endoreg-db 0.8.8.0__py3-none-any.whl → 0.8.9.2__py3-none-any.whl

endoreg_db/management/commands/load_base_db_data.py

@@ -1,5 +1,4 @@
 from django.core.management import BaseCommand, call_command
-from io import StringIO
 
 
 class Command(BaseCommand):
@@ -16,9 +15,9 @@ class Command(BaseCommand):
         # verbose = options['verbose']
         """
         Orchestrates the sequential execution of data loading commands to populate base database models.
-        
-        This management command displays an initial message and then runs a series of data loading routines 
-        (via call_command) in a specified order. It ignores any verbose setting from the command-line options 
+
+        This management command displays an initial message and then runs a series of data loading routines
+        (via call_command) in a specified order. It ignores any verbose setting from the command-line options
         and forces verbose output. A final success message is printed after all commands complete.
         """
         verbose = True
@@ -45,10 +44,10 @@ class Command(BaseCommand):
         call_command("load_event_data", stdout=out, verbose=verbose)
         call_command("load_organ_data", stdout=out, verbose=verbose)
         call_command("load_contraindication_data", stdout=out, verbose=verbose)
-        call_command("load_examination_data", stdout=out, verbose=verbose)
-        call_command("load_lab_value_data", stdout=out, verbose=verbose)
         call_command("load_finding_data", stdout=out, verbose=verbose)
         call_command("load_examination_indication_data", stdout=out, verbose=verbose)
+        call_command("load_examination_data", stdout=out, verbose=verbose)
+        call_command("load_lab_value_data", stdout=out, verbose=verbose)
         call_command("load_medication_data", stdout=out, verbose=verbose)
 
