endoreg-db 0.6.4__py3-none-any.whl → 0.8.2__py3-none-any.whl

endoreg_db/models/questionnaires/__init__.py

@@ -1,114 +0,0 @@
-from django.db import models
-
-YES_NO_CHOICES = (
-    ('yes', 'Ja'),
-    ('no', 'Nein'),
-)
-
-class TtoQuestionnaire(models.Model):
-
-    # Patient Information
-    patient_name = models.CharField(max_length=255, verbose_name="Identifikation des Patienten (Name)")
-    birth_date = models.DateField(verbose_name="Geburtsdatum")
-
-    # Base documentation
-    emergency_patient = models.CharField(max_length=3, choices=YES_NO_CHOICES, verbose_name="Notfallpatient/kürzlich untersuchter Patient (Verzicht auf Team-Time-Out möglich)")
-    consent_signed = models.CharField(max_length=3, choices=YES_NO_CHOICES, verbose_name="Einverständniserklärung unterschrieben (Arzt, Patient)")
-    documents_present = models.CharField(max_length=3, choices=YES_NO_CHOICES, verbose_name="Alle Dokumente liegen vor (Labor, Befunde, etc.)")
-    communication_possible = models.CharField(max_length=3, choices=YES_NO_CHOICES, verbose_name="Kommunikation mit Patient möglich")
-    work_incapacity_certificate = models.CharField(max_length=3, choices=YES_NO_CHOICES, verbose_name="Arbeitsunfähigkeitsbescheinigung")
-
-    # priority items
-    pregnancy = models.CharField(max_length=3, choices=YES_NO_CHOICES, verbose_name="Schwangerschaft")
-    asa_classification_checked = models.CharField(max_length=3, choices=YES_NO_CHOICES, verbose_name="ASA-Klassifikation/Komorbidität geprüft")
-    previous_anesthesia_complications = models.CharField(max_length=3, choices=YES_NO_CHOICES, verbose_name="Komplikationen bei bisherigen Narkosen?")
-    last_meal_over_6_hours_ago = models.CharField(max_length=3, choices=YES_NO_CHOICES, verbose_name="Zeitpunkt letzte Mahlzeit > 6 Stunden")
-    allergies = models.CharField(max_length=3, choices=YES_NO_CHOICES, verbose_name="Allergien, welche?")
-    outpatient_accompaniment_post_sedation = models.CharField(max_length=3, choices=YES_NO_CHOICES, verbose_name="Nur bei ambulanter Vorstellung: Begleitung nach Sedierung?")
-    
-    # Possessions
-    dental_prosthesis = models.BooleanField(default=False, verbose_name="Zahnprothese")
-    glasses = models.BooleanField(default=False, verbose_name="Brille")
-    implants = models.BooleanField(default=False, verbose_name="Implantate")
-    hearing_aids = models.BooleanField(default=False, verbose_name="Hörgeräte")
-    
-
-    # Medical History
-    anticoagulants_ass = models.CharField(max_length=3, choices=YES_NO_CHOICES, verbose_name="Antikoagulation, ASS")
-    blood_pressure_medication = models.CharField(max_length=3, choices=YES_NO_CHOICES, verbose_name="Blutdruckmedikamente")
-    glaucoma = models.CharField(max_length=3, choices=YES_NO_CHOICES, verbose_name="Glaukom")
-
-    metal_implants = models.CharField(max_length=3, choices=YES_NO_CHOICES, verbose_name="Metallimplantate")
-    pacemaker_icd = models.CharField(max_length=3, choices=YES_NO_CHOICES, verbose_name="Herzschrittmacher/ICD")
-    
-    copd = models.CharField(max_length=3, choices=YES_NO_CHOICES, verbose_name="COPD")
-    liver_cirrhosis = models.CharField(max_length=3, choices=YES_NO_CHOICES, verbose_name="Leberzirrhose")
-    
-    ibd = models.CharField(max_length=3, choices=YES_NO_CHOICES, verbose_name="CED (Chronisch entzündliche Darmerkrankungen)")
-    radiation = models.CharField(max_length=3, choices=YES_NO_CHOICES, verbose_name="Bestrahlung")
-    surgeries = models.CharField(max_length=3, choices=YES_NO_CHOICES, verbose_name="OP´s")
-
-    # preflight
-    team_introduction = models.CharField(max_length=3, choices=YES_NO_CHOICES, verbose_name="Teamvorstellung mit Name und Aufgabe")
-    instruments_available = models.CharField(max_length=3, choices=YES_NO_CHOICES, verbose_name="Notwendige Instrumente vorhanden?")
-    monitoring_medications_equipment_checked = models.CharField(max_length=3, choices=YES_NO_CHOICES, verbose_name="Monitoring, Medikamente, Equipment zum Atemwegsmanagement zur Verfügung und überprüft?")
-    complete_documentation_inclusive_care_notes = models.TextField(verbose_name="Vollständige Dokumentation inklusive Hinweise für Nachsorge")
-    
-    # notes
-    notes = models.TextField(verbose_name="Bemerkungen", default = "Keine Bemerkungen")
-    
-    # postflight  
-    specimens_secured = models.BooleanField(default=False, verbose_name="Histologische Proben gesichert")
-    patient_condition_documented = models.TextField(verbose_name="Patientenzustand dokumentiert (je nach Ausgangszustand)")
-
-    
-
-    def __str__(self):
-        return f"Endoscopy Questionnaire for {self.patient_name} on {self.birth_date}"
-    
-    def get_id_attributes(self):
-        _ = [self.patient_name, self.birth_date]
-        return _
-    
-    def get_base_documentation_attributes(self):
-        _ = [self.emergency_patient, self.consent_signed, self.documents_present, self.communication_possible, self.work_incapacity_certificate]
-        return _
-    
-    def get_priority_items_attributes(self):
-        _ = [self.pregnancy, self.asa_classification_checked, self.previous_anesthesia_complications, self.last_meal_over_6_hours_ago, self.allergies, self.outpatient_accompaniment_post_sedation]
-        return _
-    
-    def get_possessions_attributes(self):
-        _ = [self.dental_prosthesis, self.glasses, self.implants, self.hearing_aids]
-        return _
-    
-    def get_medical_history_attributes(self): 
-        _ = [
-            self.anticoagulants_ass,
-            self.blood_pressure_medication,
-            self.glaucoma,
-            self.metal_implants,
-            self.pacemaker_icd,
-            self.copd,
-            self.liver_cirrhosis,
-            self.ibd,
-            self.radiation,
-            self.surgeries,
-        ]
-
-    def get_preflight_attributes(self):
-        _ = [
-            self.team_introduction,
-            self.instruments_available,
-            self.monitoring_medications_equipment_checked,
-        ]
-
-    def get_note_attributes(self):
-        _ = [self.notes]
-
-    def get_postflight_attributes(self):
-        _ = [
-            self.specimens_secured,
-            self.patient_condition_documented
-        ]
-

