ExitCodes refactoring so that their number fit in the range 0-255

DTIPrep/DTIPrepRegister.pl

@@ -131,7 +131,7 @@
 my ($protXMLrefs)   = &DTI::readDTIPrepXMLprot($DTIPrepProtocol);
 if (!$protXMLrefs) {
     print LOG "\n\tERROR: DTIPrep XML protocol could not be read.\n";
-    exit $NeuroDB::ExitCodes::UNREADABLE_DTIPREP_PROTOCOL;
+    exit $NeuroDB::ExitCodes::UNREADABLE_FILE;
 }
 
 # 1.b Create a hash containing names of all outputs created by DTIPrep/mincdiffusion pipeline
@@ -151,7 +151,7 @@
 if ((!$mincdiffVersion) && ($DTIrefs->{$dti_file}->{'Postproc'}->{'Tool'} eq "mincdiffusion")) {
     print LOG "\n$Usage\nERROR:\n\tYou must specify which version of "
               . "mincdiffusion tools was used to post-process the DTI.\n";
-    exit $NeuroDB::ExitCodes::NO_MINCDIFFUSION_VERSION;
+    exit $NeuroDB::ExitCodes::MISSING_TOOL_VERSION;
 }
 
 
@@ -168,13 +168,13 @@
 # If $QCed_minc is not defined, means that getFiles returned undef for all output files => ERROR.
 if  (!$QCReport) {
     print LOG "\nERROR:\n\tSome process files are missing in $DTIPrep_subdir.\n";
-    exit $NeuroDB::ExitCodes::MISSING_PREPROCESSED_FILES;
+    exit $NeuroDB::ExitCodes::MISSING_FILES;
 }
 # If $QCed2_step is set, QCed2_minc should be defined in %mri_files hash! 
 if  (($QCed2_step) && (!$mri_files->{'Preproc'}{'QCed2'}{'minc'})) {
     print LOG "\nERROR:\n\tSecondary QCed DTIPrep nrrd & minc outputs are "
               . "missing in $DTIPrep_subdir.\n";
-    exit $NeuroDB::ExitCodes::MISSING_POSTPROCESSED_FILES;
+    exit $NeuroDB::ExitCodes::MISSING_FILES;
 }
 # => If we could pass step 2, then all the files to be registered were found in the filesystem!
 
@@ -191,7 +191,7 @@
                                                     "DTIPrep");
 if (!$registeredXMLprotocolID) {
     print LOG "\nERROR: no XML protocol file was registered in the database\n";
-    exit $NeuroDB::ExitCodes::FILE_REGISTRATION_FAILURE;
+    exit $NeuroDB::ExitCodes::INSERT_FAILURE;
 } else {
     print LOG "\nRegistered XML protocol with ID $registeredXMLprotocolID.\n";
     $mri_files->{'Preproc'}{'QCProt'}{'xml'} = $registeredXMLprotocolID; 
@@ -216,7 +216,7 @@
                                                     $DTIPrepVersion);
 if (!$registeredXMLReportFile) {
     print LOG "\nERROR: no XML report file was registered in the database\n";
-    exit $NeuroDB::ExitCodes::FILE_REGISTRATION_FAILURE;
+    exit $NeuroDB::ExitCodes::INSERT_FAILURE;
 } else {
     print LOG "\nRegistered XML report $registeredXMLReportFile.\n";
     $mri_files->{'Preproc'}{'QCReport'}{'xml'}  = $registeredXMLReportFile;
@@ -239,7 +239,7 @@
                                                      $DTIPrepVersion);
 if (!$registeredQCReportFile) {
     print LOG "\nERROR: no QC report file was registered in the database\n";
-    exit $NeuroDB::ExitCodes::FILE_REGISTRATION_FAILURE;
+    exit $NeuroDB::ExitCodes::INSERT_FAILURE;
 } else {
     print LOG "\nRegistered QC report $registeredQCReportFile.\n";
     $mri_files->{'Preproc'}{'QCReport'}{'txt'}  = $registeredQCReportFile;
@@ -575,7 +575,7 @@ sub register_XMLFile {
     if  (!$toolName)    {
         print STDERR "WARNING: This should not happen as long as the pipeline "
                      . "versioning of DTIPrep is not fixed!";
-        exit $NeuroDB::ExitCodes::NO_TOOL_NAME_VERSION;
+        exit $NeuroDB::ExitCodes::MISSING_TOOL_VERSION;
         # Will need to program this part once DTIPrep fixed!
         #($src_pipeline, $src_tool)=getToolName($XMLFile);
     }else   {
@@ -655,7 +655,7 @@ sub register_QCReport {
     if  (!$toolName)    {
         print STDERR "WARNING: This should not happen as long as the pipeline "
                      . "versioning of DTIPrep is not fixed!";
-        exit $NeuroDB::ExitCodes::NO_TOOL_NAME_VERSION;
+        exit $NeuroDB::ExitCodes::MISSING_TOOL_VERSION;
         # Will need to program this part once DTIPrep fixed!
         #($src_pipeline, $src_tool)=getToolName($QCReport);
     }else   {
@@ -961,7 +961,7 @@ sub getToolName {
                   . "which tool was used manually with the option "
                   . "-DTIPrepVersion or -mincdiffusionVersion as input of the "
                   . "script DTIPrepRegister.pl.";
-        exit $NeuroDB::ExitCodes::NO_TOOL_NAME_VERSION;
+        exit $NeuroDB::ExitCodes::MISSING_TOOL_VERSION;
     }else   {
         #remove leading spaces, trailing spaces and all instances of "
         $src_tool       =~s/"//g;
@@ -1332,7 +1332,7 @@ sub register_nrrd {
     if  (!$toolName)    {
         print STDERR "WARNING: This should not happen as long as the pipeline "
                      . "versioning of DTIPrep is not fixed!";
-        exit $NeuroDB::ExitCodes::NO_TOOL_NAME_VERSION;
+        exit $NeuroDB::ExitCodes::MISSING_TOOL_VERSION;
         # Will need to program this part once DTIPrep fixed!
         #($src_pipeline, $src_tool)=getToolName($XMLFile);
     }else   {

