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Allowing a suffix at the end of filename in batch upload imageuploader, like is done in imaging uploader now #159

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Merged
merged 7 commits into from
Oct 28, 2016
Merged

Allowing a suffix at the end of filename in batch upload imageuploader, like is done in imaging uploader now #159

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b6fbc14
Allowing a suffix at the end of filename in batch upload imageuploade…
MounaSafiHarab Sep 21, 2016
4955b2d
added a Usage-Help section
MounaSafiHarab Oct 20, 2016
7291415
typos
MounaSafiHarab Oct 20, 2016
f95a53e
Usage section prints by just typing filename
MounaSafiHarab Oct 21, 2016
3657761
change error message
MounaSafiHarab Oct 21, 2016
9b45fcb
Greg feedback on ARGV[0]
MounaSafiHarab Oct 27, 2016
a3dffab
profile not initialized to undef, but empty: Greg feedback
MounaSafiHarab Oct 27, 2016
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38 changes: 34 additions & 4 deletions batch_uploads_imageuploader
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Original file line number Diff line number Diff line change
Expand Up @@ -7,7 +7,7 @@ use Getopt::Tabular;
use NeuroDB::DBI;
use NeuroDB::Notify;

my $profile = undef;
my $profile = '';
my $upload_id = undef;
my $fullpath = undef;
my $phantom = undef;
Expand All @@ -25,6 +25,30 @@ my @opt_table = (
["-verbose", "boolean", 1, \$verbose, "Be verbose."]
);

my $Help = <<HELP;
******************************************************************************
Run imaging_upload_file.pl in batch mode
******************************************************************************

This script runs the Loris-MRI insertion on multiple scans. The list of scans are
provided through a text file (e.g. list_of_scans.txt) with one scan details per line.
The scan details includes the path to the scan, identification as to whether the
scan is for a phantom (Y) or not (N), and the candidate name for non-phantom entries.

Like the Loris Imaging Uploader interface, this script also validates the candidate
name against the (start of the) filename and creates an entry in the mri_upload table.

An example of what list_of_scans.txt might contain for 3 uploads to be inserted:
/data/incoming/PSC0001_123457_V1.tar.gz N PSC0000_123456_V1
/data/incoming/Lego_Phantom_MNI_20140101.zip Y
/data/incoming/PSC0001_123457_V1_RES.tar.gz N PSC0000_123456_V1

HELP
my $Usage = <<USAGE;
usage: ./batch_uploads_imageuploader -profile prod < list_of_scans.txt >log_batch_imageuploader.txt 2>&1 [options]
$0 -help to list options
USAGE
&Getopt::Tabular::SetHelp( $Help, $Usage );
&Getopt::Tabular::GetOptions( \@opt_table, \@ARGV ) || exit 1;

################################################################
Expand All @@ -38,6 +62,12 @@ if ( $profile && !@Settings::db ) {
exit 2;
}

if (!$profile ) {
print $Help;
print "\n$Usage\n";
exit 3;
}

################################################################
################ Establish database connection #################
################################################################
Expand Down Expand Up @@ -111,10 +141,10 @@ foreach my $input (@resultsarray)
exit(4);
}
if ($phantom eq 'N') {
if ($base ne $patientname) {
if ($patientname ne (substr ($base, 0, length($patientname)))) {
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@MounaSafiHarab MounaSafiHarab Oct 28, 2016

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better to use regular expression

print "Make sure the patient name $patientname " .
"for non-phantom entries matches the file " .
"name $base in $path\n";
"for non-phantom entries matches the start of the ".
"filename $base in $path\n";
exit(5);
}
}
Expand Down