endoreg-db 0.5.3__py3-none-any.whl → 0.6.1__py3-none-any.whl

endoreg_db/data/lx_permission/base.yaml

@@ -0,0 +1,24 @@
+
+# BASE_PERMISSION_NAMES = [
+#     "local_admin",
+#     "local_user",
+#     "local_base_db_read",
+#     "local_base_db_write",
+# ]
+
+- model: endoreg_db.lx_permission
+  fields:
+    name: "local_admin"
+
+- model: endoreg_db.lx_permission
+  fields:
+    name: "local_user"
+
+- model: endoreg_db.lx_permission 
+  fields:
+    name: "local_base_db_read"  
+
+- model: endoreg_db.lx_permission 
+  fields:
+    name: "local_base_db_write"
+

endoreg_db/data/lx_permission/endoreg.yaml

@@ -0,0 +1,52 @@
+# EndoReg Base DB
+- model: endoreg_db.lx_permission
+  fields:
+    name: "endoreg_base_db_read"
+
+- model: endoreg_db.lx_permission
+  fields:
+    name: "endoreg_base_db_write"
+
+- model: endoreg_db.lx_permission
+  fields:
+    name: "endoreg_base_db_admin"
+
+- model: endoreg_db.lx_permission
+  fields:
+    name: "endoreg_base_db_user"
+
+
+# EndoReg Backup DB
+- model: endoreg_db.lx_permission
+  fields:
+    name: "endoreg_backup_db_read"
+
+- model: endoreg_db.lx_permission
+  fields:
+    name: "endoreg_backup_db_write"
+
+- model: endoreg_db.lx_permission
+  fields:
+    name: "endoreg_backup_db_admin"
+
+- model: endoreg_db.lx_permission
+  fields:
+    name: "endoreg_backup_db_user"
+
+
+# EndoReg Test DB
+- model: endoreg_db.lx_permission
+  fields:
+    name: "endoreg_test_db_read"
+
+- model: endoreg_db.lx_permission
+  fields:
+    name: "endoreg_test_db_write"
+
+- model: endoreg_db.lx_permission
+  fields:
+    name: "endoreg_test_db_admin"
+
+- model: endoreg_db.lx_permission
+  fields:
+    name: "endoreg_test_db_user"

endoreg_db/data/medication_indication/anticoagulation.yaml

@@ -3,37 +3,37 @@
   fields:
     name: "te_prevention-after_hip-apixaban"
     events: ["hip_replacement"]
+    diseases: []
+    disease_classification_choices: []
     medication_schedules: [
-      "apixaban-2.5mg-twice_daily_32d", # min 32d, max 38d
-    ]
+        "apixaban-2.5mg-twice_daily_32d", # min 32d, max 38d
+      ]
     indication_type: "thromboembolism-prevention-after_hip_replacement"
-    sources: [
-      "fachinformation-apixaban-eliquis_2.5mg-bristol_meyer_squibbs"
-    ]
+    sources: ["fachinformation-apixaban-eliquis_2.5mg-bristol_meyer_squibbs"]
 
 - model: endoreg_db.medication_indication
   fields:
     name: "te_prevention-after_knee-apixaban"
     events: ["knee_replacement"]
+    diseases: []
+    disease_classification_choices: []
     medication_schedules: [
-      "apixaban-2.5mg-twice_daily_10d", # min 10d, max 14d
-    ]
+        "apixaban-2.5mg-twice_daily_10d", # min 10d, max 14d
+      ]
     indication_type: "thromboembolism-prevention-after_knee_replacement"
-    sources: [
-      "fachinformation-apixaban-eliquis_2.5mg-bristol_meyer_squibbs"
-    ]
+    sources: ["fachinformation-apixaban-eliquis_2.5mg-bristol_meyer_squibbs"]
 
 - model: endoreg_db.medication_indication
   fields:
     name: "te_prevention-non_valvular_af-apixaban"
+    events: []
     diseases: ["non_valvular_af"]
+    disease_classification_choices: []
     medication_schedules: [
-      "apixaban-5mg-twice_daily", # no limit
-    ]
+        "apixaban-5mg-twice_daily", # no limit
+      ]
     indication_type: "thromboembolism-prevention-non_valvular_af"
-    sources: [
-      "fachinformation-apixaban-eliquis_2.5mg-bristol_meyer_squibbs"
-    ]
+    sources: ["fachinformation-apixaban-eliquis_2.5mg-bristol_meyer_squibbs"]
 
