Refactor remaining array configs to use ConfigOB instead of the DBI l…

…ibrary (#770)

* use configOB for array configs

* use configOB for minc_to_bids script

* fix bug in delete script

* fix bugs with new perl

* use array for some bids config

* bug fix

* fix pod error + Nic's comment

* take care of Nic's comments

* recreate markdown files

* correct documentation of grep_FileIDs_to_deface in run_defacing_script

* Nic's review

docs/scripts_md/ConfigOB.md

@@ -207,6 +207,43 @@ Get the compute\_snr\_modalities Config setting
 
 RETURN: an array (possibly empty) of the modality IDs (i.e t1w, etc..) for which to compute the SNR
 
+### getExcludedSeriesDescription()
+
+Get the excluded\_series\_description Config setting
+
+RETURN: an array (possibly empty) of the series description to exclude from import
+
+### getModalitiesToDeface()
+
+Get the modalities\_to\_deface Config setting
+
+RETURN: an array (possibly empty) of the modalities to run the defacing pipeline on
+
+### getBidsDatasetAuthors()
+
+Get the bids\_dataset\_authors Config setting
+
+RETURN: an array (possibly empty) of the authors to use for a BIDS dataset
+
+### getBidsAcknowledgmentsText()
+
+Get the bids\_acknowledgments\_text Config setting
+
+RETURN: a string of the acknowledgment text to use for a BIDS dataset (or undef)
+
+### getBidsReadmeText()
+
+Get the bids\_readme\_text Config setting
+
+RETURN: a string of the README text to use for a BIDS dataset (or undef)
+
+### getBidsValidatorOptionsToIgnore()
+
+Get the bids\_validator\_options\_to\_ignore Config setting
+
+RETURN: an array of the BIDS validator options to ignore
+to use when creating a BIDS dataset
+
 # TO DO
 
 Nothing planned.

docs/scripts_md/DBI.md

@@ -35,18 +35,6 @@ INPUTS:
 
 RETURNS: DBI database handler when connection is successful
 
-### getConfigSetting($dbh, $name)
-
-This method fetches the value (`$value`) stored in the `Config` table for a
-specific config setting (`$name`) specified as an input.
-
-INPUTS:
-  - $dbh : database handler
-  - $name: name of the config setting
-
-RETURNS: value corresponding to the config setting in the `Config` table
-         of LORIS
-
 # TO DO
 
 Expand the package with more functions.

docs/scripts_md/MRIProcessingUtility.md

@@ -329,17 +329,17 @@ INPUTS:
 
 RETURNS: acquisition protocol ID of the MINC file
 
-### dicom\_to\_minc($study\_dir, $converter, $get\_dicom\_info, $exclude, $mail\_user, $upload\_id)
+### dicom\_to\_minc($study\_dir, $converter, $get\_dicom\_info, $mail\_user, $upload\_id, @exclude)
 
 Converts a DICOM study into MINC files.
 
 INPUTS:
   - $study\_dir      : DICOM study directory to convert
   - $converter      : converter to be used
   - $get\_dicom\_info : get DICOM information setting from the `Config` table
-  - $exclude        : which files to exclude from the `dcm2mnc` command
   - $mail\_user      : mail of the user
   - $upload\_id      : upload ID of the study
+  - @exclude        : which files to exclude from the `dcm2mnc` command
 
 ### get\_mincs($minc\_files, $upload\_id)
 

docs/scripts_md/run_defacing_script.md

@@ -22,15 +22,15 @@ specified in the Config module of LORIS.
 
 # METHODS
 
-### grep\_FileIDs\_to\_deface($session\_id\_arr, $modalities\_to\_deface\_arr)
+### grep\_FileIDs\_to\_deface($session\_id\_ref, @modalities\_to\_deface)
 
 Queries the database for the list of acquisitions' FileID to be used to run the
 defacing algorithm based on the provided list of SessionID and Scan\_type to
 restrict the search.
 
