endoreg-db 0.3.4__py3-none-any.whl → 0.3.6__py3-none-any.whl

endoreg_db/migrations/0061_remove_patientlabvalue_date_patientlabvalue_datetime.py

@@ -0,0 +1,24 @@
+# Generated by Django 5.0.4 on 2024-06-18 19:07
+
+import datetime
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ('endoreg_db', '0060_labvalue__default_date_value_distribution_and_more'),
+    ]
+
+    operations = [
+        migrations.RemoveField(
+            model_name='patientlabvalue',
+            name='date',
+        ),
+        migrations.AddField(
+            model_name='patientlabvalue',
+            name='datetime',
+            field=models.DateTimeField(auto_now_add=True, default=datetime.datetime(2024, 6, 18, 19, 7, 56, 929033, tzinfo=datetime.timezone.utc)),
+            preserve_default=False,
+        ),
+    ]

endoreg_db/migrations/0062_labvalue_numeric_precision.py

@@ -0,0 +1,18 @@
+# Generated by Django 5.0.4 on 2024-06-20 17:37
+
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ('endoreg_db', '0061_remove_patientlabvalue_date_patientlabvalue_datetime'),
+    ]
+
+    operations = [
+        migrations.AddField(
+            model_name='labvalue',
+            name='numeric_precision',
+            field=models.CharField(default='.2f', max_length=5),
+        ),
+    ]

endoreg_db/migrations/0063_alter_labvalue_numeric_precision.py

@@ -0,0 +1,18 @@
+# Generated by Django 5.0.4 on 2024-06-20 17:44
+
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ('endoreg_db', '0062_labvalue_numeric_precision'),
+    ]
+
+    operations = [
+        migrations.AlterField(
+            model_name='labvalue',
+            name='numeric_precision',
+            field=models.IntegerField(default=3),
+        ),
+    ]

endoreg_db/migrations/0064_casetemplaterule_extra_parameters_and_more.py

@@ -0,0 +1,23 @@
+# Generated by Django 5.0.4 on 2024-06-24 09:10
+
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ('endoreg_db', '0063_alter_labvalue_numeric_precision'),
+    ]
+
+    operations = [
+        migrations.AddField(
+            model_name='casetemplaterule',
+            name='extra_parameters',
+            field=models.JSONField(blank=True, null=True),
+        ),
+        migrations.AddField(
+            model_name='casetemplaterule',
+            name='parent_field',
+            field=models.CharField(blank=True, max_length=255, null=True),
+        ),
+    ]

endoreg_db/migrations/0065_rename__date_value_distribution_casetemplaterule_date_value_distribution_and_more.py

@@ -0,0 +1,58 @@
+# Generated by Django 5.0.4 on 2024-06-24 10:27
+
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ('endoreg_db', '0064_casetemplaterule_extra_parameters_and_more'),
+    ]
+
+    operations = [
+        migrations.RenameField(
+            model_name='casetemplaterule',
+            old_name='_date_value_distribution',
+            new_name='date_value_distribution',
+        ),
+        migrations.RenameField(
+            model_name='casetemplaterule',
+            old_name='_multiple_categorical_value_distribution',
+            new_name='multiple_categorical_value_distribution',
+        ),
+        migrations.RenameField(
+            model_name='casetemplaterule',
+            old_name='_numerical_value_distribution',
+            new_name='numerical_value_distribution',
+        ),
+        migrations.RenameField(
+            model_name='casetemplaterule',
+            old_name='_single_categorical_value_distribution',
+            new_name='single_categorical_value_distribution',
+        ),
+        migrations.RenameField(
+            model_name='labvalue',
+            old_name='_default_date_value_distribution',
+            new_name='default_date_value_distribution',
+        ),
+        migrations.RenameField(
+            model_name='labvalue',
+            old_name='_default_multiple_categorical_value_distribution',
+            new_name='default_multiple_categorical_value_distribution',
+        ),
+        migrations.RenameField(
+            model_name='labvalue',
+            old_name='_default_numerical_value_distribution',
+            new_name='default_numerical_value_distribution',
+        ),
+        migrations.RenameField(
+            model_name='labvalue',
+            old_name='_default_single_categorical_value_distribution',
+            new_name='default_single_categorical_value_distribution',
+        ),
+        migrations.AlterField(
+            model_name='casetemplate',
+            name='name',
+            field=models.CharField(max_length=255, unique=True),
+        ),
+    ]

