endoreg-db 0.6.3__py3-none-any.whl → 0.8.1__py3-none-any.whl

endoreg_db/management/commands/load_examination_indication_data.py

@@ -2,11 +2,11 @@ from django.conf import settings
 from django.core.management.base import BaseCommand
 from ...models import (
     ExaminationIndicationClassification,
-    ExaminationIndication,  # Replace 'your_app_name' with the actual app name
+    ExaminationIndication,
     ExaminationIndicationClassificationChoice,
     Examination,
+    FindingIntervention,
 )
-import os
 from ...utils import load_model_data_from_yaml
 from ...data import (
     EXAMINATION_INDICATION_CLASSIFICATION_CHOICE_DATA_DIR,
@@ -15,51 +15,72 @@ from ...data import (
 )
 
 
-IMPORT_MODELS = [ # string as model key, serves as key in IMPORT_METADATA
-    ExaminationIndicationClassification.__name__,
+IMPORT_MODELS = [  # string as model key, serves as key in IMPORT_METADATA
     ExaminationIndication.__name__,
+    ExaminationIndicationClassification.__name__,
     ExaminationIndicationClassificationChoice.__name__,
 ]
 
 IMPORT_METADATA = {
-    ExaminationIndicationClassification.__name__: {
-        "dir": EXAMINATION_INDICATION_CLASSIFICATION_DATA_DIR, # e.g. "interventions"
-        "model": ExaminationIndicationClassification, # e.g. Intervention
-        "foreign_keys": [], # e.g. ["intervention_types"]
-        "foreign_key_models": [] # e.g. [InterventionType]
-    },
     ExaminationIndication.__name__: {
-        "dir": EXAMINATION_INDICATION_DATA_DIR, # e.g. "interventions"
-        "model": ExaminationIndication, # e.g. Intervention
-        "foreign_keys": ["classification", "examination"], # e.g. ["intervention_types"]
-        "foreign_key_models": [ExaminationIndicationClassification, Examination] # e.g. [InterventionType]
+        "dir": EXAMINATION_INDICATION_DATA_DIR,
+        "model": ExaminationIndication,
+        "foreign_keys": [
+            "examinations",
+            "expected_interventions",
+        ],
+        "foreign_key_models": [
+            Examination,
+            FindingIntervention,
+        ],
+    },
+    ExaminationIndicationClassification.__name__: {
+        "dir": EXAMINATION_INDICATION_CLASSIFICATION_DATA_DIR,
+        "model": ExaminationIndicationClassification,
+        "foreign_keys": [
+            "examinations",
+            "indications",  # This is a many-to-many field
+        ],
+        "foreign_key_models": [
+            Examination,
+            ExaminationIndication,
+        ],
     },
     ExaminationIndicationClassificationChoice.__name__: {
-        "dir": EXAMINATION_INDICATION_CLASSIFICATION_CHOICE_DATA_DIR, # e.g. "interventions"
-        "model": ExaminationIndicationClassificationChoice, # e.g. Intervention
-        "foreign_keys": ["classification"], # e.g. ["intervention_types"]
-        "foreign_key_models": [ExaminationIndicationClassification] # e.g. [InterventionType]
+        "dir": EXAMINATION_INDICATION_CLASSIFICATION_CHOICE_DATA_DIR,
+        "model": ExaminationIndicationClassificationChoice,
+        "foreign_keys": ["classification"],
+        "foreign_key_models": [ExaminationIndicationClassification],
     },
 }
 
+
 class Command(BaseCommand):
     help = """Load all .yaml files in the data/intervention directory
     into the Intervention and InterventionType model"""
 
     def add_arguments(self, parser):
+        """
+        Add the --verbose flag to the command-line argument parser.
+        
+        This method augments the parser with a '--verbose' option to enable detailed output
+        during command execution.
+        """
         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']
+        """
+        Executes YAML data import for configured models.
+        
+        Retrieves the verbosity flag from the options and iterates through each model
+        in IMPORT_MODELS. For every model, it obtains the associated metadata from
+        IMPORT_METADATA and invokes load_model_data_from_yaml to load data from its YAML files.
+        """
+        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_finding_data.py

