'minc_insertion.pl', $upload_id, 'Y',
$notify_notsummary
);
}

exit ($subjectIDsref->{'createVisitLabel'} == 1
? $NeuroDB::ExitCodes::CREATE_SESSION_FAILURE
: $NeuroDB::ExitCodes::GET_SESSION_ID_FAILURE);
Expand All @@ -606,11 +618,13 @@ =head2 Methods
if ($not_unique_message) {
print STDERR $not_unique_message if $verbose;
print LOG $not_unique_message;
$notifier->spool(
'tarchive validation', $not_unique_message, 0,
'minc_insertion.pl', $upload_id, 'Y',
$notify_notsummary
);
if (defined $upload_id) {
$notifier->spool(
'tarchive validation', $not_unique_message, 0,
'minc_insertion.pl', $upload_id, 'Y',
$notify_notsummary
);
}
exit $NeuroDB::ExitCodes::FILE_NOT_UNIQUE;
}

Expand Down Expand Up @@ -655,15 +669,19 @@ =head2 Methods
);

if($acquisitionProtocol =~ /unknown/ && !defined $acquisitionProtocolID) {
$message = "\n --> The MINC file cannot be registered since the ".
"AcquisitionProtocol is unknown and AcquisitionProtocol ID is undefined \n";

print LOG $message;
print $message;
$notifier->spool('minc insertion', $message, 0,
'minc_insertion.pl', $upload_id, 'Y',
$notify_notsummary);
exit $NeuroDB::ExitCodes::UNKNOWN_PROTOCOL;
$message = "\n --> The MINC file cannot be registered since the ".
"AcquisitionProtocol is unknown and AcquisitionProtocol ID is undefined \n";

print LOG $message;
print $message;
if (defined $upload_id) {
$notifier->spool(
'minc insertion', $message, 0,
'minc_insertion.pl', $upload_id, 'Y',
$notify_notsummary
);
}
exit $NeuroDB::ExitCodes::UNKNOWN_PROTOCOL;
}

################################################################
Expand All @@ -688,15 +706,19 @@ =head2 Methods
if ((!defined$success)
&& (defined(&Settings::isFileToBeRegisteredGivenProtocol))
) {
$message = "\n --> The minc file cannot be registered ".
"since $acquisitionProtocol ".
"does not exist in $profile ".
"or it did not pass the extra_file_checks\n";
print LOG $message;
print $message;
$notifier->spool('minc insertion', $message, 0,
'minc_insertion', $upload_id, 'Y',
$notify_notsummary);
$message = "\n --> The minc file cannot be registered ".
"since $acquisitionProtocol ".
"does not exist in $profile ".
"or it did not pass the extra_file_checks\n";
print LOG $message;
print $message;
if (defined $upload_id) {
$notifier->spool(
'minc insertion', $message, 0,
'minc_insertion', $upload_id, 'Y',
$notify_notsummary
);
}
exit $NeuroDB::ExitCodes::PROJECT_CUSTOMIZATION_FAILURE;
}
################################################################
Expand All @@ -716,11 +738,14 @@ =head2 Methods


my $spool_type = $hrrt ? 'hrrt pet new series' : 'mri new series';
$notifier->spool(
$spool_type, $message, 0,
'minc_insertion.pl', $upload_id, 'N',
$notify_detailed
);
if (defined $upload_id) {
$notifier->spool(
$spool_type, $message, 0,
'minc_insertion.pl', $upload_id, 'N',
$notify_detailed
);
}

if ($verbose) {
print "\nFinished file: ".$file->getFileDatum('File')." \n";
}
Expand Down
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