 # - model: endoreg_db.medication_indication
 #   fields:
@@ -51,70 +51,65 @@
 
 # generally same as ckd4 above but technically different definition
 # Applies for example when risk factors (2 of three: age >= 80; KG <= 60 kg; Kreatinin >= 1.5 mg/dl)
-- model: endoreg_db.medication_indication 
+- model: endoreg_db.medication_indication
   fields:
     name: "te_prevention-non_valvular_af-apixaban-dr" #dr = dose reduction
+    events: []
     diseases: ["non_valvular_af"]
+    disease_classification_choices: []
     medication_schedules: [
-      "apixaban-2.5mg-twice_daily", # no limit
-    ]
+        "apixaban-2.5mg-twice_daily", # no limit
+      ]
     indication_type: "thromboembolism-prevention-non_valvular_af"
-    sources: [
-      "fachinformation-apixaban-eliquis_2.5mg-bristol_meyer_squibbs"
-    ]
+    sources: ["fachinformation-apixaban-eliquis_2.5mg-bristol_meyer_squibbs"]
 
 - model: endoreg_db.medication_indication
   fields:
     name: "dvt_treatment-apixaban-3mo"
     events: ["deep_vein_thrombosis"]
+    diseases: []
+    disease_classification_choices: []
     medication_schedules: [
-      "apixaban-5g-twice_daily_7d", # first 7d of treatment 10 mg twice daily
-      "apixaban-5g-twice_daily_3mo", # no limit
-    ]
+        "apixaban-5g-twice_daily_7d", # first 7d of treatment 10 mg twice daily
+        "apixaban-5g-twice_daily_3mo", # no limit
+      ]
     indication_type: "deep_vein_thrombosis-treatment"
-    sources: [
-      "fachinformation-apixaban-eliquis_2.5mg-bristol_meyer_squibbs"
-    ]
+    sources: ["fachinformation-apixaban-eliquis_2.5mg-bristol_meyer_squibbs"]
 
 - model: endoreg_db.medication_indication
   fields:
     name: "pe_treatment-apixaban-3mo"
     events: ["pulmonary_embolism"]
+    diseases: []
+    disease_classification_choices: []
     medication_schedules: [
-      "apixaban-5g-twice_daily_7d", # first 7d of treatment 10 mg twice daily
-      "apixaban-5g-twice_daily_3mo", # no limit
-    ]
+        "apixaban-5g-twice_daily_7d", # first 7d of treatment 10 mg twice daily
+        "apixaban-5g-twice_daily_3mo", # no limit
+      ]
     indication_type: "pulmonary_embolism-treatment"
-    sources: [
-      "fachinformation-apixaban-eliquis_2.5mg-bristol_meyer_squibbs"
-    ]
+    sources: ["fachinformation-apixaban-eliquis_2.5mg-bristol_meyer_squibbs"]
 
 - model: endoreg_db.medication_indication
   fields:
     name: "pe_treatment-apixaban-6mo"
     events: ["pulmonary_embolism"]
+    diseases: []
+    disease_classification_choices: []
     medication_schedules: [
-      "apixaban-5g-twice_daily_7d", # first 7d of treatment 10 mg twice daily
-      "apixaban-5g-twice_daily_6mo", # no limit
-    ]
+        "apixaban-5g-twice_daily_7d", # first 7d of treatment 10 mg twice daily
+        "apixaban-5g-twice_daily_6mo", # no limit
+      ]
     indication_type: "pulmonary_embolism-treatment"
-    sources: [
-      "fachinformation-apixaban-eliquis_2.5mg-bristol_meyer_squibbs"
-    ]
+    sources: ["fachinformation-apixaban-eliquis_2.5mg-bristol_meyer_squibbs"]
 
 - model: endoreg_db.medication_indication
   fields:
     name: "te_prevention-recurrent-te-apixaban"
-    events: [
-      "recurrent_thrombembolism"
-    ]
-    medication_schedules: [
-      "apixaban-2.5mg-twice_daily"
-    ]
+    events: ["recurrent_thrombembolism"]
+    diseases: []
+    disease_classification_choices: []
+    medication_schedules: ["apixaban-2.5mg-twice_daily"]
     indication_type: "thrombembolism-prevention-recurrent_thrombembolism"
-    sources: [
-      "fachinformation-apixaban-eliquis_2.5mg-bristol_meyer_squibbs"
-    ]
-
+    sources: ["fachinformation-apixaban-eliquis_2.5mg-bristol_meyer_squibbs"]
 # templates to create:
 # medication_schedules:

