Batch upload and insertion of scans for projects not using the front-end imaging uploader

batch_uploads_imageuploader

@@ -0,0 +1,129 @@
+#!/usr/bin/perl -w
+use strict;
+use warnings;
+use File::Basename;
+use Getopt::Tabular;
+
+my $profile   = undef;
+my ($debug, $verbose) = (0,1);
+my $stdout = '';
+my $stderr = '';
+
+my @opt_table           = (
+    [ "Basic options", "section" ],
+    [
+        "-profile", "string", 1, \$profile,
+        "name of config file in ../dicom-archive/.loris_mri"
+    ],
+    ["-verbose", "boolean", 1,   \$verbose, "Be verbose."]
+);
+
+&Getopt::Tabular::GetOptions( \@opt_table, \@ARGV ) || exit 1;
+
+#####Get config setting#######################################################
+{ package Settings; do "$ENV{LORIS_CONFIG}/.loris_mri/$profile" }
+##############################################################################
+
+my ($stdoutbase, $stderrbase) = ("$Settings::data_dir/batch_output/imuploadstdout.log", "$Settings::data_dir/batch_output/imuploadstderr.log");
+
+
+
+while($_ = $ARGV[0], /^-/) {
+    shift;
+    last if /^--$/; ## -- ends argument processing
+    if (/^-D/) { $debug++ } ## debug level
+    if (/^-v/) { $verbose++ } ## verbosity
+}
+
+
+## read input from STDIN, store into array @inputs (`find ....... | this_script`)
+my @linearray = ();
+my @resultsarray = ();
+my @patientname = ();
+my @patientnamearray = ();
+my @fullpath = ();
+my @fullpatharray = ();
+my @phantom = ();
+my @phantomarray = ();
+my @submitted = ();
+
+my $counter = 0;
+
+while(my $line = <STDIN>)
+{
+    chomp $line;
+    my @linearray = split(" " , $line);
+    push (@resultsarray, @linearray);
+    @patientname = $linearray[0];
+    @fullpath = $linearray[1];
+    @phantom = $linearray[2];
+    push (@patientnamearray, @patientname);
+    push (@fullpatharray, @fullpath);
+    push (@phantomarray, @phantom);
+}
+close STDIN;
+
+## foreach series, batch magic
+foreach my $input (@resultsarray)
+{
+    $counter++;
+    $stdout = $stdoutbase.$counter;
+    $stderr = $stderrbase.$counter;
+
+    #$stdout = '/dev/null';
+    #$stderr = '/dev/null';
+
+    my $patientname = $patientnamearray[$counter-1];
+    my $fullpath = $fullpatharray[$counter-1];
+    my $phantom = $phantomarray[$counter-1];
+
+    ## Ensure that 
+    ## 1) the uploaded file is of type .tgz or .tar.gz or .zip
+    ## 2) the patient name and path entries are identical; this mimics the imaging uploader in the front-end
+    ## 3) check that input file provides phantom details (Y for phantom, N for real candidates)
+    my ($base,$path,$type) = fileparse($fullpath, qr{\..*});
+    if (($type ne '.tgz') && ($type ne '.tar.gz') && ($type ne '.zip')) {
+	print "The file on line $counter is not of type .tgz, tar.gz, or .zip and will not be processed\n";
+	exit(1);
+    }
+    if ($base ne $patientname) {
+	print "Make sure the patient name $patientname " .
+	      "matches the file name $base in $path\n";
+	exit(2);
+    }
+    if (($phantom eq '') || ($phantom ne 'N') || ($phantom eq 'Y')) {
+	print "Make sure the Phantom entry is filled out " .
+	      "with Y if the scan if for a phantom, and N otherwise\n";
+	exit(3);
+    }
+
+    ## this is where the subprocesses are created...  should basically run processor script with study directory as argument.
+    ## processor will do all the real magic
+
+    my $command = "$Settings::bin_dir/uploadNeuroDB/imaging_upload_file.pl "
+		. "-profile $profile -phantom $phantom -patient_name $patientname $fullpath";
+    if ($verbose) {
+        $command .= " -verbose";
+    }
+
+    ##if qsub is enabled use it
+    if ($Settings::is_qsub) {
+	     open QSUB, "| qsub -V -e $stderr -o $stdout -N process_imageuploader_${counter}";
+    	 print QSUB $command;
+    	 close QSUB;
+    }
+    ##if qsub is not enabled
+    else {
+         system($command);
+    }
+
+     push @submitted, $input;
+}
+open MAIL, "|mail $Settings::mail_user";
+print MAIL "Subject: BATCH_UPLOADS_IMAGEUPLOADER: ".scalar(@submitted)." studies submitted.\n";
+print MAIL join("\n", @submitted)."\n";
+close MAIL;
+
+## exit 0 for find to consider this -cmd true (in case we ever run it that way...)
+exit(0);
+