@@ -1,63 +1,45 @@
 from django.core.management.base import BaseCommand
 from endoreg_db.models import (
     Finding, FindingType, Examination,
-    FindingLocationClassification, FindingLocationClassificationChoice,
+    FindingClassification, FindingClassificationType, FindingClassificationChoice,
     Organ,
-    FindingMorphologyClassificationType, FindingMorphologyClassification,
-    FindingMorphologyClassificationChoice,
     FindingIntervention, FindingInterventionType, LabValue, Contraindication
 
 )
 from ...utils import load_model_data_from_yaml
 from ...data import (
     FINDING_DATA_DIR, FINDING_TYPE_DATA_DIR,
-    FINDING_LOCATION_CLASSIFICATION_DATA_DIR, 
-    FINDING_LOCATION_CLASSIFICATION_CHOICE_DATA_DIR,
-    FINDING_MORPHOLOGY_CLASSIFICATION_CHOICE_DATA_DIR, 
-    FINDING_MORPHOLOGY_CLASSIFICATION_DATA_DIR,
-    FINDING_MORPGOLOGY_CLASSIFICATION_TYPE_DATA_DIR,
     FINDING_INTERVETION_DATA_DIR,
-    FINIDNG_INTERVENTION_TYPE_DATA_DIR
+    FINIDNG_INTERVENTION_TYPE_DATA_DIR,
+    FINDING_CLASSIFICATION_TYPE_DATA_DIR,
+    FINDING_CLASSIFICATION_DATA_DIR,
+    FINDING_CLASSIFICATION_CHOICE_DATA_DIR
 )
 
-MODEL_0 = FindingType
-MODEL_1 = Finding
-MODEL_2 = FindingLocationClassificationChoice
-MODEL_3 = FindingLocationClassification
-MODEL_4 = FindingMorphologyClassificationType
-MODEL_5 = FindingMorphologyClassification
-MODEL_6 = FindingMorphologyClassificationChoice
-MODEL_7 = FindingInterventionType
-MODEL_8 = FindingIntervention
-
 IMPORT_MODELS = [ # string as model key, serves as key in IMPORT_METADATA
-    MODEL_7.__name__,
-    MODEL_8.__name__,
-    MODEL_0.__name__,
-    MODEL_1.__name__,
-    MODEL_2.__name__,
-    MODEL_3.__name__,
-    MODEL_4.__name__,
-    MODEL_5.__name__,
-    MODEL_6.__name__,
+    FindingInterventionType.__name__,
+    FindingIntervention.__name__,
+    FindingType.__name__,
+    Finding.__name__,
+    FindingClassificationType.__name__,
+    FindingClassificationChoice.__name__,
+    FindingClassification.__name__,
 ]
 