 INPUTS:
-  - $session\_id\_arr          : array of SessionIDs to use when grepping FileIDs
-  - $modalities\_to\_deface\_arr: array of Scan\_type to use when grepping FileIDs
+  - $session\_id\_ref      : array of SessionIDs to use when grepping FileIDs
+  - @modalities\_to\_deface: array of Scan\_type to use when grepping FileIDs
 
 RETURNS: hash of matching FileIDs to be used to run the defacing algorithm
          organized in a hash as follows:

tools/delete_imaging_upload.pl

@@ -2014,8 +2014,8 @@ sub getScanTypesToDelete {
     return () if !defined $scanTypeList && !$keepDefaced;
 
     if($keepDefaced) {
-        my $scanTypesRef = &NeuroDB::DBI::getConfigSetting(\$dbh, 'modalities_to_deface');
-        return defined $scanTypesRef ? (map { $_ => 1 } @$scanTypesRef) : ();
+        my @scanTypes = $configOB->getModalitiesToDeface();
+        return (map { $_ => 1 } @scanTypes);
     }
 
     my %types = map { $_=> 1 } split(/,/, $scanTypeList);

tools/minc_to_bids_converter.pl

@@ -81,6 +81,7 @@ =head2 METHODS
 use NeuroDB::MRI;
 use NeuroDB::ExitCodes;
 use NeuroDB::File;
+use NeuroDB::objectBroker::ConfigOB;
 
 
 # # Set script's constants here
@@ -203,15 +204,25 @@ =head2 METHODS
 my $dbh = &NeuroDB::DBI::connect_to_db(@Settings::db);
 print "\n==> Successfully connected to database \n";
 
-# Get settings from the ConfigSettings table
-my $data_dir        = &NeuroDB::DBI::getConfigSetting(\$dbh,'dataDirBasepath');
-my $bin_dir         = &NeuroDB::DBI::getConfigSetting(\$dbh,'MRICodePath');
-my $authors         = &NeuroDB::DBI::getConfigSetting(\$dbh, 'bids_dataset_authors');
-my $acknowledgments = &NeuroDB::DBI::getConfigSetting(\$dbh, 'bids_acknowledgments_text');
-my $readme_content  = &NeuroDB::DBI::getConfigSetting(\$dbh, 'bids_readme_text');
-my $validator_ignore_opts = &NeuroDB::DBI::getConfigSetting(\$dbh, 'bids_validator_options_to_ignore');
-
-unless (defined $authors && defined $acknowledgments && defined $readme_content) {
+# new Moose database connection
+my $db  = NeuroDB::Database->new(
+    databaseName => $Settings::db[0],
+    userName     => $Settings::db[1],
+    password     => $Settings::db[2],
+    hostName     => $Settings::db[3]
+);
+$db->connect();
+
+# Get settings from the Config table
+my $configOB = NeuroDB::objectBroker::ConfigOB->new(db => $db);
+my $data_dir        = $configOB->getDataDirPath();
+my $bin_dir         = $configOB->getMriCodePath();
+my @authors         = $configOB->getBidsDatasetAuthors();
+my $acknowledgments = $configOB->getBidsAcknowledgmentsText();
+my $readme_content  = $configOB->getBidsReadmeText();
+my @validator_ignore_opts = $configOB->getBidsValidatorOptionsToIgnore();
+
+unless (@authors && defined $acknowledgments && defined $readme_content) {
     print STDERR "\n ERROR: Some 'MINC to BIDS Converter Tool Options' are not set in the configuration module."
                  . " 'BIDS Dataset Authors', 'BIDS Dataset Acknowledgments' and 'BIDS Dataset README' need to be"
                  . " defined.\n\n";
@@ -259,7 +270,7 @@ =head2 METHODS
     'BIDSVersion'           => $BIDS_VERSION,
     'Name'                  => $dataset_name,
     'LORISScriptVersion'    => $LORIS_SCRIPT_VERSION,
-    'Authors'               => $authors,
+    'Authors'               => @authors,
     'HowToAcknowledge'      => $acknowledgments,
     'LORISReleaseVersion'   => $loris_mri_version
 );
@@ -290,11 +301,9 @@ =head2 METHODS
 # specifications, not the same number of files per session etc...)
 # =============================================================================
 my $bids_validator_config_file = $dest_dir . "/.bids-validator-config.json";
-if (!-e $bids_validator_config_file && defined $validator_ignore_opts) {
+if (!-e $bids_validator_config_file && @validator_ignore_opts) {
     print "\n******* Creating the .bids-validator-config.json file $bids_validator_config_file *******\n";
-    my $validator_ignore_string = ref($validator_ignore_opts) eq 'ARRAY'
-        ? join(", ", @$validator_ignore_opts)
-        : $validator_ignore_opts;
+    my $validator_ignore_string = join(", ", @validator_ignore_opts);
     my $bids_validator_config_content = <<TEXT;
 {
   "ignore": [$validator_ignore_string]

tools/run_defacing_script.pl

@@ -184,14 +184,14 @@ =head1 METHODS
 
 my $data_dir      = $configOB->getDataDirPath();
 my $ref_scan_type = $configOB->getDefacingRefScanType();
+my @to_deface     = $configOB->getModalitiesToDeface();
 