DTIPrep/DTIPrep_pipeline.pl

@@ -83,7 +83,7 @@
                  . "via the path to DTIPrep binary. You need to specify which "
                  . "version of DTIPrep you will be using with -DTIPrepVersion "
                  . "option.\n\n";
-    exit $NeuroDB::ExitCodes::NO_DTIPREP_VERSION;
+    exit $NeuroDB::ExitCodes::MISSING_TOOL_VERSION;
 }
 
 # Establish database connection
@@ -169,14 +169,14 @@
         if (!$mincdiffVersion) {
             print STDERR "\n\tERROR: mincdiffusion tool's version could "
                   . "not be determined.\n\n";
-            exit $NeuroDB::ExitCodes::NO_MINCDIFFUSION_VERSION;
+            exit $NeuroDB::ExitCodes::MISSING_TOOL_VERSION;
         }
         # Exit program if $niak_path is not set
         if  (!$niak_path) {
             print STDERR "\n\tERROR: variable niak_path need to be set in the "
                          . "config file if you plan to use mincdiffusion tools "
                          . "to process the DTI files.\n\n";
-            exit $NeuroDB::ExitCodes::NO_NIAK_PATH;
+            exit $NeuroDB::ExitCodes::INVALID_PATH;
         }
     }
 
@@ -230,7 +230,7 @@
     } else {
         print LOG "\n\tERROR: Post processing tools won't be run for this dataset. \n";
         print LOG "--------------------------------\n";
-        exit $NeuroDB::ExitCodes::NO_POST_PROCESSING_TO_RUN;
+        exit $NeuroDB::ExitCodes::PROGRAM_EXECUTION_FAILURE;
     }
 
 

batch_uploads_imageuploader

@@ -148,7 +148,7 @@ foreach my $input (@resultsarray)
     if (($type ne '.tgz') && ($type ne '.tar.gz') && ($type ne '.zip')) {
 	print STDERR "The file on line $counter is not of type .tgz, tar.gz, or "
                  . ".zip and will not be processed\n";
-	exit $NeuroDB::ExitCodes::UPLOADED_FILE_TYPE_FAILURE;
+	exit $NeuroDB::ExitCodes::FILE_TYPE_CHECK_FAILURE;
     }
     if (($phantom eq '') || (($phantom ne 'N') && ($phantom ne 'Y'))) {
 	print STDERR "Make sure the Phantom entry is filled out "
@@ -167,7 +167,7 @@ foreach my $input (@resultsarray)
         if ($patientname ne '') {
        	    print STDERR "Please leave the patient name blank for phantom "
        	                 . "entries\n";
-	        exit $NeuroDB::ExitCodes::PNAME_PHANTOM_MISMATCH;
+	        exit $NeuroDB::ExitCodes::PNAME_FILENAME_MISMATCH;
 	}
 	else {
 	    $patientname = 'NULL';

dicom-archive/dicomTar.pl

@@ -98,7 +98,7 @@
     $targetlocation =~ s/^(.*)\/$/$1/;
 } else {
     print STDERR "\nERROR: source and target must be existing directories!\n\n";
-    exit $NeuroDB::ExitCodes::ARG_FILE_DOES_NOT_EXIST;
+    exit $NeuroDB::ExitCodes::INVALID_PATH;
 }
 
 # The tar target 
@@ -220,7 +220,7 @@
         print "\nDone adding archive info into database\n" if $verbose;
     } else {
         print STDERR "\nThe database command failed\n";
-        exit $NeuroDB::ExitCodes::TARCHIVE_INSERT_FAILURE;
+        exit $NeuroDB::ExitCodes::INSERT_FAILURE;
     }
 }
 
