Updated rules to set the default project, cohort

dicom-archive/profileTemplate.pl

@@ -40,34 +40,45 @@ sub getSubjectIDs {
      # If patientName is phantom scan or test scan
      # CandID is scanner DCCID (based on site alias)
      # visitLabel is scan patient name
-     # Set createVisitLable to 
-     #      a. 1 if imaging pipeline should create the visit label (when visit label has not been created yet in the database. 
-     #      b. 0 if imaging pipeline should not create the visit label (when visit label has not been created yet in the database. 
     if ($patientName =~ /PHA/i or $patientName =~ /TEST/i) {
 
         $subjectID{'CandID'}     = NeuroDB::MRI::my_trim(NeuroDB::MRI::getScannerCandID($scannerID, $db));
         $subjectID{'visitLabel'} = NeuroDB::MRI::my_trim($patientName);
         $subjectID{'isPhantom'} = 1;
 
-        $subjectID{'createVisitLabel'} = 1;
-
-        # When createVisitLabel is set to 1, CohortID must also
-        # be set to the ID of the cohort that the newly created
-        # visit should have. Assuming for example that all patient
-        # names end with "_<myCohortID>", then we could write:
-        # ($subjectID{'CohortID'}) = $patientName =~ /_(\d+)$/;
-        # When createVisitLabel is set to 0, $subjectID{'CohortID'} is ignored.
-
-        # If config setting 'createVisitLabel' is true
-        # then $subjectID{'ProjectID'} must be set to the project ID of the
-        # newly created visit. Assuming for example that all patients
-        # names that contain the string 'HOSPITAL' are associated to visit
+        # Override createVisitLabel here if its value needs to be different than the createVisit DB config
+        # $subjectID{'createVisitLabel'} = undef;
+        # Set createVisitLabel to
+        #      a. 1 if imaging pipeline should create the visit label (when visit label has not been created yet in the database.
+        #      b. 0 if imaging pipeline should not create the visit label (when visit label has not been created yet in the database.
+        #
+        # When $subjectID{'createVisitLabel'} is set to 1:
+        #   - $subjectID{'ProjectID'} must be set to the project ID of the newly created visit
+        #   - $subjectID{'CohortID'} must be set to the cohort ID of the newly created visit
+        #
+        # If $subjectID{'ProjectID'} is undef, the following rules will be tried in order to assign a default value:
+        #	- the ProjectID from the session table, if the PSCID and visit labels exist
+        #       - the ProjectID from the candidate table, if the PSCID exists
+        #       - the default_project DB config value
+        #
+        # If $subjectID{'CohortID'} is undef, the following rules will be tried in order to assign a default value:
+        #       - the CohortID from the session table, if the PSCID and visit labels exist
+        #       - the default_cohort DB config value
+        #
+        # When createVisitLabel is set to 0, $subjectID{'ProjectID'} and $subjectID{'CohortID'} are ignored.
+
+        # $subjectID{'ProjectID'} = undef;
+        # Assuming that all patient names that contain the string 'HOSPITAL' are associated to visit
         # done for project with ID 1 and all others to projects with ID 2, we
         # could write:
-        # $subjectID{'ProjectID'} = $patientName =~ /HOSPITAL/  
-        #     ? 1 : 2;
+        # $subjectID{'ProjectID'} = $patientName =~ /HOSPITAL/ ? 1 : 2;
         # When createVisitLabel is set to 0, $subjectID{'ProjectID'} is ignored.
 
+        # $subjectID{'CohortID'} = undef;
+        # Assuming that all patient names end with "_<myCohortID>", then we could write:
+        # $subjectID{'CohortID'} = $patientName =~ /_(\d+)$/;
+        # When createVisitLabel is set to 0, $subjectID{'CohortID'} is ignored.
+
      # If patient match PSCID_DCCID_VisitLabel
      # Determine PSCID, DCCID and visitLabel based on patient name
     } elsif ($patientName =~ /([^_]+)_(\d+)_([^_]+)/) {
@@ -77,30 +88,43 @@ sub getSubjectIDs {
         $subjectID{'visitLabel'} = NeuroDB::MRI::my_trim($3);
         $subjectID{'isPhantom'}  = 0;
 
