endoreg-db 0.6.3__py3-none-any.whl → 0.6.4__py3-none-any.whl

endoreg_db/data/requirement_type/requirement_types.yaml

@@ -0,0 +1,83 @@
+- model: endoreg_db.requirement_type
+  fields:
+    name: "patient_examination"
+    name_de: "Patientenuntersuchung"
+    name_en: "Patient examination"
+    description: "Requirements of this type are used on PatientExamination Objects."
+
+- model: endoreg_db.requirement_type
+  fields:
+    name: "examination"
+    name_de: "Untersuchung"
+    name_en: "Examination"
+    description: "Examination-related requirements"
+
+- model: endoreg_db.requirement_type
+  fields:
+    name: "examination_indication"
+    name_de: "Untersuchungsindikation"
+    name_en: "Examination Indication"
+    description: "Examination indication requirements"
+
+- model: endoreg_db.requirement_type
+  fields:
+    name: "disease"
+    name_de: "Erkrankung"
+    name_en: "Disease"
+    description: "Disease-related requirements"
+
+- model: endoreg_db.requirement_type
+  fields:
+    name: "disease_classification_choice"
+    name_de: "Erkrankungsklassifikation"
+    name_en: "Disease Classification"
+    description: "Disease classification choice requirements"
+
+- model: endoreg_db.requirement_type
+  fields:
+    name: "event"
+    name_de: "Ereignis"
+    name_en: "Event"
+    description: "Event-related requirements"
+
+- model: endoreg_db.requirement_type
+  fields:
+    name: "lab_value"
+    name_de: "Laborwert"
+    name_en: "Lab Value"
+    description: "Lab value requirements"
+
+- model: endoreg_db.requirement_type
+  fields:
+    name: "finding"
+    name_de: "Befund"
+    name_en: "Finding"
+    description: "Finding requirements"
+
+- model: endoreg_db.requirement_type
+  fields:
+    name: "finding_morphology"
+    name_de: "Befundmorphologie"
+    name_en: "Finding Morphology"
+    description: "Finding morphology requirements"
+
+- model: endoreg_db.requirement_type
+  fields:
+    name: "finding_location"
+    name_de: "Befundlokalisation"
+    name_en: "Finding Location"
+    description: "Finding location requirements"
+
+- model: endoreg_db.requirement_type
+  fields:
+    name: "finding_intervention"
+    name_de: "Befundintervention"
+    name_en: "Finding Intervention"
+    description: "Finding intervention requirements"
+
+- model: endoreg_db.requirement_type
+  fields:
+    name: "finding_interventions"
+    name_de: "Befundinterventionen (multiple)"
+    name_en: "Finding Interventions (multiple)"
+    description: "Finding interventions (multiple) requirements"

endoreg_db/data/risk/bleeding.yaml

@@ -0,0 +1,26 @@
+- model: endoreg_db.risk
+  fields:
+    name: "bleeding_low"
+    name_de: "Blutung (niedrig)"
+    name_en: "Bleeding (low)"
+    description: "Low bleeding risk"
+    risk_type: "bleeding"
+    risk_value: 1
+
+- model: endoreg_db.risk
+  fields:
+    name: "bleeding_high"
+    name_de: "Blutung (hoch)"
+    name_en: "Bleeding (high)"
+    description: "High bleeding risk"
+    risk_type: "bleeding"
+    risk_value: 3
+
+- model: endoreg_db.risk
+  fields:
+    name: "bleeding_unknown"
+    name_de: "Blutung (unbekannt)"
+    name_en: "Bleeding (unknown)"
+    description: "Unknown bleeding risk"
+    risk_type: "bleeding"
+    risk_value: 0