         call_command("load_requirement_data", stdout=out, verbose=verbose)
@@ -62,131 +61,3 @@ class Command(BaseCommand):
                 "All data loading commands executed successfully."
             )
         )
-
-        # # Run the load_network_data command
-        # self.stdout.write(self.style.SUCCESS("Running load_network_data..."))
-        # call_command('load_network_data', verbose=verbose)
-        # Run the load_network_data command
-        # self.stdout.write(self.style.SUCCESS("Running load_network_data..."))
-        # call_command("load_network_data", verbose=verbose)
-
-        # # Run the load_logging_data command
-        # self.stdout.write(self.style.SUCCESS("Running load_logging_data..."))
-        # call_command("load_logging_data", verbose=verbose)
-
-        # # Run the load_profession_data command
-        # self.stdout.write(self.style.SUCCESS("Running load_profession_data..."))
-        # call_command("load_profession_data", verbose=verbose)
-
-        # # run the load_gender_data command
-        # self.stdout.write(self.style.SUCCESS("Running load_gender_data..."))
-        # call_command("load_gender_data", verbose=verbose)
-
-        # # Run the load_examination_data command
-        # self.stdout.write(self.style.SUCCESS("Running load_examination_data..."))
-        # call_command("load_examination_data", verbose=verbose)
-
-        # # run the load_finding_data command
-        # self.stdout.write(self.style.SUCCESS("Running load_finding_data..."))
-        # call_command("load_finding_data", verbose=verbose)
-
-        # # Run the load_disease data command
-        # self.stdout.write(self.style.SUCCESS("Running load_disease_data..."))
-        # call_command("load_disease_data", verbose=verbose)
-
-        # # # Run the load_disease_classification data command
-        # # self.stdout.write(self.style.SUCCESS("Running load_disease_classification_data..."))
-        # # call_command('load_disease_classification_data', verbose=verbose)
-
-        # # # Run the load_disease_classification_choices data command
-        # # self.stdout.write(self.style.SUCCESS("Running load_disease_classification_choices_data..."))
-        # # call_command('load_disease_classification_choices_data', verbose=verbose)
-
-        # # rund the load_user_groups command
-        # self.stdout.write(self.style.SUCCESS("Running load_user_groups..."))
-        # call_command("load_user_groups", verbose=verbose)
-
-        # # run the load_report_reader_flag command
-        # self.stdout.write(self.style.SUCCESS("Running load_report_reader_flag..."))
-        # call_command("load_report_reader_flag", verbose=verbose)
-
-        # # Run the load_pdf_type_data command
-        # self.stdout.write(self.style.SUCCESS("Running load_pdf_type_data..."))
-        # call_command("load_pdf_type_data", verbose=verbose)
-
-        # # Run the load_endoscopy_processor_data command
-        # self.stdout.write(
-        #     self.style.SUCCESS("Running load_endoscopy_processor_data...")
-        # )
-        # call_command("load_endoscopy_processor_data", verbose=verbose)
-
-        # # Run the load_endoscope_type_data command
-        # self.stdout.write(self.style.SUCCESS("Running load_endoscope_type_data..."))
-        # call_command("load_endoscope_type_data", verbose=verbose)
-
-        # # Run the load_unit_data command
-        # self.stdout.write(self.style.SUCCESS("Running load_unit_data..."))
-        # call_command("load_unit_data", verbose=verbose)
-
-        # # Run the load_lab_value_data command
-        # self.stdout.write(self.style.SUCCESS("Running load_lab_value_data..."))
-        # call_command("load_lab_value_data", verbose=verbose)
-
-        # # Run the load_information_source command
-        # self.stdout.write(self.style.SUCCESS("Running load_information_source..."))
-        # call_command("load_information_source", verbose=verbose)
-
-        # # Run the load_center_data command
-        # self.stdout.write(self.style.SUCCESS("Running load_center_data..."))
-        # call_command("load_center_data", verbose=verbose)
-
-        # # Run the load_label_data command
-        # self.stdout.write(self.style.SUCCESS("Running load_label_data..."))
-        # call_command("load_label_data", verbose=verbose)
-
-        # # Run the load_ai_model_data command
-        # self.stdout.write(self.style.SUCCESS("Running load_ai_model_data..."))
-        # call_command("load_ai_model_data", verbose=verbose)
-
-        # # Run the load_event_data command
-        # self.stdout.write(self.style.SUCCESS("Running load_event_data..."))
-        # call_command("load_event_data", verbose=verbose)
-
-        # # run the load_medication_data command
-        # self.stdout.write(self.style.SUCCESS("Running load_medication_data..."))
-        # call_command("load_medication_data", verbose=verbose)
-
-        # # # Run the load_medication_indication_type_data command
-        # # self.stdout.write(self.style.SUCCESS("Running load_medication_indication_type_data..."))
-        # # call_command('load_medication_indication_type_data', verbose=verbose)
-
-        # # # Run the load_medication_intake_time_data command
-        # # self.stdout.write(self.style.SUCCESS("Running load_medication_intake_time_data..."))
-        # # call_command('load_medication_intake_time_data', verbose=verbose)
-
-        # # # Run the load_medication_schedule_data command
-        # # self.stdout.write(self.style.SUCCESS("Running load_medication_schedule_data..."))
-        # # call_command('load_medication_schedule_data', verbose=verbose)
-
-        # # # Run the load_medication_indication_data command
-        # # self.stdout.write(self.style.SUCCESS("Running load_medication_indication_data..."))
-        # # call_command('load_medication_indication_data', verbose=verbose)
-
-        # # Run the load_green_endoscopy_wuerzburg_data command
-        # self.stdout.write(
-        #     self.style.SUCCESS("Running load_green_endoscopy_wuerzburg_data...")
-        # )
-        # call_command("load_green_endoscopy_wuerzburg_data", verbose=verbose)
-
-        # # Load G-Play Data
-        # # run the load_distribution_data command
-        # self.stdout.write(self.style.SUCCESS("Running load_distribution_data..."))
-        # call_command("load_distribution_data", verbose=verbose)
-        # # Run the load_g_play_data command
-        # self.stdout.write(self.style.SUCCESS("Running load_g_play_data..."))
-        # call_command("load_g_play_data", verbose=verbose)
-
-        # # Necessary? Migrate? FIXME
-        # # # Run the load_active_model_data command
-        # # self.stdout.write(self.style.SUCCESS("Running load_active_model_data..."))
-        # # call_command('load_active_model_data', verbose=verbose)

endoreg_db/management/commands/load_contraindication_data.py

@@ -1,41 +1,39 @@
 from django.core.management.base import BaseCommand
+
 from endoreg_db.models import Contraindication
-from ...utils import load_model_data_from_yaml
+
 from ...data import CONTRAINDICATION_DATA_DIR as SOURCE_DIR
+from ...utils import load_model_data_from_yaml
 
 MODEL_0 = Contraindication
 
-IMPORT_MODELS = [ # string as model key, serves as key in IMPORT_METADATA
+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]
+        "dir": SOURCE_DIR,  # e.g. "interventions"
+        "model": MODEL_0,
+        "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',
+            "--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_disease_classification_choices_data.py

