[Moose] ConfigOB - grepping the boolean config settings using ConfigOB

batch_uploads_imageuploader.pl

@@ -153,13 +153,7 @@ =head2 Methods
 my $data_dir  = $configOB->getDataDirPath();
 my $mail_user = $configOB->getMailUser();
 my $bin_dir   = $configOB->getMriCodePath();
-
-
-# -----------------------------------------------------------------
-## Get config setting using the old database calls
-# -----------------------------------------------------------------
-
-my $is_qsub   = &NeuroDB::DBI::getConfigSetting(\$dbh, 'is_qsub');
+my $is_qsub   = $configOB->getIsQsub();
 
 
 

batch_uploads_tarchive.pl

@@ -185,14 +185,9 @@ =head1 AUTHORS
 my $data_dir           = $configOB->getDataDirPath();
 my $tarchiveLibraryDir = $configOB->getTarchiveLibraryDir();
 my $mail_user          = $configOB->getMailUser();
+my $is_qsub            = $configOB->getIsQsub();
 
 
-# -----------------------------------------------------------------
-## Get config setting using the old database calls
-# -----------------------------------------------------------------
-
-my $is_qsub = &NeuroDB::DBI::getConfigSetting(\$dbh, 'is_qsub');
-
 
 # define project space
 my ($debug) = (0);

docs/scripts_md/ConfigOB.md

@@ -71,12 +71,129 @@ INPUT: name of the setting to fetch.
 RETURN: the setting value (as a string). If the setting value is NULL, then this
          method will return `undef`.
 
+### &$getBoolean($value)
+
+Private method. This methods returns 1 if a boolean value is set to either 'true'
+or '1'; 0 otherwise. This ensures harmonization of the boolean settings.
+
+INPUT: boolean value extracted from the Config table
+
+RETURN: 1 if the value provided is 'true' or '1'; 0 otherwise
+
 ### getTarchiveLibraryDir()
 
 Gets the tarchive library dir.
 
 RETURN: value (string) of the tarchive library dir in the Config table.
 
+### getDataDirPath()
+
+Get the data directory path.
+
+RETURN: value (sting) of the data directory path in the Config table.
+
+### getMriCodePath()
+
+Get the MRI code path.
+
+RETURN: value (string) of the MRI code path in the Config table.
+
+### getNiakPath()
+
+Get the NIAK package path.
+
+RETURN: value (string) of the NIAK package path in the Config table.
+
+### getMailUser()
+
+Get the mail user.
+
+RETURN: value (string) of the mail user in the Config table.
+
+### getPrefix()
+
+Get the study prefix.
+
+RETURN: value (string) of the study prefix in the Config table.
+
+### getDtiVolumes()
+
+Get the number of DTI volumes.
+
+RETURN: value (string) of the number of DTI volumes in the Config table.
+
+### getT1ScanType()
+
+Get the T1 scan type.
+
+RETURN: value (string) of the T1 scan type in the Config table.
+
+### getQced2Step()
+
+Get the QCed2 step dataset name.
+
+RETURN: value (string) of the QCed2 step dataset name in the Config table.
+
+### getDicomInfo()
+
+Get the get\_dicom\_info.pl path.
+
+RETURN: value (string) of the get\_dicom\_info.pl path in the Config table.
+
+### getConverter()
+
+Get the converter name.
+
+RETURN: value (string) of the converter name in the Config table.
+
+### getLookupCenterNameUsing()
+
+Get the lookup center name using.
+
+RETURN: value (string) of the lookup center name using in the Config table.
+
+### getDefacingRefScanType()
+
+Get the defacing reference scan type.
+
+RETURN: value (string) of the defacing reference scan type in the Config table.
+
+### getLegoPhantomRegex()
+
+Get the lego phantom regular expression.
+
+RETURN: value (string) of the lego phantom regular expression in the Config table.
+
+### getLivingPhantomRegex()
+
+Get the living phantom regular expression.
+
+RETURN: value (string) of the living phantom regular expression in the Config table.
+
+### getCreateNii()
+
+Get the create\_nii Config setting.
+
+RETURN: (boolean) 1 if create\_nii is set to Yes in the Config module, 0 otherwise
+
+### getHorizontalPics()
+
+Get the horizontalPics Config setting.
+
+RETURN: (boolean) 1 if horizontalPics is set to Yes in the Config module, 0 otherwise
+
+### getIsQsub()
+
+Get the is\_qsub Config setting.
+
+RETURN: (boolean) 1 if is\_qsub is set to Yes in the Config module, 0 otherwise
+
+### getCreateCandidates()
+
+Get the createCandidates Config setting.
+
+RETURN: (boolean) 1 if createCandidates is set to Yes in the Config module, 0 otherwise
+
 # TO DO
 
