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

endoreg_db/models/patient_examination/__init__.py

@@ -1,35 +1,35 @@
-from django.db import models
-
-# Serializer located in serializers/examination.py
-class PatientExamination(models.Model):
-    patient = models.ForeignKey('Patient', on_delete=models.CASCADE, related_name='patient_examinations')
-    examination = models.ForeignKey('Examination', on_delete=models.CASCADE, null = True, blank = True)
-    video = models.OneToOneField('Video', on_delete=models.CASCADE, null = True, blank = True, related_name='patient_examination')
-    report_file = models.OneToOneField('ReportFile', on_delete=models.CASCADE, null = True, blank = True, related_name='patient_examination')
-
-    class Meta:
-        verbose_name = 'Patient Examination'
-        verbose_name_plural = 'Patient Examinations'
-        ordering = ['patient', 'examination']
-
-    def __str__(self):
-        return f"{self.patient} - {self.report_file}"
-    
-    def find_matching_video_from_patient(self):
-        """
-        Finds a video for this patient examination based on the patient's videos.
-        For this, the videos date must be the same as the report file's date.
-        #TODO add more criteria for matching: Examination type
-        """
-        videos = self.patient.video_set.filter(date=self.report_file.date, patient_examination__isnull=True)
-        if videos:
-            if len(videos) > 1:
-                print(f"Warning: Found more than one video for patient {self.patient} on date {self.report_file.date}. Choosing the first one.")
-            return videos[0]
-        else:
-            videos = self.patient.video_set.filter(patient_examination__isnull=True)
-            if len(videos)==1:
-                return videos[0]
-            
-        return None
-
+from django.db import models
+
+# Serializer located in serializers/examination.py
+class PatientExamination(models.Model):
+    patient = models.ForeignKey('Patient', on_delete=models.CASCADE, related_name='patient_examinations')
+    examination = models.ForeignKey('Examination', on_delete=models.CASCADE, null = True, blank = True)
+    video = models.OneToOneField('Video', on_delete=models.CASCADE, null = True, blank = True, related_name='patient_examination')
+    report_file = models.OneToOneField('ReportFile', on_delete=models.CASCADE, null = True, blank = True, related_name='patient_examination')
+
+    class Meta:
+        verbose_name = 'Patient Examination'
+        verbose_name_plural = 'Patient Examinations'
+        ordering = ['patient', 'examination']
+
+    def __str__(self):
+        return f"{self.patient} - {self.report_file}"
+    
+    def find_matching_video_from_patient(self):
+        """
+        Finds a video for this patient examination based on the patient's videos.
+        For this, the videos date must be the same as the report file's date.
+        #TODO add more criteria for matching: Examination type
+        """
+        videos = self.patient.video_set.filter(date=self.report_file.date, patient_examination__isnull=True)
+        if videos:
+            if len(videos) > 1:
+                print(f"Warning: Found more than one video for patient {self.patient} on date {self.report_file.date}. Choosing the first one.")
+            return videos[0]
+        else:
+            videos = self.patient.video_set.filter(patient_examination__isnull=True)
+            if len(videos)==1:
+                return videos[0]
+            
+        return None
+