-        $subjectID{'createVisitLabel'} = 0;
-
-        # When createVisitLabel is set to 1, CohortID must also
-        # be set to the ID of the cohort that the newly created
-        # visit should have. Assuming for example that visits V01 and V02
-        # are associated with cohort with ID 1 and all others to cohort
-        # with ID 2, then we could write:
-        # ($subjectID{'CohortID'}) = $subjectID{'visitLabel'} =~ /^V0[12]$/ 
-        #     ? 1 : 2;
-        # When createVisitLabel is set to 0, $subjectID{'CohortID'} is ignored.
-
-        # If config setting 'createVisitLabel' is true
-        # then $subjectID{'ProjectID'} must be set to the project ID of the
-        # newly created visit. Assuming for example that candidates with a
-        # candidate ID greater than 400000 are seen in project 1 and others are
-        # seen in project 2, we could write
-        # could write:
+        # Override createVisitLabel here if its value needs to be different than the createVisit DB config
+        # $subjectID{'createVisitLabel'} = undef;
+        # Set createVisitLabel to
+        #      a. 1 if imaging pipeline should create the visit label (when visit label has not been created yet in the database.
+        #      b. 0 if imaging pipeline should not create the visit label (when visit label has not been created yet in the database.
+        #
+        # When $subjectID{'createVisitLabel'} is set to 1:
+        #   - $subjectID{'ProjectID'} must be set to the project ID of the newly created visit
+        #   - $subjectID{'CohortID'} must be set to the cohort ID of the newly created visit
+        #
+        # If $subjectID{'ProjectID'} is undef, the following rules will be tried in order to assign a default value:
+        #       - the ProjectID from the session table, if the PSCID and visit labels exist
+        #       - the ProjectID from the candidate table, if the PSCID exists
+        #       - the default_project DB config value
+        #
+        # If $subjectID{'CohortID'} is undef, the following rules will be tried in order to assign a default value:
+        #       - the CohortID from the session table, if the PSCID and visit labels exist
+        #       - the default_cohort DB config value
+        #
+        # When createVisitLabel is set to 0, $subjectID{'ProjectID'} and $subjectID{'CohortID'} are ignored.
+
+        # $subjectID{'ProjectID'} = undef;
+        # Assuming for example that candidates with a candidate ID greater than 400000 are seen in project 1
+        # and others are seen in project 2, we could write:
         # $subjectID{'ProjectID'} = $subjectID{'CandID'} > 400000 ? 1 : 2;
-        #     ? 1 : 2;
         # When createVisitLabel is set to 0, $subjectID{'ProjectID'} is ignored.
 
-        print "PSCID is: "            . $subjectID{'PSCID'}      . 
-                "\n CandID id: "      . $subjectID{'CandID'}     .
-                "\n visit_label is: " . $subjectID{'visitLabel'} . "\n";
+        # $subjectID{'CohortID'} = undef;
+        # Assuming for example that visits V01 and V02 are associated with cohort with ID 1 and all others
+        # to cohort with ID 2, then we could write:
+        # $subjectID{'CohortID'} = $subjectID{'visitLabel'} =~ /^V0[12]$/ ? 1 : 2;
+        # When createVisitLabel is set to 0, $subjectID{'CohortID'} is ignored.
+
+        print "PSCID is: "            . $subjectID{'PSCID'}  .
+                "\n CandID id: "      . $subjectID{'CandID'} .
+                "\n visit_label is: " . $subjectID{'visitLabel'} . "\n" .
+                "\n ProjectID is: "   . $subjectID{'ProjectID'} . "\n";
     }
 
