Merge pull request #143 from bptlab/improvement/136-extraction-pipeline

Improvement/136 extraction pipeline

requirements.txt

@@ -6,3 +6,4 @@ plotly~=5.22.0
 pandas~=2.1.3
 numpy~=1.26.2
 jinja2~=3.1.4
+regex~=2024.5.15

tracex_project/extraction/admin.py

@@ -1,25 +1,59 @@
 """Admin file for extraction app."""
+from typing import Union
+
 from django.contrib import admin
+
 from extraction.models import Event, PatientJourney, Prompt, Trace, Cohort, Metric
 
 
 class CohortInline(admin.StackedInline):
-    """Inline for the Cohort model, used to display the related Cohort object in the Trace admin page."""
+    """
+    Django admin interface for the Cohort model.
+
+    This inline admin interface is used to manage Cohort instances directly from the Trace admin page.
+    No extra blank forms are displayed for adding new Cohort instances, and deletion of Cohort instances
+    from the Trace admin page is not allowed.
+
+    Attributes:
+        model: Specifies the model that this inline admin interface is for.
+        extra: Defines how many extra blank forms are displayed on the admin page when a new Trace is created.
+        can_delete: Determines whether the deletion of instances of the model is allowed from the admin interface.
+    """
 
     model = Cohort
     extra = 0
     can_delete = False
 
 
 class TraceInline(admin.TabularInline):
-    """Inline for the Trace model, used to display the related Trace objects in the PatientJourney admin page."""
+    """
+    Django admin interface for the Trace model.
+
+    This inline admin interface is used to manage Trace instances directly from the PatientJourney admin page.
+    No extra blank forms are displayed for adding new Trace instances.
+
+    Attributes:
+        model: Specifies the model that this inline admin interface is for.
+        extra: Defines how many extra blank forms are displayed on the admin page when a new PatientJourney is created.
+    """
 
     model = Trace
     extra = 0  # Controls the number of empty forms displayed for adding related objects
 
 
 class EventInline(admin.TabularInline):
-    """Inline for the Event model, used to display the related Event objects in the Trace admin page."""
+    """
+    Django admin interface for the Event model.
+
+    This inline admin interface is used to manage Event instances directly from the Trace admin page.
+    No extra blank forms are displayed for adding new Event instances. Certain fields related to metrics
+    are read-only.
+
+    Attributes:
+        model: Specifies the model that this inline admin interface is for.
+        extra: Defines how many extra blank forms are displayed on the admin page when a new Trace is created.
+        readonly_fields: Specifies which fields on the admin interface are read-only.
+    """
 
     model = Event
     extra = 0
@@ -29,36 +63,39 @@ class EventInline(admin.TabularInline):
         "metrics_correctness_confidence",
     )
 
-    def metrics_activity_relevance(self, obj):
+    @staticmethod
+    def metrics_activity_relevance(obj: Event) -> Union[str, int]:
         """Returns the activity relevance metric for the event."""
         return obj.metrics.activity_relevance if hasattr(obj, "metrics") else "-"
 
-    def metrics_timestamp_correctness(self, obj):
+    @staticmethod
+    def metrics_timestamp_correctness(obj: Event) -> Union[str, int]:
         """Returns the timestamp correctness metric for the event."""
         return obj.metrics.timestamp_correctness if hasattr(obj, "metrics") else "-"
 
-    def metrics_correctness_confidence(self, obj):
+    @staticmethod
+    def metrics_correctness_confidence(obj: Event) -> Union[str, int]:
         """Returns the correctness confidence metric for the event."""
         return obj.metrics.correctness_confidence if hasattr(obj, "metrics") else "-"
 
 
 @admin.register(PatientJourney)
 class PatientJourneyAdmin(admin.ModelAdmin):
-    """Admin page for the PatientJourney model."""
+    """Django admin interface for managing PatientJourney instances and related Trace instances."""
 
     inlines = [TraceInline]
 
 
 @admin.register(Trace)
 class TraceAdmin(admin.ModelAdmin):
-    """Admin page for the Trace model."""
+    """Django admin interface for managing Trace instances and related Cohort and Event instances."""
 
     inlines = [CohortInline, EventInline]
 
 
 @admin.register(Event)
 class EventAdmin(admin.ModelAdmin):
-    """Admin page for the Event model."""
+    """Django admin interface for managing Event instances."""
 
 
 admin.site.register(Metric)

tracex_project/extraction/apps.py

@@ -3,7 +3,16 @@
 
 
 class ExtractionConfig(AppConfig):
-    """App configuration class for django UI."""
+    """
+    Configuration class for the 'extraction' Django application.
+
+    This class allows customization of application configuration. It sets the default type of auto-created
+    primary key fields to be 64-bit integers and specifies the name of the application.
+
+    Attributes:
+        default_auto_field: The type of auto-created primary key fields for models in this application.
+        name: The name of the application that is being configured.
+    """
 
     default_auto_field = "django.db.models.BigAutoField"
     name = "extraction"