Feature/discard gsms (#9)

kilombo/model/study_hierarchy.py

@@ -1,4 +1,7 @@
+import logging
+
 from kilombo.model.failed_study import FailedStudy
+from kilombo.model.failed_study_reason import FailedStudyReason
 
 
 class StudyHierarchy:
@@ -15,6 +18,9 @@ def __init__(self, pending=None):
  def add_pending_study(self, study_id):
  self.pending[study_id] = {}
 
+ def remove_study(self, study_id):
+ del self.pending[study_id]
+
  def move_study_to_failed(self, failed_study: FailedStudy):
  self.failed[failed_study.study_id] = self.pending[failed_study.study_id]
  self.failed[failed_study.study_id] = failed_study.reason
@@ -36,12 +42,24 @@ def add_srrs(self, study_id, srrs: []):
  self.successful[study_id]["srrs"] = srrs
 
  def reconcile(self):
- successful_study_ids_to_remove = [study_id[0] for study_id in self.successful.items() if study_id[0] in self.pending.keys()]
- failed_study_ids_to_remove = [study_id[0] for study_id in self.failed.items() if study_id[0] in self.pending.keys()]
+ successful_study_ids_to_remove_from_pending = [study_id[0] for study_id in self.successful.items() if study_id[0] in self.pending.keys()]
+ failed_study_ids_to_remove_from_pending = [study_id[0] for study_id in self.failed.items() if study_id[0] in self.pending.keys()]
 
- study_ids = successful_study_ids_to_remove + failed_study_ids_to_remove
+ study_ids = successful_study_ids_to_remove_from_pending + failed_study_ids_to_remove_from_pending
 
  for study_id in study_ids:
  self.pending.pop(study_id)
+
  if len(self.pending) == 0:
  del self.pending
+
+ self._clean_gsms()
+
+ def _clean_gsms(self):
+ gsms_to_remove = [study_id for study_id in self.failed.keys() if self.failed[study_id] == FailedStudyReason.GSM_FOUND]
+ if gsms_to_remove:
+ logging.debug(f"GSMs to remove: {gsms_to_remove}")
+ for study_id in gsms_to_remove:
+ self.failed.pop(study_id)
+ self.count_failed -= 1
+ self.count_total -= 1