Merge pull request #363 from 4dn-dcic/check_problematic_runs

Check problematic runs

chalicelib/check_setup.json

@@ -1483,6 +1483,38 @@
             }
         }
     },
+    "problematic_wfrs_status" : {
+        "title": "x) Errored Runs",
+        "group": "Pipeline checks",
+        "schedule": {
+            "hourly_checks": {
+                "cgap": {
+                    "kwargs": {"primary": true},
+                    "dependencies": []
+                },
+                "cgapwolf": {
+                    "kwargs": {"primary": true},
+                    "dependencies": []
+                }
+            }
+        }
+    },
+    "long_running_wfrs_status" : {
+        "title": "x) Long Running Runs",
+        "group": "Pipeline checks",
+        "schedule": {
+            "hourly_checks": {
+                "cgap": {
+                    "kwargs": {"primary": true},
+                    "dependencies": []
+                },
+                "cgapwolf": {
+                    "kwargs": {"primary": true},
+                    "dependencies": []
+                }
+            }
+        }
+    },
     "elastic_search_space" : {
         "title": "ES Disk Space Check",
         "group": "Elasticsearch checks",

chalicelib/checks/helpers/cgap_utils.py

@@ -1036,3 +1036,30 @@ def is_there_my_qc_metric(file_meta, qc_metric_name, my_auth):
         if qc_metric_name not in qc_results['display_title']:
             return False
     return True
+
+
+def fetch_wfr_associated(wfr_info):
+    """Given wfr embedded frame, find associated output files and qcs"""
+    wfr_as_list = []
+    wfr_as_list.append(wfr_info['uuid'])
+    if wfr_info.get('output_files'):
+        for o in wfr_info['output_files']:
+            if o.get('value'):
+                wfr_as_list.append(o['value']['uuid'])
+            elif o.get('value_qc'):
+                wfr_as_list.append(o['value_qc']['uuid'])
+    if wfr_info.get('output_quality_metrics'):
+        for qc in wfr_info['output_quality_metrics']:
+            if qc.get('value'):
+                wfr_as_list.append(qc['value']['uuid'])
+    if wfr_info.get('quality_metric'):
+        wfr_as_list.append(wfr_info['quality_metric']['uuid'])
+    return list(set(wfr_as_list))
+
+
+def string_to_list(string):
+    "Given a string that is either comma separated values, or a python list, parse to list"
+    for a_sep in "'\":[] ":
+        values = string.replace(a_sep, ",")
+    values = [i.strip() for i in values.split(',') if i]
+    return values