uploadNeuroDB/imaging_upload_file.pl

@@ -28,9 +28,12 @@
                 $year + 1900,
                 $mon + 1, $mday, $hour, $min, $sec
               );
-my $profile = undef;    # this should never be set unless you are in a
+my $profile   = undef;    # this should never be set unless you are in a
                         # stable production environment
 my $upload_id = undef;         # The uploadID
+my $phantom   = undef;         # Y if Phantom
+my $patient_name_batch = undef;         # Patient Name as obtained from batch upload
+my $pname = undef;         
 my $template  = "ImagingUpload-$hour-$min-XXXXXX";    # for tempdir
 my $TmpDir_decompressed_folder =
      tempdir( $template, TMPDIR => 1, CLEANUP => 1 );
@@ -52,6 +55,16 @@
         "-upload_id", "string", 1, \$upload_id,
         "The uploadID of the given scan uploaded"
     ],
+    [
+        "-patient_name_batch", "string", 1, \$patient_name_batch,
+        "The patient name; needed only when using batch_upload_imaguploader"
+    ],
+    [
+        "-phantom", "string", 1, \$phantom,
+        "Y for phantom and N for real study participants; " .
+	" needed only when using batch_upload_imaguploader"
+
+    ],
     ["-verbose", "boolean", 1,   \$verbose, "Be verbose."],
     [ "Advanced options", "section" ],
     [ "Fancy options", "section" ]
@@ -109,10 +122,14 @@
     exit 3;
 }
 
-if ( !$upload_id ) {
-    print $Help;
-    print "$Usage\n\tERROR: The Upload_id is missing \n\n";
-    exit 4;
+# check if patient name is provided in case of no upload_id; 
+# expected when script is called from batch_upload_imageuploader 
+if ( !$upload_id ) { 
+    if (!$patient_name_batch) { 
+        print $Help;
+        print "$Usage\n\tERROR: No upload_id or patient name provided \n\n";
+        exit 4;
+    }
 }
 
 $uploaded_file = abs_path( $ARGV[0] );
@@ -158,7 +175,30 @@
 ############### Get Patient_name using UploadID#################
 ################################################################
 ################################################################
-my $pname = getPnameUsingUploadID($upload_id);
+if (!$patient_name_batch) { 
+    $pname = getPnameUsingUploadID($upload_id);
+}
+else {
+    $pname = $patient_name_batch;
+}
+
+################################################################
+############# For entries coming from batch_upload #############
+########### Created entries into the mri_upload table ##########
+################################################################
+if ($patient_name_batch) {
+    if (!$phantom) {
+        print "Please ensure that entries from " .
+              "batch_upload_imageuploader contain " .
+	      "a Y or N for phantoms or no phantoms, ".
+	      "respectively\n";
+    } 
+    else {
+         $upload_id = insertIntoMRIUpload($patient_name_batch, 
+				          $phantom, 
+				          $uploaded_file);
+    }
+}
 
 ################################################################
 ################ ImagingUpload  Object #########################
@@ -280,6 +320,47 @@ sub getPnameUsingUploadID {
     return $patient_name;
 }
 
+################################################################
+############### insertIntoMRIUpload ############################
+################################################################
+=pod
+insertIntoMRIUpload()
+Description:
+  - Insert into the mri_upload table entries for data coming 
+    from batch_upload_imageuploader
+
+Arguments:
+  $patient_name_batch: The patient name
+  $phantom : 'Y' if the entry is for a phantom, and 'N' othwrwose
+  $uploaded_file: Path to the uploaded file
+
+  Returns: $upload_id : The Upload ID
+=cut
+
+
+sub insertIntoMRIUpload {
+
+    my ( $patient_name_batch, $phantom, $uploaded_file ) = @_;
+    my $User = `whoami`;
+
+    my $query = "INSERT INTO mri_upload ".
+      		"(UploadedBy, UploadDate, PatientName, ".
+		"IsPhantom, UploadLocation) ".
+    		"VALUES (?, now(), ?, ?, ?)";
+    my $mri_upload_insert = $dbh->prepare($query);
+    $mri_upload_insert->execute($User,$patient_name_batch,
+				$phantom, $uploaded_file);
+
+    my $where = " WHERE mu.UploadLocation =?";
+    $query = "SELECT mu.UploadID FROM mri_upload mu";
+    $query .= $where;
+    my $sth = $dbh->prepare($query);
+    $sth->execute($uploaded_file);
+    my $upload_id = $sth->fetchrow_array;
+
+    return $upload_id;
+}
+
 ################################################################
 ############### spool()#########################################
 ################################################################