endoreg_db/models/quiz/__init__.py

@@ -1,9 +0,0 @@
-from .quiz_answer import QuizAnswer, QuizAnswerType
-from .quiz_question import QuizQuestion, QuizQuestionType
-
-__all__ = [
-    "QuizAnswer",
-    "QuizAnswerType",
-    "QuizQuestion",
-    "QuizQuestionType",
-] 

endoreg_db/models/quiz/quiz_answer.py

@@ -1,41 +0,0 @@
-from django.db import models
-
-class QuizAnswerTypeManager(models.Manager):
-    def get_by_natural_key(self, name):
-        return self.get(name=name)
-
-class QuizAnswerType(models.Model):
-    objects = QuizAnswerTypeManager()
-
-    name = models.CharField(max_length=255)
-    description = models.TextField(blank=True, null=True)
-
-    def natural_key(self):
-        return (self.name,)
-
-    def __str__(self):
-        return self.name
-
-class QuizAnswerManager(models.Manager):
-    def get_by_natural_key(self, text):
-        return self.get(text=text)
-    
-class QuizAnswer(models.Model):
-    objects = QuizAnswerManager()
-
-    text_value = models.CharField(max_length=255, null=True, blank=True)
-    number_value = models.FloatField(null=True, blank=True)
-    answer_type = models.ForeignKey("QuizAnswerType", on_delete=models.CASCADE)
-    question = models.ForeignKey("QuizQuestion", on_delete=models.CASCADE)
-
-    last_updated = models.DateTimeField(auto_now=True)
-
-    #TODO add user as foreign key
-
-    def natural_key(self):
-        return (self.text,)
-    
-    def __str__(self):
-        return self.text
-    
-

