endoreg-db 0.3.4__py3-none-any.whl → 0.3.5__py3-none-any.whl

endoreg_db/management/commands/load_medication_data.py

@@ -0,0 +1,41 @@
+from django.core.management.base import BaseCommand
+from endoreg_db.models import Medication, Unit
+from ...utils import load_model_data_from_yaml
+from ...data import MEDICATION_DATA_DIR as SOURCE_DIR
+
+MODEL_0 = Medication
+
+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": ["default_unit"], # e.g. ["intervention_types"]
+        "foreign_key_models": [Unit] # 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_medication_indication_data.py

@@ -0,0 +1,63 @@
+from django.core.management.base import BaseCommand
+from endoreg_db.models import (
+    MedicationIndication,
+    MedicationIndicationType,
+    MedicationSchedule,
+    Disease,
+    Event,
+    DiseaseClassificationChoice,
+    InformationSource
+)
+from ...utils import load_model_data_from_yaml
+from ...data import MEDICATION_INDICATION_DATA_DIR as SOURCE_DIR
+
+MODEL_0 = MedicationIndication
+
+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": [
+            "indication_type",
+            "medication_schedules",
+            "diseases",
+            "events",
+            "classification_choices",
+            "sources"
+        ], # e.g. ["intervention_types"]
+        "foreign_key_models": [
+            MedicationIndicationType,
+            MedicationSchedule,
+            Disease,
+            Event,
+            DiseaseClassificationChoice,
+            InformationSource
+        ] # 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_medication_indication_type_data.py

@@ -0,0 +1,41 @@
+from django.core.management.base import BaseCommand
+from endoreg_db.models import MedicationIndicationType
+from ...utils import load_model_data_from_yaml
+from ...data import MEDICATION_INDICATION_TYPE_DATA_DIR as SOURCE_DIR
+
+MODEL_0 = MedicationIndicationType
+
+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_medication_intake_time_data.py

@@ -0,0 +1,41 @@
+from django.core.management.base import BaseCommand
+from endoreg_db.models import MedicationIntakeTime
+from ...utils import load_model_data_from_yaml
+from ...data import MEDICATION_INTAKE_TIME_DATA_DIR as SOURCE_DIR
+
+MODEL_0 = MedicationIntakeTime
+
+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_medication_schedule_data.py

@@ -0,0 +1,55 @@
+from django.core.management.base import BaseCommand
+from endoreg_db.models import (
+    MedicationSchedule,
+    Medication,
+    MedicationIntakeTime,
+    Unit,
+    InformationSource
+)
+from ...utils import load_model_data_from_yaml
+from ...data import MEDICATION_SCHEDULE_DATA_DIR as SOURCE_DIR
+
+MODEL_0 = MedicationSchedule
+
+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": [
+            "medication",
+            "intake_times",
+            "unit",
+        ], # e.g. ["intervention_types"]
+        "foreign_key_models": [
+            Medication,
+            MedicationIntakeTime,
+            Unit,
+        ] # 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/migrations/0025_event_alter_rawpdffile_file_patientevent.py

@@ -0,0 +1,42 @@
+# Generated by Django 4.2.11 on 2024-04-25 21:31
+
+import django.core.files.storage
+import django.core.validators
+from django.db import migrations, models
+import django.db.models.deletion
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ('endoreg_db', '0024_remove_ttoquestionnaire_infections_and_more'),
+    ]
+
+    operations = [
+        migrations.CreateModel(
+            name='Event',
+            fields=[
+                ('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
+                ('name', models.CharField(max_length=100, unique=True)),
+                ('name_de', models.CharField(blank=True, max_length=100, null=True)),
+                ('name_en', models.CharField(blank=True, max_length=100, null=True)),
+                ('description', models.TextField(blank=True, null=True)),
+            ],
+        ),
+        migrations.AlterField(
+            model_name='rawpdffile',
+            name='file',
+            field=models.FileField(storage=django.core.files.storage.FileSystemStorage(location='/home/agl-admin/case-generator/agl_case_generator/erc_data/raw_pdf'), upload_to='raw_pdf/', validators=[django.core.validators.FileExtensionValidator(allowed_extensions=['pdf'])]),
+        ),
+        migrations.CreateModel(
+            name='PatientEvent',
+            fields=[
+                ('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
+                ('date_start', models.DateField()),
+                ('date_end', models.DateField(blank=True, null=True)),
+                ('description', models.TextField(blank=True, null=True)),
+                ('event', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='endoreg_db.event')),
+                ('patient', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='endoreg_db.patient')),
+            ],
+        ),
+    ]