@@ -1,41 +1,38 @@
 from django.core.management.base import BaseCommand
-from endoreg_db.models import DiseaseClassificationChoice as MODEL_0
-from ...utils import load_model_data_from_yaml
-from ...data import DISEASE_CLASSIFICATION_CHOICE_DATA_DIR as SOURCE_DIR
 
 from endoreg_db.models import DiseaseClassification
+from endoreg_db.models import DiseaseClassificationChoice as MODEL_0
 
-IMPORT_MODELS = [ # string as model key, serves as key in IMPORT_METADATA
+from ...data import DISEASE_CLASSIFICATION_CHOICE_DATA_DIR as SOURCE_DIR
+from ...utils import load_model_data_from_yaml
+
+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": ["disease_classification"], # e.g. ["intervention_types"]
-        "foreign_key_models": [DiseaseClassification] # e.g. [InterventionType]
+        "dir": SOURCE_DIR,  # e.g. "interventions"
+        "model": MODEL_0,
+        "foreign_keys": ["disease_classification"],  # e.g. ["intervention_types"]
+        "foreign_key_models": [DiseaseClassification],  # 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',
+            "--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_disease_classification_data.py

@@ -1,41 +1,38 @@
 from django.core.management.base import BaseCommand
-from endoreg_db.models import DiseaseClassification as MODEL_0
-from ...utils import load_model_data_from_yaml
-from ...data import DISEASE_CLASSIFICATION_DATA_DIR as SOURCE_DIR
 
 from endoreg_db.models import Disease
+from endoreg_db.models import DiseaseClassification as MODEL_0
 
-IMPORT_MODELS = [ # string as model key, serves as key in IMPORT_METADATA
+from ...data import DISEASE_CLASSIFICATION_DATA_DIR as SOURCE_DIR
+from ...utils import load_model_data_from_yaml
+
+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": ["disease"], # e.g. ["intervention_types"]
-        "foreign_key_models": [Disease] # e.g. [InterventionType]
+        "dir": SOURCE_DIR,  # e.g. "interventions"
+        "model": MODEL_0,
+        "foreign_keys": ["disease"],  # e.g. ["intervention_types"]
+        "foreign_key_models": [Disease],  # 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',
+            "--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_disease_data.py

@@ -1,18 +1,19 @@
 from django.core.management.base import BaseCommand
+
 from endoreg_db.models import (
-    Disease, 
+    Disease,
     DiseaseClassification,
     DiseaseClassificationChoice,
 )
-from ...utils import load_model_data_from_yaml
+
 from ...data import (
-    DISEASE_DATA_DIR, 
-    DISEASE_CLASSIFICATION_DATA_DIR,
     DISEASE_CLASSIFICATION_CHOICE_DATA_DIR,
+    DISEASE_CLASSIFICATION_DATA_DIR,
+    DISEASE_DATA_DIR,
 )
+from ...utils import load_model_data_from_yaml
 
-
-IMPORT_MODELS = [ # string as model key, serves as key in IMPORT_METADATA
+IMPORT_MODELS = [  # string as model key, serves as key in IMPORT_METADATA
     Disease.__name__,
     DiseaseClassification.__name__,
     DiseaseClassificationChoice.__name__,
@@ -20,43 +21,39 @@ IMPORT_MODELS = [ # string as model key, serves as key in IMPORT_METADATA
 
