Script to remove mnc file based on a query

tools/deletemincandinsertfromtar.pl

@@ -0,0 +1,94 @@
+#!/usr/bin/perl
+use strict;
+use warnings;
+no warnings 'once';
+use Data::Dumper;
+use File::Basename;
+use File::Copy;
+use Term::ANSIColor qw(:constants);
+use NeuroDB::DBI;
+
+{ package Settings; do "$ENV{LORIS_CONFIG}/.loris_mri/prod" }
+my $dbh = &NeuroDB::DBI::connect_to_db(@Settings::db);
+
+# my $queryF = "SELECT f.SeriesUID, a.ArchiveLocation, SUBSTRING_INDEX(a.ArchiveLocation, '/', -1) as tarchive, ".
+#             "CASE WHEN t.SeriesDescription LIKE '%t1%' THEN 't1w' WHEN t.SeriesDescription LIKE '%t2%' THEN 't2w' END AS protocol FROM files AS f ".
+#             "LEFT JOIN tarchive_series AS t ON t.SeriesUID=f.SeriesUID LEFT JOIN tarchive AS a ON f.TarchiveSource=a.TarchiveID ".
+#             "where f.file LIKE '%dti%' AND (t.SeriesDescription LIKE '%t1%' OR t.SeriesDescription LIKE '%t2%') ".
+#             "AND f.SeriesUID NOT IN ('1.3.12.2.1107.5.2.32.35182.2008073113303686337017814.0.0.0','1.3.12.2.1107.5.2.43.67010.2015042819301841366299600.0.0.0') ".
+#             "ORDER BY f.FileID, t.SeriesDescription";
+
+my $queryF = <<SQL;
+    SELECT DISTINCT
+    f.FileID, f.File, f.SeriesUID, t.ArchiveLocation, SUBSTRING_INDEX(t.ArchiveLocation, '/', -1) as tarchive
+    FROM files AS f
+    LEFT JOIN session s ON (f.SessionID=s.ID)
+    LEFT JOIN parameter_file AS pf USING (FileID)
+    LEFT JOIN files_qcstatus AS fq USING (FileID)
+    LEFT JOIN tarchive AS t ON f.TarchiveSource=t.TarchiveID
+    WHERE f.SeriesUID='1.3.12.2.1107.5.2.32.35177.2015072521545163128256406.0.0.0' or f.SeriesUID='1.3.12.2.1107.5.2.32.35177.2015072822492087585653675.0.0.0' and
+    ((pf.ParameterTypeID=329 and pf.`VALUE` like '%acquisition:direction_x = 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0.%')
+     or (pf.ParameterTypeID=329 and pf.`VALUE` like '%acquisition:direction_y = 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0.%')
+     or (pf.ParameterTypeID=329 and pf.`VALUE` like '%acquisition:direction_z = 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0.%')
+     or (pf.ParameterTypeID=333 and pf.`VALUE` like '%0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0.%')
+     or (pf.ParameterTypeID=334 and pf.`VALUE` like '%0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0.%')
+     or (pf.ParameterTypeID=343 and pf.`VALUE` like '%0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0.%'))
+    ORDER BY f.FileID
+SQL
+
+
+my $sthF = $dbh->prepare($queryF);
+
+my $keepgoing = 1;
+my ($rF, $fF, $stdin, $i);
+
+printf ("%-6s", '| L# ');
+printf ("%-64s",'| SeriesUID');
+printf ("%-36s",'| ArchiveLocation');
+printf ("%-36s",'| CorrectLocation');
+
+print "|\n";
+
+$rF = $sthF->execute();
+
+while ($fF = $sthF->fetchrow_hashref()) {
+
+  if ($sthF->rows > 0) {
+    $i++;
+
+    # copy("/data/not_backed_up/ibis_t1t2/backup/" . $fF->{'tarchive'}, "/data/not_backed_up/ibis_t1t2/");
+
+    my $minc_delete_cmd = "../uploadNeuroDB/minc_deletion.pl -profile prod -seriesuid " . $fF->{'SeriesUID'} . " confirm";
+    print $minc_delete_cmd . "\n";
+    my $minc_delete_log = `$minc_delete_cmd`;
+    print $minc_delete_log . "\n";
+
+    print "Press ENTER to continue:";
+    <STDIN>;
+
+    # -acquisition_protocol " . $fF->{'protocol'}
+    # -profile prod
+    # ../../../../" . $fF->{'ArchiveLocation'}
+    my $tar_loader_cmd  = "../uploadNeuroDB/tarchiveLoader -profile null_grads -seriesuid " . $fF->{'SeriesUID'} .
+                          " -verbose -globLocation " . $fF->{'ArchiveLocation'};
+
+    print $tar_loader_cmd . "\n";
+    my $tar_loader_log  = `$tar_loader_cmd`;
+    print $tar_loader_log . "\n";
+
+    printf ("%-6s", '| '. $i);
+    printf ("%-64s",'| '. $fF->{'seriesuid'});
+    printf ("%-36s",'| '. $fF->{'ArchiveLocation'});
+    printf ("%-36s",'| '. $fF->{'tarchive'});
+    print  "|\n";
+
+    if ($keepgoing) {
+      print "Press ENTER (or A and ENTER to do it all)\n";
+      $stdin = <STDIN>;
+      if ($stdin eq "A\n") {
+        print "Ok, I will keep going until it's done.\n";
+        $keepgoing = 0;
+      }
+    }
+  }
+}