endoreg_db/models/permissions/__init__.py

@@ -1,44 +1,44 @@
-from django.contrib.contenttypes.models import ContentType
-from django.contrib.auth.models import Permission
-from endoreg_db.models import *  # Import your models here
-from django.db import transaction
-
-# Step 1: Define model to category mappings
-# Assuming every model class name is unique across your entire Django project
-model_categories = {
-    'SensitiveModel1': 'sensitive',
-    'SensitiveModel2': 'sensitive',
-    'DevelopmentModel1': 'development',
-    'DevelopmentModel2': 'development',
-    # Add all models you have, mapping them to either 'sensitive', 'development', or 'all'
-}
-
-# Step 2: Define permissions for each category
-category_permissions = {
-    'sensitive': ['view', 'edit', 'delete'],
-    'development': ['view', 'edit'],
-    'all': ['view'],
-}
-
-@transaction.atomic
-def create_permissions_for_all_models():
-    for model_class_name, category in model_categories.items():
-        model_class = globals().get(model_class_name)
-        if model_class is None:
-            print(f"Model {model_class_name} not found.")
-            continue
-        
-        content_type = ContentType.objects.get_for_model(model_class)
-        permissions = category_permissions.get(category, [])
-
-        for permission_codename in permissions:
-            permission_name = f"Can {permission_codename} {model_class_name}"
-            permission, created = Permission.objects.get_or_create(
-                codename=f"{permission_codename}_{model_class_name.lower()}",
-                defaults={'name': permission_name, 'content_type': content_type},
-            )
-            if created:
-                print(f"Created permission: {permission_name}")
-
-# Run the function to create and assign permissions based on categories
-create_permissions_for_all_models()
+from django.contrib.contenttypes.models import ContentType
+from django.contrib.auth.models import Permission
+from endoreg_db.models import *  # Import your models here
+from django.db import transaction
+
+# Step 1: Define model to category mappings
+# Assuming every model class name is unique across your entire Django project
+model_categories = {
+    'SensitiveModel1': 'sensitive',
+    'SensitiveModel2': 'sensitive',
+    'DevelopmentModel1': 'development',
+    'DevelopmentModel2': 'development',
+    # Add all models you have, mapping them to either 'sensitive', 'development', or 'all'
+}
+
+# Step 2: Define permissions for each category
+category_permissions = {
+    'sensitive': ['view', 'edit', 'delete'],
+    'development': ['view', 'edit'],
+    'all': ['view'],
+}
+
+@transaction.atomic
+def create_permissions_for_all_models():
+    for model_class_name, category in model_categories.items():
+        model_class = globals().get(model_class_name)
+        if model_class is None:
+            print(f"Model {model_class_name} not found.")
+            continue
+        
+        content_type = ContentType.objects.get_for_model(model_class)
+        permissions = category_permissions.get(category, [])
+
+        for permission_codename in permissions:
+            permission_name = f"Can {permission_codename} {model_class_name}"
+            permission, created = Permission.objects.get_or_create(
+                codename=f"{permission_codename}_{model_class_name.lower()}",
+                defaults={'name': permission_name, 'content_type': content_type},
+            )
+            if created:
+                print(f"Created permission: {permission_name}")
+
+# Run the function to create and assign permissions based on categories
+create_permissions_for_all_models()

endoreg_db/models/persons/__init__.py

@@ -1,6 +1,7 @@
-from .person import Person
-from .patient import Patient, PatientForm
-from .examiner import Examiner, ExaminerSerializer
-from .portal_user_information import PortalUserInfo, Profession
-from .first_name import FirstName
-from .last_name import LastName
+from .gender import Gender
+from .person import Person
+from .patient import *
+from .examiner import Examiner, ExaminerSerializer
+from .portal_user_information import PortalUserInfo, Profession
+from .first_name import FirstName
+from .last_name import LastName

endoreg_db/models/persons/examiner/__init__.py

@@ -1,2 +1,2 @@
-from .examiner import Examiner, ExaminerSerializer
+from .examiner import Examiner, ExaminerSerializer
 # from .examiner_type import ExaminerType

endoreg_db/models/persons/examiner/examiner.py

@@ -1,16 +1,16 @@
-from django.db import models
-from ..person import Person
-from rest_framework import serializers
-
-class Examiner(Person):
-    center = models.ForeignKey('Center', on_delete=models.CASCADE, blank=True, null=True)
-
-    def __str__(self):
-        return self.first_name + " " + self.last_name
-    
-
-class ExaminerSerializer(serializers.ModelSerializer):
-    
-    class Meta:
-        model = Examiner
+from django.db import models
+from ..person import Person
+from rest_framework import serializers
+
+class Examiner(Person):
+    center = models.ForeignKey('Center', on_delete=models.CASCADE, blank=True, null=True)
+
+    def __str__(self):
+        return self.first_name + " " + self.last_name
+    
+
+class ExaminerSerializer(serializers.ModelSerializer):
+    
+    class Meta:
+        model = Examiner
         fields = '__all__'

endoreg_db/models/persons/examiner/examiner_type.py

@@ -1,2 +1,2 @@
-from .examiner import Examiner
+from .examiner import Examiner
 # from .examiner_type import ExaminerType