 IMPORT_METADATA = {
-    MODEL_0.__name__: {
+    FindingType.__name__: {
         "dir": FINDING_TYPE_DATA_DIR, # e.g. "interventions"
-        "model": MODEL_0, # e.g. Intervention
+        "model": FindingType, # e.g. Intervention
         "foreign_keys": [], # e.g. ["intervention_types"]
         "foreign_key_models": [] # e.g. [InterventionType]
     },
     Finding.__name__: {
         "dir": FINDING_DATA_DIR, # e.g. "interventions"
-        "model": MODEL_1, # e.g. Intervention
+        "model": Finding, # e.g. Intervention
         "foreign_keys": [
             "finding_types",
             "examinations",
             "finding_interventions",
-            "causing_finding_interventions",
-            "opt_causing_finding_interventions",
         ], # e.g. ["intervention_types"]
         "foreign_key_models": [
             FindingType,
@@ -67,65 +49,6 @@ IMPORT_METADATA = {
             FindingIntervention,
         ] # e.g. [InterventionType]
     },
-    MODEL_2.__name__: {
-        "dir": FINDING_LOCATION_CLASSIFICATION_CHOICE_DATA_DIR, # e.g. "interventions"
-        "model": MODEL_2, # e.g. Intervention
-        "foreign_keys": [
-            "organs"
-        ], # e.g. ["intervention_types"]
-        "foreign_key_models": [
-            Organ
-        ] # e.g. [InterventionType]
-    },
-    MODEL_3.__name__: {
-        "dir": FINDING_LOCATION_CLASSIFICATION_DATA_DIR, # e.g. "interventions"
-        "model": MODEL_3, # e.g. Intervention
-        "foreign_keys": [
-            "examinations",
-            "finding_types",
-            "findings",
-            "choices"
-        ], # e.g. ["intervention_types"]
-        "foreign_key_models": [
-            Examination,
-            FindingType,
-            Finding,
-            FindingLocationClassificationChoice
-        ] # e.g. [InterventionType]
-    },
-    MODEL_4.__name__: {
-        "dir": FINDING_MORPGOLOGY_CLASSIFICATION_TYPE_DATA_DIR, # e.g. "interventions"
-        "model": MODEL_4, # e.g. Intervention
-        "foreign_keys": [
-            "required_by_findings",
-            "optional_for_findings"
-        ], # e.g. ["intervention_types"]
-        "foreign_key_models": [
-            Finding,
-            Finding
-        ] # e.g. [InterventionType]
-    },
-
-    MODEL_5.__name__: {
-        "dir": FINDING_MORPHOLOGY_CLASSIFICATION_DATA_DIR, # e.g. "interventions"
-        "model": MODEL_5, # e.g. Intervention
-        "foreign_keys": [
-            "classification_type",
-        ],
-        "foreign_key_models": [
-            FindingMorphologyClassificationType,
-        ] 
-    },
-    MODEL_6.__name__: {
-        "dir": FINDING_MORPHOLOGY_CLASSIFICATION_CHOICE_DATA_DIR, # e.g. "interventions"
-        "model": MODEL_6, # e.g. Intervention
-        "foreign_keys": [
-            "classification",
-        ],
-        "foreign_key_models": [
-            FindingMorphologyClassification,
-        ] 
-    },
     FindingInterventionType.__name__: {
         "dir": FINIDNG_INTERVENTION_TYPE_DATA_DIR, # e.g. "interventions"
         "model": FindingInterventionType, # e.g. Intervention
@@ -146,6 +69,40 @@ IMPORT_METADATA = {
             Contraindication
         ] # e.g. [InterventionType]
     },
+    FindingClassificationType.__name__: {
+        "dir": FINDING_CLASSIFICATION_TYPE_DATA_DIR, # e.g. "interventions"
+        "model": FindingClassificationType, # e.g. Intervention
+        "foreign_keys": [], # e.g. ["intervention_types"]
+        "foreign_key_models": [] # e.g. [InterventionType]
+    },
+    FindingClassification.__name__: {
+        "dir": FINDING_CLASSIFICATION_DATA_DIR, # e.g. "interventions"
+        "model": FindingClassification, # e.g. Intervention
+        "foreign_keys": [
+            "classification_types",
+            "findings",
+            "examinations",
+            "finding_types",
+            "choices"
+        ], # e.g. ["intervention_types"]
+        "foreign_key_models": [
+            FindingClassificationType,
+            Finding,
+            Examination,
+            FindingType,
+            FindingClassificationChoice,
+        ] # e.g. [InterventionType]
+    },
+    FindingClassificationChoice.__name__: {
+        "dir": FINDING_CLASSIFICATION_CHOICE_DATA_DIR, # e.g. "interventions"
+        "model": FindingClassificationChoice, # e.g. Intervention
+        "foreign_keys": [
+            # "classifications",
+        ], # e.g. ["intervention_types"]
+        "foreign_key_models": [
+            # FindingClassification
+        ] # e.g. [InterventionType]
+    },
 }
 
