endoreg-db 0.8.8.9__py3-none-any.whl → 0.8.9.10__py3-none-any.whl

endoreg_db/management/commands/import_report.py

@@ -38,7 +38,7 @@ local_version_available = ensure_local_lx_anonymizer()
 
 # Now import from lx_anonymizer
 try:
-    from lx_anonymizer.ollama_service import ollama_service
+    from lx_anonymizer.ollama.ollama_service import ollama_service
 except ImportError:
     print("Could not import init_ollama_service from local or installed lx_anonymizer")
     raise
@@ -344,8 +344,6 @@ class Command(BaseCommand):
         finally:
             # Clean up Ollama process if we started it
             if ollama_proc is not None:
-                import signal
-
                 self.stdout.write(
                     self.style.SUCCESS("Cleaning up Ollama server process...")
                 )

endoreg_db/management/commands/list_routes.py

@@ -1,6 +1,7 @@
 from django.core.management.base import BaseCommand
 from django.urls import get_resolver, URLPattern, URLResolver
 
+
 def iter_patterns(prefix, patterns):
     for p in patterns:
         if isinstance(p, URLPattern):
@@ -8,6 +9,7 @@ def iter_patterns(prefix, patterns):
         elif isinstance(p, URLResolver):
             yield from iter_patterns(prefix, p.url_patterns)
 
+
 class Command(BaseCommand):
     help = "List all URL names (useful to fill policy.py)"
 

endoreg_db/management/commands/load_ai_model_data.py

@@ -53,8 +53,14 @@ IMPORT_METADATA = {
     AiModel.__name__: {
         "dir": AI_MODEL_DATA_DIR,  # e.g. "intervention_types"
         "model": AiModel,
-        "foreign_keys": ["video_segmentation_labelset", "model_type"],  # e.g. ["interventions"]
-        "foreign_key_models": [VideoSegmentationLabelSet, ModelType],  # e.g. [Intervention]
+        "foreign_keys": [
+            "video_segmentation_labelset",
+            "model_type",
+        ],  # e.g. ["interventions"]
+        "foreign_key_models": [
+            VideoSegmentationLabelSet,
+            ModelType,
+        ],  # e.g. [Intervention]
     },
 }
 

endoreg_db/management/commands/load_ai_model_label_data.py

@@ -1,6 +1,5 @@
 import os
 
-from django.conf import settings
 from django.core.management.base import BaseCommand
 
 from ...data import LABEL_DATA_DIR

endoreg_db/management/commands/load_center_data.py

@@ -41,7 +41,7 @@ class Command(BaseCommand):
     def add_arguments(self, parser):
         """
         Adds the '--verbose' flag to the argument parser.
-        
+
         When specified, this flag enables verbose output for the management command.
         """
         parser.add_argument(
@@ -53,11 +53,11 @@ class Command(BaseCommand):
     def handle(self, *args, **options):
         """
         Load YAML data for each predefined model.
-        
+
         Iterates over the models specified in IMPORT_MODELS, retrieving each model's metadata from
         IMPORT_METADATA and invoking load_model_data_from_yaml to load YAML data. The verbosity of
         the output is determined by the 'verbose' flag in the command options.
-        
+
         Args:
             *args: Additional positional arguments.
             **options: Command options; must include a 'verbose' key to control output detail.

endoreg_db/management/commands/load_distribution_data.py

@@ -3,8 +3,7 @@ from endoreg_db.models import (
     NumericValueDistribution,
     SingleCategoricalValueDistribution,
     MultipleCategoricalValueDistribution,
-    DateValueDistribution
-
+    DateValueDistribution,
 )
 from collections import OrderedDict
 
@@ -16,32 +15,35 @@ from ...data import (
     DISTRIBUTION_DATE_DATA_DIR,
 )
 