endoreg_db/migrations/0066_alter_patientlabvalue_patient_and_more.py

@@ -0,0 +1,29 @@
+# Generated by Django 5.0.4 on 2024-06-24 15:36
+
+import django.db.models.deletion
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ('endoreg_db', '0065_rename__date_value_distribution_casetemplaterule_date_value_distribution_and_more'),
+    ]
+
+    operations = [
+        migrations.AlterField(
+            model_name='patientlabvalue',
+            name='patient',
+            field=models.ForeignKey(blank=True, null=True, on_delete=django.db.models.deletion.CASCADE, related_name='lab_values', to='endoreg_db.patient'),
+        ),
+        migrations.CreateModel(
+            name='PatientMedicationSchedule',
+            fields=[
+                ('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
+                ('created_at', models.DateTimeField(auto_now_add=True)),
+                ('updated_at', models.DateTimeField(auto_now=True)),
+                ('medication', models.ManyToManyField(related_name='patient_medication_schedules', to='endoreg_db.patientmedication')),
+                ('patient', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='endoreg_db.patient')),
+            ],
+        ),
+    ]

endoreg_db/migrations/0067_alter_medicationindication_indication_type.py

@@ -0,0 +1,19 @@
+# Generated by Django 5.0.4 on 2024-06-24 15:49
+
+import django.db.models.deletion
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ('endoreg_db', '0066_alter_patientlabvalue_patient_and_more'),
+    ]
+
+    operations = [
+        migrations.AlterField(
+            model_name='medicationindication',
+            name='indication_type',
+            field=models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, related_name='medication_indications', to='endoreg_db.medicationindicationtype'),
+        ),
+    ]

endoreg_db/models/__init__.py

@@ -1,57 +1,74 @@
-from .unit import Unit
-from .information_source import InformationSource
-from .center import Center
-from .report_reader import ReportReaderConfig, ReportReaderFlag
-from .persons import (
-    Person,
-    Patient,
-    PatientForm,
-    Examiner,
-    ExaminerSerializer,
-    PortalUserInfo,
-    Profession,
-    FirstName, LastName
-)
-
-from .examination import (
-    Examination,
-    ExaminationType,
-    ExaminationTime,
-    ExaminationTimeType,
-)
-
-from .data_file import *
-
-from .patient_examination import PatientExamination
-
-from .label import Label, LabelType, LabelSet
-
-from .annotation import (
-    ImageClassificationAnnotation,
-    LegacyBinaryClassificationAnnotationTask,
-    BinaryClassificationAnnotationTask,
-)
-
-from .legacy_data import (
-    LegacyImage,
-)
-
-from .ai_model import (
-    ModelMeta,
-    ModelType,
-    ActiveModel,
-)
-
-from .prediction import (
-    ImageClassificationPrediction,
-    LegacyVideoPredictionMeta,
-    VideoPredictionMeta,
-)
-
-from .hardware import (
-    EndoscopyProcessor,
-    Endoscope,
-    EndoscopeType,
-)
-
-from .questionnaires import TtoQuestionnaire
+from .unit import Unit
+from .information_source import InformationSource
+from .center import *
+from .report_reader import ReportReaderConfig, ReportReaderFlag
+from .emission import *
+from .persons import *
+
+from .case_template import *
+# from .other.distribution import (
+#     SingleCategoricalValueDistribution,
+#     NumericValueDistribution,
+#     MultipleCategoricalValueDistribution,
+#     DateValueDistribution,
+# )
+from .rules import (
+    Rule,
+    RuleType,
+    Ruleset,
+    RuleApplicator,
+    Rule
+)
+
+from .disease import Disease, DiseaseClassification, DiseaseClassificationChoice
+from .event import Event
+from .laboratory import LabValue
+from .medication import *
+
+from .examination import (
+    Examination,
+    ExaminationType,
+    ExaminationTime,
+    ExaminationTimeType,
+)
+from .data_file import *
+
+from .patient_examination import PatientExamination
+
+from .label import Label, LabelType, LabelSet
+
+from .annotation import (
+    ImageClassificationAnnotation,
+    LegacyBinaryClassificationAnnotationTask,
+    BinaryClassificationAnnotationTask,
+)
+
+from .legacy_data import (
+    LegacyImage,
+)
+
+from .other import *
+
+from .product import *
+
+from .ai_model import (
+    ModelMeta,
+    ModelType,
+    ActiveModel,
+)
+
+from .quiz import *
+
+from .prediction import (
+    ImageClassificationPrediction,
+    LegacyVideoPredictionMeta,
+    VideoPredictionMeta,
+)
+
+from .hardware import (
+    EndoscopyProcessor,
+    Endoscope,
+    EndoscopeType,
+)
+
+from .questionnaires import TtoQuestionnaire

