fixed a bug where heredicare annotation yielded an error

GC-HBOC · Nov 20, 2023 · 6d06f98 · 6d06f98
1 parent bca30cb
commit 6d06f98
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Showing 2 changed files with 22 additions and 18 deletions.
diff --git a/src/annotation_service/annotation_jobs/heredicare_job.py b/src/annotation_service/annotation_jobs/heredicare_job.py
@@ -54,23 +54,26 @@ def save_to_db(self, info, variant_id, conn):
                 if tries > 0:
                     time.sleep(30 * tries)
             if status == "error":
-                raise Exception("There was an error during variant retrieval from heredicare: " + str(message))
-
-            n_fam = heredicare_variant["N_FAM"]
-            n_pat = heredicare_variant["N_PAT"]
-            consensus_class = heredicare_variant["PATH_TF"] if heredicare_variant["PATH_TF"] != "-1" else None
-            comment = heredicare_variant["VUSTF_15"] if heredicare_variant["VUSTF_15"] is not None else ''
-            comment = comment.strip()
-            comment = comment if comment != '' else None
-            classification_date = heredicare_variant["VUSTF_DATUM"] if heredicare_variant["VUSTF_DATUM"] != '' else None
-            if classification_date is not None:
-                try:
-                    classification_date = datetime.strptime(classification_date, "%d.%m.%Y")
-                except:
-                    raise Exception("The date could not be saved in the database. Format should be dd.mm.yyyy, but was: " + str(classification_date))
-
-            conn.insert_heredicare_annotation(variant_id, vid, n_fam, n_pat, consensus_class, classification_date, comment)
-
-            return status_code, err_msg
+                err_msg += "There was an error during variant retrieval from heredicare: " + str(message)
+                status_code = 1
+            else:
+                n_fam = heredicare_variant["N_FAM"]
+                n_pat = heredicare_variant["N_PAT"]
+                consensus_class = heredicare_variant["PATH_TF"] if heredicare_variant["PATH_TF"] != "-1" else None
+                comment = heredicare_variant["VUSTF_15"] if heredicare_variant["VUSTF_15"] is not None else ''
+                comment = comment.strip()
+                comment = comment if comment != '' else None
+                classification_date = heredicare_variant["VUSTF_DATUM"] if heredicare_variant["VUSTF_DATUM"] != '' else None
+                if classification_date is not None:
+                    try:
+                        classification_date = datetime.strptime(classification_date, "%d.%m.%Y")
+                    except:
+                        err_msg += "The date could not be saved in the database. Format should be dd.mm.yyyy, but was: " + str(classification_date)
+                        status_code = 1
+
+                if status_code == 0:
+                    conn.insert_heredicare_annotation(variant_id, vid, n_fam, n_pat, consensus_class, classification_date, comment)
+
+        return status_code, err_msg
 
 
diff --git a/src/annotation_service/main.py b/src/annotation_service/main.py
@@ -168,6 +168,7 @@ def process_one_request(annotation_queue_id, job_config = get_default_job_config
 
             info = line.split('\t')[7]
             for job in all_jobs:
+                print(job.job_name)
                 status_code, err_msg = job.save_to_db(info, variant_id, conn=conn)
                 if status_code > 0:
                     status = "error"