endoreg_db/data/names_first/first_names.yaml

@@ -0,0 +1,51 @@
+- model: endoreg_db.first_name
+  fields:
+    name: Alexander
+- model: endoreg_db.first_name
+  fields:
+    name: Angelika
+- model: endoreg_db.first_name
+  fields:
+    name: Anja
+- model: endoreg_db.first_name
+  fields:
+    name: Doro
+- model: endoreg_db.first_name
+  fields:
+    name: Dorothea
+- model: endoreg_db.first_name
+  fields:
+    name: Florian
+- model: endoreg_db.first_name
+  fields:
+    name: Hans
+- model: endoreg_db.first_name
+  fields:
+    name: Kathrin
+- model: endoreg_db.first_name
+  fields:
+    name: Laura
+- model: endoreg_db.first_name
+  fields:
+    name: Linhel
+- model: endoreg_db.first_name
+  fields:
+    name: Mandy
+- model: endoreg_db.first_name
+  fields:
+    name: Markus
+- model: endoreg_db.first_name
+  fields:
+    name: Philip
+- model: endoreg_db.first_name
+  fields:
+    name: Rainer
+- model: endoreg_db.first_name
+  fields:
+    name: Sven
+- model: endoreg_db.first_name
+  fields:
+    name: Tanja
+- model: endoreg_db.first_name
+  fields:
+    name: Theodor

endoreg_db/data/names_last/last_names.yaml

@@ -0,0 +1,51 @@
+- model: endoreg_db.last_name
+  fields:
+    name: Brand
+- model: endoreg_db.last_name
+  fields:
+    name: Dela Cruz
+- model: endoreg_db.last_name
+  fields:
+    name: Hann
+- model: endoreg_db.last_name
+  fields:
+    name: Henniger
+- model: endoreg_db.last_name
+  fields:
+    name: Hose
+- model: endoreg_db.last_name
+  fields:
+    name: Hossner
+- model: endoreg_db.last_name
+  fields:
+    name: Kozielski
+- model: endoreg_db.last_name
+  fields:
+    name: Kudlich
+- model: endoreg_db.last_name
+  fields:
+    name: Lux
+- model: endoreg_db.last_name
+  fields:
+    name: Meining
+- model: endoreg_db.last_name
+  fields:
+    name: Purrer
+- model: endoreg_db.last_name
+  fields:
+    name: Reiter
+- model: endoreg_db.last_name
+  fields:
+    name: Retzbach
+- model: endoreg_db.last_name
+  fields:
+    name: Sodmann
+- model: endoreg_db.last_name
+  fields:
+    name: Weich
+- model: endoreg_db.last_name
+  fields:
+    name: Wiese
+- model: endoreg_db.last_name
+  fields:
+    name: Wiesemann

endoreg_db/data/network_device/data.yaml

@@ -22,6 +22,36 @@
     device_type: "agl-server"
     ip: "172.16.255.4"
 
+- model: endoreg_db.network_device
+  fields:
+    name: "agl-gpu-client-01"
+    device_type: "agl-server"
+    ip: "172.16.255.141"
+
+- model: endoreg_db.network_device
+  fields:
+    name: "agl-gpu-client-02"
+    device_type: "agl-server"
+    ip: "172.16.255.142"
+
+- model: endoreg_db.network_device
+  fields:
+    name: "agl-gpu-client-03"
+    device_type: "agl-server"
+    ip: "172.16.255.143"
+
+- model: endoreg_db.network_device
+  fields:
+    name: "agl-gpu-client-04"
+    device_type: "agl-server"
+    ip: "172.16.255.144"
+
+- model: endoreg_db.network_device
+  fields:
+    name: "agl-gpu-client-05"
+    device_type: "agl-server"
+    ip: "172.16.255.145"
+
 - model: endoreg_db.network_device
   fields:
     name: "agl-gpu-client-dev"

endoreg_db/data/organ/data.yaml

@@ -0,0 +1,29 @@
+- model: endoreg_db.organ
+  fields:
+    name: "colon"
+    name_de: "Kolon"
+    name_en: "Colon"
+  
+- model: endoreg_db.organ
+  fields:
+    name: "rectum"
+    name_de: "Rektum"
+    name_en: "Rectum"
+
+- model: endoreg_db.organ
+  fields:
+    name: "anal_canal"
+    name_de: "Analkanal"
+    name_en: "Anal Canal"
+
+- model: endoreg_db.organ
+  fields:
+    name: "ileum"
+    name_de: "Ileum"
+    name_en: "Ileum"
+
+- model: endoreg_db.organ
+  fields:
+    name: "small_bowel"
+    name_de: "Dünndarm"
+    name_en: "Small Bowel"