endoreg_db/data/risk/thrombosis.yaml

@@ -0,0 +1,37 @@
+# high medium low thrombosis risk
+
+- model: endoreg_db.risk
+  fields:
+    name: "thrombosis_high"
+    name_de: "Thrombose hoch"
+    name_en: "Thrombosis high"
+    description: "High thrombosis risk"
+    risk_type: "thrombosis"
+    risk_value: 3
+
+- model: endoreg_db.risk
+  fields:
+    name: "thrombosis_medium"
+    name_de: "Thrombose mittel"
+    name_en: "Thrombosis medium"
+    description: "Medium thrombosis risk"
+    risk_type: "thrombosis"
+    risk_value: 2
+
+- model: endoreg_db.risk
+  fields:
+    name: "thrombosis_low"
+    name_de: "Thrombose niedrig"
+    name_en: "Thrombosis low"
+    description: "Low thrombosis risk"
+    risk_type: "thrombosis"
+    risk_value: 1
+
+- model: endoreg_db.risk
+  fields:
+    name: "thrombosis_unknown"
+    name_de: "Thrombose unbekannt"
+    name_en: "Thrombosis unknown"
+    description: "Unknown thrombosis risk"
+    risk_type: "thrombosis"
+    risk_value: 0

endoreg_db/data/risk_type/data.yaml

@@ -0,0 +1,27 @@
+- model: endoreg_db.risk_type
+  fields:
+    name: "bleeding"
+    name_de: "Blutung"
+    name_en: "Bleeding"
+    description: "Bleeding risk"
+
+- model: endoreg_db.risk_type
+  fields:
+    name: "perforation"
+    name_de: "Perforation"
+    name_en: "Perforation"
+    description: "Perforation risk"
+
+- model: endoreg_db.risk_type
+  fields:
+    name: "infection"
+    name_de: "Infektion"
+    name_en: "Infection"
+    description: "Infection risk"
+
+- model: endoreg_db.risk_type
+  fields:
+    name: "thrombosis"
+    name_de: "Thrombose"
+    name_en: "Thrombosis"
+    description: "Thrombosis risk"

endoreg_db/data/unit/time.yaml

@@ -10,4 +10,39 @@
     name: "minutes"
     abbreviation: "min"
     name_de: "Minuten"
-    name_en: "Minutes"
+    name_en: "Minutes"
+
+- model: endoreg_db.unit
+  fields:
+    name: "hours"
+    abbreviation: "h"
+    name_de: "Stunden"
+    name_en: "Hours"
+
+- model: endoreg_db.unit
+  fields:
+    name: "days"
+    abbreviation: "d"
+    name_de: "Tage"
+    name_en: "Days"
+
+- model: endoreg_db.unit
+  fields:
+    name: "weeks"
+    abbreviation: "w"
+    name_de: "Wochen"
+    name_en: "Weeks"
+
+- model: endoreg_db.unit
+  fields:
+    name: "months"
+    abbreviation: "mo"
+    name_de: "Monate"
+    name_en: "Months"
+
+- model: endoreg_db.unit
+  fields:
+    name: "years"
+    abbreviation: "y"
+    name_de: "Jahre"
+    name_en: "Years"

endoreg_db/management/commands/load_base_db_data.py

@@ -14,12 +14,23 @@ class Command(BaseCommand):
 
     def handle(self, *args, **options):
         # 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 
+        and forces verbose output. A final success message is printed after all commands complete.
+        """
         verbose = True
 
         self.stdout.write(self.style.SUCCESS("Populating base db models with data..."))
 
         out = self.stdout
 
+        call_command("load_information_source", stdout=out, verbose=verbose)
+
+        call_command("load_risk_data", stdout=out, verbose=verbose)
+
         # Load Center Data
         call_command("load_center_data", stdout=out, verbose=verbose)
         call_command("load_endoscope_data", stdout=out, verbose=verbose)
@@ -34,11 +45,13 @@ class Command(BaseCommand):
         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_examination_indication_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_medication_data", stdout=out, verbose=verbose)
 
+        call_command("load_requirement_data", stdout=out, verbose=verbose)
+
         # Load AI Model Data
         call_command("load_ai_model_label_data", stdout=out, verbose=verbose)
         call_command("load_ai_model_data", stdout=out, verbose=verbose)

endoreg_db/management/commands/load_center_data.py

@@ -1,43 +1,68 @@
 from django.core.management.base import BaseCommand
 from ...utils import load_model_data_from_yaml
 from ...models import Center, FirstName, LastName
-from ...data import CENTER_DATA_DIR
+from ...data import CENTER_DATA_DIR, NAMES_FIRST_DATA_DIR, NAMES_LAST_DATA_DIR
 
