endoreg-db 0.6.0__py3-none-any.whl → 0.6.2__py3-none-any.whl

endoreg_db/data/resource/green_endoscopy_dashboard_Resource.yaml

@@ -0,0 +1,15 @@
+- fields:
+    name: gas
+    name_de: Erdgas
+    name_en: Gas
+  model: endoreg_db.Resource
+- fields:
+    name: oil
+    name_de: "Heizöl"
+    name_en: Oil
+  model: endoreg_db.Resource
+- fields:
+    name: electricity
+    name_de: Strom
+    name_en: Electricity
+  model: endoreg_db.Resource

endoreg_db/data/transport_route/green_endoscopy_dashboard_TransportRoute.yaml

@@ -0,0 +1,12 @@
+- fields:
+    distance: 1000
+    emission_factor: transport_product_emission_generic_europe
+    name: generic_europe
+    unit: kilometer
+  model: endoreg_db.TransportRoute
+- fields:
+    distance: 10000
+    emission_factor: transport_product_emission_generic_overseas
+    name: generic_overseas
+    unit: kilometer
+  model: endoreg_db.TransportRoute

endoreg_db/data/unit/concentration.yaml

@@ -0,0 +1,92 @@
+# g / l and equivalents; ascending by gram, then ascending by liter
+- model: endoreg_db.unit
+  fields: 
+    name: "picogram per mililiter"
+    name_de: "Pikogramm pro Mililiter"
+    name_en: "picogram per mililiter"
+    abbreviation: "pg/ml"
+
+
+- model: endoreg_db.unit
+  fields:
+    name: "nanogram per mililiter"
+    name_de: "Nanogramm pro Mililiter"
+    name_en: "nanogram per mililiter"
+    abbreviation: "ng/ml"
+
+- model: endoreg_db.unit
+  fields:
+    name: "nanogram per deciliter"
+    name_de: "Nanogramm pro Deziliter"
+    name_en: "nanogram per deciliter"
+
+- model: endoreg_db.unit
+  fields:
+    name: "microgram per mililiter"
+    name_de: "Microgramm pro Mililiter"
+    name_en: "microgram per mililiter"
+    abbreviation: "µg/ml"
+
+- model: endoreg_db.Unit
+  fields:
+    name: "microgram per deciliter"
+    abbreviation: "µg/dL"
+    name_de: "Mikrogramm pro Deziliter"
+    name_en: "microgram per deciliter"
+    description: "Micrograms per deciliter, a unit of measurement for concentration."
+
+- model: endoreg_db.unit
+  fields:
+    name: "gram per deciliter"
+    name_de: "Gramm pro Deziliter"
+    name_en: "gram per deciliter"
+  
+
+# mol / l
+- model: endoreg_db.Unit
+  fields:
+    name: "milimole per liter"
+    abbreviation: "mmol/L"
+    name_de: "milimol pro Liter"
+    name_en: "milimole per liter"
+    description: "milimoles per liter, a unit of measurement for concentration in blood."
+
+- model: endoreg_db.Unit
+  fields:
+    name: "miliequivalent per liter"
+    abbreviation: "mEq/L"
+    name_de: "miliäquivalent pro Liter"
+    name_en: "miliequivalent per liter"
+    description: "miliequivalents per liter, used for electrolytes concentration."
+
+- model: endoreg_db.Unit
+  fields:
+    name: "miligram per deciliter"
+    abbreviation: "mg/dL"
+    name_de: "miligramm pro Deziliter"
+    name_en: "miligram per deciliter"
+    description: "miligrams per deciliter, commonly used for various blood measurements."
+
+# x 10^9 per liter
+- model: endoreg_db.Unit
+  fields:
+    name: "x 10^9 per liter"
+    abbreviation: "x 10^9/L"
+    name_de: "x 10^9 pro Liter"
+    name_en: "x 10^9 per liter"
+    description: "Number of cells per liter, often used for blood cell counts."
+
+# U / l
+- model: endoreg_db.unit
+  fields:
+    name: "units per liter"
+    name_de: "Units pro Liter"
+    name_en: "units per liter"
+    abbreviation: "U/l"
+
+- model: endoreg_db.unit
+  fields:
+    name: "microinternational units per mililiter"
+    name_de: "Mikro-Internationale Einheiten pro Mililiter"
+    name_en: "micro-international units per mililiter"
+    abbreviation: "µU/ml"