 class Command(BaseCommand):

endoreg_db/management/commands/load_green_endoscopy_wuerzburg_data.py

@@ -7,7 +7,6 @@ from endoreg_db.models import (
     Product,
     ProductGroup,
     ReferenceProduct,
-    ProductGroup,
     TransportRoute,
     CenterWaste,
     CenterResource,

endoreg_db/management/commands/load_information_source.py

@@ -1,24 +1,30 @@
 from django.conf import settings
 import os
 from django.core.management.base import BaseCommand
-from ...models import InformationSource
+from ...models import InformationSource, InformationSourceType
 from ...utils import load_model_data_from_yaml
-from ...data import INFORMATION_DATA_DIR
+from ...data import INFORMATION_DATA_DIR, INFORMATION_SOURCE_TYPE_DATA_DIR
 
 SOURCE_DIR = INFORMATION_DATA_DIR # e.g. settings.DATA_DIR_INTERVENTION
 
-MODEL_0 = InformationSource
 
 IMPORT_MODELS = [ # string as model key, serves as key in IMPORT_METADATA
-    MODEL_0.__name__,
+    InformationSourceType.__name__,
+    InformationSource.__name__,
 ]
 
 IMPORT_METADATA = {
-    MODEL_0.__name__: {
-        "dir": SOURCE_DIR, # e.g. "interventions"
-        "model": MODEL_0, # e.g. Intervention
+    InformationSourceType.__name__: {
+        "dir": INFORMATION_SOURCE_TYPE_DATA_DIR, # e.g. "intervention_type"
+        "model": InformationSourceType, # e.g. InterventionType
         "foreign_keys": [], # e.g. ["intervention_types"]
         "foreign_key_models": [] # e.g. [InterventionType]
+    },
+    InformationSource.__name__: {
+        "dir": SOURCE_DIR, # e.g. "interventions"
+        "model": InformationSource, # e.g. Intervention
+        "foreign_keys": ["information_source_types"], # e.g. ["intervention_types"]
+        "foreign_key_models": [InformationSourceType] # e.g. [InterventionType]
     }
 }
 

endoreg_db/management/commands/load_qualification_data.py

@@ -0,0 +1,59 @@
+from django.core.management.base import BaseCommand
+from ...models import Qualification, QualificationType
+from ...utils import load_model_data_from_yaml
+from ...data import QUALIFICATION_DATA_DIR
+
+SOURCE_DIR = QUALIFICATION_DATA_DIR       # qualification data directory
+
+model_0 = QualificationType
+model_1 = Qualification
+
+IMPORT_MODELS = [ # string as model key, serves as key in IMPORT_METADATA
+    model_0.__name__,
+    model_1.__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]
+    },
+    model_1.__name__: {
+        "dir": SOURCE_DIR, # e.g. "interventions"
+        "model": model_1, # e.g. Intervention
+        "foreign_keys": ["qualification_types"], # e.g. ["intervention_types"]
+        "foreign_key_models": [model_0] # e.g. [InterventionType]
+    }
+}
+
+class Command(BaseCommand):
+    help = """Load all .yaml files in the data/qualification directory
+    into the Qualification / Qualification Type model"""
+
+    def add_arguments(self, parser):
+        """
+        Adds the --verbose flag to the command-line parser to enable detailed output.
+        """
+        parser.add_argument(
+            '--verbose',
+            action='store_true',
+            help='Display verbose output',
+        )
+
+    def handle(self, *args, **options):
+        """
+        Loads data from YAML files into the QualificationType and Qualification models.
+        
+        Iterates over predefined models and imports their data from YAML files using associated metadata. Supports verbose output if enabled via command-line 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_requirement_data.py