endoreg_db/models/quiz/quiz_question.py

@@ -1,54 +0,0 @@
-from django.db import models
-
-class QuizQuestionTypeManager(models.Manager):
-    def get_by_natural_key(self, name):
-        return self.get(name=name)
-    
-class QuizQuestionType(models.Model):
-    """
-    A class representing a quiz question type.
-
-    Attributes:
-        name (str): The name of the quiz question type.
-        description (str): A description of the quiz question type.
-
-    """
-    name = models.CharField(max_length=255)
-    description = models.TextField(blank=True, null=True)
-
-    objects = QuizQuestionTypeManager()
-
-    def natural_key(self):
-        return (self.name,)
-
-    def __str__(self):
-        return self.name
-    
-class QuizQuestionManager(models.Manager):
-    def get_by_natural_key(self, text):
-        return self.get(text=text)
-    
-class QuizQuestion(models.Model):
-    """
-    A class representing a quiz question.
-
-    Attributes:
-        text (str): The text of the quiz question.
-        question_type (QuizQuestionType): The type of the quiz question.
-        description (str): A description of the quiz question.
-
-    """
-    text = models.TextField()
-    description = models.TextField(blank=True, null=True)
-    question_type = models.ForeignKey("QuizQuestionType", on_delete=models.CASCADE)
-
-    objects = QuizQuestionManager()
-
-    def natural_key(self):
-        return (self.text,)
-    
-    def __str__(self):
-        return self.text
-    
-    def get_question_type(self):
-        return self.question_type.name

endoreg_db/models/report_reader/report_reader_config.py

@@ -1,53 +0,0 @@
-# ReportReaderConfig Class
-# Description: This class is used to store the configuration of the ReportReader
-
-# PATIENT_INFO_LINE_FLAG = "Patient: "
-# ENDOSCOPE_INFO_LINE_FLAG = "Gerät: "
-# EXAMINER_INFO_LINE_FLAG = "1. Unters.:"
-# CUT_OFF_BELOW_LINE_FLAG = "________________"
-
-
-# CUT_OFF_ABOVE_LINE_FLAGS = [
-#     ENDOSCOPE_INFO_LINE_FLAG,
-#     EXAMINER_INFO_LINE_FLAG,
-# ]
-
-# CUT_OFF_BELOW_LINE_FLAGS = [
-#         CUT_OFF_BELOW_LINE_FLAG
-#     ]
-
-from django.db import models
-from .report_reader_flag import ReportReaderFlag
-from ..center import Center
-from ..data_file import PdfType
-
-class ReportReaderConfig(models.Model):
-
-    locale = models.CharField(default="de_DE", max_length=10)
-    first_names = models.ManyToManyField('FirstName', related_name='report_reader_configs')
-    last_names = models.ManyToManyField('LastName', related_name='report_reader_configs')
-    text_date_format = models.CharField(default = "%d.%m.%Y", max_length=10)
-    patient_info_line_flag = models.ForeignKey(ReportReaderFlag, related_name='report_reader_configs_patient_info_line', on_delete=models.CASCADE)
-    endoscope_info_line_flag = models.ForeignKey(ReportReaderFlag, related_name='report_reader_configs_endoscope_info_line', on_delete=models.CASCADE)
-    examiner_info_line_flag = models.ForeignKey(ReportReaderFlag, related_name='report_reader_configs_examiner_info_line', on_delete=models.CASCADE)
-    cut_off_below = models.ManyToManyField(ReportReaderFlag, related_name='report_reader_configs_cut_off_below')
-    cut_off_above = models.ManyToManyField(ReportReaderFlag, related_name='report_reader_configs_cut_off_above')
-    
-    def __str__(self):
-        return self.locale
-    
-    def update_names_by_center(self, center:Center, save = True):
-        self.first_names.set(center.first_names.all())
-        self.last_names.set(center.last_names.all())
-        if save:
-            self.save()
-
-    def update_flags_by_pdf_type(self, pdf_type:PdfType, save = True):
-        self.patient_info_line_flag = pdf_type.patient_info_line_flag
-        self.endoscope_info_line_flag = pdf_type.endoscope_info_line_flag
-        self.examiner_info_line_flag = pdf_type.examiner_info_line_flag
-        self.cut_off_below.set(pdf_type.cut_off_below.all())
-        self.cut_off_above.set(pdf_type.cut_off_above.all())
-        if save:
-            self.save()
-

