Added option to also re-insert deleted minc files (Same as PR#179)

tools/example_scripts/README.md

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+### Example scripts
+
+ - **deletemincsqlwrapper.pl**
+   - An example script to delete multiple minc files fitting a common criterion from the database. 
+   - The script also provides the option to re-insert deleted scans with their seriesUID when using the `-insertminc` flag.
+   - **Projects should modify the query as needed to suit their needs**. 
+   - For the example query provided (in `$queryF`), all inserted scans with types like `t1` or `t2`, having a `slice thickness` in the range of `4 mm` will be deleted.
+      - A use case of this deletion query might be that initially the project did not exclude `t1` or `t2` modalities having 4 mm slice thickness, and subsequently, the
+        study `mri_protocol` has been changed to add tighter checks on slice thickness.  
+
+

tools/example_scripts/deletemincsqlwrapper.pl

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+#!/usr/bin/perl
+use strict;
+use warnings;
+use Getopt::Tabular;
+no warnings 'once';
+use Data::Dumper;
+use File::Basename;
+use File::Copy;
+use Term::ANSIColor qw(:constants);
+use NeuroDB::DBI;
+
+my $profile = undef;
+my $insertminc;
+
+my @opt_table           = (
+    [ "Basic options", "section" ],
+    [
+        "-profile", "string", 1, \$profile,
+        "name of config file in ../../dicom-archive/.loris_mri"
+    ],
+    [   
+         "-insertminc", "boolean", 0, \$insertminc, "Re-insert the deleted minc"
+    ]
+);
+
+my $Help = <<HELP;
+******************************************************************************
+Wrapper to minc_deletion.pl for bulk deletion based on a SQL customisable Query
+******************************************************************************
+
+This script is a wrapper for deleting multiple mincs at a time and optionally 
+re-inserting them.
+
+It will pause before for confirmation before deleting.
+
+Please note that this is an example script. Projects need to customize the query
+based on their needs. Please refer to the README in the tools/example_scripts/ 
+directory for more details.
+
+HELP
+
+my $Usage = <<USAGE;
+usage: tools/example_scripts/deletemincsqlwrapper.pl -profile prod
+       $0 -help to list options
+USAGE
+&Getopt::Tabular::SetHelp( $Help, $Usage );
+&Getopt::Tabular::GetOptions( \@opt_table, \@ARGV ) || exit 1;
+
+{ package Settings; do "$ENV{LORIS_CONFIG}/.loris_mri/" . $profile}
+my $dbh = &NeuroDB::DBI::connect_to_db(@Settings::db);
+
+
+
+# Only the f.SeriesUID is really needed for minc_deletion, other fields are for information only
+# If you plan to re-insert, you'll also need ArchiveLocation
+my $queryF = <<SQL;
+  SELECT DISTINCT f.fileid, f.SeriesUID, f.SessionID, f.file, t.ArchiveLocation, FROM_UNIXTIME(f.InsertTime), p.Value, q.QCStatus, c.Alias, m.Scan_type
+  FROM files AS f
+  LEFT JOIN parameter_file AS p using (FileID)
+  LEFT JOIN parameter_type AS pt using (ParameterTypeID)
+  LEFT JOIN files_qcstatus AS q using (FileID)
+  LEFT JOIN session AS s ON (f.SessionID=s.ID)
+  LEFT JOIN psc AS c ON (c.CenterID=s.CenterID)
+  LEFT JOIN mri_scan_type AS m ON (m.ID=f.AcquisitionProtocolID)
+  LEFT JOIN tarchive AS t ON f.TarchiveSource=t.TarchiveID
+  WHERE pt.Name = 'acquisition:slice_thickness'
+  AND p.Value LIKE '%4.%'
+  AND (m.Scan_type LIKE '%t1%' OR m.Scan_type LIKE '%t2%')
+  ORDER BY FROM_UNIXTIME(f.InsertTime)
+SQL
+
+
+my $sthF = $dbh->prepare($queryF);
+
+my $keepgoing = 1;
+my ($fF, $stdin, $i);
+
+printf ("%-6s", '| L# ');
+printf ("%-64s",'| SeriesUID');
+printf ("%-20s",'| Value');
+printf ("%-20s",'| Scan Type');
+printf ("%-60s",'| File');
+print "|\n";
+
+$sthF->execute();
+
+if ($sthF->rows > 0) {
+
+  while ($fF = $sthF->fetchrow_hashref()) {
+
+    $i++;
+
+    printf ("%-6s", '| '. $i);
+    printf ("%-64s",'| '. $fF->{'SeriesUID'});
+    printf ("%-20s",'| '. $fF->{'Value'});
+    printf ("%-20s",'| '. $fF->{'Scan_type'});
+    printf ("%-60s",'| '. $fF->{'file'});
+    print  "|\n";
+
+    if ($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;
+      }
+    }
+
+    my $minc_delete_cmd = "uploadNeuroDB/minc_deletion.pl -profile " . $profile . " -seriesuid " . $fF->{'SeriesUID'} . " confirm";
+    print $minc_delete_cmd . "\n";
+    my $minc_delete_log = `$minc_delete_cmd`;
+    print $minc_delete_log . "\n";
+
+    if ($insertminc) {
+      # Running tarchiveLoader on the archived tar as a whole will only insert new minc files that are not already in the files table 
+      my $tar_loader_cmd  = "uploadNeuroDB/tarchiveLoader -profile " . $profile . " -verbose -globLocation " . $fF->{'ArchiveLocation'};
+      print $tar_loader_cmd . "\n";
+      my $tar_loader_log  = `$tar_loader_cmd`;
+      print $tar_loader_log . "\n";
+    }
+  }
+} else {
+    print "\n***No files were found that match the following query:***\n\n" . $queryF . "\n";
+}