 IMPORT_METADATA = {
     Disease.__name__: {
-        "dir": DISEASE_DATA_DIR, # e.g. "interventions"
-        "model": Disease, # e.g. Intervention
-        "foreign_keys": [], # e.g. ["intervention_types"]
-        "foreign_key_models": [] # e.g. [InterventionType]
+        "dir": DISEASE_DATA_DIR,  # e.g. "interventions"
+        "model": Disease,
+        "foreign_keys": [],  # e.g. ["intervention_types"]
+        "foreign_key_models": [],  # e.g. [InterventionType]
     },
     DiseaseClassification.__name__: {
-        "dir": DISEASE_CLASSIFICATION_DATA_DIR, # e.g. "interventions"
-        "model": DiseaseClassification, # e.g. Intervention
-        "foreign_keys": ["disease"], # e.g. ["intervention_types"]
-        "foreign_key_models": [Disease] # e.g. [InterventionType]
+        "dir": DISEASE_CLASSIFICATION_DATA_DIR,  # e.g. "interventions"
+        "model": DiseaseClassification,
+        "foreign_keys": ["disease"],  # e.g. ["intervention_types"]
+        "foreign_key_models": [Disease],  # e.g. [InterventionType]
     },
     DiseaseClassificationChoice.__name__: {
-        "dir": DISEASE_CLASSIFICATION_CHOICE_DATA_DIR, # e.g. "interventions"
-        "model": DiseaseClassificationChoice, # e.g. Intervention
-        "foreign_keys": ["disease_classification"], # e.g. ["intervention_types"]
-        "foreign_key_models": [DiseaseClassification] # e.g. [InterventionType]
+        "dir": DISEASE_CLASSIFICATION_CHOICE_DATA_DIR,  # e.g. "interventions"
+        "model": DiseaseClassificationChoice,
+        "foreign_keys": ["disease_classification"],  # e.g. ["intervention_types"]
+        "foreign_key_models": [DiseaseClassification],  # 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',
+            "--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_endoscope_data.py

@@ -1,24 +1,21 @@
-from django.conf import settings
 import os
+
+from django.conf import settings
 from django.core.management.base import BaseCommand
-from ...models import (
-    EndoscopeType,
-    Endoscope,
-    EndoscopyProcessor,
-    Center
-)
-from ...utils import load_model_data_from_yaml
+
 from ...data import (
+    ENDOSCOPE_DATA_DIR,
     ENDOSCOPE_TYPE_DATA_DIR,
     ENDOSCOPY_PROCESSOR_DATA_DIR,
-    ENDOSCOPE_DATA_DIR,
 )
+from ...models import Center, Endoscope, EndoscopeType, EndoscopyProcessor
+from ...utils import load_model_data_from_yaml
 
-SOURCE_DIR = ENDOSCOPE_TYPE_DATA_DIR # e.g. settings.DATA_DIR_INTERVENTION
+SOURCE_DIR = ENDOSCOPE_TYPE_DATA_DIR  # e.g. settings.DATA_DIR_INTERVENTION
 
 MODEL_0 = EndoscopeType
 
-IMPORT_MODELS = [ # string as model key, serves as key in IMPORT_METADATA
+IMPORT_MODELS = [  # string as model key, serves as key in IMPORT_METADATA
     EndoscopeType.__name__,
     EndoscopyProcessor.__name__,
     Endoscope.__name__,
@@ -26,43 +23,39 @@ IMPORT_MODELS = [ # string as model key, serves as key in IMPORT_METADATA
 
 IMPORT_METADATA = {
     EndoscopeType.__name__: {
-        "dir": ENDOSCOPE_TYPE_DATA_DIR, # e.g. "interventions"
-        "model": EndoscopeType, # e.g. Intervention
-        "foreign_keys": [], # e.g. ["intervention_types"]
-        "foreign_key_models": [] # e.g. [InterventionType]
+        "dir": ENDOSCOPE_TYPE_DATA_DIR,  # e.g. "interventions"
+        "model": EndoscopeType,
+        "foreign_keys": [],  # e.g. ["intervention_types"]
+        "foreign_key_models": [],  # e.g. [InterventionType]
     },
     EndoscopyProcessor.__name__: {
         "dir": ENDOSCOPY_PROCESSOR_DATA_DIR,
         "model": EndoscopyProcessor,
         "foreign_keys": ["centers"],
-        "foreign_key_models": [Center]
+        "foreign_key_models": [Center],
     },
     Endoscope.__name__: {
         "dir": ENDOSCOPE_DATA_DIR,
         "model": Endoscope,
         "foreign_keys": ["center", "endoscope_type"],
-        "foreign_key_models": [Center, EndoscopeType]
+        "foreign_key_models": [Center, EndoscopeType],
     },
 }
 
+
 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_event_data.py

@@ -1,41 +1,39 @@
 from django.core.management.base import BaseCommand
+
 from endoreg_db.models import Event
-from ...utils import load_model_data_from_yaml
+
 from ...data import EVENT_DATA_DIR as SOURCE_DIR
+from ...utils import load_model_data_from_yaml
 
 MODEL_0 = Event
 
-IMPORT_MODELS = [ # string as model key, serves as key in IMPORT_METADATA
+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]
+        "dir": SOURCE_DIR,  # e.g. "interventions"
+        "model": MODEL_0,
+        "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',
+            "--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)