endoreg_db/models/rules/__init__.py

@@ -1,5 +0,0 @@
-from .rule_type import RuleType
-from .rule import Rule
-from .ruleset import Ruleset
-from .rule_attribute_dtype import RuleAttributeDType
-from .rule_applicator import RuleApplicator

endoreg_db/queries/get/__init__.py

@@ -1,6 +0,0 @@
-from .annotation import *
-from .center import *
-from .model import *
-from .patient import *
-from .patient_examination import *
-from .video import *

endoreg_db/queries/get/center.py

@@ -1,42 +0,0 @@
-from endoreg_db.models import Center
-from typing import Optional
-
-def get_centers() -> Center:
-    """
-    Returns all Center objects from the database.
-    """
-    return Center.objects.all()
-
-def get_center_by_name(name) -> Optional[Center]:
-    """Retrieve a Center object by its name.
-
-    Args:
-        name (str): The name of the center to retrieve.
-
-    Returns:
-        Optional[Center]: The Center object with the given name, or None if it does not exist.
-    """
-    return Center.objects.get(name=name)
-
-def get_center_by_id(id) -> Optional[Center]:
-    """Retrieve a Center object by its id.
-
-    Args:
-        id (int): The id of the center to retrieve.
-
-    Returns:
-        Optional[Center]: The Center object with the given id, or None if it does not exist.
-    """
-    return Center.objects.get(id=id)
-
-def get_center_by_natural_key(name: str) -> Optional[Center]:
-    """
-    Retrieve a Center object by its natural key.
-
-    Args:
-        name: The name of the center to retrieve.
-
-    Returns:
-        The Center object with the given name, or None if it does not exist.
-    """
-    return Center.objects.get_by_natural_key(name=name)

endoreg_db/queries/get/model.py

@@ -1,13 +0,0 @@
-from endoreg_db.models import (
-    ModelMeta,
-)
-
-def get_latest_model_by_name(model_name):
-    """
-    Expects model name. Fetches models by name from database, sorts by version and returns latest version.
-    """
-    models = ModelMeta.objects.filter(name=model_name).order_by('-version')
-    if len(models) == 0:
-        return None
-    else:
-        return models[0]

endoreg_db/queries/get/patient.py

@@ -1,14 +0,0 @@
-from endoreg_db.models import Patient
-
-def get_patients() -> Patient:
-    """
-    Returns all Patient objects from the database.
-    """
-    return Patient.objects.all()
-
-def get_patients_without_dob() -> Patient:
-    """
-    Returns all Patient objects from the database without a date of birth.
-    """
-    return Patient.objects.filter(dob__isnull=True)
-

endoreg_db/queries/get/patient_examination.py

@@ -1,20 +0,0 @@
-from endoreg_db.models import PatientExamination
-from typing import Optional
-
-def get_patient_examinations() -> PatientExamination:
-    """
-    Returns all PatientExamination objects from the database.
-    """
-    return PatientExamination.objects.all()
-
-def get_patient_examinations_without_report_file() -> PatientExamination:
-    """
-    Returns all PatientExamination objects from the database without a report_file.
-    """
-    return PatientExamination.objects.filter(report_file__isnull=True)
-
-def get_patient_examinations_without_video() -> PatientExamination:
-    """
-    Returns all PatientExamination objects from the database without a video.
-    """
-    return PatientExamination.objects.filter(video__isnull=True)