 Nothing planned.
@@ -91,5 +208,5 @@ License: GPLv3
 
 # AUTHORS
 
-LORIS community <loris.info@mcin.ca> and McGill Centre for Integrative
+LORIS community <loris.info@mcin.ca> and McGill Centre for Integrative
 Neuroscience

tools/batch_run_defacing_script.pl

@@ -144,13 +144,7 @@ =head1 AUTHORS
 my $data_dir  = $configOB->getDataDirPath();
 my $mail_user = $configOB->getMailUser();
 my $bin_dir   = $configOB->getMriCodePath();
-
-
-# -----------------------------------------------------------------
-## Get config setting using the old database calls
-# -----------------------------------------------------------------
-
-my $is_qsub   = &NeuroDB::DBI::getConfigSetting(\$dbh, 'is_qsub');
+my $is_qsub   = $configOB->getIsQsub();
 
 
 

tools/batch_run_pipeline_qc_face_script.pl

@@ -157,13 +157,7 @@ =head1 AUTHORS
 my $data_dir  = $configOB->getDataDirPath();
 my $mail_user = $configOB->getMailUser();
 my $bin_dir   = $configOB->getMriCodePath();
-
-
-# -----------------------------------------------------------------
-## Get config setting using the old database calls
-# -----------------------------------------------------------------
-
-my $is_qsub   = &NeuroDB::DBI::getConfigSetting(\$dbh, 'is_qsub');
+my $is_qsub   = $configOB->getIsQsub();
 
 
 

tools/create_nifti_bval_bvec.pl

@@ -143,15 +143,10 @@ =head1 AUTHORS
 
 my $configOB = NeuroDB::objectBroker::ConfigOB->new(db => $db);
 
-my $data_dir  = $configOB->getDataDirPath();
+my $data_dir   = $configOB->getDataDirPath();
+my $create_nii = $configOB->getCreateNii();
 
 
-# -----------------------------------------------------------------
-## Get config setting using the old database calls
-# -----------------------------------------------------------------
-
-my $create_nii = NeuroDB::DBI::getConfigSetting(\$dbh, 'create_nii');
-
 
 
 ## exit if create_nii is set to No

uploadNeuroDB/NeuroDB/MRIProcessingUtility.pm

@@ -498,7 +498,7 @@ sub determinePSC {
     # ----------------------------------------------------------------
     ## Get config settings using ConfigOB
     # ----------------------------------------------------------------
-    my $configOB              = $this->{configOB};
+    my $configOB              = $this->{'configOB'};
     my $lookupCenterNameUsing = $configOB->getLookupCenterNameUsing();
 
 
@@ -1175,7 +1175,7 @@ sub registerScanIntoDB {
     # ----------------------------------------------------------------
     ## Get config settings using ConfigOB
     # ----------------------------------------------------------------
-    my $configOB = $this->{configOB};
+    my $configOB = $this->{'configOB'};
     my $data_dir = $configOB->getDataDirPath();
     my $prefix   = $configOB->getPrefix();
 
@@ -1506,7 +1506,7 @@ sub moveAndUpdateTarchive {
     # ----------------------------------------------------------------
     ## Get config settings using ConfigOB
     # ----------------------------------------------------------------
-    my $configOB = $this->{configOB};
+    my $configOB = $this->{'configOB'};
     my $tarchivePath = $configOB->getTarchiveLibraryDir();
 
 
@@ -1585,15 +1585,18 @@ sub CreateMRICandidates {
         $sex = "Male";
     }
 
+    # ----------------------------------------------------------------
+    ## Get the createCandidates config settings using ConfigOB
+    # ----------------------------------------------------------------
+    my $configOB = $this->{'configOB'};
+    my $createCandidates = $configOB->getCreateCandidates();
+
     ################################################################
     ## Create non-existent candidate if the profile allows for #####
     ## Candidate creation ##########################################
     ################################################################
-    if (!NeuroDB::MRI::subjectIDExists(
-            $subjectIDsref->{'CandID'},
-            $this->{dbhr}
-        ) 
-        && (NeuroDB::DBI::getConfigSetting($this->{dbhr},'createCandidates'))
+    if (!NeuroDB::MRI::subjectIDExists($subjectIDsref->{'CandID'}, $this->{dbhr})
+        && ($createCandidates)
     ) {
            chomp($User);
             unless ($subjectIDsref->{'CandID'}) {
@@ -1888,7 +1891,7 @@ sub computeSNR {
     # ----------------------------------------------------------------
     ## Get config settings using ConfigOB
     # ----------------------------------------------------------------
-    my $configOB = $this->{configOB};
+    my $configOB = $this->{'configOB'};
     my $data_dir = $configOB->getDataDirPath();
 