@@ -0,0 +1,180 @@
+from django.core.management.base import BaseCommand
+from endoreg_db.models import (
+    RequirementType,
+    RequirementOperator,
+    Requirement,
+    RequirementSetType,
+    RequirementSet,
+    Examination,
+    ExaminationIndication,
+    Disease,
+    DiseaseClassificationChoice,
+    Event,
+    LabValue,
+    Finding,
+    FindingClassification,
+    FindingClassificationChoice,
+    FindingIntervention,
+    InformationSource,
+    Unit,
+    Risk,
+    RiskType,
+    MedicationIndication,
+    MedicationIndicationType,
+    MedicationSchedule,
+    Medication,  # Added Medication model
+    MedicationIntakeTime,
+    Tag,
+    ExaminationRequirementSet,  # Added to avoid circular import issues
+)
+from endoreg_db.models.other.gender import Gender
+from ...utils import load_model_data_from_yaml
+from ...data import (
+    REQUIREMENT_TYPE_DATA_DIR,
+    REQUIREMENT_OPERATOR_DATA_DIR,
+    REQUIREMENT_DATA_DIR,
+    REQUIREMENT_SET_TYPE_DATA_DIR,
+    REQUIREMENT_SET_DATA_DIR,
+    EXAMINATION_REQUIREMENT_SET_DATA_DIR
+)
+
+
+IMPORT_MODELS = [  # string as model key, serves as key in IMPORT_METADATA
+    RequirementType.__name__,
+    RequirementOperator.__name__,
+    Requirement.__name__,
+    RequirementSetType.__name__,
+    ExaminationRequirementSet.__name__,
+    RequirementSet.__name__,
+]
+
+IMPORT_METADATA = {
+    RequirementType.__name__: {
+        "dir": REQUIREMENT_TYPE_DATA_DIR,  # e.g. "interventions"
+        "model": RequirementType,  # e.g. Intervention
+        "foreign_keys": [],  # e.g. ["intervention_types"]
+        "foreign_key_models": [],  # e.g. [InterventionType]
+    },
+    RequirementOperator.__name__: {
+        "dir": REQUIREMENT_OPERATOR_DATA_DIR,  # e.g. "interventions"
+        "model": RequirementOperator,  # e.g. Intervention
+        "foreign_keys": [],  # e.g. ["intervention_types"]
+        "foreign_key_models": [],  # e.g. [InterventionType]
+    },
+    ExaminationRequirementSet.__name__: {
+        "dir": EXAMINATION_REQUIREMENT_SET_DATA_DIR,  # e.g. "interventions"
+        "model": ExaminationRequirementSet,  # e.g. Intervention
+        "foreign_keys": ["examinations",], # Through model uses foreign keys of both models
+        "foreign_key_models": [Examination,],
+    },
+    # ExaminationRequirementSet.__name__,
+    Requirement.__name__: {
+        "dir": REQUIREMENT_DATA_DIR,  # e.g. "interventions"
+        "model": Requirement,  # e.g. Intervention
+        "foreign_keys": [
+            "requirement_types",
+            "operators",
+            "unit",
+            "examinations",
+            "examination_indications",
+            "diseases",
+            "disease_classification_choices",
+            "events",
+            "lab_values",
+            "findings",
+            "finding_classifications",
+            "finding_classification_choices",  # updated from finding_morphology_classification_choices
+            "finding_interventions",
+            "risks",
+            "risk_types",
+            "medication_indications",
+            "medication_indication_types",
+            "medication_schedules",
+            "medications",  # Added medications
+            "medication_intake_times",
+            "genders"
+        ],
+        "foreign_key_models": [
+            RequirementType,
+            RequirementOperator,
+            Unit,
+            Examination,
+            ExaminationIndication,
+            Disease,
+            DiseaseClassificationChoice,
+            Event,
+            LabValue,
+            Finding,
+            FindingClassification,
+            FindingClassificationChoice,
+            FindingIntervention,
+            Risk,
+            RiskType,
+            MedicationIndication,
+            MedicationIndicationType,
+            MedicationSchedule,
+            Medication,  # Added Medication model
+            MedicationIntakeTime,
+            Gender
+        ],
+    },
+    RequirementSetType.__name__: {
+        "dir": REQUIREMENT_SET_TYPE_DATA_DIR,  # e.g. "interventions"
+        "model": RequirementSetType,  # e.g. Intervention
+        "foreign_keys": [],  # e.g. ["intervention_types"]
+        "foreign_key_models": [],  # e.g. [InterventionType]
+    },
+    RequirementSet.__name__: {
+        "dir": REQUIREMENT_SET_DATA_DIR,  # e.g. "interventions"
+        "model": RequirementSet,  # e.g. Intervention
+        "foreign_keys": [
+            "requirement_set_type",
+            "requirements",  # This is a many-to-many field
+            "links_to_sets",
+            "information_sources",
+            "tags",
+            "reqset_exam_links"
+        ],  # e.g. ["intervention_types"]
+        "foreign_key_models": [
+            RequirementSetType,
+            Requirement,
+            RequirementSet,
+            InformationSource,
+            Tag,
+            ExaminationRequirementSet
+        ],  # e.g. [InterventionType]
+    },
+}
+
+
+class Command(BaseCommand):
+    help = """Load all requirement-related YAML files from their respective directories
+    into the database, including RequirementType, RequirementOperator, Requirement, 
+    RequirementSetType, and RequirementSet models"""
+
+    def add_arguments(self, parser):
+        """
+        Add command-line arguments to enable verbose output.
+        
+        Adds an optional '--verbose' flag to the command parser. When specified,
+        this flag causes the command to display detailed output during execution.
+        """
+        parser.add_argument(
+            "--verbose",
+            action="store_true",
+            help="Display verbose output",
+        )
+
+    def handle(self, *args, **options):
+        """
+        Executes data import for requirement models from YAML files.
+        
+        Retrieves the verbosity setting from the command options and iterates over each model 
+        listed in IMPORT_MODELS. For each model, it obtains the corresponding metadata from 
+        IMPORT_METADATA and calls a helper to load the YAML data into the database. Verbose mode 
+        enables detailed output during the process.
+        """
+        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_risk_data.py