endoreg_db/data/pdf_type/data.yaml

@@ -6,8 +6,9 @@
     endoscope_info_line: "ukw-examination-generic-endoscope-info-line"
     examiner_info_line: "ukw-examination-generic-examiner-info-line"
     cut_off_above_lines: [
+      "ukw-examination-generic-anamnese-info-line",
       "ukw-examination-generic-endoscope-info-line",
-      "ukw-examination-generic-examiner-info-line"
+      "ukw-examination-generic-examiner-info-line",
     ]
     cut_off_below_lines: [
       "ukw-examination-generic-cut-off-below-line-01"

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

@@ -24,3 +24,7 @@
     name: "ukw-examination-generic-cut-off-below-line-01"
     value: "________________"
 
+- model: endoreg_db.report_reader_flag
+  fields:
+    name: "ukw-examination-generic-anamnese-info-line"
+    value: "Anamnese: "

endoreg_db/forms/__init__.py

@@ -1,3 +1,5 @@
 from .unit import Unit
 from .settings import ActiveModelForm
-from .questionnaires import *
+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/management/commands/load_ai_model_data.py

@@ -1,45 +1,79 @@
 from django.conf import settings
 import os
 from django.core.management.base import BaseCommand
-from ...models import ModelType
+from ...models import (
+    ModelMeta,
+    ModelType,
+    LabelSet,
+    VideoSegmentationLabel,
+    VideoSegmentationLabelSet,
+    AiModel,
+)
 from ...utils import load_model_data_from_yaml
-from ...data import MODEL_TYPE_DATA_DIR
+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,
+)
 
-SOURCE_DIR = MODEL_TYPE_DATA_DIR # e.g. settings.DATA_DIR_INTERVENTION
 
-MODEL_0 = ModelType
-
-IMPORT_MODELS = [ # string as model key, serves as key in IMPORT_METADATA
-    MODEL_0.__name__,
+IMPORT_MODELS = [  # string as model key, serves as key in IMPORT_METADATA
+    ModelType.__name__,
+    # ModelMeta.__name__,
+    VideoSegmentationLabel.__name__,
+    VideoSegmentationLabelSet.__name__,
+    AiModel.__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]
-    }
+    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',
+            "--verbose",
+            action="store_true",
+            help="Display verbose output",
         )
 
     def handle(self, *args, **options):
-        verbose = options['verbose']
+        verbose = options["verbose"]
         for model_name in IMPORT_MODELS:
             _metadata = IMPORT_METADATA[model_name]
-            load_model_data_from_yaml(
-                self,
-                model_name,
-                _metadata,
-                verbose
-            )
+            load_model_data_from_yaml(self, model_name, _metadata, verbose)

endoreg_db/management/commands/load_ai_model_label_data.py

@@ -0,0 +1,59 @@
+from django.conf import settings
+from django.core.management.base import BaseCommand
+from ...models import Label, LabelType, LabelSet
+import os
+from ...utils import load_model_data_from_yaml
+from ...data import LABEL_DATA_DIR
+
+SOURCE_DIR = LABEL_DATA_DIR
+
+IMPORT_MODELS = [  # string as model key, serves as key in IMPORT_METADATA
+    "LabelType",
+    "Label",
+    "LabelSet",
+]
+
+IMPORT_METADATA = {
+    # "": { # same as model name in "import models", e.g. "Intervention"
+    #     "subdir": 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]
+    # },
+    "LabelType": {
+        "dir": os.path.join(SOURCE_DIR, "label-type"),  # e.g. "interventions"
+        "model": LabelType,  # e.g. Intervention
+        "foreign_keys": [],  # e.g. ["intervention_types"]
+        "foreign_key_models": [],  # e.g. [InterventionType]
+    },
+    "Label": {
+        "dir": os.path.join(SOURCE_DIR, "label"),  # e.g. "interventions"
+        "model": Label,  # e.g. Intervention
+        "foreign_keys": ["label_type"],  # e.g. ["intervention_types"]
+        "foreign_key_models": [LabelType],  # e.g. [InterventionType]
+    },
+    "LabelSet": {
+        "dir": os.path.join(SOURCE_DIR, "label-set"),  # e.g. "interventions"
+        "model": LabelSet,  # e.g. Intervention
+        "foreign_keys": ["labels"],  # e.g. ["intervention_types"]
+        "foreign_key_models": [Label],  # 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)