endoreg-db 0.5.2__py3-none-any.whl → 0.6.0__py3-none-any.whl

endoreg_db/data/reference_product/green_endoscopy_dashboard_ReferenceProduct.yaml

@@ -1,55 +0,0 @@
-- fields:
-    name: reference_balloon_wuerzburg
-    product: extraction_balloon_escort_2
-    product_group: Balloon
-  model: endoreg_db.ReferenceProduct
-- fields:
-    name: reference_bougie_wuerzburg
-    product: esophageal_dilator
-    product_group: Bougie
-  model: endoreg_db.ReferenceProduct
-- fields:
-    name: reference_wire_wuerzburg
-    product: visiglide_2
-    product_group: Wire
-  model: endoreg_db.ReferenceProduct
-- fields:
-    name: reference_peg_wuerzburg
-    product: peg_freka_15_ch
-    product_group: PEG
-  model: endoreg_db.ReferenceProduct
-- fields:
-    name: reference_instrument_wuerzburg
-    product: biopsy_grasper_hot_radial_jaw_4
-    product_group: Instrument
-  model: endoreg_db.ReferenceProduct
-- fields:
-    name: reference_metalstent_wuerzburg
-    product: nitinol_stent_aix_oel
-    product_group: Metal-Stent
-  model: endoreg_db.ReferenceProduct
-- fields:
-    name: reference_plasticstent_wuerzburg
-    product: biliary_stent_cotton_leung_sof_flex
-    product_group: Plastic-Stent
-  model: endoreg_db.ReferenceProduct
-- fields:
-    name: reference_plastic_wuerzburg
-    product: bite_protector
-    product_group: Plastic
-  model: endoreg_db.ReferenceProduct
-- fields:
-    name: reference_plastic-large_wuerzburg
-    product: pressure_syringe_60_ml
-    product_group: Plastic-Large
-  model: endoreg_db.ReferenceProduct
-- fields:
-    name: reference_coat_wuerzburg
-    product: foliodress_gown_standard
-    product_group: Coat
-  model: endoreg_db.ReferenceProduct
-- fields:
-    name: reference_absorbant-pad_wuerzburg
-    product: absorbant_pad
-    product_group: Absorbant-Pad
-  model: endoreg_db.ReferenceProduct

endoreg_db/data/report_reader_flag/ukw-examination-generic.yaml

@@ -1,26 +0,0 @@
-# yaml definitions for report reader flag objects
-# PATIENT_INFO_LINE_FLAG = "Patient: "
-# ENDOSCOPE_INFO_LINE_FLAG = "Gerät: "
-# EXAMINER_INFO_LINE_FLAG = "1. Unters.:"
-# CUT_OFF_BELOW_LINE_FLAG = "________________"
-
-- model: endoreg_db.report_reader_flag
-  fields:
-    name: "ukw-examination-generic-patient-info-line"
-    value: "Patient: "
-
-- model: endoreg_db.report_reader_flag
-  fields:
-    name: "ukw-examination-generic-endoscope-info-line"
-    value: "Gerät: "
-
-- model: endoreg_db.report_reader_flag
-  fields:
-    name: "ukw-examination-generic-examiner-info-line"
-    value: "1. Unters.:"
-
-- model: endoreg_db.report_reader_flag
-  fields:
-    name: "ukw-examination-generic-cut-off-below-line-01"
-    value: "________________"
-

endoreg_db/data/report_reader_flag/ukw-histology-generic.yaml

@@ -1,19 +0,0 @@
-- model: endoreg_db.report_reader_flag
-  fields:
-    name: "ukw-histology-generic-patient-info-line"
-    value: "Patient:"
-
-- model: endoreg_db.report_reader_flag
-  fields:
-    name: "ukw-histology-generic-examiner-info-line"
-    value: "Eingang am:"
-
-- model: endoreg_db.report_reader_flag
-  fields:
-    name: "ukw-histology-generic-cut-off-below-line-01"
-    value: "$$-3"
-
-- model: endoreg_db.report_reader_flag
-  fields:
-    name: "ukw-histology-generic-endoscope-info-line"
-    value: ""

endoreg_db/data/resource/green_endoscopy_dashboard_Resource.yaml

@@ -1,15 +0,0 @@
-- 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

@@ -1,12 +0,0 @@
-- 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

@@ -1,92 +0,0 @@
-# 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

@@ -1,17 +0,0 @@
-- 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

@@ -1,31 +0,0 @@
-- 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

@@ -1,20 +0,0 @@
-- 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

@@ -1,6 +0,0 @@
-- 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

@@ -1,13 +0,0 @@
-- 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

@@ -1,35 +0,0 @@
-# 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

@@ -1,38 +0,0 @@
-- 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

@@ -1,12 +0,0 @@
-- 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

@@ -1,3 +0,0 @@
-from .unit import Unit
-from .settings import ActiveModelForm
-from .questionnaires import *

endoreg_db/forms/questionnaires/__init__.py

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

endoreg_db/forms/questionnaires/tto_questionnaire.py

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

@@ -1,8 +0,0 @@
-# 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

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

endoreg_db/management/commands/_load_model_template.py

@@ -1,41 +0,0 @@
-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

@@ -1,18 +0,0 @@
-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/delete_legacy_images.py

@@ -1,19 +0,0 @@
-# django command to delete all LegacyImage objects
-
-from django.core.management.base import BaseCommand, CommandError
-from endoreg_db.models import LegacyImage
-from tqdm import tqdm
-
-class Command(BaseCommand):
-    help = 'Deletes all LegacyImage objects including the linked files (legacy_image.image)'
-
-    def handle(self, *args, **options):
-        legacy_images = LegacyImage.objects.all()
-
-        for legacy_image in tqdm(legacy_images):
-            legacy_image.image.delete()
-            legacy_image.delete()
-
-        self.stdout.write(self.style.SUCCESS('Successfully deleted all LegacyImage objects and linked image files'))
-
-

endoreg_db/management/commands/delete_legacy_videos.py

@@ -1,17 +0,0 @@
-# Django command to fetch all LegacyVideo objects, delete the associated file and delete the object from the database
-
-from endoreg_db.models.data_file.video import LegacyVideo
-from tqdm import tqdm
-from django.core.management.base import BaseCommand
-
-class Command(BaseCommand):
-    """
-    Deletes all LegacyVideos in the database.
-    """
-    help = 'Deletes all LegacyVideos in the database.'
-
-    def handle(self, *args, **options):
-        videos = LegacyVideo.objects.all()
-        for video in tqdm(videos):
-            video.file.delete()
-            video.delete()

endoreg_db/management/commands/extract_legacy_video_frames.py

@@ -1,18 +0,0 @@
-# Django Command to:
-# fetch all LegacyVideos and extract frames from them 
-# track progress for all videos and for each video with tqdm
-
-from endoreg_db.models.data_file.video import LegacyVideo
-from tqdm import tqdm
-from django.core.management.base import BaseCommand
-
-class Command(BaseCommand):
-    """
-    Extracts frames from all LegacyVideos in the database.
-    """
-    help = 'Extracts frames from all LegacyVideos in the database.'
-
-    def handle(self, *args, **options):
-        videos = LegacyVideo.objects.all()
-        for video in tqdm(videos):
-            video.extract_all_frames()

endoreg_db/management/commands/fetch_legacy_image_dataset.py

@@ -1,32 +0,0 @@
-# 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

@@ -1,20 +0,0 @@
-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}'))