 
 # -----------------------------------------------------------------
 ## Get config setting using the old database calls
 # -----------------------------------------------------------------
 
-my $to_deface = &NeuroDB::DBI::getConfigSetting(\$dbh, 'modalities_to_deface');
-unless ($ref_scan_type && $to_deface) {
+unless ($ref_scan_type && @to_deface) {
     print STDERR "\n==> ERROR: you need to configure both the "
                  . "reference_scan_type_for_defacing & modalities_to_deface config "
                  . "settings in the imaging pipeline section of the Config module.\n"
@@ -235,14 +235,14 @@ =head1 METHODS
 print "\n==> Fetching all FileIDs to deface.\n" if $verbose;
 my @session_ids = defined $session_ids ? split(",", $session_ids) : ();
 
-unless ($to_deface) {
+unless (@to_deface) {
     print "\nNo modalities were set to be defaced in the Config module. Ensure"
           . " to select modalities to deface in the Config module under the imaging"
           . " pipeline section (setting called modalities_to_deface. \n\n";
     exit $NeuroDB::ExitCodes::SUCCESS;
 }
 
-my %files_hash  = grep_FileIDs_to_deface(\@session_ids, $to_deface);
+my %files_hash  = grep_FileIDs_to_deface(\@session_ids, @to_deface);
 
 
 
@@ -293,15 +293,15 @@ =head1 METHODS
 
 =pod
 
-=head3 grep_FileIDs_to_deface($session_id_arr, $modalities_to_deface_arr)
+=head3 grep_FileIDs_to_deface($session_id_ref, @modalities_to_deface)
 
 Queries the database for the list of acquisitions' FileID to be used to run the
 defacing algorithm based on the provided list of SessionID and Scan_type to
 restrict the search.
 
 INPUTS:
-  - $session_id_arr          : array of SessionIDs to use when grepping FileIDs
-  - $modalities_to_deface_arr: array of Scan_type to use when grepping FileIDs
+  - $session_id_ref      : array of SessionIDs to use when grepping FileIDs
+  - @modalities_to_deface: array of Scan_type to use when grepping FileIDs
 
 RETURNS: hash of matching FileIDs to be used to run the defacing algorithm
          organized in a hash as follows:
@@ -318,18 +318,18 @@ =head3 grep_FileIDs_to_deface($session_id_arr, $modalities_to_deface_arr)
 =cut
 
 sub grep_FileIDs_to_deface {
-    my ($session_id_arr, $modalities_to_deface_arr) = @_;
+    my ($session_id_ref, @modalities_to_deface) = @_;
 
     # separate the special modalities specified in %SPECIAL_ACQUISITIONS from the
     # standard scan types
     my @special_scan_types = keys %SPECIAL_ACQUISITIONS_FILTER;
     my @special_cases;
     foreach my $special (@special_scan_types) {
         # push the special modalities to a new array @special_cases
-        push @special_cases, grep(/$special/, @$modalities_to_deface_arr);
+        push @special_cases, grep(/$special/, @modalities_to_deface);
         # remove the special modalities from the modalities array as they will be
         # dealt with differently than standard modalities
-        @$modalities_to_deface_arr = grep(! /$special/, @$modalities_to_deface_arr);
+        @modalities_to_deface = grep(! /$special/, @modalities_to_deface);
     }
 
     # base query
@@ -342,8 +342,8 @@ sub grep_FileIDs_to_deface {
 
     # add where clause for the different standard scan types to deface
     my @where;
-    if (@$modalities_to_deface_arr) {
-        @where = map { "mst.Scan_type = ?" } @$modalities_to_deface_arr;
+    if (@modalities_to_deface) {
+        @where = map { "mst.Scan_type = ?" } @modalities_to_deface;
         $query   .= sprintf(" %s ", join(" OR ", @where));
     }
 