uploadNeuroDB/NeuroDB/MRIProcessingUtility.pm

@@ -180,10 +180,10 @@ sub extract_tarchive {
     $dcmdir =~ s/\.tar\.gz$//;
 
     if (defined($seriesuid)) {
-        print "seriesuid: $seriesuid\n";
+        print "seriesuid: $seriesuid\n" if $this->{verbose};
         my @alltarfiles = `cd $this->{TmpDir} ; tar -tzf $dcmtar`;
         $tarnames = getFileNamesfromSeriesUID($seriesuid, @alltarfiles);
-        print "tarnames: $tarnames\n";
+        print "tarnames: $tarnames\n" if $this->{verbose};
     }
 
     `cd $this->{TmpDir} ; tar -xzf $dcmtar $tarnames`;

uploadNeuroDB/minc_insertion.pl

@@ -49,6 +49,7 @@
 my $bypass_extra_file_checks=0;# If you need to bypass the extra_file_checks, set to 1.
 my $acquisitionProtocol;       # Specify the acquisition Protocol also bypasses the checks
 my $acquisitionProtocolID;     # acquisition Protocol id
+my $seriesuid   = undef;          # if you are inserting a specific SeriesUID, the caveat flag will be set.
 my @checks      = ();          # Initialise the array
 my $create_minc_pics    = 0;   # Default is 0, set the option to overide.
 my $globArchiveLocation = 0;   # whether to use strict ArchiveLocation strings
@@ -100,7 +101,9 @@
 
                  ["General options","section"],
                  ["-verbose", "boolean", 1, \$verbose, "Be verbose."],
-
+
+                 ["-seriesuid", "boolean", 1, \$seriesuid, "Inserting by SeriesUID"],
+
                  ["-acquisition_protocol","string", 1, \$acquisitionProtocol,
                   "Suggest the acquisition protocol to use."],
 
@@ -387,7 +390,11 @@
 $file->setFileData('OutputType', 'native');
 $file->setFileData('FileType', 'mnc');
 $file->setFileData('TarchiveSource', $tarchiveInfo{'TarchiveID'});
-$file->setFileData('Caveat', 0);
+if (defined($seriesuid)) {
+    $file->setFileData('Caveat', 1);
+} else {
+    $file->setFileData('Caveat', 0);
+}
 
 ################################################################
 ## Get acquisition protocol (identify the volume) ##############

uploadNeuroDB/tarchiveLoader

@@ -79,7 +79,7 @@ my $no_jiv      = 0;           # Should bet set to 1, if jivs should not be
                                # created
 my $valid_study = 0;
 my $newTarchiveLocation = undef;
-my $seriesuid   = '';          # if you want to insert a specific SeriesUID
+my $seriesuid   = undef;       # if you want to insert a specific SeriesUID
 my $bypass_extra_file_checks=0;# If you need to bypass the extra_file_checks, set to 1.
 my $acquisitionProtocol;       # Specify the acquisition Protocol also bypasses the checks
 my @opt_table = (
@@ -452,6 +452,10 @@ foreach my $minc (@minc_files) {
         $script .= " -verbose";
     }
 
+    if ($seriesuid) {
+        $script .= " -seriesuid";
+    }
+
     if ($acquisitionProtocol) {
         $script .= " -acquisition_protocol " . $acquisitionProtocol;
     }