Command Line Tool to obtain FileID of inserted mincs using a lists of SeriesUID as STDIN

tools/seriesuid2fileid

@@ -0,0 +1,142 @@
+#!/usr/bin/perl
+use strict;
+use warnings;
+no warnings 'once';
+use Data::Dumper;
+use File::Basename;
+use Term::ANSIColor qw(:constants);
+use NeuroDB::DBI;
+
+my $Help = <<HELP;
+*******************************************************************************
+SeriesUID 2 fileID
+*******************************************************************************
+
+Author  :   Gregory Luneau
+Date    :   October 2016
+Version :   1
+
+
+The program does the following:
+
+Takes SeriesUID from STDIN and returns a report with
+
+- SeriesUID
+- SeriesDescription
+- TarchiveID
+- m_p_v_s_ID
+- mri_v_log
+- FileID
+- FileName
+
+There are no arguments so far.
+
+HELP
+
+{ package Settings; do "$ENV{LORIS_CONFIG}/.loris_mri/prod" }
+my $dbh = &NeuroDB::DBI::connect_to_db(@Settings::db);
+
+my $queryF = "SELECT * FROM files as f WHERE f.SeriesUID=?";
+my $queryT = "SELECT * FROM tarchive_series as t LEFT JOIN tarchive as a USING (TarchiveID) WHERE t.SeriesUID=?";
+my $queryM = "SELECT * FROM mri_protocol_violated_scans as m WHERE m.SeriesUID=? OR (m.PatientName=? AND m.series_description=?)";
+my $queryV = "SELECT * FROM mri_violations_log as v WHERE v.SeriesUID=?";
+my $queryP = "SELECT (SELECT pf.`VALUE` FROM parameter_file AS pf WHERE pf.FileID=? AND pf.ParameterTypeID=(SELECT p.ParameterTypeID FROM parameter_type as p WHERE p.Name='xspace')) AS xspace, (SELECT pf.`VALUE` FROM parameter_file AS pf WHERE pf.FileID=? AND pf.ParameterTypeID=(SELECT p.ParameterTypeID FROM parameter_type as p WHERE p.Name='zspace')) AS zspace, IFNULL((SELECT pf.`VALUE` FROM parameter_file AS pf WHERE pf.FileID=? AND pf.ParameterTypeID=(SELECT p.ParameterTypeID FROM parameter_type as p WHERE p.Name='time')), 1) as time";
+
+my $sthF = $dbh->prepare($queryF);
+my $sthT = $dbh->prepare($queryT);
+my $sthM = $dbh->prepare($queryM);
+my $sthV = $dbh->prepare($queryV);
+my $sthP = $dbh->prepare($queryP);
+
+my ($rF, $rT, $rM, $rV, $rP);
+my ($fF, $fT, $fM, $fV, $fP);
+
+my ($SeriesDescription, $TarchiveID, $FileID, $ID, $Severity, $PatientName, $NumberOfFiles, $ZxT, $FileName);
+
+printf ("%-6s", '| L# ');
+printf ("%-64s",'| SeriesUID');
+printf ("%-36s",'| SeriesDescription');
+printf ("%-16s",'| TarchiveID');
+printf ("%-13s",'| m_p_v_s_ID');
+printf ("%-12s",'| mri_v_log');
+printf ("%-16s",'| FileID');
+printf ("%-36s",'| FileName');
+
+print "|\n";
+
+while (<STDIN>) {
+
+  chomp($_);
+
+  $rF = $sthF->execute($_);
+  $fF = $sthF->fetchrow_hashref();
+
+  $rT = $sthT->execute($_);
+  $fT = $sthT->fetchrow_hashref();
+
+  $rV = $sthV->execute($_);
+  $fV = $sthV->fetchrow_hashref();
+
+  #print Dumper($f);
+
+  if ($sthT->rows > 0) {
+    $SeriesDescription = $fT->{'SeriesDescription'};
+    $TarchiveID        = $fT->{'TarchiveID'};
+    $PatientName       = $fT->{'PatientName'};
+    $NumberOfFiles     = ' (' . $fT->{'NumberOfFiles'} . ')';
+  } else {
+    $SeriesDescription = '';
+    $TarchiveID        = '';
+    $NumberOfFiles     = '';
+  }
+
+  $rM = $sthM->execute($_, $PatientName, $SeriesDescription);
+  $fM = $sthM->fetchrow_hashref();
+
+  if ($sthM->rows > 0) {
+    $ID = $fM->{'ID'} . " (" . $sthM->rows . ")";
+  } else {
+    $ID = '';
+  }
+
+  if ($sthF->rows > 0) {
+    $FileID = $fF->{'FileID'};
+    $FileName = basename($fF->{'File'});
+    $rP = $sthP->execute($FileID, $FileID, $FileID);
+    $fP = $sthP->fetchrow_hashref();
+
+    if ($sthP->rows > 0) {
+      $ZxT = ' (' . $fP->{'zspace'} * $fP->{'time'} . ')';
+      # $ZxT = ' (' . $fP->{'xspace'} * $fP->{'time'} . ')';
+    } else {
+      $ZxT = '';
+    }
+  } elsif (index($SeriesDescription, "localizer") != -1) {
+    $FileID = 'exclude';
+    $ZxT = '';
+    $FileName = '';
+  } else {
+    $FileID = '';
+    $ZxT = '';
+    $FileName = '';
+  }
+
+  if ($sthV->rows > 0) {
+    $Severity = $fV->{'Severity'};
+  } else {
+    $Severity = '';
+  }
+
+#  print "$.,$_,$SeriesDescription,$TarchiveID,$FileID\n";
+
+  printf ("%-6s", '| '. $.);
+  printf ("%-64s",'| '. $_);
+  printf ("%-36s",'| '. $SeriesDescription);
+  printf ("%-16s",'| '. $TarchiveID . $NumberOfFiles);
+  printf ("%-13s",'| '. $ID);
+  printf ("%-12s",'| '. $Severity);
+  printf ("%-16s",'| '. $FileID . $ZxT);
+  printf ("%-36s",'| '. $FileName);
+  print  "|\n";
+
+}