endoreg_db/data/unit/data.yaml

@@ -0,0 +1,17 @@
+- model: endoreg_db.Unit
+  fields:
+    name: "liters-per-minute"
+    abbreviation: "l/min"
+    name_de: "Liter pro Minute"
+    name_en: "Liters per Minute"
+    description: "liters per minute"
+
+
+# kilowatt-hours
+- model: endoreg_db.Unit
+  fields:
+    name: "kilowatt-hours"
+    abbreviation: "kWh"
+    name_de: "Kilowattstunden"
+    name_en: "Kilowatt-hours"
+    description: "kilowatt-hours"

endoreg_db/data/unit/length.yaml

@@ -0,0 +1,31 @@
+- model: endoreg_db.Unit
+  fields:
+    name: "milimeter"
+    abbreviation: "mm"
+    name_de: "milimeter"
+    name_en: "milimeter"
+    description: "milimeters"
+
+- model: endoreg_db.Unit
+  fields:
+    name: "centimeter"
+    abbreviation: "cm"
+    name_de: "Zentimeter"
+    name_en: "Centimeter"
+    description: "centimeters"
+
+- model: endoreg_db.Unit
+  fields:
+    name: "meter"
+    abbreviation: "m"
+    name_de: "Meter"
+    name_en: "Meter"
+    description: "meters"
+
+- model: endoreg_db.Unit
+  fields:
+    name: "kilometer"
+    abbreviation: "km"
+    name_de: "Kilometer"
+    name_en: "Kilometer"
+    description: "kilometers"

endoreg_db/data/unit/misc.yaml

@@ -0,0 +1,20 @@
+- model: endoreg_db.unit
+  fields:
+    name: "percent"
+    abbreviation: "%"
+    name_de: "Prozent"
+    name_en: "percent"
+
+- model: endoreg_db.unit
+  fields:
+    name: "ratio"
+    abbreviation: ""
+    name_de: "Ratio"
+    name_en: "ratio"
+
+- model: endoreg_db.unit
+  fields:
+    name: "dose"
+    name_de: "Dosierung(en)"
+    name_en: "dose(s)"
+    abbreviation: ""

endoreg_db/data/unit/rate.yaml

@@ -0,0 +1,6 @@
+- model: endoreg_db.unit
+  fields:
+    name: "mililiter per minute per 1.73m^2"
+    name_de: "ml/min/1.73m²"
+    name_en: "ml/min/1.73m²"
+    abbreviation: "ml/min/1.73m²"

endoreg_db/data/unit/time.yaml

@@ -0,0 +1,13 @@
+- model: endoreg_db.unit
+  fields:
+    name: "seconds"
+    abbreviation: "s"
+    name_de: "Sekunden"
+    name_en: "Sekunden"
+
+- model: endoreg_db.unit
+  fields:
+    name: "minutes"
+    abbreviation: "min"
+    name_de: "Minuten"
+    name_en: "Minutes"

endoreg_db/data/unit/volume.yaml

@@ -0,0 +1,35 @@
+# Units/data.yaml
+
+# femptolitre
+- model: endoreg_db.Unit
+  fields:
+    name: "femtoliter"
+    abbreviation: "fl"
+    name_de: "Femtoliter"
+    name_en: "Femtolitre"
+    description: "femtoliters"
+
+- model: endoreg_db.Unit
+  fields:
+    name: "mililiter"
+    abbreviation: "ml"
+    name_de: "mililiter"
+    name_en: "mililiter"
+    description: "mililiters"
+
+- model: endoreg_db.Unit
+  fields:
+    name: "liter"
+    abbreviation: "l"
+    name_de: "Liter"
+    name_en: "Liter"
+    description: "liters"
+
+# cubic_meter
+- model: endoreg_db.Unit
+  fields:
+    name: "cubic_meter"
+    abbreviation: "m³"
+    name_de: "Kubikmeter"
+    name_en: "Cubic Meter"
+    description: "cubic meters"

endoreg_db/data/unit/weight.yaml

@@ -0,0 +1,38 @@
+- model: endoreg_db.unit
+  fields:
+    name: "picogram"
+    abbreviation: "pg"
+    name_de: "Picogramm"
+    name_en: "Picogram"
+
+- model: endoreg_db.Unit
+  fields:
+    name: "microgram"
+    abbreviation: "µg"
+    name_de: "Mikrogramm"
+    name_en: "Microgram"
+    description: "micrograms"
+
+- model: endoreg_db.Unit
+  fields:
+    name: "miligram"
+    abbreviation: "mg"
+    name_de: "miligramm"
+    name_en: "miligram"
+    description: "miligrams"
+
+- model: endoreg_db.Unit
+  fields:
+    name: "gram"
+    abbreviation: "g"
+    name_de: "Gramm"
+    name_en: "Gram"
+    description: "grams"
+
+- model: endoreg_db.Unit
+  fields:
+    name: "kilogram"
+    abbreviation: "kg"
+    name_de: "Kilogramm"
+    name_en: "Kilogram"
+    description: "kilograms"