@@ -232,7 +232,7 @@
     my $output = system($script);
     if ($output!=0)  {
         print STDERR "\n\tERROR: the script updateMRI_Upload.pl has failed\n\n";
-        exit $NeuroDB::ExitCodes::UPDATE_MRI_UPLOAD_FAILURE;
+        exit $NeuroDB::ExitCodes::UPDATE_FAILURE;
     }
 }
 

dicom-archive/updateMRI_Upload.pl

@@ -102,7 +102,7 @@
 unless (-e $tarchive) {
     print STDERR "\nERROR: Could not find archive $tarchive.\n"
                  . "Please, make sure the path to the archive is valid.\n\n";
-    exit $NeuroDB::ExitCodes::ARG_FILE_DOES_NOT_EXIST;
+    exit $NeuroDB::ExitCodes::INVALID_PATH;
 }
 
 ################################################################
@@ -111,7 +111,7 @@
 unless (-e $source_location) {
     print STDERR "\nERROR: Could not find sourcelocation $source_location\n"
                  . "Please, make sure the sourcelocation is valid.\n\n";
-    exit $NeuroDB::ExitCodes::ARG_FILE_DOES_NOT_EXIST;
+    exit $NeuroDB::ExitCodes::INVALID_PATH;
 }
 ################################################################
 #####establish database connection if database option is set####
@@ -154,7 +154,7 @@
 my $count = $sth->fetchrow_array;
 if($count>0) {
    print STDERR "\n\tERROR: the tarchive is already uploaded \n\n";
-   exit $NeuroDB::ExitCodes::TARCHIVE_ALREADY_UPLOADED;
+   exit $NeuroDB::ExitCodes::FILE_NOT_UNIQUE;
 } 
 
 

docs/scripts_md/ExitCodes.md

@@ -29,41 +29,37 @@ input error checking and setting failures). Note that not all of the possible
 exit codes are used by each script, giving some room to add some later on if
 needed.
 
-Below is a list of the possible exit codes organized per script:
+Below is a list of the possible exit codes:
 
-1\. Common exit codes to most insertion scripts (exit codes from 0 to 19, 0 =
-exit script with success status)
+\##### ---- SECTION 1:  EXIT CODES COMMON TO MOST IMAGING INSERTION SCRIPTS
 
-2\. Exit codes from batch\_uploads\_imageuploader (exit codes from 20 to 39)
+1\. Success: exit code = 0 upon success.
 
-3\. Exit codes from batch\_uploads\_tarchive (no exit codes available yet, exit
-codes will be from 40 to 59)
+2\. Common input error checking and setting failures (exit codes from 1 to 19)
 
-4\. Exit codes from dicom-archive/dicomTar.pl (exit codes from 60 to 79)
+3\. Common database related failures (exit codes from 20 to 39)
 
-5\. Exit codes from dicom-archive/updateMRI\_upload (exit codes from 80 to 99)
+4\. Common configuration failures (exit codes from 40 to 59)
 
-6\. Exit codes from DTIPrep/DTIPrep\_pipeline.pl (exit codes from 100 to 119)
+5\. Common file manipulation failures (exit codes from 60 to 79)
 
-7\. Exit codes from DTIPrep/DTIPrepRegister.pl (exit codes from 120 to 139)
+6\. Common other generic failures (exit codes from 80 to 149)
 
-8\. Exit codes from uploadNeuroDB/imaging\_upload\_file.pl (exit codes from 140
-to 159)
+\##### ---- SECTION 2: SCRIPT SPECIFIC EXIT CODES NOT COVERED IN SECTION 1
 
-9\. Exit codes from uploadNeuroDB/NeuroDB/ImagingUpload.pm (exit codes from 160
-to 179)
+7\. Exit codes from batch\_uploads\_imageuploader (exit codes from 150 to 159)
 
-10\. Exit codes from uploadNeuroDB/NeuroDB/MRIProcessingUtility.pm (exit codes
- from 180 to 199)
+8\. Exit codes from DTIPrep/DTIPrepRegister.pl (exit codes from 160 to 169)
 
-11\. Exit codes from uploadNeuroDB/minc\_deletion.pl (exit codes from 200 to 219)
+9\. Exit codes from uploadNeuroDB/NeuroDB/ImagingUpload.pm (exit codes from
+170 to 179)
 
-12\. Exit codes from uploadNeuroDB/minc\_insertion.pl (exit codes from 220 to 239)
+11\. Exit codes from uploadNeuroDB/minc\_insertion.pl (exit codes from 180 to 189)
 
-13\. Exit codes from uploadNeuroDB/register\_processed\_data.pl (exit codes from
-240 to 259)
+12\. Exit codes from uploadNeuroDB/tarchiveLoader (exit codes from 190 to 199)
 
-14\. Exit codes from uploadNeuroDB/tarchiveLoader (exit codes from 260 to 279)
+13\. Exit codes from uploadNeuroDB/NeuroDB/bin/minc2jiv.pl (exit codes from 200
+to 210)
 
 # LICENSING