endoreg-db 0.4.5__py3-none-any.whl → 0.8.6.3__py3-none-any.whl

endoreg_db/models/medication/medication.py

@@ -1,148 +0,0 @@
-from django.db import models
-
-class MedicationManager(models.Manager):
-    def get_by_natural_key(self, name):
-        return self.get(name=name)
-
-class Medication(models.Model):
-    name = models.CharField(max_length=255, unique=True)
-    name_de = models.CharField(max_length=255, blank=True, null=True)
-    name_en = models.CharField(max_length=255, blank=True, null=True)
-    adapt_to_renal_function = models.BooleanField(default = False)
-    adapt_to_hepatic_function = models.BooleanField(default=False)
-    adapt_to_indication = models.BooleanField(default=False)
-    adapt_to_age = models.BooleanField(default=False)
-    adapt_to_weight = models.BooleanField(default=False)
-    adapt_to_risk = models.BooleanField(default=False)
-    default_unit = models.ForeignKey('Unit', on_delete=models.CASCADE)
-
-
-    objects = MedicationManager()
-
-    def natural_key(self):
-        return (self.name,)
-
-    def __str__(self):
-        return self.name
-    
-class MedicationScheduleManager(models.Manager):
-    def get_by_natural_key(self, name):
-        return self.get(name=name)
-    
-class MedicationSchedule(models.Model):
-    name = models.CharField(max_length=255)
-    name_de = models.CharField(max_length=255, blank=True, null=True)
-    name_en = models.CharField(max_length=255, blank=True, null=True)
-    description = models.TextField(blank=True, null=True)
-    medication = models.ForeignKey("Medication", on_delete=models.CASCADE)
-    unit = models.ForeignKey("Unit", on_delete=models.CASCADE)
-    therapy_duration_d = models.FloatField(blank=True, null=True)
-    dose = models.FloatField()
-    intake_times = models.ManyToManyField(
-        "MedicationIntakeTime", 
-    )
-
-    objects = MedicationScheduleManager()
-
-    def natural_key(self):
-        return (self.name,)
-    
-    def __str__(self):
-        return self.name
-    
-    
-class MedicationIntakeTimeManager(models.Manager):
-    def get_by_natural_key(self, name):
-        return self.get(name=name)
-    
-class MedicationIntakeTime(models.Model):
-    name = models.CharField(max_length=255)
-    name_de = models.CharField(max_length=255, blank=True, null=True)
-    name_en = models.CharField(max_length=255, blank=True, null=True)
-    repeats = models.CharField(max_length=20, default = "daily")
-    time = models.TimeField()
-
-    objects = MedicationIntakeTimeManager()
-
-    def natural_key(self):
-        return (self.name,)
-    
-    def __str__(self):
-        return self.name
-
-# IMPLEMENT MEDICATION INDICATION TYPE
-class MedicationIndicationTypeManager(models.Manager):
-    def get_by_natural_key(self, name):
-        return self.get(name=name)
-
-class MedicationIndicationType(models.Model):
-    name = models.CharField(max_length=255, unique=True)
-    name_de = models.CharField(max_length=255, blank=True, null=True)
-    name_en = models.CharField(max_length=255, blank=True, null=True)
-
-    objects = MedicationIndicationTypeManager()
-
-    def natural_key(self):
-        return (self.name,)
-
-    def __str__(self):
-        return self.name
-    
-    @classmethod
-    def get_random_indication_by_type(cls, name) -> "MedicationIndication":
-        return cls.objects.get(name=name).medication_indications.order_by('?').first()
-    
-
-    def get_random_medication_indication(self):
-        from endoreg_db.models import MedicationIndication
-        return MedicationIndication.objects.filter(indication_type=self).order_by('?').first()
-
-
-class MedicationIndicationManager(models.Manager):
-    def get_by_natural_key(self, name):
-        return self.get(name=name)
-
-class MedicationIndication(models.Model):
-    name = models.CharField(max_length=255, unique=True)
-    indication_type = models.ForeignKey(
-        "MedicationIndicationType", on_delete=models.CASCADE, related_name="medication_indications"
-    )
-    medication_schedules = models.ManyToManyField(
-        "MedicationSchedule"
-    )
-    diseases = models.ManyToManyField(
-        "Disease"
-    )
-    events = models.ManyToManyField(
-        "Event"
-    )
-    classification_choices = models.ManyToManyField(
-        "DiseaseClassificationChoice"
-    )
-    sources = models.ManyToManyField(
-        "InformationSource"
-    )
-
-    def get_indication_links(self):
-        links = {
-            "medication_schedules": self.medication_schedules,
-            "diseases": self.diseases,
-            "events": self.events,
-            "classification_choices": self.classification_choices
-        }
-
-    objects = MedicationIndicationManager()
-
-    def natural_key(self):
-        return (self.name,)
-    
-    def __str__(self):
-        return self.name
-    
-    def create_patient_medication_schedules(self, patient):
-        from endoreg_db.models import PatientMedicationSchedule
-        for medication_schedule in self.medication_schedules.all():
-            PatientMedicationSchedule.objects.create(
-                patient=patient,
-                medication_schedule=medication_schedule
-            )