-IMPORT_METADATA = OrderedDict({
-    NumericValueDistribution.__name__: {
-        "dir": DISTRIBUTION_NUMERIC_DATA_DIR,
-        "model": NumericValueDistribution, 
-        "foreign_keys": [], 
-        "foreign_key_models": [] 
-    },
-    SingleCategoricalValueDistribution.__name__: {
-        "dir": DISTRIBUTION_SINGLE_CATEGORICAL_DATA_DIR,
-        "model": SingleCategoricalValueDistribution, 
-        "foreign_keys": [], 
-        "foreign_key_models": [] 
-    },
-    MultipleCategoricalValueDistribution.__name__: {
-        "dir": DISTRIBUTION_MULTIPLE_CATEGORICAL_DATA_DIR,
-        "model": MultipleCategoricalValueDistribution, 
-        "foreign_keys": [], 
-        "foreign_key_models": [] 
-    },
-    DateValueDistribution.__name__: {
-        "dir": DISTRIBUTION_DATE_DATA_DIR,
-        "model": DateValueDistribution, 
-        "foreign_keys": [], 
-        "foreign_key_models": [] 
-    },
-})
+IMPORT_METADATA = OrderedDict(
+    {
+        NumericValueDistribution.__name__: {
+            "dir": DISTRIBUTION_NUMERIC_DATA_DIR,
+            "model": NumericValueDistribution,
+            "foreign_keys": [],
+            "foreign_key_models": [],
+        },
+        SingleCategoricalValueDistribution.__name__: {
+            "dir": DISTRIBUTION_SINGLE_CATEGORICAL_DATA_DIR,
+            "model": SingleCategoricalValueDistribution,
+            "foreign_keys": [],
+            "foreign_key_models": [],
+        },
+        MultipleCategoricalValueDistribution.__name__: {
+            "dir": DISTRIBUTION_MULTIPLE_CATEGORICAL_DATA_DIR,
+            "model": MultipleCategoricalValueDistribution,
+            "foreign_keys": [],
+            "foreign_key_models": [],
+        },
+        DateValueDistribution.__name__: {
+            "dir": DISTRIBUTION_DATE_DATA_DIR,
+            "model": DateValueDistribution,
+            "foreign_keys": [],
+            "foreign_key_models": [],
+        },
+    }
+)
+
 
 class Command(BaseCommand):
     help = """Load all .yaml files in the data/intervention directory
@@ -49,18 +51,13 @@ class Command(BaseCommand):
 
     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_METADATA.keys():
             _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_endoscope_data.py

@@ -1,6 +1,3 @@
-import os
-
-from django.conf import settings
 from django.core.management.base import BaseCommand
 
 from ...data import (

endoreg_db/management/commands/load_examination_data.py

@@ -1,10 +1,16 @@
 import os
 
-from django.conf import settings
 from django.core.management.base import BaseCommand
 
 from ...data import EXAMINATION_DATA_DIR
-from ...models import Examination, ExaminationIndication, ExaminationTime, ExaminationTimeType, ExaminationType, Finding
+from ...models import (
+    Examination,
+    ExaminationIndication,
+    ExaminationTime,
+    ExaminationTimeType,
+    ExaminationType,
+    Finding,
+)
 from ...utils import load_model_data_from_yaml
 
 SOURCE_DIR = EXAMINATION_DATA_DIR
@@ -26,8 +32,18 @@ IMPORT_METADATA = {
     "Examination": {
         "dir": os.path.join(SOURCE_DIR, "examinations"),
         "model": Examination,
-        "foreign_keys": ["findings", "examination_types", "examination_times", "indications"],
-        "foreign_key_models": [Finding, ExaminationType, ExaminationTime, ExaminationIndication],
+        "foreign_keys": [
+            "findings",
+            "examination_types",
+            "examination_times",
+            "indications",
+        ],
+        "foreign_key_models": [
+            Finding,
+            ExaminationType,
+            ExaminationTime,
+            ExaminationIndication,
+        ],
     },
     "ExaminationTimeType": {
         "dir": os.path.join(SOURCE_DIR, "time-type"),

endoreg_db/management/commands/load_finding_data.py

@@ -41,8 +41,18 @@ IMPORT_METADATA = {
     Finding.__name__: {
         "dir": FINDING_DATA_DIR,
         "model": Finding,
-        "foreign_keys": ["finding_types", "finding_interventions", "finding_classifications", "caused_by_interventions"],
-        "foreign_key_models": [FindingType, FindingIntervention, FindingClassification, FindingIntervention],
+        "foreign_keys": [
+            "finding_types",
+            "finding_interventions",
+            "finding_classifications",
+            "caused_by_interventions",
+        ],
+        "foreign_key_models": [
+            FindingType,
+            FindingIntervention,
+            FindingClassification,
+            FindingIntervention,
+        ],
     },
     FindingInterventionType.__name__: {
         "dir": FINIDNG_INTERVENTION_TYPE_DATA_DIR,
@@ -65,7 +75,12 @@ IMPORT_METADATA = {
     FindingClassification.__name__: {
         "dir": FINDING_CLASSIFICATION_DATA_DIR,
         "model": FindingClassification,
-        "foreign_keys": ["classification_types", "findings", "finding_types", "choices"],
+        "foreign_keys": [
+            "classification_types",
+            "findings",
+            "finding_types",
+            "choices",
+        ],
         "foreign_key_models": [
             FindingClassificationType,
             Finding,

endoreg_db/management/commands/load_gender_data.py

@@ -1,10 +1,5 @@
 from django.core.management.base import BaseCommand
-from endoreg_db.models import (
-    Gender,
-
-    # Other models for ForeignKeys
-    Unit, Center
-)
+from endoreg_db.models import Gender
 from collections import OrderedDict
 
 from ...utils import load_model_data_from_yaml
@@ -12,14 +7,17 @@ from ...data import (
     GENDER_DATA_DIR,
 )
 