     # Return subjectIDs

docs/02-Install.md

@@ -152,8 +152,24 @@ Under the `Imaging Pipeline` section:
     typically `/data/$PROJECT/data/tarchive/`
  * `Patient identifiers and center name lookup variable`: DICOM header that
     contains the LORIS candidate identifiers; typically `PatientName`
- * `Upload creation of candidates`: enable or disable candidate creation into LORIS
+ * `Enable candidate creation`: enable or disable candidate creation into LORIS
     when running the insertion pipeline
+ * `Enable visit creation`: enable or disable visit creation into LORIS
+    when running the insertion pipeline
+ * `Default project`: Default cohort used when Enable visit creation is set to true. This value is used when
+   the following rules fails:
+      - the $subjectID{'ProjectID'} is undef in the profileTemplate (prod) file;
+      - the ProjectID from the session table, if the PSCID and visit labels exist;
+      - the ProjectID from the candidate table, if the PSCID exists.
+ * `Default cohort`: Default cohort used when Enable visit creation is set to true. This value is used when
+   the following rules fails:
+      - the $subjectID{'CohortID'} is undef in the profileTemplate (prod) file;
+      - the CohortID from the session table, if the PSCID and visit labels exist;
+      - the default_cohort DB config value.
+ * `Default visit label for BIDS dataset`: the visit directory in BIDS
+    structure is optional in the case of only one visit for the whole dataset. In
+    this case, we need to specify to LORIS what would be the default visit label
+    the project wants to use to store the electrophysiology datasets (*e.g.* V01).
  * `Project batch management used`: enable or disable batch management
  * `Number of volumes in native DTI acquisitions`: used by the DTIPrep pipeline
  * `Scan type of native T1 acquisition`: name as specified in the `mri_scan_type`
@@ -170,10 +186,6 @@ Under the `Imaging Pipeline` section:
     control. Feature to be integrated in the code base in a **future** release.
  * `Name of the Perl MRI config file`: name of the perl-based MRI config file to use when running
     the Perl insertion scripts; typically `prod`; used when Auto launch is turned on.
- * `Default visit label for BIDS dataset`: the visit directory in BIDS 
-    structure is optional in the case of only one visit for the whole dataset. In
-    this case, we need to specify to LORIS what would be the default visit label 
-    the project wants to use to store the electrophysiology datasets (*e.g.* V01).
  * `Name of the environment file`: name of the MRI environment file to source before
     running the insertion scripts; typically `environment`; used when Auto-launch
     is turned on for the pipeline.

docs/scripts_md/ConfigOB.md

@@ -195,6 +195,24 @@ Get the createCandidates Config setting.
 
 RETURN: (boolean) 1 if createCandidates is set to Yes in the Config module, 0 otherwise
 
+### getCreateVisit()
+
+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.

docs/scripts_md/MRI.md

@@ -243,6 +243,18 @@ RETURNS: a two element array:
   - first is the MRI alias of the PSC or "UNKN"
   - second is the `CenterID` or 0
 
+### getProject($patientName, $dbhr, $db)
+
+Looks for the project id using the C<session> table C<ProjectID> as
+a first resource, then using the C<candidate> table C<RegistrationProjectID>,
+otherwise, look for the default_project config value, and return C<ProjectID>.
+
+INPUTS:
+  - $subjectIDsref: subject's information hash ref
+  - $dbhr       : database handle reference
+
+RETURNS: the C<ProjectID> or an error if not found
+
 ### compute\_hash($file\_ref)
 
 Semi-intelligently generates a hash (MD5 digest) for the `NeuroDB::File` object

uploadNeuroDB/NeuroDB/ExitCodes.pm

@@ -125,7 +125,7 @@ our $INVALID_ENVIRONMENT_VAR       = 40; # used when an environment variable is
                                          # value
 our $PROJECT_CUSTOMIZATION_FAILURE = 41; # used when either missing a function
                                          # or a customization variable
-
+our $PROJECT_INIT_FAILURE          = 42; # used when project can't be initialized
 
 ## -- Common file manipulation failures (exit codes from 60 to 79)
 our $EXTRACTION_FAILURE      = 60; # if archive extraction failed

uploadNeuroDB/NeuroDB/MRI.pm

@@ -1104,7 +1104,7 @@ sub getPSC {
 
         my $sth = $${dbhr}->prepare($query);
         $sth->execute($PSCID, $visitLabel);
-        if ( $sth->rows > 0) {
+        if ($sth->rows > 0) {
             my $row = $sth->fetchrow_hashref();
             return ($row->{'MRI_alias'},$row->{'CenterID'});
         }
@@ -1125,6 +1125,136 @@ sub getPSC {
 