endoreg_db/models/ai_model/__init__.py

@@ -1,3 +1,3 @@
-from .model_meta import ModelMeta
-from .model_type import ModelType
-from .active_model import ActiveModel
+from .model_meta import ModelMeta
+from .model_type import ModelType
+from .active_model import ActiveModel

endoreg_db/models/ai_model/active_model.py

@@ -1,9 +1,9 @@
-from django.db import models
-
-class ActiveModelManager(models.Manager):
-    def get_by_natural_key(self, name):
-        return self.get(name=name)
-    
-class ActiveModel(models.Model):
-    name = models.CharField(max_length=255, unique=True)
-    model_meta = models.OneToOneField('ModelMeta', on_delete=models.SET_NULL, blank=True, null=True)
+from django.db import models
+
+class ActiveModelManager(models.Manager):
+    def get_by_natural_key(self, name):
+        return self.get(name=name)
+    
+class ActiveModel(models.Model):
+    name = models.CharField(max_length=255, unique=True)
+    model_meta = models.OneToOneField('ModelMeta', on_delete=models.SET_NULL, blank=True, null=True)

endoreg_db/models/ai_model/model_meta.py

@@ -1,24 +1,24 @@
-from django.db import models
-
-class ModelMetaManager(models.Manager):
-    # natural key is name and version
-    def get_by_natural_key(self, name, version):
-        return self.get(name=name, version=version)
-
-class ModelMeta(models.Model):
-    name = models.CharField(max_length=255)
-    version = models.CharField(max_length=255)
-    type = models.ForeignKey("ModelType", on_delete=models.CASCADE, related_name="models")
-    labelset = models.ForeignKey("LabelSet", on_delete=models.CASCADE, related_name="models")
-    weights = models.FileField(upload_to='weights/')
-    
-    description = models.TextField(blank=True, null=True)
-    date_created = models.DateTimeField(auto_now_add=True)
-    objects = ModelMetaManager()
-
-    def natural_key(self):
-        return (self.name, self.version)
-
-    def __str__(self):
-        return f"{self.name} (v: {self.version})"
-
+from django.db import models
+
+class ModelMetaManager(models.Manager):
+    # natural key is name and version
+    def get_by_natural_key(self, name, version):
+        return self.get(name=name, version=version)
+
+class ModelMeta(models.Model):
+    name = models.CharField(max_length=255)
+    version = models.CharField(max_length=255)
+    type = models.ForeignKey("ModelType", on_delete=models.CASCADE, related_name="models")
+    labelset = models.ForeignKey("LabelSet", on_delete=models.CASCADE, related_name="models")
+    weights = models.FileField(upload_to='weights/')
+    
+    description = models.TextField(blank=True, null=True)
+    date_created = models.DateTimeField(auto_now_add=True)
+    objects = ModelMetaManager()
+
+    def natural_key(self):
+        return (self.name, self.version)
+
+    def __str__(self):
+        return f"{self.name} (v: {self.version})"
+

endoreg_db/models/ai_model/model_type.py

@@ -1,26 +1,26 @@
-from django.db import models
-from django.core import serializers
-
-class ModelTypeManager(models.Manager):
-    def get_by_natural_key(self, name):
-        return self.get(name=name)
-    
-class ModelType(models.Model):
-    """
-    A class representing a model type.
-
-    Attributes:
-        name (str): The name of the model type.
-        description (str): A description of the model type.
-
-    """
-    name = models.CharField(max_length=255)
-    description = models.TextField(blank=True, null=True)
-
-    objects = ModelTypeManager()
-
-    def natural_key(self):
-        return (self.name,)
-
-    def __str__(self):
+from django.db import models
+from django.core import serializers
+
+class ModelTypeManager(models.Manager):
+    def get_by_natural_key(self, name):
+        return self.get(name=name)
+    
+class ModelType(models.Model):
+    """
+    A class representing a model type.
+
+    Attributes:
+        name (str): The name of the model type.
+        description (str): A description of the model type.
+
+    """
+    name = models.CharField(max_length=255)
+    description = models.TextField(blank=True, null=True)
+
+    objects = ModelTypeManager()
+
+    def natural_key(self):
+        return (self.name,)
+
+    def __str__(self):
         return self.name

