endoreg-db 0.8.6.4__py3-none-any.whl

endoreg_db/management/commands/load_name_data.py

@@ -0,0 +1,37 @@
+# endoreg_db/management/commands/generate_names.py
+
+import os
+from django.core.management.base import BaseCommand
+from endoreg_db.utils import collect_center_names  # Import your function here
+from pathlib import Path
+
+class Command(BaseCommand):
+    help = "Generate first_names.yaml and last_names.yaml from center data"
+
+    def add_arguments(self, parser):
+        # Adding an argument for the input file path
+        # parser.add_argument(
+        #     '--input_file_path',
+        #     type=str,
+        #     required=False,
+        #     help="Path to the input YAML file containing center data",
+        #     default="data/center/data.yaml",
+        # )
+        # parser.add_argument(
+        #     '--output-dir',
+        #     type=str,
+        #     default=os.getcwd(),
+        #     help="Directory where the output files will be saved (default: current directory)",
+        # )
+        pass
+
+    def handle(self, *args, **options):
+
+        # Run the function with the provided arguments
+        try:
+            collect_center_names()
+            self.stdout.write(self.style.SUCCESS("Successfully generated YAML files."))
+        except Exception as e:
+            self.stderr.write(self.style.ERROR(f"An error occurred: {e}"))
+
+            self.stderr.write(self.style.ERROR(f"PWD: {os.getcwd()}"))

endoreg_db/management/commands/load_organ_data.py

@@ -0,0 +1,43 @@
+from django.core.management.base import BaseCommand
+from endoreg_db.models import Organ
+from ...utils import load_model_data_from_yaml
+from ...data import (
+    ORGAN_DATA_DIR
+)
+
+MODEL_0 = Organ
+
+IMPORT_MODELS = [ # string as model key, serves as key in IMPORT_METADATA
+    MODEL_0.__name__,#
+]
+
+IMPORT_METADATA = {
+    MODEL_0.__name__: {
+        "dir": ORGAN_DATA_DIR, # e.g. "interventions"
+        "model": MODEL_0, # e.g. Intervention
+        "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',
+        )
+
+    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
+            )

endoreg_db/management/commands/load_pdf_type_data.py

@@ -0,0 +1,61 @@
+from django.conf import settings
+import os
+from django.core.management.base import BaseCommand
+
+import yaml
+from ...utils import load_model_data_from_yaml
+
+
+#### CUSTOMIZE
+from ...models import PdfType, ReportReaderFlag
+from ...data import PDF_TYPE_DATA_DIR
+
+SOURCE_DIR = PDF_TYPE_DATA_DIR # e.g. settings.DATA_DIR_INTERVENTION
+
+MODEL_0 = PdfType
+
+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": [
+            "patient_info_line",
+            "endoscope_info_line",
+            "examiner_info_line",
+            "cut_off_below_lines",
+            "cut_off_above_lines"
+        ], # e.g. ["intervention_types"]
+        "foreign_key_models": [
+            ReportReaderFlag,
+            ReportReaderFlag,
+            ReportReaderFlag,
+            ReportReaderFlag,
+            ReportReaderFlag
+        ] # e.g. [InterventionType]
+    }
+}
+
+class Command(BaseCommand):
+    help = f"""Load all .yaml files in the {SOURCE_DIR} directory"""
+
+    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
+            )

endoreg_db/management/commands/load_profession_data.py

@@ -0,0 +1,44 @@
+from django.conf import settings
+from django.core.management.base import BaseCommand
+from ...models import Profession
+from ...utils import load_model_data_from_yaml
+from ...data import PROFESSION_DATA_DIR
+
+SOURCE_DIR = PROFESSION_DATA_DIR # e.g. settings.DATA_DIR_INTERVENTION
+
+MODEL_0 = Profession
+
+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]
+    }
+}
+
+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
+            )

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_report_reader_flag_data.py

@@ -0,0 +1,46 @@
+from django.conf import settings
+import os
+from django.core.management.base import BaseCommand
+from ...models import ReportReaderFlag
+import yaml
+from ...utils import load_model_data_from_yaml
+from ...data import REPORT_READER_FLAG_DATA_DIR
+
+SOURCE_DIR = REPORT_READER_FLAG_DATA_DIR # e.g. settings.DATA_DIR_INTERVENTION
+
+MODEL_0 = ReportReaderFlag
+
+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]
+    }
+}
+
+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
+            )

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)

endoreg_db/management/commands/load_shift_data.py

@@ -0,0 +1,60 @@
+from django.core.management.base import BaseCommand
+from ...models import Shift, ShiftType
+from ...utils import load_model_data_from_yaml
+from ...data import REPORT_READER_FLAG_DATA_DIR
+
+SOURCE_DIR = REPORT_READER_FLAG_DATA_DIR # e.g. settings.DATA_DIR_INTERVENTION
+
+model_0 = ShiftType
+model_1 = Shift
+
+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]
+    },
+    model_1.__name__: {
+        "dir": SOURCE_DIR, # e.g. "interventions"
+        "model": model_1, # e.g. Intervention
+        "foreign_keys": ["shift_types"], # e.g. ["intervention_types"]
+        "foreign_key_models": [model_0]   # e.g. [InterventionType]
+    }
+}
+
+class Command(BaseCommand):
+    help = """Load all .yaml files in the data/shift directory
+    into the Shift and ShiftType model"""
+
+    def add_arguments(self, parser):
+        """
+        Adds the --verbose command-line option to enable detailed output during execution.
+        """
+        parser.add_argument(
+            '--verbose',
+            action='store_true',
+            help='Display verbose output',
+        )
+
+    def handle(self, *args, **options):
+        """
+        Loads YAML data files into models defined in IMPORT_MODELS using provided metadata.
+        
+        Iterates over each model specified in IMPORT_MODELS, retrieves its import metadata,
+        and calls the data loading utility to populate the database from YAML files. Supports
+        optional 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_tag_data.py

@@ -0,0 +1,57 @@
+from django.core.management.base import BaseCommand
+from endoreg_db.models import (
+    Tag,
+
+)
+
+from ...utils import load_model_data_from_yaml
+from ...data import (
+    TAG_DATA_DIR
+)
+
+
+IMPORT_MODELS = [  # string as model key, serves as key in IMPORT_METADATA
+    Tag.__name__,
+]
+
+IMPORT_METADATA = {
+    Tag.__name__: {
+        "dir": TAG_DATA_DIR,  # e.g. "interventions"
+        "model": Tag,  # e.g. Intervention
+        "foreign_keys": [],  # e.g. ["intervention_types"]
+        "foreign_key_models": [],  # 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)