endoreg_db/queries/get/report_file.py

@@ -1,33 +0,0 @@
-from endoreg_db.models import ReportFile
-from typing import Optional
-
-def get_report_files() -> ReportFile:
-    """
-    Returns all ReportFile objects from the database.
-    """
-    return ReportFile.objects.all()
-
-def get_report_file_by_id(id) -> Optional[ReportFile]:
-    """Retrieve a ReportFile object by its id.
-
-    Args:
-        id (int): The id of the report_file to retrieve.
-
-    Returns:
-        Optional[ReportFile]: The ReportFile object with the given id, or None if it does not exist.
-    """
-    return ReportFile.objects.get(id=id)
-
-def get_report_files_without_examination() -> ReportFile:
-    """
-    Returns all ReportFile objects from the database without an examination.
-    """
-    return ReportFile.objects.filter(patient_examination__isnull=True)
-
-def get_report_files_without_patient() -> ReportFile:
-    """
-    Returns all ReportFile objects from the database without a patient.
-    """
-    return ReportFile.objects.filter(patient__isnull=True)
-
-

endoreg_db/queries/get/video.py

@@ -1,31 +0,0 @@
-from endoreg_db.models import Video, PatientExamination
-from typing import Optional
-
-def get_videos() -> Video:
-    """
-    Returns all Video objects from the database.
-    """
-    return Video.objects.all()
-
-def get_video_by_id(id) -> Optional[Video]:
-    """Retrieve a Video object by its id.
-
-    Args:
-        id (int): The id of the video to retrieve.
-
-    Returns:
-        Optional[Video]: The Video object with the given id, or None if it does not exist.
-    """
-    return Video.objects.get(id=id)
-
-def get_video_without_examination() -> Video:
-    """
-    Returns all Video objects from the database without an examination.
-    """
-    return Video.objects.filter(patient_examination__isnull=True)
-
-def get_video_without_patient() -> Video:
-    """
-    Returns all Video objects from the database without a patient.
-    """
-    return Video.objects.filter(patient__isnull=True)

endoreg_db/serializers/ai_model.py

@@ -1,19 +0,0 @@
-from endoreg_db.models import ModelMeta, ModelType, ActiveModel
-from rest_framework import serializers
-
-class ModelMetaSerializer(serializers.ModelSerializer):
-    weights = serializers.FileField(use_url=True)  # use_url=True will provide the file's URI
-
-    class Meta:
-        model = ModelMeta
-        fields = '__all__'
-
-class ModelTypeSerializer(serializers.ModelSerializer):
-    class Meta:
-        model = ModelType
-        fields = '__all__'
-
-class ActiveModelSerializer(serializers.ModelSerializer):
-    class Meta:
-        model = ActiveModel
-        fields = '__all__'

endoreg_db/serializers/annotation.py

@@ -1,14 +0,0 @@
-from rest_framework import serializers
-from endoreg_db.models import  BinaryClassificationAnnotationTask, ImageClassificationAnnotation
-
-
-
-class BinaryClassificationAnnotationTaskSerializer(serializers.ModelSerializer):
-    class Meta:
-        model = BinaryClassificationAnnotationTask
-        fields = '__all__'
-
-class ImageClassificationAnnotationSerializer(serializers.ModelSerializer):
-    class Meta:
-        model = ImageClassificationAnnotation
-        fields = '__all__'

endoreg_db/serializers/center.py

@@ -1,11 +0,0 @@
-from rest_framework import serializers
-from endoreg_db.models import (
-    Center,
-)
-
-class CenterSerializer(serializers.ModelSerializer):
-    class Meta:
-        model = Center
-        fields = '__all__'
-
-

