endoreg-db 0.6.3__py3-none-any.whl → 0.8.1__py3-none-any.whl

endoreg_db/exceptions.py

@@ -0,0 +1,19 @@
+
+
+class InsufficientStorageError(Exception):
+    """Raised when there's not enough disk space for an operation."""
+    
+    def __init__(self, message, required_space=None, available_space=None):
+        super().__init__(message)
+        self.required_space = required_space
+        self.available_space = available_space
+
+
+class TranscodingError(Exception):
+    """Raised when video transcoding fails."""
+    pass
+
+
+class VideoProcessingError(Exception):
+    """Base class for video processing errors."""
+    pass

endoreg_db/forms/patient_finding_intervention_form.py

@@ -1,7 +1,7 @@
 from django import forms
 from endoreg_db.models import (
     Patient, PatientExamination, Finding, 
-    FindingLocationClassification, FindingMorphologyClassification, 
+    FindingClassification, FindingClassificationChoice,
     FindingIntervention, PatientFindingIntervention
 )
 
@@ -9,11 +9,10 @@ class PatientFindingInterventionForm(forms.ModelForm):
     patient = forms.ModelChoiceField(queryset=Patient.objects.all(), required=True)
     examination = forms.ModelChoiceField(queryset=PatientExamination.objects.none(), required=True)
     finding = forms.ModelChoiceField(queryset=Finding.objects.none(), required=True)
-    location = forms.ModelChoiceField(queryset=FindingLocationClassification.objects.none(), required=True)
-    location_choice = forms.ModelChoiceField(queryset=FindingLocationClassification.objects.none(), required=True)
-    morphology = forms.ModelChoiceField(queryset=FindingMorphologyClassification.objects.none(), required=True)
+    classification = forms.ModelChoiceField(queryset=FindingClassification.objects.none(), required=True)
+    classification_choice = forms.ModelChoiceField(queryset=FindingClassificationChoice.objects.none(), required=True)
     interventions = forms.ModelMultipleChoiceField(queryset=FindingIntervention.objects.none(), widget=forms.CheckboxSelectMultiple, required=True)
 
     class Meta:
         model = PatientFindingIntervention
-        fields = ["patient", "examination", "finding", "location", "location_choice", "morphology", "interventions"]
+        fields = ["patient", "examination", "finding", "classification", "classification_choice", "interventions"]

endoreg_db/forms/patient_form.py

@@ -1,11 +1,12 @@
 from django import forms
 from django.forms import ModelForm, Select
-from endoreg_db.models.persons.patient.patient import Patient
-from django import forms
-from django.forms import ModelForm, Select
-from endoreg_db.models.persons.patient.patient import Patient
-from endoreg_db.models.persons.gender import Gender  
-from endoreg_db.models.center import Center  
+from endoreg_db.models import (
+    Patient,
+    Gender,
+    Center
+)
+
+
 class PatientForm(ModelForm):
     gender = forms.ModelChoiceField(
         queryset=Gender.objects.all(),  

endoreg_db/forms/questionnaires/__init__.py

@@ -1 +1 @@
-from .tto_questionnaire import TtoQuestionnaireForm, TtoQuestionnaireCreate
+# from .tto_questionnaire import TtoQuestionnaireForm, TtoQuestionnaireCreate

endoreg_db/forms/questionnaires/tto_questionnaire.py

@@ -1,23 +1,23 @@
-# Path: endoreg_db/forms/questionnaires/tto_questionnaire.py
-from endoreg_db.models import TtoQuestionnaire
-from django import forms
+# # Path: endoreg_db/forms/questionnaires/tto_questionnaire.py
+# from endoreg_db.models import TtoQuestionnaire
+# from django import forms
 
-class TtoQuestionnaireForm(forms.ModelForm):
-    class Meta:
-        model = TtoQuestionnaire
-        fields = '__all__'
-        widgets = {
-            # Specify Bootstrap classes for other fields as needed
-            'patient_name': forms.TextInput(attrs={'class': 'form-control'}),
-            'birth_date': forms.DateInput(attrs={'class': 'form-control', 'type': 'date'}),
-            # You can continue to specify widgets for other fields
-        }
+# class TtoQuestionnaireForm(forms.ModelForm):
+#     class Meta:
+#         model = TtoQuestionnaire
+#         fields = '__all__'
+#         widgets = {
+#             # Specify Bootstrap classes for other fields as needed
+#             'patient_name': forms.TextInput(attrs={'class': 'form-control'}),
+#             'birth_date': forms.DateInput(attrs={'class': 'form-control', 'type': 'date'}),
+#             # You can continue to specify widgets for other fields
+#         }
 