endoreg_db/models/persons/first_name.py

@@ -1,18 +1,18 @@
-# class to represent unique first-names
-# name attribute is natural key
-
-from django.db import models
-
-class FirstNameManager(models.Manager):
-    def get_by_natural_key(self, name):
-        return self.get(name=name)
-    
-class FirstName(models.Model):
-    objects = FirstNameManager()
-    name = models.CharField(max_length=255, unique=True)
-    
-    def natural_key(self):
-        return (self.name,)
-    
-    def __str__(self):
+# class to represent unique first-names
+# name attribute is natural key
+
+from django.db import models
+
+class FirstNameManager(models.Manager):
+    def get_by_natural_key(self, name):
+        return self.get(name=name)
+    
+class FirstName(models.Model):
+    objects = FirstNameManager()
+    name = models.CharField(max_length=255, unique=True)
+    
+    def natural_key(self):
+        return (self.name,)
+    
+    def __str__(self):
         return self.name

endoreg_db/models/persons/gender.py

@@ -0,0 +1,22 @@
+from django.db import models
+
+class GenderManager(models.Manager):
+    def get_by_natural_key(self, name):
+        return self.get(name=name)
+    
+class Gender(models.Model):
+    """A class representing gender."""
+    objects = GenderManager()
+
+    name = models.CharField(max_length=255)
+    name_de = models.CharField(max_length=255, null=True)
+    name_en = models.CharField(max_length=255, null=True)
+    abbreviation = models.CharField(max_length=255, null=True)
+    description = models.TextField(blank=True, null=True)
+
+    def natural_key(self):
+        return (self.name,)
+    
+    def __str__(self):
+        return self.name
+

endoreg_db/models/persons/last_name.py

@@ -1,20 +1,20 @@
-# class to represent unique last_names
-# name attribute is natural key
-from django.db import models
-
-class LastNameManager(models.Manager):
-    def get_by_natural_key(self, name):
-        return self.get(name=name)
-
-class LastName(models.Model):
-    objects = LastNameManager()
-    name = models.CharField(max_length=255, unique=True)
-
-    def natural_key(self):
-        return (self.name,)
-
-    def __str__(self):
-        return self.name
-    
-# Path: endoreg_db/models/persons/first_name.py
+# class to represent unique last_names
+# name attribute is natural key
+from django.db import models
+
+class LastNameManager(models.Manager):
+    def get_by_natural_key(self, name):
+        return self.get(name=name)
+
+class LastName(models.Model):
+    objects = LastNameManager()
+    name = models.CharField(max_length=255, unique=True)
+
+    def natural_key(self):
+        return (self.name,)
+
+    def __str__(self):
+        return self.name
+    
+# Path: endoreg_db/models/persons/first_name.py
         

endoreg_db/models/persons/patient/__init__.py

@@ -0,0 +1,8 @@
+from .patient import Patient, PatientForm
+from .patient_event import PatientEvent
+from .patient_disease import PatientDisease
+from .patient_lab_sample import PatientLabSample, PatientLabSampleType
+from .patient_lab_value import PatientLabValue
+from .patient_medication import PatientMedication
+from .patient_medication_schedule import PatientMedicationSchedule
+from .case import *

endoreg_db/models/persons/patient/case/case.py

@@ -0,0 +1,30 @@
+from django.db import models
+
+class Case(models.Model):
+    """
+    A class representing a case.
+
+    Attributes:
+        name (str): The name of the case.
+        description (str): A description of the case.
+        case_template (CaseTemplate): The case template of the case.
+        patient (Patient): The patient of the case.
+        start_date (datetime): The start date of the case.
+        end_date (datetime): The end date of the case.
+        is_active (bool): A flag indicating whether the case is active.
+        is_closed (bool): A flag indicating whether the case is closed.
+        is_deleted (bool): A flag indicating whether the case is deleted.
+        created_at (datetime): The creation date of the case.
+        updated_at (datetime): The last update date of the case.
+
+    """
+    start_date = models.DateTimeField()
+    end_date = models.DateTimeField(null=True)
+    is_active = models.BooleanField(default=True)
+    is_closed = models.BooleanField(default=False)
+    is_deleted = models.BooleanField(default=False)
+    created_at = models.DateTimeField(auto_now_add=True)
+    updated_at = models.DateTimeField(auto_now=True)
+
+    def __str__(self):
+        return self.name