endoreg_db/models/ai_model/utils.py

@@ -1,8 +1,8 @@
-from .model_meta import ModelMeta
-
-# get latest model meta by model name
-
-# TODO MOVE THIS TO A QUERY FILE
-def get_latest_model_meta_by_model_name(model_name):
-    model_meta = ModelMeta.objects.filter(name=model_name).order_by('-version').first()
-    return model_meta
+from .model_meta import ModelMeta
+
+# get latest model meta by model name
+
+# TODO MOVE THIS TO A QUERY FILE
+def get_latest_model_meta_by_model_name(model_name):
+    model_meta = ModelMeta.objects.filter(name=model_name).order_by('-version').first()
+    return model_meta

endoreg_db/models/annotation/__init__.py

@@ -1,2 +1,2 @@
-from .image_classification import ImageClassificationAnnotation
+from .image_classification import ImageClassificationAnnotation
 from .binary_classification_annotation_task import LegacyBinaryClassificationAnnotationTask, BinaryClassificationAnnotationTask

endoreg_db/models/annotation/binary_classification_annotation_task.py

@@ -1,80 +1,80 @@
-from django.db import models
-from rest_framework import serializers
-from ..label import Label
-from ..data_file.video_segment import LegacyLabelVideoSegment
-from .image_classification import ImageClassificationAnnotation
-
-ANNOTATION_PER_S_THRESHOLD = 2
-
-def clear_finished_legacy_tasks():
-    # fetch all BinaryClassificationAnnotationTasks that are finished and delete them
-    tasks = LegacyBinaryClassificationAnnotationTask.objects.filter(finished=True)
-
-    # delete tasks with a bulk operation
-    tasks.delete()
-
-def get_legacy_binary_classification_annotation_tasks_by_label(label:Label, n:int=100, legacy=False):
-    clear_finished_legacy_tasks()
-
-    if legacy:
-        # fetch all LegacyLabelVideoSegments with the given label
-        _segments = LegacyLabelVideoSegment.objects.filter(label=label)
-        frames_for_tasks = []
-
-        for segment in _segments:
-            # check if the segment has already been annotated
-            annotations = list(ImageClassificationAnnotation.objects.filter(legacy_frame__in=segment.get_frames(), label=label))
-            segment_len_in_s = segment.get_segment_len_in_s()
-
-            target_annotation_number = segment_len_in_s * ANNOTATION_PER_S_THRESHOLD
-
-            if len(annotations) < target_annotation_number:
-                get_frame_number = int(target_annotation_number - len(annotations))
-                frames = segment.get_frames_without_annotation(get_frame_number)
-                frames_for_tasks.extend(frames)
-
-            if len(frames_for_tasks) >= n:
-                break
-
-        # create tasks
-        tasks = []
-        for frame in frames_for_tasks:
-
-            # get_or_create task
-            task, created = LegacyBinaryClassificationAnnotationTask.objects.get_or_create(
-                label=label,
-                image_path=frame.image.path,
-                frame_id=frame.pk,
-            )
-        
-
-class AbstractBinaryClassificationAnnotationTask(models.Model):
-    label = models.ForeignKey("Label", on_delete=models.CASCADE)
-    is_finished = models.BooleanField(default=False)
-    date_created = models.DateTimeField(auto_now_add=True)
-    date_finished = models.DateTimeField(blank=True, null=True)
-    image_path = models.CharField(max_length=255, blank=True, null=True)
-    image_type = models.CharField(max_length=255, blank=True, null=True)
-    frame_id = models.IntegerField(blank=True, null=True)
-    labelstudio_project_id = models.IntegerField(blank=True, null=True)
-    labelstudio_task_id = models.IntegerField(blank=True, null=True)
-
-    class Meta:
-        abstract = True
-
-class BinaryClassificationAnnotationTask(AbstractBinaryClassificationAnnotationTask):
-    frame = models.ForeignKey("Frame", on_delete=models.CASCADE, related_name="binary_classification_annotation_tasks")