 =pod
 
+=head3 getProject($subjectIDsref, $dbhr, $db)
+
+Looks for the project id using the C<session> table C<ProjectID> as
+a first resource, then using the C<candidate> table C<RegistrationProjectID>,
+otherwise, look for the default_project config value, and return C<ProjectID>.
+
+INPUTS:
+  - $subjectIDsref: subject's information hash ref
+  - $dbhr       : database handle reference
+  - $db         : database object
+
+RETURNS: the C<ProjectID> or an error if not found
+
+=cut
+
+sub getProject {
+    my ($subjectIDsref, $dbhr, $db) = @_;
+    my $PSCID = $subjectIDsref->{'PSCID'};
+    my $visitLabel = $subjectIDsref->{'visitLabel'};
+    my $configOB = NeuroDB::objectBroker::ConfigOB->new(db => $db);
+
+    ## Get the ProjectID from the session table, if the PSCID and visit labels exist
+    ## and could be extracted
+    if ($PSCID && $visitLabel) {
+        my $query = "SELECT s.ProjectID FROM session s
+                    JOIN candidate c on c.CandID=s.CandID
+                    WHERE c.PSCID = ? AND s.Visit_label = ?";
+
+        my $sth = $${dbhr}->prepare($query);
+        $sth->execute($PSCID, $visitLabel);
+        if ($sth->rows > 0) {
+            my $row = $sth->fetchrow_hashref();
+            return $row->{'ProjectID'};
+        }
+    }
+
+    ## Otherwise get the ProjectID from the candidate table, if the PSCID exists
+    if ($PSCID) {
+        my $query = "SELECT RegistrationProjectID
+                    FROM candidate
+                    WHERE PSCID = ?";
+
+        my $sth = $${dbhr}->prepare($query);
+        $sth->execute($PSCID);
+        if ($sth->rows > 0) {
+            my $row = $sth->fetchrow_hashref();
+            return $row->{'RegistrationProjectID'};
+        }
+    }
+
+    ## Otherwise, use the default_project config value
+    my $query = "SELECT ProjectID
+                 FROM Project
+                 WHERE Name = ?";
+
+    my $default_project = $configOB->getDefaultProject();
+    my $sth = $${dbhr}->prepare($query);
+    $sth->execute($default_project);
+    if ( $sth->rows > 0) {
+        my $row = $sth->fetchrow_hashref();
+        if ($row->{'ProjectID'}) {
+            return $row->{'ProjectID'};
+        }
+    }
+
+    print STDERR "\nERROR: ProjectID cannot be initialized. ".
+                 "Please set the default_project config.\n\n";
+    exit $NeuroDB::ExitCodes::PROJECT_CUSTOMIZATION_FAILURE;
+}
+
+=pod
+
+=head3 getCohort($subjectIDsref, $projectID, $dbhr, $db)
+
+Looks for the cohort id using the C<session> table C<ProjectID> as
+a first resource, for the cases where it is created using the front-end,
+otherwise, look for the default_cohort config value, and return C<CohortID>.
+
+INPUTS:
+  - $subjectIDsref: subject's information hash ref
+  - $projectID    : the project ID
+  - $dbhr         : database handle reference
+  - $db           : database object
+
+RETURNS: the C<CohortID> or 0
+
+=cut
+
+sub getCohort {
+    my ($subjectIDsref, $projectID, $dbhr, $db) = @_;
+    my $PSCID = $subjectIDsref->{'PSCID'};
+    my $visitLabel = $subjectIDsref->{'visitLabel'};
+    my $configOB = NeuroDB::objectBroker::ConfigOB->new(db => $db);
+
+    ## Get the CohortID from the session table, if the PSCID and visit labels exist
+    ## and could be extracted
+    if ($PSCID && $visitLabel) {
+        my $query = "SELECT s.CohortID FROM session s
+                    JOIN candidate c on c.CandID=s.CandID
+                    WHERE c.PSCID = ? AND s.Visit_label = ?";
+
+        my $sth = $${dbhr}->prepare($query);
+        $sth->execute($PSCID, $visitLabel);
+        if ( $sth->rows > 0) {
+            my $row = $sth->fetchrow_hashref();
+            return $row->{'CohortID'};
+        }
+    }
+
+    ## Otherwise, use the default_cohort config value
+    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);
+    $sth->execute($default_cohort, $default_project);
+    if ( $sth->rows > 0) {
+        my $row = $sth->fetchrow_hashref();
+        return $row->{'CohortID'};
+    }
+
+    return ("UNKN", 0);
+}
+
+=pod
+
 =head3 compute_hash($file_ref)
 
 Semi-intelligently generates a hash (MD5 digest) for the C<NeuroDB::File> object