endoreg_db/data/waste/data.yaml

@@ -0,0 +1,12 @@
+- model: endoreg_db.Waste
+  fields:
+    name: general_waste
+    name_de: Allgemeiner Abfall
+    name_en: General Waste
+
+- model: endoreg_db.Waste
+  fields:
+    name: medical_waste
+    name_de: Medizinischer Abfall
+    name_en: Medical Waste
+    

endoreg_db/forms/__init__.py

@@ -0,0 +1,5 @@
+from .unit import Unit
+from .settings import ActiveModelForm
+from .questionnaires import *
+from .patient_form import PatientForm
+

endoreg_db/forms/examination_form.py

@@ -0,0 +1,11 @@
+from django import forms
+from endoreg_db.models.examination.examination import Examination
+
+class ExaminationForm(forms.ModelForm):
+    class Meta:
+        model = Examination
+        fields = '__all__'
+        widgets = {
+            'date': forms.DateInput(attrs={'type': 'date', 'class': 'form-control'}),
+            'time': forms.TimeInput(attrs={'type': 'time', 'class': 'form-control'}),
+        }

endoreg_db/forms/patient_finding_intervention_form.py

@@ -0,0 +1,19 @@
+from django import forms
+from endoreg_db.models import (
+    Patient, PatientExamination, Finding, 
+    FindingLocationClassification, FindingMorphologyClassification, 
+    FindingIntervention, PatientFindingIntervention
+)
+
+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)
+    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"]

endoreg_db/forms/patient_form.py

@@ -0,0 +1,26 @@
+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  
+class PatientForm(ModelForm):
+    gender = forms.ModelChoiceField(
+        queryset=Gender.objects.all(),  
+        empty_label="Select Gender",  
+        widget=Select(attrs={'class': 'form-control'})
+    )
+    center = forms.ModelChoiceField(
+        queryset=Center.objects.all(),  
+        empty_label="Select Center",  
+        widget=Select(attrs={'class': 'form-control'})
+    )
+
+    class Meta:
+        model = Patient
+        fields = '__all__'
+        widgets = {
+            'dob': forms.DateInput(attrs={'type': 'date', 'class': 'form-control'}),
+        }

endoreg_db/forms/questionnaires/__init__.py

@@ -0,0 +1 @@
+from .tto_questionnaire import TtoQuestionnaireForm, TtoQuestionnaireCreate

endoreg_db/forms/questionnaires/tto_questionnaire.py

@@ -0,0 +1,23 @@
+# 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
+        }
+
+
+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

endoreg_db/forms/settings/__init__.py

@@ -0,0 +1,8 @@
+# forms.py
+from django import forms
+from endoreg_db.models import ActiveModel
+
+class ActiveModelForm(forms.ModelForm):
+    class Meta:
+        model = ActiveModel
+        fields = ["model_meta"]  # Or list the specific fields you want to include in the form.

endoreg_db/forms/unit.py

@@ -0,0 +1,6 @@
+from django import forms
+from ..models import Unit
+
+class UnitForm(forms.Form):
+    class Meta:
+        model = Unit

endoreg_db/management/commands/_load_model_template.py

@@ -0,0 +1,41 @@
+from django.conf import settings
+from django.core.management.base import BaseCommand
+from reports.models import Intervention, InterventionType  # Replace 'your_app_name' with the actual app name
+import os
+from reports.dataloader_utils import load_model_data
+
+SOURCE_DIR = None # e.g. settings.DATA_DIR_INTERVENTION
+
+IMPORT_MODELS = [ # string as model key, serves as key in IMPORT_METADATA
+]
+
+IMPORT_METADATA = {
+    # "": { # same as model name in "import models", e.g. "Intervention"
+    #     "dir": os.path.join(SOURCE_DIR,""), # e.g. "interventions"
+    #     "model": None, # e.g. Intervention
+    #     "foreign_keys": [], # e.g. ["intervention_types"]
+    #     "foreign_key_models": [] # e.g. [InterventionType]
+    # },
+}
+
+class Command(BaseCommand):
+    help = """Load all .yaml files in the data/intervention directory
+    into the Intervention and InterventionType model"""
+
+    def add_arguments(self, parser):
+        parser.add_argument(
+            '--verbose',
+            action='store_true',
+            help='Display verbose output',
+        )
+
+    def handle(self, *args, **options):
+        verbose = options['verbose']
+        for model_name in IMPORT_MODELS:
+            _metadata = IMPORT_METADATA[model_name]
+            load_model_data(
+                self,
+                model_name,
+                _metadata,
+                verbose
+            )