-SOURCE_DIR = CENTER_DATA_DIR # e.g. settings.DATA_DIR_INTERVENTION
 
-MODEL_0 = Center
+SOURCE_DIR = CENTER_DATA_DIR  # e.g. settings.DATA_DIR_INTERVENTION
 
-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
+    FirstName.__name__,
+    LastName.__name__,
+    Center.__name__,
 ]
 
 IMPORT_METADATA = {
-    MODEL_0.__name__: {
-        "dir": SOURCE_DIR, # e.g. "interventions"
-        "model": MODEL_0, # e.g. Intervention
-        "foreign_keys": ["first_names", "last_names"], # e.g. ["intervention_types"]
-        "foreign_key_models": [FirstName, LastName] # e.g. [InterventionType]
-    }
+    FirstName.__name__: {
+        "dir": NAMES_FIRST_DATA_DIR,  # e.g. "interventions"
+        "model": FirstName,  # e.g. Intervention
+        "foreign_keys": [],  # e.g. ["intervention_types"]
+        "foreign_key_models": [],  # e.g. [InterventionType]
+    },
+    LastName.__name__: {
+        "dir": NAMES_LAST_DATA_DIR,  # e.g. "interventions"
+        "model": LastName,  # e.g. Intervention
+        "foreign_keys": [],  # e.g. ["intervention_types"]
+        "foreign_key_models": [],  # e.g. [InterventionType]
+    },
+    Center.__name__: {
+        "dir": SOURCE_DIR,  # e.g. "interventions"
+        "model": Center,  # e.g. Intervention
+        "foreign_keys": ["first_names", "last_names"],  # e.g. ["intervention_types"]
+        "foreign_key_models": [FirstName, LastName],  # 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.
+        
+        When specified, this flag enables verbose output for the management command.
+        """
         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']
+        """
+        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.
+        """
+        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_examination_indication_data.py

@@ -2,9 +2,10 @@ 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
@@ -15,51 +16,72 @@ 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": [
+            "examination",
+            "expected_interventions",
+        ],
+        "foreign_key_models": [
+            Examination,
+            FindingIntervention,
+        ],
+    },
+    ExaminationIndicationClassification.__name__: {
+        "dir": EXAMINATION_INDICATION_CLASSIFICATION_DATA_DIR,
+        "model": ExaminationIndicationClassification,
+        "foreign_keys": [
+            "examination",
+            "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_requirement_data.py

@@ -0,0 +1,156 @@
+from django.core.management.base import BaseCommand
+from endoreg_db.models import (
+    RequirementType,
+    RequirementOperator,
+    Requirement,
+    RequirementSetType,
+    RequirementSet,
+    Examination,
+    ExaminationIndication,
+    Disease,
+    DiseaseClassificationChoice,
+    Event,
+    LabValue,
+    Finding,
+    FindingMorphologyClassificationChoice,
+    FindingLocationClassificationChoice,
+    FindingIntervention,
+    InformationSource,
+    Unit,
+    Risk,
+    RiskType,
+    MedicationIndication,
+    MedicationIndicationType,
+    MedicationSchedule,
+)
+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,
+)
+
+
+IMPORT_MODELS = [  # string as model key, serves as key in IMPORT_METADATA
+    RequirementType.__name__,
+    RequirementOperator.__name__,
+    Requirement.__name__,
+    RequirementSetType.__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]
+    },
+    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_morphology_classification_choices",
+            "finding_location_classification_choices",
+            "finding_interventions",
+            "risks",
+            "risk_types",
+            "medication_indications",
+            "medication_indication_types",
+            "medication_schedules",
+        ],
+        "foreign_key_models": [
+            RequirementType,
+            RequirementOperator,
+            Unit,
+            Examination,
+            ExaminationIndication,
+            Disease,
+            DiseaseClassificationChoice,
+            Event,
+            LabValue,
+            Finding,
+            FindingMorphologyClassificationChoice,
+            FindingLocationClassificationChoice,
+            FindingIntervention,
+            Risk,
+            RiskType,
+            MedicationIndication,
+            MedicationIndicationType,
+            MedicationSchedule,
+        ],
+    },
+    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",
+        ],  # e.g. ["intervention_types"]
+        "foreign_key_models": [
+            RequirementSetType,
+            Requirement,
+            RequirementSet,
+            InformationSource,
+        ],  # 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)