endoreg_db/models/network/__init__.py

@@ -1,3 +0,0 @@
-from .network_device import NetworkDevice
-from .network_device_type import NetworkDeviceType
-from .agl_service import AglService

endoreg_db/models/network/agl_service.py

@@ -1,38 +0,0 @@
-from django.db import models
-
-class AglServiceManager(models.Manager):
-    # Custom manager for AglService; defines name as natural key
-    def get_by_natural_key(self, name):
-        return self.get(name=name)
-    
-class AglService(models.Model):
-    name = models.CharField(max_length=255)
-    description = models.CharField(max_length=255)
-    online = models.BooleanField(default=False)
-    created = models.DateTimeField(auto_now_add=True)
-    updated = models.DateTimeField(auto_now=True)
-    objects = AglServiceManager()
-    devices = models.ManyToManyField("NetworkDevice", related_name="services")
-    port = models.IntegerField(blank=True, null=True)
-    protocol = models.CharField(max_length=255, blank=True, null=True)
-    url = models.URLField(blank=True, null=True)
-
-    def alive_log(self, user, ip_address, user_agent):
-        from ..logging import AglServiceLogEntry
-        AglServiceLogEntry.objects.create(
-            user=user,
-            ip_address=ip_address,
-            user_agent=user_agent,
-            message=f"Service {self.name} is alive.",
-            service=self
-        )
-
-    def __str__(self):
-        return self.name
-
-    class Meta:
-        ordering = ['name']
-        
-    def natural_key(self):
-        return (self.name,)
-    

endoreg_db/models/network/network_device.py

@@ -1,53 +0,0 @@
-# Django db class to store network devices (e.g., servers, clients, switches, etc.)
-
-from django.db import models
-
-class NetworkDeviceManager(models.Manager):
-    # Custom manager for NetworkDevice; defines name as natural key
-    def get_by_natural_key(self, name):
-        return self.get(name=name)
-    
-class NetworkDevice(models.Model):
-    name = models.CharField(max_length=255)
-    ip = models.GenericIPAddressField(blank=True, null=True)
-    description = models.CharField(max_length=255)
-    device_type = models.ForeignKey("NetworkDeviceType", on_delete=models.CASCADE)
-    online = models.BooleanField(default=False)
-    created = models.DateTimeField(auto_now_add=True)
-    updated = models.DateTimeField(auto_now=True)
-    objects = NetworkDeviceManager()
-
-    def __str__(self):
-        return self.name
-
-    class Meta:
-        db_table = 'network_devices'
-        ordering = ['name']
-        
-    def natural_key(self):
-        return (self.name,)
-    
-    def ping(self):
-        target_ip = self.ip
-
-        # Import the required module
-        import subprocess
-
-        # Define the command
-        command = ['ping', '-c', '1', target_ip]
-
-        # Run the command
-        process = subprocess.Popen(command, stdout=subprocess.PIPE, stderr=subprocess.PIPE)
-
-        # Wait for the process to terminate
-        process.wait()
-
-        # Check the return code
-        return_code = process.returncode
-        
-        # Return True if the return code is 0, False otherwise
-        self.online = return_code == 0
-        self.save()
-        return self.online
-    
-

endoreg_db/models/network/network_device_type.py

@@ -1,23 +0,0 @@
-# Django db class to store network device types (e.g., server, client, switch, etc.)
-
-from django.db import models
-
-class NetworkDeviceTypeManager(models.Manager):
-    # Custom manager for NetworkDeviceType; defines name as natural key
-    def get_by_natural_key(self, name):
-        return self.get(name=name)
-
-class NetworkDeviceType(models.Model):
-    name = models.CharField(max_length=255)
-    description = models.CharField(max_length=255)
-    created = models.DateTimeField(auto_now_add=True)
-    updated = models.DateTimeField(auto_now=True)
-    objects = NetworkDeviceTypeManager()
-
-    def __str__(self):
-        return self.name
-
-    class Meta:
-        db_table = 'network_device_types'
-        ordering = ['name']
-