endoreg_db/management/commands/delete_all.py

@@ -0,0 +1,18 @@
+from django.core.management.base import BaseCommand
+from django.apps import apps
+from django.db import transaction
+
+class Command(BaseCommand):
+    help = 'Deletes all objects from all models in the "endoreg_db" app.'
+
+    def handle(self, *args, **options):
+        app_models = apps.get_models()
+        app_models = [model for model in app_models if "endoreg_db" in model._meta.app_label]  # Filter models by the "endoreg_db" app
+        for model in app_models:
+            with transaction.atomic():  # Use a separate transaction for each model
+                try:
+                    model.objects.all().delete()
+                    self.stdout.write(self.style.SUCCESS(f'Successfully deleted all objects in {model._meta.db_table}'))
+                except Exception as e:
+                    # This catches exceptions and continues with the next model
+                    self.stdout.write(self.style.ERROR(f'Error deleting objects in {model._meta.db_table}: {e}'))

endoreg_db/management/commands/fetch_legacy_image_dataset.py

@@ -0,0 +1,32 @@
+# command to fetch the legacy dataset and save it to a json file.
+from django.core.management.base import BaseCommand, CommandError
+from endoreg_db.queries import generate_legacy_dataset_output 
+import json
+
+LABELSET_NAME = "multilabel_classification"
+LABELSET_VERSION = 0
+
+class Command(BaseCommand):
+    help = 'Fetches the legacy dataset and saves it to a jsonl file'
+
+    def handle(self, *args, **options):
+        output, labelset = generate_legacy_dataset_output(LABELSET_NAME, LABELSET_VERSION)
+        # output is a list of dicts, each dict is an image
+        labels_in_order = labelset.get_labels_in_order()
+
+        # write to file
+        with open('legacy_dataset.jsonl', 'w') as f:
+            for img_dict in output:
+                f.write(json.dumps(img_dict) + '\n')
+
+
+        _dict = {
+            "labels": [label.name for label in labels_in_order],
+            "name": LABELSET_NAME,
+            "version": LABELSET_VERSION
+        }
+
+        with open('legacy_dataset_info.json', 'w') as f:
+            f.write(json.dumps(_dict))
+
+        self.stdout.write(self.style.SUCCESS('Successfully fetched and saved the legacy dataset'))

endoreg_db/management/commands/fix_auth_permission.py

@@ -0,0 +1,20 @@
+from django.core.management.base import BaseCommand
+from django.contrib.auth.models import Permission
+from django.contrib.contenttypes.models import ContentType
+from django.apps import apps
+
+class Command(BaseCommand):
+    help = 'Sets up default permissions for each model in the app.'
+
+    def handle(self, *args, **options):
+        for model in apps.get_models():
+            content_type = ContentType.objects.get_for_model(model)
+            permissions = ['view', 'add', 'change', 'delete']
+            for perm in permissions:
+                codename = f'{perm}_{model._meta.model_name}'
+                name = f'Can {perm} {model._meta.verbose_name}'
+                Permission.objects.get_or_create(
+                    codename=codename,
+                    defaults={'name': name, 'content_type': content_type},
+                )
+            self.stdout.write(self.style.SUCCESS(f'Set up permissions for {model._meta.verbose_name}'))