-IMPORT_METADATA = OrderedDict({
-    Gender.__name__: {
-        "dir": GENDER_DATA_DIR,
-        "model": Gender, 
-        "foreign_keys": [], 
-        "foreign_key_models": [] 
-    },    
-})
+IMPORT_METADATA = OrderedDict(
+    {
+        Gender.__name__: {
+            "dir": GENDER_DATA_DIR,
+            "model": Gender,
+            "foreign_keys": [],
+            "foreign_key_models": [],
+        },
+    }
+)
+
 
 class Command(BaseCommand):
     help = """Load all .yaml files in the data/intervention directory
@@ -27,18 +25,13 @@ class Command(BaseCommand):
 
     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_METADATA.keys():
             _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_green_endoscopy_wuerzburg_data.py

@@ -12,9 +12,9 @@ from endoreg_db.models import (
     CenterResource,
     ProductMaterial,
     ProductWeight,
-
     # Other models for ForeignKeys
-    Unit, Center
+    Unit,
+    Center,
 )
 from collections import OrderedDict
 
@@ -34,80 +34,95 @@ from ...data import (
     PRODUCT_WEIGHT_DATA_DIR,
 )
 
-IMPORT_METADATA = OrderedDict({
-    EmissionFactor.__name__: {
-        "dir": EMISSION_FACTOR_DATA_DIR,
-        "model": EmissionFactor, 
-        "foreign_keys": ["unit"], 
-        "foreign_key_models": [Unit] 
-    },
-    Resource.__name__: {
-        "dir": RESOURCE_DATA_DIR,
-        "model": Resource,
-        "foreign_keys": [],
-        "foreign_key_models": []
-    },
-    Waste.__name__: {
-        "dir": WASTE_DATA_DIR,
-        "model": Waste,
-        "foreign_keys": [],
-        "foreign_key_models": []
-    },
-    Material.__name__: {
-        "dir": MATERIAL_DATA_DIR,
-        "model": Material,
-        "foreign_keys": ["emission_factor"],
-        "foreign_key_models": [EmissionFactor]
-    },
-    ProductGroup.__name__: {
-        "dir": PRODUCT_GROUP_DATA_DIR,
-        "model": ProductGroup,
-        "foreign_keys": [],
-        "foreign_key_models": []
-    },
-    TransportRoute.__name__: {
-        "dir": TRANSPORT_ROUTE_DATA_DIR,
-        "model": TransportRoute,
-        "foreign_keys": ["emission_factor", "unit"],
-        "foreign_key_models": [EmissionFactor, Unit]
-    },
-    Product.__name__: {
-        "dir": PRODUCT_DATA_DIR,
-        "model": Product,
-        "foreign_keys": ["product_group", "transport_route"],
-        "foreign_key_models": [ProductGroup, TransportRoute]
-    },
-    ReferenceProduct.__name__: {
-        "dir": REFERENCE_PRODUCT_DATA_DIR,
-        "model": ReferenceProduct,
-        "foreign_keys": ["product","product_group"],
-        "foreign_key_models": [Product,ProductGroup]
-    },
-    CenterWaste.__name__: {
-        "dir": CENTER_WASTE_DATA_DIR,
-        "model": CenterWaste,
-        "foreign_keys": ["waste", "center", "unit", "emission_factor"],
-        "foreign_key_models": [Waste, Center, Unit, EmissionFactor]
-    },
-    CenterResource.__name__: {
-        "dir": CENTER_RESOURCE_DATA_DIR,
-        "model": CenterResource,
-        "foreign_keys": ["center","resource", "unit", "transport_emission_factor", "use_emission_factor"],
-        "foreign_key_models": [Center,Resource, Unit, EmissionFactor, EmissionFactor]
-    },
-    ProductMaterial.__name__: {
-        "dir": PRODUCT_MATERIAL_DATA_DIR,
-        "model": ProductMaterial,
-        "foreign_keys": ["product", "material", "unit"],
-        "foreign_key_models": [Product, Material, Unit]
-    },
-    ProductWeight.__name__: {
-        "dir": PRODUCT_WEIGHT_DATA_DIR,
-        "model": ProductWeight,
-        "foreign_keys": ["product", "unit"],
-        "foreign_key_models": [Product, Unit]
+IMPORT_METADATA = OrderedDict(
+    {
+        EmissionFactor.__name__: {
+            "dir": EMISSION_FACTOR_DATA_DIR,
+            "model": EmissionFactor,
+            "foreign_keys": ["unit"],
+            "foreign_key_models": [Unit],
+        },
+        Resource.__name__: {
+            "dir": RESOURCE_DATA_DIR,
+            "model": Resource,
+            "foreign_keys": [],
+            "foreign_key_models": [],
+        },
+        Waste.__name__: {
+            "dir": WASTE_DATA_DIR,
+            "model": Waste,
+            "foreign_keys": [],
+            "foreign_key_models": [],
+        },
+        Material.__name__: {
+            "dir": MATERIAL_DATA_DIR,
+            "model": Material,
+            "foreign_keys": ["emission_factor"],
+            "foreign_key_models": [EmissionFactor],
+        },
+        ProductGroup.__name__: {
+            "dir": PRODUCT_GROUP_DATA_DIR,
+            "model": ProductGroup,
+            "foreign_keys": [],
+            "foreign_key_models": [],
+        },
+        TransportRoute.__name__: {
+            "dir": TRANSPORT_ROUTE_DATA_DIR,
+            "model": TransportRoute,
+            "foreign_keys": ["emission_factor", "unit"],
+            "foreign_key_models": [EmissionFactor, Unit],
+        },
+        Product.__name__: {
+            "dir": PRODUCT_DATA_DIR,
+            "model": Product,
+            "foreign_keys": ["product_group", "transport_route"],
+            "foreign_key_models": [ProductGroup, TransportRoute],
+        },
+        ReferenceProduct.__name__: {
+            "dir": REFERENCE_PRODUCT_DATA_DIR,
+            "model": ReferenceProduct,
+            "foreign_keys": ["product", "product_group"],
+            "foreign_key_models": [Product, ProductGroup],
+        },
+        CenterWaste.__name__: {
+            "dir": CENTER_WASTE_DATA_DIR,
+            "model": CenterWaste,
+            "foreign_keys": ["waste", "center", "unit", "emission_factor"],
+            "foreign_key_models": [Waste, Center, Unit, EmissionFactor],
+        },
+        CenterResource.__name__: {
+            "dir": CENTER_RESOURCE_DATA_DIR,
+            "model": CenterResource,
+            "foreign_keys": [
+                "center",
+                "resource",
+                "unit",
+                "transport_emission_factor",
+                "use_emission_factor",
+            ],
+            "foreign_key_models": [
+                Center,
+                Resource,
+                Unit,
+                EmissionFactor,
+                EmissionFactor,
+            ],
+        },
+        ProductMaterial.__name__: {
+            "dir": PRODUCT_MATERIAL_DATA_DIR,
+            "model": ProductMaterial,
+            "foreign_keys": ["product", "material", "unit"],
+            "foreign_key_models": [Product, Material, Unit],
+        },
+        ProductWeight.__name__: {
+            "dir": PRODUCT_WEIGHT_DATA_DIR,
+            "model": ProductWeight,
+            "foreign_keys": ["product", "unit"],
+            "foreign_key_models": [Product, Unit],
+        },
     }
-})
+)
+
 