-    image_type = models.CharField(max_length=255, default="frame")
-
-    def get_frame(self):
-        return self.video_segment.get_frame_by_id(self.frame_id)
-
-class LegacyBinaryClassificationAnnotationTask(AbstractBinaryClassificationAnnotationTask):
-    frame = models.ForeignKey("LegacyFrame", on_delete=models.CASCADE, related_name="binary_classification_annotation_tasks")
-    image_type = models.CharField(max_length=255, default="legacy")
-
-    def get_frame(self):
-        return self.frame
-
-
-
+from django.db import models
+from rest_framework import serializers
+from ..label import Label
+from ..data_file.video_segment import LegacyLabelVideoSegment
+from .image_classification import ImageClassificationAnnotation
+
+ANNOTATION_PER_S_THRESHOLD = 2
+
+def clear_finished_legacy_tasks():
+    # fetch all BinaryClassificationAnnotationTasks that are finished and delete them
+    tasks = LegacyBinaryClassificationAnnotationTask.objects.filter(finished=True)
+
+    # delete tasks with a bulk operation
+    tasks.delete()
+
+def get_legacy_binary_classification_annotation_tasks_by_label(label:Label, n:int=100, legacy=False):
+    clear_finished_legacy_tasks()
+
+    if legacy:
+        # fetch all LegacyLabelVideoSegments with the given label
+        _segments = LegacyLabelVideoSegment.objects.filter(label=label)
+        frames_for_tasks = []
+
+        for segment in _segments:
+            # check if the segment has already been annotated
+            annotations = list(ImageClassificationAnnotation.objects.filter(legacy_frame__in=segment.get_frames(), label=label))
+            segment_len_in_s = segment.get_segment_len_in_s()
+
+            target_annotation_number = segment_len_in_s * ANNOTATION_PER_S_THRESHOLD
+
+            if len(annotations) < target_annotation_number:
+                get_frame_number = int(target_annotation_number - len(annotations))
+                frames = segment.get_frames_without_annotation(get_frame_number)
+                frames_for_tasks.extend(frames)
+
+            if len(frames_for_tasks) >= n:
+                break
+
+        # create tasks
+        tasks = []
+        for frame in frames_for_tasks:
+
+            # get_or_create task
+            task, created = LegacyBinaryClassificationAnnotationTask.objects.get_or_create(
+                label=label,
+                image_path=frame.image.path,
+                frame_id=frame.pk,
+            )
+        
+
+class AbstractBinaryClassificationAnnotationTask(models.Model):
+    label = models.ForeignKey("Label", on_delete=models.CASCADE)
+    is_finished = models.BooleanField(default=False)
+    date_created = models.DateTimeField(auto_now_add=True)
+    date_finished = models.DateTimeField(blank=True, null=True)
+    image_path = models.CharField(max_length=255, blank=True, null=True)
+    image_type = models.CharField(max_length=255, blank=True, null=True)
+    frame_id = models.IntegerField(blank=True, null=True)
+    labelstudio_project_id = models.IntegerField(blank=True, null=True)
+    labelstudio_task_id = models.IntegerField(blank=True, null=True)
+
+    class Meta:
+        abstract = True
+
+class BinaryClassificationAnnotationTask(AbstractBinaryClassificationAnnotationTask):
+    frame = models.ForeignKey("Frame", on_delete=models.CASCADE, related_name="binary_classification_annotation_tasks")
+    image_type = models.CharField(max_length=255, default="frame")
+
+    def get_frame(self):
+        return self.video_segment.get_frame_by_id(self.frame_id)
+
+class LegacyBinaryClassificationAnnotationTask(AbstractBinaryClassificationAnnotationTask):
+    frame = models.ForeignKey("LegacyFrame", on_delete=models.CASCADE, related_name="binary_classification_annotation_tasks")
+    image_type = models.CharField(max_length=255, default="legacy")
+
+    def get_frame(self):
+        return self.frame
+
+
+