endoreg_db/migrations/0026_disease_diseaseclassification_and_more.py

@@ -0,0 +1,166 @@
+# Generated by Django 4.2.11 on 2024-04-26 09:59
+
+from django.db import migrations, models
+import django.db.models.deletion
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ('endoreg_db', '0025_event_alter_rawpdffile_file_patientevent'),
+    ]
+
+    operations = [
+        migrations.CreateModel(
+            name='Disease',
+            fields=[
+                ('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
+                ('name', models.CharField(max_length=255, unique=True)),
+                ('name_de', models.CharField(blank=True, max_length=255, null=True)),
+                ('name_en', models.CharField(blank=True, max_length=255, null=True)),
+            ],
+        ),
+        migrations.CreateModel(
+            name='DiseaseClassification',
+            fields=[
+                ('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
+                ('name', models.CharField(max_length=255, unique=True)),
+                ('name_de', models.CharField(blank=True, max_length=255, null=True)),
+                ('name_en', models.CharField(blank=True, max_length=255, null=True)),
+                ('disease', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='endoreg_db.disease')),
+            ],
+        ),
+        migrations.CreateModel(
+            name='DiseaseClassificationChoice',
+            fields=[
+                ('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
+                ('name', models.CharField(max_length=255, unique=True)),
+                ('name_de', models.CharField(blank=True, max_length=255, null=True)),
+                ('name_en', models.CharField(blank=True, max_length=255, null=True)),
+                ('disease_classification', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='endoreg_db.diseaseclassification')),
+            ],
+        ),
+        migrations.CreateModel(
+            name='LabValue',
+            fields=[
+                ('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
+                ('name', models.CharField(max_length=255, unique=True)),
+                ('name_de', models.CharField(blank=True, max_length=255, null=True)),
+                ('name_en', models.CharField(blank=True, max_length=255, null=True)),
+                ('default_unit', models.ForeignKey(blank=True, null=True, on_delete=django.db.models.deletion.CASCADE, to='endoreg_db.unit')),
+            ],
+        ),
+        migrations.CreateModel(
+            name='Medication',
+            fields=[
+                ('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
+                ('name', models.CharField(max_length=255, unique=True)),
+                ('name_de', models.CharField(blank=True, max_length=255, null=True)),
+                ('name_en', models.CharField(blank=True, max_length=255, null=True)),
+                ('default_unit', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='endoreg_db.unit')),
+            ],
+        ),
+        migrations.CreateModel(
+            name='Rule',
+            fields=[
+                ('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
+                ('name', models.CharField(max_length=255, unique=True)),
+                ('name_de', models.CharField(blank=True, max_length=255, null=True)),
+                ('name_en', models.CharField(blank=True, max_length=255, null=True)),
+                ('description', models.TextField(blank=True, null=True)),
+                ('attribute_key', models.CharField(max_length=255)),
+            ],
+            options={
+                'verbose_name': 'Rule',
+                'verbose_name_plural': 'Rules',
+            },
+        ),
+        migrations.CreateModel(
+            name='RuleAttributeDType',
+            fields=[
+                ('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
+                ('name', models.CharField(max_length=255, unique=True)),
+                ('name_de', models.CharField(blank=True, max_length=255, null=True)),
+                ('name_en', models.CharField(blank=True, max_length=255, null=True)),
+            ],
+        ),
+        migrations.CreateModel(
+            name='RuleType',
+            fields=[
+                ('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
+                ('name', models.CharField(max_length=255, unique=True)),
+                ('name_de', models.CharField(blank=True, max_length=255, null=True)),
+                ('name_en', models.CharField(blank=True, max_length=255, null=True)),
+            ],
+            options={
+                'verbose_name': 'Rule Type',
+                'verbose_name_plural': 'Rule Types',
+            },
+        ),
+        migrations.AddField(
+            model_name='patientevent',
+            name='last_update',
+            field=models.DateTimeField(auto_now=True),
+        ),
+        migrations.CreateModel(
+            name='Ruleset',
+            fields=[
+                ('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
+                ('name', models.CharField(max_length=255, unique=True)),
+                ('name_de', models.CharField(blank=True, max_length=255, null=True)),
+                ('name_en', models.CharField(blank=True, max_length=255, null=True)),
+                ('rules', models.ManyToManyField(to='endoreg_db.rule')),
+            ],
+        ),
+        migrations.AddField(
+            model_name='rule',
+            name='attribute_dtype',
+            field=models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='endoreg_db.ruleattributedtype'),
+        ),
+        migrations.AddField(
+            model_name='rule',
+            name='rule_type',
+            field=models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='endoreg_db.ruletype'),
+        ),
+        migrations.CreateModel(
+            name='PatientMedication',
+            fields=[
+                ('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
+                ('name', models.CharField(max_length=255, unique=True)),
+                ('name_de', models.CharField(blank=True, max_length=255, null=True)),
+                ('name_en', models.CharField(blank=True, max_length=255, null=True)),
+                ('dosage', models.JSONField()),
+                ('active', models.BooleanField(default=True)),
+                ('medication', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='endoreg_db.medication')),
+                ('unit', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='endoreg_db.unit')),
+            ],
+            options={
+                'verbose_name': 'Patient Medication',
+                'verbose_name_plural': 'Patient Medications',
+            },
+        ),
+        migrations.CreateModel(
+            name='PatientLabValue',
+            fields=[
+                ('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
+                ('value', models.FloatField(blank=True, null=True)),
+                ('value_str', models.CharField(blank=True, max_length=255, null=True)),
+                ('date', models.DateTimeField()),
+                ('lab_value', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='endoreg_db.labvalue')),
+                ('patient', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='endoreg_db.patient')),
+                ('unit', models.ForeignKey(blank=True, null=True, on_delete=django.db.models.deletion.CASCADE, to='endoreg_db.unit')),
+            ],
+        ),
+        migrations.CreateModel(
+            name='PatientDisease',
+            fields=[
+                ('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
+                ('start_date', models.DateField(blank=True, null=True)),
+                ('end_date', models.DateField(blank=True, null=True)),
+                ('last_update', models.DateTimeField(auto_now=True)),
+                ('classification_choices', models.ManyToManyField(to='endoreg_db.diseaseclassificationchoice')),
+                ('disease', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='endoreg_db.disease')),
+                ('patient', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='endoreg_db.patient')),
+            ],
+        ),
+    ]