@@ -0,0 +1,56 @@
+from django.core.management.base import BaseCommand
+from endoreg_db.models import Risk, RiskType
+from ...utils import load_model_data_from_yaml
+from ...data import RISK_DATA_DIR, RISK_TYPE_DATA_DIR
+
+
+IMPORT_MODELS = [  # string as model key, serves as key in IMPORT_METADATA
+    RiskType.__name__,
+    Risk.__name__,
+]
+
+IMPORT_METADATA = {
+    RiskType.__name__: {
+        "dir": RISK_TYPE_DATA_DIR,  # e.g. "interventions"
+        "model": RiskType,  # e.g. Intervention
+        "foreign_keys": [],  # e.g. ["intervention_types"]
+        "foreign_key_models": [],  # e.g. [InterventionType]
+    },
+    Risk.__name__: {
+        "dir": RISK_DATA_DIR,  # e.g. "interventions"
+        "model": Risk,  # e.g. Intervention
+        "foreign_keys": ["risk_type"],  # e.g. ["intervention_types"]
+        "foreign_key_models": [RiskType],  # 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):
+        """
+        Adds the '--verbose' flag to the argument parser for detailed output.
+        
+        This method extends the given parser by adding an option that, when specified,
+        enables verbose output during command execution.
+        """
+        parser.add_argument(
+            "--verbose",
+            action="store_true",
+            help="Display verbose output",
+        )
+
+    def handle(self, *args, **options):
+        """
+        Execute the command to load YAML data into configured models.
+        
+        Retrieves the verbosity setting from the options and iterates over each model in IMPORT_MODELS.
+        For each model, it obtains the corresponding metadata from IMPORT_METADATA and calls the utility
+        function load_model_data_from_yaml to load data from the associated YAML files.
+        """
+        verbose = options["verbose"]
+        for model_name in IMPORT_MODELS:
+            _metadata = IMPORT_METADATA[model_name]
+            load_model_data_from_yaml(self, model_name, _metadata, verbose)