endoreg_db/models/persons/patient/patient.py

@@ -0,0 +1,216 @@
+from ..person import Person
+from django import forms
+from django.forms import DateInput
+from rest_framework import serializers
+from ...patient_examination import PatientExamination
+from ...data_file import ReportFile
+from django.db import models
+from faker import Faker
+import random
+from datetime import datetime
+
+class Patient(Person):
+    """
+    A class representing a patient.
+
+    Attributes inhereted from Person:
+        first_name (str): The first name of the patient.
+        last_name (str): The last name of the patient.
+        dob (datetime.date): The date of birth of the patient.
+        gender (Foreign Key): The gender of the patient.
+        email (str): The email address of the patient.
+        phone (str): The phone number of the patient.
+
+    """
+    center = models.ForeignKey("Center", on_delete=models.CASCADE, blank=True, null=True)
+    
+
+    def __str__(self):
+        return self.first_name + " " + self.last_name + " (" + str(self.dob) + ")"
+    
+    def get_unmatched_report_files(self): #field: self.report_files; filter: report_file.patient_examination = None
+        '''Returns all report files for this patient that are not matched to a patient examination.'''
+
+        return self.reportfile_set.filter(patient_examination=None)
+
+    def get_unmatched_video_files(self): #field: self.videos; filter: video.patient_examination = None
+        '''Returns all video files for this patient that are not matched to a patient examination.'''
+        return self.videos.filter(patient_examination=None)
+
+    def get_patient_examinations(self): #field: self.patient_examinations
+        '''Returns all patient examinations for this patient ordered by date (most recent is first).'''
+        return self.patient_examinations.order_by('-date')
+    
+    def create_examination_by_report_file(self, report_file:ReportFile):
+        '''Creates a patient examination for this patient based on the given report file.'''
+        patient_examination = PatientExamination(patient=self, report_file=report_file)
+        patient_examination.save()
+        return patient_examination
+    
+    @classmethod
+    def get_random_gender(self, p_male=0.5, p_female=0.5):
+        """
+        Get a Gender object by name (male, female) from the database with given probability.
+
+        :param p_male: Probability of selecting 'male' gender.
+        :param p_female: Probability of selecting 'female' gender.
+        :return: Gender object selected based on given probabilities.
+        """
+        from endoreg_db.models import Gender
+        
+        # Extract names and probabilities
+        gender_names = ["male", "female"]
+        probabilities = [0.5, 0.5]
+        
+        # Debug: print the names and probabilities
+        print(f"Gender names: {gender_names}")
+        print(f"Probabilities: {probabilities}")
+        
+        # Select a gender based on the given probabilities
+        selected_gender = random.choices(gender_names, probabilities)[0]
+        # Debug: print the selected gender
+        print(f"Selected gender: {selected_gender}")
+        
+        # Fetch the corresponding Gender object from the database
+        gender_obj = Gender.objects.get(name=selected_gender)
+        
+        return gender_obj
+
+
+    @classmethod
+    def get_random_age(self, 
+            min_age = 55,
+            max_age = 90,
+            mean_age = 65,
+            std_age = 10,
+            distribution = "normal"
+    ):
+        """
+        Get a random age based on the given distribution.
+
+        :param min_age: Minimum age.
+        :param max_age: Maximum age.
+        :param mean_age: Mean age.
+        :param std_age: Standard deviation of the age.
+        :param distribution: Distribution of the age.
+        :return: Random age based on the given distribution.
+        """
+        if distribution == "normal":
+            age = int(random.normalvariate(mean_age, std_age))
+        else:
+            age = int(random.uniform(min_age, max_age))
+        
+        return age
+    
+    @classmethod
+    def get_dob_from_age(self, age, current_date=None):
+        """
+        Get a date of birth based on the given age and current date.
+
+        :param age: Age of the patient.
+        :param current_date: Current date.
+        :return: Date of birth based on the given age and current date.
+        """
+        if current_date is None:
+            current_date = datetime.now()
+        dob = current_date.replace(year=current_date.year - age).date()
+
+        # TODO
+        # randomize the day and month by adding a random number of days (0-364) to the date
+
+        return dob
+        
+    @classmethod
+    def get_random_name_for_gender(self, gender_obj, locale="de_DE"):
+        gender = gender_obj.name
+        fake = Faker(locale)
+        
+        if gender == "male":
+            first_name = fake.first_name_male()
+            last_name = fake.last_name_male()
+
+        else: 
+            first_name = fake.first_name_female()
+            last_name = fake.last_name_female()
+
+        return last_name, first_name
+    
+    @classmethod
+    def create_generic(self, center="gplay_case_generator"):
+        """
+        Create a generic patient with random attributes.
+
+        :param center: The center of the patient.
+        :return: The created patient.
+        """
+        from endoreg_db.models import Center
+        gender = Patient.get_random_gender()
+        last_name, first_name = Patient.get_random_name_for_gender(gender)
+
+        age = Patient.get_random_age()
+        dob = Patient.get_dob_from_age(age)
+
+        center = Center.objects.get(name=center)
+
+        patient = Patient.objects.create(
+            first_name=first_name,
+            last_name=last_name,
+            dob=dob
+        )
+        patient.save()
+        return patient
+
+    def age(self):
+        """
+        Get the age of the patient.
+
+        :return: The age of the patient.
+        """
+        # calculate correct age based on current date including day and month
+        current_date = datetime.now()
+        dob = self.dob
+        age = current_date.year - dob.year - ((current_date.month, current_date.day) < (dob.month, dob.day))
+        return age
+
+    def create_lab_sample(self, sample_type="generic", date=None, save=True):
+        """
+        Create a lab sample for this patient.
+
+        :param sample_type: The sample type. Should be either string of the sample types
+            name or the sample type object. If not set, the default sample type ("generic") is used.
+        :param date: The date of the lab sample.
+        :return: The created lab sample.
+        """
+        from endoreg_db.models import PatientLabSample, PatientLabSampleType
+        if date is None:
+            date = datetime.now()
+
+        if isinstance(sample_type, str):
+            sample_type = PatientLabSampleType.objects.get(name=sample_type)
+            assert sample_type is not None, f"Sample type with name '{sample_type}' not found."#
+        elif not isinstance(sample_type, PatientLabSampleType):
+            raise ValueError("Sample type must be either a string or a PatientLabSampleType object.")
+        
+        patient_lab_sample = PatientLabSample.objects.create(
+            patient=self,
+            sample_type=sample_type,
+            date=date
+        )
+
+        if save:
+            patient_lab_sample.save()
+
+        return patient_lab_sample
+
+class PatientForm(forms.ModelForm):
+    class Meta:
+        model = Patient
+        fields = '__all__'
+        widgets = {
+            'dob': DateInput(attrs={'type': 'date'}),
+        }
+
+    def __init__(self, *args, **kwargs):
+        super().__init__(*args, **kwargs)
+        for field in self.fields.values():
+            field.widget.attrs['class'] = 'form-control'

