Merge pull request #58 from c3g/curation-entity-attribute

Curation entity attribute

backend/fms_core/management/commands/_update_field_value.py

@@ -0,0 +1,89 @@
+from django.apps import apps
+import reversion
+import json
+import logging
+from reversion.models import Version
+from fms_core.models import *
+
+# Parameters required for this curation
+ACTION = "action"                     # = update_field_value
+CURATION_INDEX = "curation_index"     # Number indicating the order in which this action was performed during the curation.
+COMMENT = "comment"                   # An optional comment to be stored in the logs
+ENTITY_MODEL = "entity_model"         # The name of the model for the target entity.
+ENTITY_DICT_ID = "entity_identifier"  # An array of dictionary that contains the fields required to uniquely identify the targeted entity.
+FIELD_NAME = "field_name"             # The name of the field that need to be updated.
+VALUE_OLD = "value_old"               # The old value of the entity's field (used for validation). Optional, validation skipped if empty.
+VALUE_NEW = "value_new"               # The new value of the entity's field.
+USER_ID = "requester_user_id"         # The user id of the person requesting the curation. Optional, if left empty use biobankadmin id.
+
+# Curation params template
+# { CURATION_INDEX: 1,
+#   ACTION: "update_field_value",
+#   COMMENT: "Dr. No asled the samples to be changed from BLOOD to PLASMA to correct an error at submission.",
+#   ENTITY_MODEL: "Sample",
+#   ENTITY_DICT_ID: [{"name": "Sample_test", "id": 42, "container_id": 5823}], # Any subset of fields that identifies uniquely the entity
+#   FIELD_NAME: "sample_kind",
+#   VALUE_OLD: 5, # Matches BLOOD
+#   VALUE_NEW: 9, # Matches PLASMA 
+#   USER_ID: 5
+# }
+
+# ENTITY_DICT_ID is an array to allow an identical change to be performed on multiple entities. If the changes are different,
+# add more field_value_actions to the curation.
+
+def update_field_value(params, log):
+    log.info("Action [" + str(params[CURATION_INDEX]) + "] Update Field Value started.")
+    log.info("Comment [" + str(params.get(COMMENT, "None")) + "].")
+    log.info("Targeted model : " + str(params[ENTITY_MODEL]))
+    log.info("Identifier used : " + str(params[ENTITY_DICT_ID]))
+    log.info("Field to update : " + str(params[FIELD_NAME]))
+    log.info("Old value : " + str(params.get(VALUE_OLD)))
+    log.info("New value : " + str(params[VALUE_NEW]))
+    log.info("Requester id : " + str(params.get(USER_ID)))
+
+    # initialize the curation
+    curation_code = params.get(CURATION_INDEX, "Invalid index")
+    error_found = False
+    model = params[ENTITY_MODEL]
+    id_array = params[ENTITY_DICT_ID]
+    field = params[FIELD_NAME]
+    old_value = params.get(VALUE_OLD)
+    new_value = params[VALUE_NEW]
+    user_id = params.get(USER_ID)
+
+
+    try:
+        entity_model = apps.get_model("fms_core", model)
+        count_updates = 0
+        for id in id_array:
+            try:
+                entity = entity_model.objects.get(**id)
+                try:
+                    db_old_value = getattr(entity, field)
+                    if old_value and old_value == db_old_value:
+                        setattr(entity, field, new_value)
+                        log.info(f"Updated model [{model}] id [{id} field [{field}] old value [{old_value}] new value [{new_value}].")
+                        if user_id:
+                            entity.save(requester_id=user_id) # Save using th id of the requester
+                        else:
+                            entity.save() # Save using the default admin user
+                        count_updates += 1
+                    else:
+                        log.error(f"Content of field [{field}] do not match the old_value expected [{old_value}].")
+                        error_found = True    
+                except AttributeError:
+                    log.error(f"Field [{field}] does not exist for model [{model}].")
+                    error_found = True  
+            except entity_model.DoesNotExist:
+                log.error(f"No entity found for id [{id}].")
+                error_found = True
+            except entity_model.MultipleObjectsReturned:
+                log.error(f"Multiple entities found for id [{id}]. Provide a unique identifier.")
+                error_found = True
+    except LookupError as e:
+        log.error("Model [" + str(model) + "] does not exist.")
+        error_found = True
+    if not error_found:
+        curation_code = None
+        log.info(f"Updated [{count_updates}] field values.")
+    return curation_code

backend/fms_core/management/commands/curation.py

@@ -13,10 +13,12 @@
 # Import the functions of the various curations available.
 from ._rollback_extraction import rollback_extraction
 from ._rollback_curation import rollback_curation
+from ._update_field_value import update_field_value
 
 # Available actions
 ACTION_ROLLBACK_CURATION = "rollback_curation"
 ACTION_ROLLBACK_EXTRACTION = "rollback_extraction"
+ACTION_UPDATE_FIELD_VALUE = "update_field_value"
 
 # Curation params template
 # [CURATION_ACTION_TEMPLATE_1,CURATION_ACTION_TEMPLATE_2,...]
@@ -35,7 +37,8 @@ class Command(BaseCommand):
 
     curation_switch = {
         ACTION_ROLLBACK_EXTRACTION: rollback_extraction,
-        ACTION_ROLLBACK_CURATION: rollback_curation
+        ACTION_ROLLBACK_CURATION: rollback_curation,
+        ACTION_UPDATE_FIELD_VALUE: update_field_value,
     }
 
     def init_logging(self, log_name, timestamp):

backend/fms_core/models/tracked_model.py

@@ -19,7 +19,11 @@ class Meta:
         abstract = True
 
     def save(self, *args, **kwargs):
-        user = get_current_user()
+        requester = kwargs.get("requester_id")
+        if requester:
+            user = User.objects.get(pk=requester)
+        else:
+            user = get_current_user()
         if not user or (user and not user.pk):
             user = User.objects.get(username=ADMIN_USERNAME)
         # if the instance has not been saved to the DB yet
@@ -29,7 +33,7 @@ def save(self, *args, **kwargs):
         # Set modified by user each time we save
         self.updated_by = user
 
-        super().save(*args, **kwargs)
+        super().save()
 
     def delete(self, *args, **kwargs):
         user = get_current_user()