endoreg_db/management/commands/load_active_model_data.py

@@ -0,0 +1,45 @@
+from django.conf import settings
+import os
+from django.core.management.base import BaseCommand
+from ...models import ActiveModel
+from ...utils import load_model_data_from_yaml
+from ...data import ACTIVE_MODEL_DATA_DIR
+
+SOURCE_DIR = ACTIVE_MODEL_DATA_DIR # e.g. settings.DATA_DIR_INTERVENTION
+
+MODEL_0 = ActiveModel
+
+IMPORT_MODELS = [ # string as model key, serves as key in IMPORT_METADATA
+    MODEL_0.__name__,
+]
+
+IMPORT_METADATA = {
+    MODEL_0.__name__: {
+        "dir": SOURCE_DIR, # e.g. "interventions"
+        "model": MODEL_0, # e.g. Intervention
+        "foreign_keys": [], # e.g. ["intervention_types"]
+        "foreign_key_models": [] # e.g. [InterventionType]
+    }
+}
+
+class Command(BaseCommand):
+    help = """Load all .yaml files in the data/intervention directory
+    into the Intervention and InterventionType model"""
+
+    def add_arguments(self, parser):
+        parser.add_argument(
+            '--verbose',
+            action='store_true',
+            help='Display verbose output',
+        )
+
+    def handle(self, *args, **options):
+        verbose = options['verbose']
+        for model_name in IMPORT_MODELS:
+            _metadata = IMPORT_METADATA[model_name]
+            load_model_data_from_yaml(
+                self,
+                model_name,
+                _metadata,
+                verbose
+            )

endoreg_db/management/commands/load_ai_model_data.py

@@ -0,0 +1,79 @@
+from django.conf import settings
+import os
+from django.core.management.base import BaseCommand
+from ...models import (
+    ModelMeta,
+    ModelType,
+    LabelSet,
+    VideoSegmentationLabel,
+    VideoSegmentationLabelSet,
+    AiModel,
+)
+from ...utils import load_model_data_from_yaml
+from ...data import (
+    MODEL_TYPE_DATA_DIR,
+    VIDEO_SEGMENTATION_LABEL_DATA_DIR,
+    VIDEO_SEGMENTATION_LABELSET_DATA_DIR,
+    AI_MODEL_DATA_DIR,
+    AI_MODEL_META_DATA_DIR,
+)
+
+
+IMPORT_MODELS = [  # string as model key, serves as key in IMPORT_METADATA
+    ModelType.__name__,
+    # ModelMeta.__name__,
+    VideoSegmentationLabel.__name__,
+    VideoSegmentationLabelSet.__name__,
+    AiModel.__name__,
+]
+
+IMPORT_METADATA = {
+    ModelType.__name__: {
+        "dir": MODEL_TYPE_DATA_DIR,  # e.g. "intervention_types"
+        "model": ModelType,  # e.g. InterventionType
+        "foreign_keys": [],  # e.g. ["interventions"]
+        "foreign_key_models": [],  # e.g. [Intervention]
+    },
+    # ModelMeta.__name__: {
+    #     "dir": AI_MODEL_META_DATA_DIR,  # e.g. "intervention_types"
+    #     "model": ModelMeta,  # e.g. InterventionType
+    #     "foreign_keys": ["labelset", "type"],  # e.g. ["interventions"]
+    #     "foreign_key_models": [LabelSet, ModelType],  # e.g. [Intervention]
+    # },
+    VideoSegmentationLabel.__name__: {
+        "dir": VIDEO_SEGMENTATION_LABEL_DATA_DIR,  # e.g. "interventions"
+        "model": VideoSegmentationLabel,  # e.g. Intervention
+        "foreign_keys": [],  # e.g. ["intervention_types"]
+        "foreign_key_models": [],  # e.g. [InterventionType]
+    },
+    VideoSegmentationLabelSet.__name__: {
+        "dir": VIDEO_SEGMENTATION_LABELSET_DATA_DIR,  # e.g. "interventions"
+        "model": VideoSegmentationLabelSet,  # e.g. Intervention
+        "foreign_keys": ["labels"],  # e.g. ["intervention_types"]
+        "foreign_key_models": [VideoSegmentationLabel],  # e.g. [Intervention]
+    },
+    AiModel.__name__: {
+        "dir": AI_MODEL_DATA_DIR,  # e.g. "intervention_types"
+        "model": AiModel,  # e.g. InterventionType
+        "foreign_keys": ["video_segmentation_labelset"],  # e.g. ["interventions"]
+        "foreign_key_models": [VideoSegmentationLabelSet],  # e.g. [Intervention]
+    },
+}
+
+
+class Command(BaseCommand):
+    help = """Load all .yaml files in the data/intervention directory
+    into the Intervention and InterventionType model"""
+
+    def add_arguments(self, parser):
+        parser.add_argument(
+            "--verbose",
+            action="store_true",
+            help="Display verbose output",
+        )
+
+    def handle(self, *args, **options):
+        verbose = options["verbose"]
+        for model_name in IMPORT_MODELS:
+            _metadata = IMPORT_METADATA[model_name]
+            load_model_data_from_yaml(self, model_name, _metadata, verbose)