endoreg_db/models/persons/patient/patient_disease.py

@@ -0,0 +1,16 @@
+from django.db import models
+
+
+
+class PatientDisease(models.Model):
+    patient = models.ForeignKey("Patient", on_delete=models.CASCADE)
+    disease = models.ForeignKey("Disease", on_delete=models.CASCADE)
+    classification_choices = models.ManyToManyField("DiseaseClassificationChoice")
+    start_date = models.DateField(blank=True, null=True)
+    end_date = models.DateField(blank=True, null=True)
+
+    last_update = models.DateTimeField(auto_now=True)
+
+    def __str__(self):
+        return f"{self.patient} - {self.disease}"
+    

endoreg_db/models/persons/patient/patient_event.py

@@ -0,0 +1,22 @@
+from django.db import models
+from .patient import Patient
+
+class PatientEvent(models.Model):
+    """
+    A class representing an event for a patient.
+
+    Attributes:
+        patient (Patient): The patient associated with this event.
+        date (datetime.date): The date of the event.
+        description (str): A description of the event.
+    """
+    patient = models.ForeignKey(Patient, on_delete=models.CASCADE)
+    event = models.ForeignKey("Event", on_delete=models.CASCADE)
+    date_start = models.DateField()
+    date_end = models.DateField(blank=True, null=True)
+    description = models.TextField(blank=True, null=True)
+
+    last_update = models.DateTimeField(auto_now=True)
+    
+    def __str__(self):
+        return str(self.date_start) + ": " + self.event