 
-from django.views.generic.edit import CreateView
-from django.urls import reverse_lazy
+# from django.views.generic.edit import CreateView
+# from django.urls import reverse_lazy
 
-class TtoQuestionnaireCreate(CreateView):
-    model = TtoQuestionnaire
-    form_class = TtoQuestionnaireForm
-    success_url = reverse_lazy('questionnaire_success')  # Redirect to a success page after submission
+# class TtoQuestionnaireCreate(CreateView):
+#     model = TtoQuestionnaire
+#     form_class = TtoQuestionnaireForm
+#     success_url = reverse_lazy('questionnaire_success')  # Redirect to a success page after submission

endoreg_db/helpers/count_db.py

@@ -0,0 +1,45 @@
+# endoreg_db/helpers/count_db.py  
+from endoreg_db.models.state.audit_ledger import AuditLedger
+
+def _distinct(object_type: str, action: str):
+    """
+    Returns the count of distinct primary keys for records in AuditLedger filtered by object type and action.
+    
+    Args:
+        object_type: The type of object to filter by.
+        action: The action to filter by.
+    
+    Returns:
+        The number of unique object primary keys matching the specified type and action.
+    """
+    return (
+        AuditLedger.objects
+        .filter(object_type=object_type, action=action)
+        .values('object_pk')
+        .distinct()
+        .count()
+    )
+
+def collect_counters():
+    """
+    Returns a dictionary with statistical counts for cases, videos, annotations, anonymizations, images, and video statuses.
+    
+    The returned dictionary includes:
+    - "totalCases": Count of distinct created video files.
+    - "totalVideos": Count of distinct created video files.
+    - "totalAnnotations": Count of audit log entries where an annotation was added.
+    - "totalAnonymizations": Count of distinct video files that have been anonymized.
+    - "totalImages": Count of distinct created images.
+    - "videosCompleted": Count of distinct video files that have been validated.
+    - "videosAnonym": Count of distinct video files that have been anonymized.
+    """
+    return {
+        #TODO @maxhild can we remove the totalCases key?
+        # "totalCases":           _distinct("VideoFile", "created"),
+        "totalVideos":          _distinct("VideoFile", "created"),
+        "totalAnnotations":     AuditLedger.objects.filter(action="annotation_added").count(),
+        "totalAnonymizations":  _distinct("VideoFile", "anonymized"),
+        "totalImages":          _distinct("Image",     "created"),
+        "videosCompleted":      _distinct("VideoFile", "validated"),
+        "videosAnonym":         _distinct("VideoFile", "anonymized"),
+    }

