Merge pull request #410 from fyvon/feature/release_skip_EFO

Added option to skip EFO traits ontology rebuilding during release post-processing

release/scripts/OnlyUpdateEFOAssociations.py

@@ -0,0 +1,45 @@
+from django.db import transaction
+from catalog.models import EFOTrait_Ontology, Score, Release
+
+
+class OnlyUpdateEFOAssociations:
+    """This class updates the EFO trait associations of the given scores without rebuilding
+    the whole EFO ontology as UpdateEFO does. This might be useful when one or several
+    EFO traits went obsolete, although we don't want to reflect this change yet in the PGS Catalog."""
+
+    def get_current_release_scores(self):
+        """Retrieve the scores of the ongoing release, assuming this process is executed
+        as part of the release post-processing."""
+        latest_release = Release.objects.latest('date')
+        return Score.objects.filter(date_released=latest_release.date)
+
+    def add_score_efo_trait_associations(self, score):
+        """Add EFO trait associations to the given score."""
+        efo_traits = score.trait_efo.all()
+        for efo_trait in efo_traits:
+            try:
+                efo_trait_ontology = EFOTrait_Ontology.objects.get(id=efo_trait.id)
+                efo_trait_ontology.scores_direct_associations.add(score)
+                efo_trait_ontology.save()
+                for efo_trait_parent in efo_trait_ontology.parent_traits.all():
+                    efo_trait_parent.scores_child_associations.add(score)
+                    efo_trait_parent.save()
+            except EFOTrait_Ontology.DoesNotExist as e:
+                print(f'ERROR: {efo_trait.id} is a new trait, UpdateEFO cannot be bypassed.')
+                raise e
+
+    def add_efo_trait_associations(self):
+        """Main function."""
+        latest_scores = self.get_current_release_scores()
+        with transaction.atomic():
+            try:
+                for score in latest_scores:
+                    self.add_score_efo_trait_associations(score)
+            except Exception as e:
+                transaction.rollback()
+                raise e
+
+
+def run():
+    only_update_efo_associations = OnlyUpdateEFOAssociations()
+    only_update_efo_associations.add_efo_trait_associations()

release/scripts/run_post_processing_script.py

@@ -1,13 +1,14 @@
-import sys, os.path, shutil, glob
 from django.db.models import Count
 from catalog.models import *
 from release.scripts.RemoveDataForRelease import NonReleasedDataToRemove
+from release.scripts.OnlyUpdateEFOAssociations import OnlyUpdateEFOAssociations
 from release.scripts.UpdateScoreAncestry import UpdateScoreAncestry
 from release.scripts.UpdateScoreEvaluated import UpdateScoreEvaluated
 from release.scripts.UpdateReleasedCohorts import UpdateReleasedCohorts
 from release.scripts.UpdateEFO import UpdateEFO
 
-def run():
+
+def run(*args):
     """
         Main method executed by the Django command:
         `python manage.py runscript run_post_processing_script`
@@ -30,8 +31,12 @@ def run():
     # Update the cohorts (update the Cohort "released" field)
     update_released_cohorts()
 
-    # Update the trait information and ontology
-    update_efo()
+    if 'update_efo_associations_only' in args:
+        # Simply update trait associations without rebuilding the ontology
+        update_efo_associations_only()
+    else:
+        # Update the trait information and ontology
+        update_efo()
 
     # Display the list of new EFO traits in the catalog
     display_new_efo()
@@ -76,6 +81,13 @@ def update_efo():
     update_efo.launch_efo_updates()
 
 
+def update_efo_associations_only():
+    """ Skipping EFO rebuilding, just adding scores and traits associations """
+    report_header("kipping EFO rebuilding, just adding scores and traits associations.")
+    update_efo_associations = OnlyUpdateEFOAssociations()
+    update_efo_associations.add_efo_trait_associations()
+
+
 def display_new_efo():
     """ Display the list of new Traits added with the new release """
     new_release = Release.objects.latest('date').date