🐛 fix bug with durations

tracex/extraction/logic/modules/module_patient_journey_generator.py

@@ -82,8 +82,9 @@ def __get_date():
                 "content": "Please give me one date between 01/01/2020 and 01/09/2023.",
             }
         ]
-        country = u.query_gpt(messages=message, max_tokens=50, temperature=0.5)
-        return country
+        date = u.query_gpt(messages=message, max_tokens=50, temperature=0.5)
+        print(date)
+        return date
 
     @staticmethod
     def __get_life_circumstances(sex):

tracex/extraction/logic/orchestrator.py

@@ -99,7 +99,6 @@ def generate_patient_journey(self):
         module = self.configuration.modules["patient_journey_generation"]()
         module.execute(self.data, self.configuration.patient_journey)
         self.configuration.update(patient_journey=module.result)
-        return module.result
 
     # Will be deleted when dataframes are implemented
     @staticmethod

tracex/extraction/logic/utils.py

@@ -61,7 +61,7 @@ def get_all_xes_output_path(
     if not (is_test or is_extracted):
         append_csv()
         all_traces_xes_path = Conversion.create_xes(
-            CSV_ALL_TRACES, name=xes_name, key=activity_key
+            csv_file=CSV_ALL_TRACES, name=xes_name, key=activity_key
         )
     else:
         all_traces_xes_path = (
@@ -112,9 +112,10 @@ def create_xes(csv_file, name, key):
         dataframe["caseID"] = dataframe["caseID"].astype(str)
         dataframe["start"] = pd.to_datetime(dataframe["start"])
         dataframe["end"] = pd.to_datetime(dataframe["end"])
-        dataframe["duration"] = pd.to_timedelta(dataframe["duration"])  # Bug: When filters are applied from the JourneyGenerationView, there seems to be some type of "offset"
+        # Bug on 118: When filters are applied from the JourneyGenerationView, there seems to be some type of "offset"
         # Hence I got the error "Could not convert 'Symptom Onset' to NumPy timedelta" when deselecting "Home" from
         # This error does not appear when configuring filters in the ResultView
+        dataframe["duration"] = pd.to_timedelta(dataframe["duration"])
         dataframe = dataframe.rename(
             columns={
                 key: "concept:name",

tracex/extraction/views.py

@@ -28,6 +28,12 @@ def redirect_to_selection(request):
     return redirect("selection")
 
 
+class SelectionView(generic.TemplateView):
+    """View for selecting a patient journey."""
+
+    template_name = "selection.html"
+
+
 class JourneyInputView(generic.FormView):
     """View for uploading a patient journey."""
 
@@ -47,12 +53,6 @@ def form_valid(self, form):
         return super().form_valid(form)
 
 
-class SelectionView(generic.TemplateView):
-    """View for selecting a patient journey."""
-
-    template_name = "selection.html"
-
-
 class JourneyGenerationView(generic.FormView):
     """View for generating a patient journey."""
 
@@ -69,11 +69,11 @@ def get_context_data(self, **kwargs):
         if IS_TEST:
             with open(str(utils.input_path / "journey_synth_covid_1.txt"), "r") as file:
                 journey = file.read()
+                orchestrator.configuration.update(patient_journey=journey)
         else:
+            # This automatically updates the configuration with the generated patient journey
             orchestrator.generate_patient_journey()
-            journey = orchestrator.configuration.patient_journey
 
-        orchestrator.configuration.update(patient_journey=journey)  # In case of test mode off, this is already executed from generate_patient_journey()
         context["generated_journey"] = orchestrator.configuration.patient_journey
         return context
 
@@ -82,6 +82,7 @@ def form_valid(self, form):
         cache.set("is_extracted", False)
         orchestrator = Orchestrator.get_instance()
         orchestrator.configuration.update(
+                patient_journey=orchestrator.configuration.patient_journey,  # This should not be necessary, unspecefied values should be unchanged
                 event_types=form.cleaned_data["event_types"],
                 locations=form.cleaned_data["locations"],
         )
@@ -159,11 +160,11 @@ def get_context_data(self, **kwargs):
     def form_valid(self, form):
         """Save the filter settings in the cache."""
         orchestrator = Orchestrator.get_instance()
-        configuration = {
-            "event_types": form.cleaned_data["event_types"],
-            "locations": form.cleaned_data["locations"],
-        }
-        orchestrator.configuration.update(**configuration)
+        orchestrator.configuration.update(
+            patient_journey=orchestrator.configuration.patient_journey,  # This should not be necessary, unspecefied values should be unchanged
+            event_types=form.cleaned_data["event_types"],
+            locations=form.cleaned_data["locations"],
+        )
         return super().form_valid(form)
 
     @staticmethod