Create getDefaultCohort and getDefaultProject in ConfigOB

aces · Mar 3, 2023 · 797eb1e · 797eb1e
1 parent 516b093
commit 797eb1e
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Showing 5 changed files with 60 additions and 23 deletions.
diff --git a/dicom-archive/profileTemplate.pl b/dicom-archive/profileTemplate.pl
@@ -51,8 +51,8 @@ sub getSubjectIDs {
 
         $subjectID{'createVisitLabel'} = 1;
 
-	# $subjectID{'CohortID'} = undef;
-        # When createVisitLabel is set to 1, CohortID  must also
+        # $subjectID{'CohortID'} = undef;
+        # When createVisitLabel is set to 1, CohortID must also
         # be set to the ID of the cohort that the newly created
         # visit should have. Assuming for example that all patient
         # names end with "_<myCohortID>", then we could write:

diff --git a/docs/scripts_md/ConfigOB.md b/docs/scripts_md/ConfigOB.md
@@ -201,6 +201,18 @@ Get the createVisit Config setting.
 
 RETURN: (boolean) 1 if createVisit is set to Yes in the Config module, 0 otherwise
 
+### getDefaultProject()
+
+Get the default_project Config setting.
+
+RETURN: value (string) of the default_project config in the Config table.
+
+### getDefaultCohort()
+
+Get the default_cohort Config setting.
+
+RETURN: value (string) of the default_cohort config in the Config table.
+
 ### getPythonConfigFile()
 
 Get the MriPythonConfigFile Config setting.

diff --git a/uploadNeuroDB/NeuroDB/MRI.pm b/uploadNeuroDB/NeuroDB/MRI.pm
@@ -1145,6 +1145,7 @@ sub getProject {
     my ($subjectIDsref, $dbhr) = @_;
     my $PSCID = $subjectIDsref->{'PSCID'};
     my $visitLabel = $subjectIDsref->{'visitLabel'};
+    my $configOB = NeuroDB::objectBroker::ConfigOB->new(db => $db);
 
     ## Get the ProjectID from the session table, if the PSCID and visit labels exist
     ## and could be extracted
@@ -1176,14 +1177,13 @@ sub getProject {
     }
 
     ## Otherwise, use the default_project config value
-    my $query = "SELECT p.ProjectID
-                 FROM Config c
-                 JOIN ConfigSettings cs ON c.ConfigID = cs.ID
-                 JOIN Project p ON p.Name = c.Value
-                 WHERE cs.Name = 'default_project'";
+    my $query = "SELECT ProjectID
+                 FROM Project
+                 WHERE Name = ?";
 
+    my $default_project = $configOB->getDefaultProject();
     my $sth = $${dbhr}->prepare($query);
-    $sth->execute();
+    $sth->execute($default_project);
     if ( $sth->rows > 0) {
         my $row = $sth->fetchrow_hashref();
         if ($row->{'ProjectID'}) {
@@ -1217,6 +1217,7 @@ sub getCohort {
     my ($subjectIDsref, $projectID, $dbhr) = @_;
     my $PSCID = $subjectIDsref->{'PSCID'};
     my $visitLabel = $subjectIDsref->{'visitLabel'};
+    my $configOB = NeuroDB::objectBroker::ConfigOB->new(db => $db);
 
     ## Get the CohortID from the session table, if the PSCID and visit labels exist
     ## and could be extracted
@@ -1234,18 +1235,16 @@ sub getCohort {
     }
 
     ## Otherwise, use the default_cohort config value
-    my $query = "SELECT c.Value
-                 FROM Config c
-                 JOIN ConfigSettings cs ON c.ConfigID = cs.ID
-                 WHERE cs.Name = 'default_cohort'
-                 AND Value IN (
-                    SELECT title
-                    FROM cohort
-                    JOIN `project_cohort_rel` USING (CohortID)
-                    WHERE ProjectID = ?)";
-
+    my $query = "SELECT CohortID
+                 FROM cohort
+                 JOIN project_cohort_rel USING (CohortID)
+                 JOIN Project USING(ProjectID)
+                 WHERE title = ? AND Name = ?";
+
+    my $default_cohort = $configOB->getDefaultCohort();
+    my $default_project = $configOB->getDefaultProject();
     my $sth = $${dbhr}->prepare($query);
-    $sth->execute($projectID);
+    $sth->execute($default_cohort, $default_project);
     if ( $sth->rows > 0) {
         my $row = $sth->fetchrow_hashref();
         if ($row->{'Value'}) {

diff --git a/uploadNeuroDB/NeuroDB/MRIProcessingUtility.pm b/uploadNeuroDB/NeuroDB/MRIProcessingUtility.pm
@@ -394,7 +394,7 @@ sub determineSubjectID {
 
     my $this = shift;
     my ($scannerID, $tarchiveInfo, $to_log, $upload_id, $User, $centerID) = @_;
-    my $dbhr   = $this->{dbhr};
+    my $dbhr = $this->{dbhr};
 
     $to_log = 1 unless defined $to_log;
     if (!defined(&Settings::getSubjectIDs)) {
@@ -421,8 +421,8 @@ sub determineSubjectID {
         $subjectIDsref->{'ProjectID'} = $projectID;
     }
 
-    if (!$subjectIDsref->{'SubprojectID'}) {
-        $subjectIDsref->{'SubprojectID'} = NeuroDB::MRI::getCohort($subjectIDsref, $subjectIDsref->{'ProjectID'}, $dbhr);
+    if (!$subjectIDsref->{'CohortID'}) {
+        $subjectIDsref->{'CohortID'} = NeuroDB::MRI::getCohort($subjectIDsref, $subjectIDsref->{'ProjectID'}, $dbhr);
     }
 
     # create the candidate if it does not exist

diff --git a/uploadNeuroDB/NeuroDB/objectBroker/ConfigOB.pm b/uploadNeuroDB/NeuroDB/objectBroker/ConfigOB.pm
@@ -65,7 +65,6 @@ use NeuroDB::objectBroker::ObjectBrokerException;
 
 use TryCatch;
 
-<<<<<<< HEAD
 use constant TARCHIVE_LIBRARY_DIR        => 'tarchiveLibraryDir';
 use constant DATA_DIR_BASE_PATH          => 'dataDirBasepath';
 use constant MAIL_USER                   => 'mail_user';
@@ -96,6 +95,7 @@ use constant BIDS_README_TEXT            => 'bids_readme_text';
 use constant BIDS_VALIDATOR_OPTIONS_TO_IGNORE => 'bids_validator_options_to_ignore';
 use constant CREATE_CANDIDATES           => 'createCandidates';
 use constant CREATE_VISIT                => 'createVisit';
+use constant DEFAULT_COHORT              => 'default_cohort';
 
 =pod
 
@@ -464,6 +464,32 @@ sub getCreateVisit {
     return $getBooleanRef->($value);
 }
 
+=head3 getDefaultProject()
+
+Get the default_project Config setting.
+
+RETURN: value (string) of the default_project config in the Config table.
+
+=cut
+sub getDefaultProject {
+    my $self = shift;
+
+    return &$getConfigSettingRef($self, DEFAULT_PROJECT);
+}
+
+=head3 getDefaultCohort()
+
+Get the default_cohort Config setting.
+
+RETURN: value (string) of the default_cohort config in the Config table.
+
+=cut
+sub getDefaultCohort {
+    my $self = shift;
+
+    return &$getConfigSettingRef($self, DEFAULT_COHORT);
+}
+
 =head3 getPythonConfigFile()
 
 Get the MriPythonConfigFile Config setting.