endoreg_db/helpers/data_loader.py

@@ -0,0 +1,208 @@
+"""
+Data Loader Helpers and others
+"""
+from django.core.management import call_command
+from pathlib import Path
+ASSET_DIR = Path(__file__).resolve().parent.parent / "assets"
+
+def load_default_ai_model(): 
+    """
+    Loads the default AI model into the database using a predefined checkpoint file.
+    
+    This function constructs the path to the default AI model checkpoint and invokes the
+    Django management command `create_multilabel_model_meta` to register the model.
+    """
+    model_path = f"{ASSET_DIR.as_posix()}/colo_segmentation_RegNetX800MF_6.ckpt"
+    # Pass arguments individually to call_command
+    call_command(
+        "create_multilabel_model_meta",
+        "--model_path",
+        model_path
+    )
+
+def load_qualification_data():
+    """
+    Loads qualification data into the database using the corresponding Django management command.
+    """
+    call_command("load_qualification_data", )
+
+def load_shift_data():
+    """
+    Loads shift data into the database by invoking the corresponding Django management command.
+    """
+    call_command("load_shift_data", )
+
+def load_base_db_data():
+    """
+    Loads the base database data by invoking the corresponding Django management command.
+    """
+    call_command("load_base_db_data", )
+
+def load_information_source():
+    """
+    Loads information source data into the database by invoking the corresponding Django management command.
+    """
+    call_command("load_information_source", )
+
+def load_risk_data():
+    """
+    Loads risk data into the database by invoking the corresponding Django management command.
+    """
+    call_command("load_risk_data", )
+
+def load_center_data():
+    """
+    Loads center data into the database by invoking the corresponding Django management command.
+    """
+    call_command("load_center_data", )
+
+def load_endoscope_data():
+    """
+    Loads endoscope data into the database by invoking the corresponding Django management command.
+    """
+    call_command("load_endoscope_data", )
+
+def load_distribution_data():
+    """
+    Loads distribution data into the database by invoking the corresponding Django management command.
+    """
+    call_command("load_distribution_data", )
+
+def load_gender_data():
+    """
+    Loads gender data into the database by invoking the corresponding Django management command.
+    """
+    call_command("load_gender_data", )
+
+def load_report_reader_flag_data():
+    """
+    Loads the report reader flag data into the database using the corresponding management command.
+    """
+    call_command("load_report_reader_flag_data", )
+    
+def load_pdf_type_data():
+    """
+    Loads PDF type data into the database by invoking the corresponding Django management command.
+    """
+    call_command("load_pdf_type_data", )
+    
+def load_unit_data():
+    """
+    Loads unit data into the database by invoking the corresponding Django management command.
+    """
+    call_command("load_unit_data", )
+    
+def load_disease_data():
+    """
+    Loads disease data into the database using the corresponding Django management command.
+    """
+    call_command("load_disease_data", )
+    
+def load_event_data():
+    """
+    Loads event data into the database by invoking the corresponding Django management command.
+    """
+    call_command("load_event_data", )
+    
+def load_organ_data():
+    """
+    Loads organ data into the database by invoking the corresponding Django management command.
+    """
+    call_command("load_organ_data", )
+    
+def load_contraindication_data():
+    """
+    Loads contraindication data into the database using the corresponding management command.
+    """
+    call_command("load_contraindication_data", )
+    
+def load_examination_data():
+    """
+    Loads examination data into the database using the corresponding Django management command.
+    """
+    call_command("load_examination_data", )
+    
+def load_lab_value_data():
+    """
+    Loads laboratory value data into the database using the corresponding Django management command.
+    """
+    call_command("load_lab_value_data", )
+    
+def load_finding_data():
+    """
+    Loads finding data into the database by invoking the corresponding Django management command.
+    """
+    call_command("load_finding_data", )
+    
+def load_examination_indication_data():
+    """
+    Loads examination indication data into the database using the corresponding Django management command.
+    """
+    call_command("load_examination_indication_data", )
+    
+def load_medication_data():
+    """
+    Loads medication data into the database using the corresponding Django management command.
+    """
+    call_command("load_medication_data", )
+
+def load_requirement_data():
+
+    """
+    Loads requirement data into the database by invoking the corresponding Django management command.
+    """
+    call_command("load_requirement_data", )
+
+def load_ai_model_label_data():
+    """
+    Loads AI model label data into the database by invoking the corresponding Django management command.
+    """
+    call_command("load_ai_model_label_data", )
+
+def load_ai_model_data():    
+    """
+    Loads AI model data into the database by invoking the corresponding Django management command.
+    """
+    call_command("load_ai_model_data", )
+
+def load_green_endoscopy_wuerzburg_data():
+    """
+    Loads the Green Endoscopy Wuerzburg dataset into the database using the corresponding Django management command.
+    """
+    call_command("load_green_endoscopy_wuerzburg_data", )
+
+def load_data():
+    """
+    Loads all predefined data sets into the database in the required sequence.
+    
+    Calls individual data loading functions in a specific order to ensure that dependencies between data sets are respected.
+    """
+    
+    load_information_source()
+    load_risk_data()
+    load_center_data()
+    load_endoscope_data()
+    load_distribution_data()
+
+    load_gender_data()
+    load_report_reader_flag_data()
+    load_pdf_type_data()
+    load_unit_data()
+    load_disease_data()
+    load_event_data()
+    load_organ_data()
+    load_contraindication_data()
+    load_examination_data()
+    load_lab_value_data()
+    load_finding_data()
+    load_examination_indication_data()
+    load_medication_data()
+    load_requirement_data()
+
+    load_ai_model_label_data()
+    load_ai_model_data()
+
+    load_green_endoscopy_wuerzburg_data()
+
+    
+