endoreg_db/models/other/distribution.py

@@ -1,215 +0,0 @@
-from django.db import models
-import numpy as np
-from scipy.stats import skewnorm
-
-class BaseValueDistribution(models.Model):
-    """
-    Abstract base class for value distributions.
-    """
-    name = models.CharField(max_length=100)
-
-    class Meta:
-        abstract = True
-
-    def generate_value(self):
-        """
-        Generate a value based on the distribution rules.
-        Must be implemented by subclasses.
-        """
-        raise NotImplementedError("Subclasses must implement this method")
-    
-    def natural_key(self):
-        return (self.name,)
-
-class NumericValueDistributionManager(models.Manager):
-    def get_by_natural_key(self, name):
-        return self.get(name=name)
-
-class NumericValueDistribution(BaseValueDistribution):
-    """
-    Numeric value distribution model.
-    Supports uniform, normal, and skewed normal distributions with hard limits.
-    """
-    objects = NumericValueDistributionManager()
-    DISTRIBUTION_CHOICES = [
-        ('uniform', 'Uniform'),
-        ('normal', 'Normal'),
-        ('skewed_normal', 'Skewed Normal'),
-    ]
-
-    distribution_type = models.CharField(max_length=20, choices=DISTRIBUTION_CHOICES)
-    min_value = models.FloatField()
-    max_value = models.FloatField()
-    mean = models.FloatField(null=True, blank=True)
-    std_dev = models.FloatField(null=True, blank=True)
-    skewness = models.FloatField(null=True, blank=True)
-
-    def generate_value(self):
-        if self.distribution_type == 'uniform':
-            return np.random.uniform(self.min_value, self.max_value)
-        elif self.distribution_type == 'normal':
-            value = np.random.normal(self.mean, self.std_dev)
-            return np.clip(value, self.min_value, self.max_value)
-        elif self.distribution_type == 'skewed_normal':
-            value = skewnorm.rvs(a=self.skewness, loc=self.mean, scale=self.std_dev)
-            return np.clip(value, self.min_value, self.max_value)
-        else:
-            raise ValueError("Unsupported distribution type")
-        
-    
-class SingleCategoricalValueDistributionManager(models.Manager):
-    def get_by_natural_key(self, name):
-        return self.get(name=name)
-
-class SingleCategoricalValueDistribution(BaseValueDistribution):
-    """
-    Single categorical value distribution model.
-    Assigns a single value based on specified probabilities.
-    """
-    objects = SingleCategoricalValueDistributionManager()
-    categories = models.JSONField()  # { "category": "probability", ... }
-
-    def generate_value(self):
-        categories, probabilities = zip(*self.categories.items())
-        return np.random.choice(categories, p=probabilities)
-    
-
-class MultipleCategoricalValueDistributionManager(models.Manager):
-    def get_by_natural_key(self, name):
-        return self.get(name=name)
-
-class MultipleCategoricalValueDistribution(BaseValueDistribution):
-    """
-    Multiple categorical value distribution model.
-    Assigns a specific number or varying number of values based on probabilities.
-    """
-    objects = MultipleCategoricalValueDistributionManager()
-    categories = models.JSONField()  # { "category": "probability", ... }
-    min_count = models.IntegerField()
-    max_count = models.IntegerField()
-    count_distribution_type = models.CharField(max_length=20, choices=[('uniform', 'Uniform'), ('normal', 'Normal')])
-    count_mean = models.FloatField(null=True, blank=True)
-    count_std_dev = models.FloatField(null=True, blank=True)
-
-    def generate_value(self):
-        if self.count_distribution_type == 'uniform':
-            count = np.random.randint(self.min_count, self.max_count + 1)
-        elif self.count_distribution_type == 'normal':
-            count = int(np.random.normal(self.count_mean, self.count_std_dev))
-            count = np.clip(count, self.min_count, self.max_count)
-        else:
-            raise ValueError("Unsupported count distribution type")
-
-        categories, probabilities = zip(*self.categories.items())
-        return list(np.random.choice(categories, size=count, p=probabilities))
-
-
-class DateValueDistributionManager(models.Manager):
-    def get_by_natural_key(self, name):
-        return self.get(name=name)
-
-from datetime import date, timedelta
-class DateValueDistribution(BaseValueDistribution):
-    """
-    Assign date values based on specified distribution.
-    Expects distribution_type (uniform, normal) and mode (date, timedelta) and based on this either
-    date_min, date_max, date_mean, date_std_dev or
-    timedelta_days_min, timedelta_days_max, timedelta_days_mean, timedelta_days_std_dev