     my $modalities = NeuroDB::DBI::getConfigSetting(

uploadNeuroDB/NeuroDB/objectBroker/ConfigOB.pm

@@ -81,6 +81,10 @@ use constant LOOK_UP_CENTER_NAME_USING => 'lookupCenterNameUsing';
 use constant DEFACING_REF_SCAN_TYPE    => 'reference_scan_type_for_defacing';
 use constant LEGO_PHANTOM_REGEX        => 'LegoPhantomRegex';
 use constant LIVING_PHANTOM_REGEX      => 'LivingPhantomRegex';
+use constant CREATE_NII                => 'create_nii';
+use constant HORIZONTAL_PICS           => 'horizontalPics';
+use constant IS_QSUB                   => 'is_qsub';
+use constant CREATE_CANDIDATES         => 'createCandidates';
 
 =pod
 
@@ -139,6 +143,23 @@ my $getConfigSettingRef = sub {
     return $result->[0]->{'value'};
 };
 
+
+=head3 &$getBoolean($value)
+
+Private method. This methods returns 1 if a boolean value is set to either 'true'
+or '1'; 0 otherwise. This ensures harmonization of the boolean settings.
+
+INPUT: boolean value extracted from the Config table
+
+RETURN: 1 if the value provided is 'true' or '1'; 0 otherwise
+
+=cut
+my $getBoolean = sub {
+    my ($value) = @_;
+
+    return ($value eq "true" || $value == 1) ? 1 : 0;
+};
+
 =head3 getTarchiveLibraryDir()
 
 Gets the tarchive library dir.
@@ -348,6 +369,66 @@ sub getLivingPhantomRegex {
     return &$getConfigSettingRef($self, LIVING_PHANTOM_REGEX);
 }
 
+=head3 getCreateNii()
+
+Get the create_nii Config setting.
+
+RETURN: (boolean) 1 if create_nii is set to Yes in the Config module, 0 otherwise
+
+=cut
+sub getCreateNii {
+    my $self = shift;
+
+    my $value = &$getConfigSettingRef($self, CREATE_NII);
+
+    return $getBoolean->($value);
+}
+
+=head3 getHorizontalPics()
+
+Get the horizontalPics Config setting.
+
+RETURN: (boolean) 1 if horizontalPics is set to Yes in the Config module, 0 otherwise
+
+=cut
+sub getHorizontalPics {
+    my $self = shift;
+
+    my $value = &$getConfigSettingRef($self, HORIZONTAL_PICS);
+
+    return $getBoolean->($value);
+}
+
+=head3 getIsQsub()
+
+Get the is_qsub Config setting.
+
+RETURN: (boolean) 1 if is_qsub is set to Yes in the Config module, 0 otherwise
+
+=cut
+sub getIsQsub {
+    my $self = shift;
+
+    my $value = &$getConfigSettingRef($self, IS_QSUB);
+
+    return $getBoolean->($value);
+}
+
+=head3 getCreateCandidates()
+
+Get the createCandidates Config setting.
+
+RETURN: (boolean) 1 if createCandidates is set to Yes in the Config module, 0 otherwise
+
+=cut
+sub getCreateCandidates {
+    my $self = shift;
+
+    my $value = &$getConfigSettingRef($self, IS_QSUB);
+
+    return $getBoolean->($value);
+}
+
 1;
 
 

uploadNeuroDB/mass_pic.pl

@@ -124,14 +124,8 @@ =head1 DESCRIPTION
 
 my $configOB = NeuroDB::objectBroker::ConfigOB->new(db => $db);
 
-my $data_dir  = $configOB->getDataDirPath();
-
-
-# -----------------------------------------------------------------
-## Get config setting using the old database calls
-# -----------------------------------------------------------------
-
-my $horizontalPics = &NeuroDB::DBI::getConfigSetting(\$dbh, 'horizontalPics');
+my $data_dir       = $configOB->getDataDirPath();
+my $horizontalPics = $configOB->getHorizontalPics();