Dev (#32)

* Adding a raise for unique constraint failed on readset when ingesting run processing

* Moving the raise for unique constraint failed on readset when ingesting run processing when flushing

* Checking which readset(s) in causing the unique constraint failure

project_tracking/db_action.py

@@ -59,7 +59,7 @@ def __init__(self, message=None, table=None, attribute=None, query=None):
         if message:
             self.message = message
         else:
-            self.message = f"'{table}' with '{attribute}' '{query}' doesn't exist on database"
+            self.message = f"'{table}' with '{attribute}' '{query}' doesn't exist in the database"
 
 class RequestError(Error):
     """RequestError"""
@@ -70,6 +70,34 @@ def __init__(self, message=None, argument=None):
         else:
             self.message = f"For current request '{argument}' is required"
 
+class UniqueConstraintError(Error):
+    """UniqueConstraintError"""
+    def __init__(self, message=None, entity=None, attribute=None, value=None):
+        super().__init__(message)
+        if message:
+            self.message = message
+        else:
+            self.message = f"'{entity}' with '{attribute}' '{value}' already exists in the database and '{attribute}' has to be unique"
+
+def unique_constraint_error(session, json_format, ingest_data):
+    """
+    When unique constraint errors, checks which entity is causing the error and returns it/them
+    """
+    ret = []
+    if json_format == "run_processing":
+        for patient_json in ingest_data[vb.PATIENT]:
+            for sample_json in patient_json[vb.SAMPLE]:
+                for readset_json in sample_json[vb.READSET]:
+                    readset_name = readset_json[vb.READSET_NAME]
+                    stmt = (
+                        select(Readset)
+                        .where(Readset.name.is_(readset_name))
+                        )
+                    if session.scalars(stmt).unique().all():
+                        ret.append(f"'Readset' with 'name' '{readset_name}' already exists in the database and 'name' has to be unique")
+    return ret
+
+
 def name_to_id(model_class, name, session=None):
     """
     Converting a given name into its id
@@ -604,7 +632,6 @@ def ingest_run_processing(project_id: str, ingest_data, session=None):
                     kit_expiration_date=kit_expiration_date,
                     session=session
                     )
-                # Let this fails if readset already exists.
                 readset = Readset(
                     name=readset_json[vb.READSET_NAME],
                     lane=LaneEnum(readset_json[vb.READSET_LANE]),
@@ -665,7 +692,12 @@ def ingest_run_processing(project_id: str, ingest_data, session=None):
                         )
 
             session.add(readset)
-            session.flush()
+            try:
+                session.flush()
+            except exc.IntegrityError as error:
+                session.rollback()
+                message = unique_constraint_error(session, "run_processing", ingest_data)
+                raise UniqueConstraintError(message=message) from error
 
     operation_id = operation.id
     job_id = job.id