endoreg_db/serializers/examination.py

@@ -1,33 +0,0 @@
-from rest_framework import serializers
-from endoreg_db.models import (
-    Examination,
-    ExaminationTimeType,
-    ExaminationTime,
-    ExaminationType,
-    PatientExamination
-)
-
-class ExaminationTimeTypeSerializer(serializers.ModelSerializer):
-    class Meta:
-        model = ExaminationTimeType
-        fields = '__all__'
-
-class ExaminationTimeSerializer(serializers.ModelSerializer):
-    class Meta:
-        model = ExaminationTime
-        fields = '__all__'
-
-class ExaminationTypeSerializer(serializers.ModelSerializer):
-    class Meta:
-        model = ExaminationType
-        fields = '__all__'
-
-class ExaminationSerializer(serializers.ModelSerializer): 
-    class Meta:
-        model = Examination
-        fields = '__all__'
-
-class PatientExaminationSerializer(serializers.ModelSerializer):
-    class Meta:
-        model = PatientExamination
-        fields = '__all__'

endoreg_db/serializers/frame.py

@@ -1,9 +0,0 @@
-from rest_framework import serializers
-from endoreg_db.models import Frame
-
-class FrameSerializer(serializers.ModelSerializer):
-    class Meta:
-        model = Frame
-        fields = '__all__'
-
-

endoreg_db/serializers/hardware.py

@@ -1,21 +0,0 @@
-from rest_framework import serializers
-from endoreg_db.models import (
-    Endoscope,
-    EndoscopeType,
-    EndoscopyProcessor,
-)
-
-class EndoscopeSerializer(serializers.ModelSerializer):
-    class Meta:
-        model = Endoscope
-        fields = '__all__'
-
-class EndoscopyProcessorSerializer(serializers.ModelSerializer):
-    class Meta:
-        model = EndoscopyProcessor
-        fields = '__all__'
-
-class EndoscopeTypeSerializer(serializers.ModelSerializer):
-    class Meta:
-        model = EndoscopeType
-        fields = '__all__'

endoreg_db/serializers/label.py

@@ -1,22 +0,0 @@
-from rest_framework import serializers
-from endoreg_db.models import (
-    Label,
-    LabelSet,
-    LabelType,
-)
-
-class LabelTypeSerializer(serializers.ModelSerializer):
-    class Meta:
-        model = LabelType
-        fields = '__all__'
-
-class LabelSetSerializer(serializers.ModelSerializer):
-    class Meta:
-        model = LabelSet
-        fields = '__all__'
-
-class LabelSerializer(serializers.ModelSerializer):
-    class Meta:
-        model = Label
-        fields = '__all__'
-        

endoreg_db/serializers/patient.py

@@ -1,33 +0,0 @@
-from rest_framework import serializers
-from endoreg_db.models import Patient, Gender
-
-class PatientSerializer(serializers.ModelSerializer):
-    # Use the slug field "name" so that the gender is represented by its string value
-    gender = serializers.SlugRelatedField(
-        slug_field='name',
-        queryset=Gender.objects.all()
-    )
-
-    class Meta:
-        model = Patient
-        fields = '__all__'
-        read_only_fields = ['id']
-
-    def get_age(self, obj):
-        return obj.age()
-
-    def create(self, validated_data):
-        center = validated_data.pop('center', None)
-        gender = validated_data.pop('gender', None)
-        patient = Patient.objects.create(center=center, gender=gender, **validated_data)
-        return patient
-
-    def update(self, instance, validated_data):
-        center = validated_data.pop('center', None)
-        gender = validated_data.pop('gender', None)
-        instance.center = center if center else instance.center
-        instance.gender = gender if gender else instance.gender
-        for attr, value in validated_data.items():
-            setattr(instance, attr, value)
-        instance.save()
-        return instance

endoreg_db/serializers/prediction.py

@@ -1,10 +0,0 @@
-from rest_framework import serializers
-from endoreg_db.models import (
-    ImageClassificationPrediction,
-)
-
-
-class ImageClassificationPredictionSerializer(serializers.ModelSerializer):
-    class Meta:
-        model = ImageClassificationPrediction
-        fields = "__all__"