-    """
-    objects = DateValueDistributionManager()
-    name = models.CharField(max_length=100)
-    name_de = models.CharField(max_length=100, blank=True, null=True)
-    name_en = models.CharField(max_length=100, blank=True, null=True)
-    description = models.TextField(blank=True, null=True)
-    DISTRIBUTION_CHOICES = [
-        ('uniform', 'Uniform'),
-        ('normal', 'Normal'),
-    ]
-    MODE_CHOICES = [
-        ('date', 'Date'),
-        ('timedelta', 'Timedelta'),
-    ]
-
-    distribution_type = models.CharField(max_length=20, choices=DISTRIBUTION_CHOICES)
-    mode = models.CharField(max_length=20, choices=MODE_CHOICES)
-
-    # Date-related fields
-    date_min = models.DateField(blank=True, null=True)
-    date_max = models.DateField(blank=True, null=True)
-    date_mean = models.DateField(blank=True, null=True)
-    date_std_dev = models.IntegerField(blank=True, null=True)  # Standard deviation in days
-
-    # Timedelta-related fields
-    timedelta_days_min = models.IntegerField(blank=True, null=True)
-    timedelta_days_max = models.IntegerField(blank=True, null=True)
-    timedelta_days_mean = models.IntegerField(blank=True, null=True)
-    timedelta_days_std_dev = models.IntegerField(blank=True, null=True)
-
-    def generate_value(self):
-        if self.mode == 'date':
-            return self._generate_date_value()
-        elif self.mode == 'timedelta':
-            return self._generate_timedelta_value()
-        else:
-            raise ValueError("Unsupported mode")
-
-    def _generate_date_value(self):
-        #UNTESTED
-        if self.distribution_type == 'uniform':
-            start_date = self.date_min.toordinal()
-            end_date = self.date_max.toordinal()
-            random_ordinal = np.random.randint(start_date, end_date)
-            return date.fromordinal(random_ordinal)
-        elif self.distribution_type == 'normal':
-            mean_ordinal = self.date_mean.toordinal()
-            std_dev_days = self.date_std_dev
-            random_ordinal = int(np.random.normal(mean_ordinal, std_dev_days))
-            random_ordinal = np.clip(random_ordinal, self.date_min.toordinal(), self.date_max.toordinal())
-            return date.fromordinal(random_ordinal)
-        else:
-            raise ValueError("Unsupported distribution type")
-
-    def _generate_timedelta_value(self):
-        if self.distribution_type == 'uniform':
-            random_days = np.random.randint(self.timedelta_days_min, self.timedelta_days_max + 1)
-            
-            
-        elif self.distribution_type == 'normal':
-            random_days = int(np.random.normal(self.timedelta_days_mean, self.timedelta_days_std_dev))
-            random_days = np.clip(random_days, self.timedelta_days_min, self.timedelta_days_max)
-            
-        else:
-            raise ValueError("Unsupported distribution type")
-        
-        current_date = date.today()
-        generated_date = current_date - timedelta(days=random_days)
-        print(generated_date)
-        return(generated_date)
-        
-# Example Usage
-# Numeric distribution for age
-# age_distribution = NumericValueDistribution.objects.create(
-#     name='Age Distribution',
-#     distribution_type='normal',
-#     min_value=0,
-#     max_value=100,
-#     mean=50,
-#     std_dev=15
-# )
-
-# # Single categorical distribution for gender
-# gender_distribution = SingleCategoricalValueDistribution.objects.create(
-#     name='Gender Distribution',
-#     categories={'male': 0.5, 'female': 0.5}
-# )
-
-# # Multiple categorical distribution for symptoms
-# symptoms_distribution = MultipleCategoricalValueDistribution.objects.create(
-#     name='Symptoms Distribution',
-#     categories={'fever': 0.3, 'cough': 0.4, 'fatigue': 0.2, 'nausea': 0.1},
-#     min_count=1,
-#     max_count=3,
-#     count_distribution_type='normal',
-#     count_mean=2,
-#     count_std_dev=0.5
-# )

endoreg_db/models/patient_examination/__init__.py

@@ -1,35 +0,0 @@
-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 +0,0 @@
-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

@@ -1,7 +0,0 @@
-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 +0,0 @@
-from .examiner import Examiner, ExaminerSerializer
-# from .examiner_type import ExaminerType

endoreg_db/models/persons/examiner/examiner.py

@@ -1,16 +0,0 @@
-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 +0,0 @@
-from .examiner import Examiner
-# from .examiner_type import ExaminerType

endoreg_db/models/persons/patient/__init__.py

@@ -1,8 +0,0 @@
-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

@@ -1,30 +0,0 @@
-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