@@ -358,20 +358,20 @@ sub grep_FileIDs_to_deface {
 
     # add where clause for the session IDs specified to the script if -sessionIDs
     # was set
-    if ($session_id_arr) {
-        @where  = map { "f.SessionID = ?" } @$session_id_arr;
+    if ($session_id_ref) {
+        @where  = map { "f.SessionID = ?" } @$session_id_ref;
         $query .= sprintf(" AND (%s) ", join(" OR ", @where));
     }
 
     my $sth = $dbh->prepare($query);
 
     # create array of parameters
-    my @bind_param = @$modalities_to_deface_arr;
+    my @bind_param = @modalities_to_deface;
     foreach my $special_scan_type (@special_cases) {
         push @bind_param, $special_scan_type;
         push @bind_param, $SPECIAL_ACQUISITIONS_FILTER{$special_scan_type};
     }
-    push @bind_param, @$session_id_arr;
+    push @bind_param, @$session_id_ref;
 
     # execute the query
     $sth->execute(@bind_param);
@@ -434,7 +434,7 @@ =head3 check_if_deface_files_already_in_db($session_files, $session_id)
 sub check_if_deface_files_already_in_db {
     my ($session_files, $session_id) = @_;
 
-    my @defaced_scan_types = map { $_ . '-defaced' } keys $session_files;
+    my @defaced_scan_types = map { $_ . '-defaced' } keys %{ $session_files };
 
     # base query
     my $query = "SELECT COUNT(*) "
@@ -554,7 +554,7 @@ sub deface_session {
 
     # add multi-constrast modalities to cmd line & remove them from $session_files
     foreach my $multi (@MULTI_CONTRAST_ACQUISITIONS_BASE_NAMES) {
-        my @scan_types         = keys $session_files;
+        my @scan_types         = keys %{ $session_files };
         my @matching_types     = grep (/$multi/i, @scan_types);
         my @non_matching_types = grep (!/$multi/i, @scan_types);
         my (@multi_files_list, @other_files);
@@ -623,7 +623,7 @@ sub fetch_defaced_files {
     $defaced_images{$deface_ref}{Scan_type}   = $$ref_file{Scan_type};
 
     # for each files in $session_files, append the defaced images to the hash
-    foreach my $scan_type (keys $session_files) {
+    foreach my $scan_type (keys %{ $session_files }) {
         my %files = %{ $$session_files{$scan_type} };
         foreach my $fileID (keys %files) {
             my $deface_file   = $deface_dir . '/' . basename($files{$fileID});
@@ -663,7 +663,7 @@ sub register_defaced_files {
                        . " -coordinateSpace native "
                        . " -outputType defaced ";
 
-    foreach my $file (keys $defaced_images) {
+    foreach my $file (keys %{ $defaced_images }) {
         my $input_fileID = $$defaced_images{$file}{InputFileID};
         my $scan_type    = $$defaced_images{$file}{Scan_type} . "-defaced";
 

uploadNeuroDB/NeuroDB/DBI.pm

@@ -72,47 +72,6 @@ sub connect_to_db
     return $dbh;
 }
 
-=pod
-
-=head3 getConfigSetting($dbh, $name)
-
-This method fetches the value (C<$value>) stored in the C<Config> table for a
-specific config setting (C<$name>) specified as an input.
-
-INPUTS:
-  - $dbh : database handler
-  - $name: name of the config setting
-
-RETURNS: value corresponding to the config setting in the C<Config> table
-         of LORIS
-
-=cut
-sub getConfigSetting
-{
-    my ($dbh, $name) = @_;
-    my ($message, $query, $where) = '';
-    my $value = undef;
-
-    $where = " WHERE c.ConfigID=(Select cs.ID from ConfigSettings cs where cs.Name=?)";
-    $query = " SELECT c.Value FROM Config c";
-    $query = $query . $where;
-    my $sth = $$dbh->prepare($query);
-    $sth->execute($name);
-
-    if ( $sth->rows > 1 ){
-        # if more than one row returned, push data into an array that will be
-        #  dereferenced into $value
-        my @values;
-        while (my $row = $sth->fetchrow_array()) {
-            push (@values, $row);
-        }
-        $value = \@values;
-    } elsif ( $sth->rows > 0 ) {
-        $value = $sth->fetchrow_array();
-    }
-    return $value;
-}
-
 1;
 
 =pod