 class Command(BaseCommand):
     help = """Load all .yaml files in the data/intervention directory
@@ -115,18 +130,13 @@ class Command(BaseCommand):
 
     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_METADATA.keys():
             _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_information_source.py

@@ -1,6 +1,3 @@
-import os
-
-from django.conf import settings
 from django.core.management.base import BaseCommand
 
 from ...data import INFORMATION_DATA_DIR, INFORMATION_SOURCE_TYPE_DATA_DIR

endoreg_db/management/commands/load_lab_value_data.py

@@ -16,10 +16,21 @@ IMPORT_METADATA = {
     MODEL_0.__name__: {
         "dir": SOURCE_DIR,  # e.g. "interventions"
         "model": MODEL_0,
-        "foreign_keys": ["default_unit", "default_numerical_value_distribution"],  # e.g. ["intervention_types"]
-        "foreign_key_models": [Unit, NumericValueDistribution],  # e.g. [InterventionType]
+        "foreign_keys": [
+            "default_unit",
+            "default_numerical_value_distribution",
+        ],  # e.g. ["intervention_types"]
+        "foreign_key_models": [
+            Unit,
+            NumericValueDistribution,
+        ],  # e.g. [InterventionType]
+    },
+    PatientLabSampleType.__name__: {
+        "dir": PATIENT_LAB_SAMPLE_TYPE_DATA_DIR,
+        "model": PatientLabSampleType,
+        "foreign_keys": [],
+        "foreign_key_models": [],
     },
-    PatientLabSampleType.__name__: {"dir": PATIENT_LAB_SAMPLE_TYPE_DATA_DIR, "model": PatientLabSampleType, "foreign_keys": [], "foreign_key_models": []},
 }