endoreg_db/migrations/0027_labvalue_abbreviation_labvalue_default_normal_range_and_more.py

@@ -0,0 +1,38 @@
+# Generated by Django 4.2.11 on 2024-04-27 07:35
+
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ('endoreg_db', '0026_disease_diseaseclassification_and_more'),
+    ]
+
+    operations = [
+        migrations.AddField(
+            model_name='labvalue',
+            name='abbreviation',
+            field=models.CharField(blank=True, max_length=10, null=True),
+        ),
+        migrations.AddField(
+            model_name='labvalue',
+            name='default_normal_range',
+            field=models.JSONField(blank=True, null=True),
+        ),
+        migrations.AddField(
+            model_name='labvalue',
+            name='normal_range_age_dependent',
+            field=models.BooleanField(default=False),
+        ),
+        migrations.AddField(
+            model_name='labvalue',
+            name='normal_range_gender_dependent',
+            field=models.BooleanField(default=False),
+        ),
+        migrations.AddField(
+            model_name='labvalue',
+            name='normal_range_special_case',
+            field=models.BooleanField(default=False),
+        ),
+    ]

endoreg_db/migrations/0028_alter_unit_abbreviation.py

@@ -0,0 +1,18 @@
+# Generated by Django 4.2.11 on 2024-04-27 08:29
+
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ('endoreg_db', '0027_labvalue_abbreviation_labvalue_default_normal_range_and_more'),
+    ]
+
+    operations = [
+        migrations.AlterField(
+            model_name='unit',
+            name='abbreviation',
+            field=models.CharField(blank=True, max_length=25, null=True),
+        ),
+    ]

endoreg_db/migrations/0029_medicationintaketime_and_more.py

@@ -0,0 +1,75 @@
+# Generated by Django 4.2.11 on 2024-04-27 09:14
+
+from django.db import migrations, models
+import django.db.models.deletion
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ('endoreg_db', '0028_alter_unit_abbreviation'),
+    ]
+
+    operations = [
+        migrations.CreateModel(
+            name='MedicationIntakeTime',
+            fields=[
+                ('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
+                ('repeats', models.CharField(default='daily', max_length=20)),
+                ('time', models.TimeField()),
+                ('unit', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='endoreg_db.unit')),
+            ],
+        ),
+        migrations.RemoveField(
+            model_name='patientmedication',
+            name='medication',
+        ),
+        migrations.RemoveField(
+            model_name='patientmedication',
+            name='name',
+        ),
+        migrations.RemoveField(
+            model_name='patientmedication',
+            name='name_de',
+        ),
+        migrations.RemoveField(
+            model_name='patientmedication',
+            name='name_en',
+        ),
+        migrations.AddField(
+            model_name='medication',
+            name='adapt_to_liver_function',
+            field=models.BooleanField(default=False),
+        ),
+        migrations.AddField(
+            model_name='medication',
+            name='adapt_to_renal_function',
+            field=models.BooleanField(default=False),
+        ),
+        migrations.AddField(
+            model_name='patientlabvalue',
+            name='normal_range',
+            field=models.JSONField(default={}),
+        ),
+        migrations.AddField(
+            model_name='patientmedication',
+            name='patient',
+            field=models.ForeignKey(default=None, on_delete=django.db.models.deletion.CASCADE, to='endoreg_db.patient'),
+            preserve_default=False,
+        ),
+        migrations.CreateModel(
+            name='MedicationSchedule',
+            fields=[
+                ('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
+                ('name', models.CharField(max_length=255)),
+                ('intake_times', models.ManyToManyField(to='endoreg_db.medicationintaketime')),
+                ('medication', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='endoreg_db.medication')),
+                ('unit', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='endoreg_db.unit')),
+            ],
+        ),
+        migrations.AddField(
+            model_name='patientmedication',
+            name='medication_schedules',
+            field=models.ManyToManyField(to='endoreg_db.medicationschedule'),
+        ),
+    ]