endoreg-db 0.6.0__py3-none-any.whl → 0.6.2__py3-none-any.whl

endoreg_db/models/persons/patient/patient.py

@@ -0,0 +1,389 @@
+from ..person import Person
+from django import forms
+from django.forms import DateInput
+from ...patient import PatientExamination
+from ...data_file import ReportFile
+from django.db import models
+from faker import Faker
+import random
+from datetime import datetime
+from icecream import ic
+from typing import TYPE_CHECKING
+
+if TYPE_CHECKING:
+    from endoreg_db.models import Center, Gender
+
+
+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.
+
+    """
+
+    # -----gc-08-dev--changings---
+    first_name = models.CharField(max_length=100)
+    last_name = models.CharField(max_length=100)
+    dob = models.DateField(null=True, blank=True)
+    gender = models.ForeignKey(
+        "Gender", on_delete=models.SET_NULL, null=True, blank=True
+    )
+    center = models.ForeignKey(
+        "Center", on_delete=models.SET_NULL, null=True, blank=True
+    )
+    patient_hash = models.CharField(max_length=255, blank=True, null=True)
+
+    def __str__(self):
+        return f"{self.first_name} {self.last_name} ({self.dob})"
+
+    @classmethod
+    def get_or_create_pseudo_patient_by_hash(
+        cls,
+        patient_hash: str,
+        center: "Center" = None,
+        gender: "Gender" = None,
+        birth_month: int = None,
+        birth_year: int = None,
+    ):
+        from endoreg_db.utils import random_day_by_year, create_mock_patient_name
+
+        created = False
+
+        existing_pathient = cls.objects.filter(patient_hash=patient_hash).first()
+        if existing_pathient:
+            ic(f"Patient with hash {patient_hash} already exists")
+            ic(f"Returning existing patient: {existing_pathient}")
+            return existing_pathient, created
+
+        # If no patient with the given hash exists, create a new pseudo patient
+        assert center, "Center must be provided to create a new pseudo patient"
+        assert gender, "Gender must be provided to create a new pseudo patient"
+        assert birth_month, (
+            "Birth month must be provided to create a new pseudo patient"
+        )
+        assert birth_year, "Birth year must be provided to create a new pseudo patient"
+
+        pseudo_dob = random_day_by_year(birth_year)
+        gender_name = gender.name
+        first_name, last_name = create_mock_patient_name(gender_name)
+
+        ic(f"Creating pseudo patient with hash {patient_hash}")
+        ic(f"Generated name: {first_name} {last_name}")
+
+        patient = cls.objects.create(
+            first_name=first_name,
+            last_name=last_name,
+            dob=pseudo_dob,
+            patient_hash=patient_hash,
+            is_real_person=False,
+        )
+
+        patient.save()
+        created = True
+
+        return patient, created
+
+    def export_patient_examinations(self):
+        """
+        Get all associated PatientExaminations, ReportFiles, and Videos for the patient.
+        """
+        from endoreg_db.models import PatientExamination, ReportFile, Video
+
+        patient_examinations = PatientExamination.objects.filter(patient=self)
+        report_files, videos = [], []
+        for patient_examination in patient_examinations:
+            rr = patient_examination.reportfile_set.all()
+            vv = patient_examination.videos.all()
+
+            report_files.extend(rr)
+            videos.extend(vv)
+
+        return patient_examinations, report_files, videos
+
+    def get_dob(self) -> datetime.date:
+        dob: datetime.date = self.dob
+        return 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(
+        self,
+        examination_name_str: str = None,
+        date_start: datetime = None,
+        date_end: datetime = None,
+    ):
+        """Creates a patient examination for this patient."""
+
+        if examination_name_str:
+            from endoreg_db.models import Examination
+
+            examination = Examination.objects.get(name=examination_name_str)
+            patient_examination = PatientExamination(
+                patient=self,
+                examination=examination,
+                date_start=date_start,
+                date_end=date_end,
+            )
+
+        else:
+            patient_examination = PatientExamination(
+                patient=self, date_start=date_start, date_end=date_end
+            )
+
+        patient_examination.save()
+
+        return patient_examination
+
+    def create_examination_by_indication(
+        self, indication, date_start: datetime = None, date_end: datetime = None
+    ):
+        from endoreg_db.models import (
+            ExaminationIndication,
+            Examination,
+            PatientExaminationIndication,
+        )
+
+        assert isinstance(indication, ExaminationIndication)
+
+        examination = indication.get_examination()
+
+        assert isinstance(examination, Examination)
+
+        patient_examination = PatientExamination.objects.create(
+            patient=self,
+            examination=examination,
+            date_start=date_start,
+            date_end=date_end,
+        )
+
+        patient_examination.save()
+
+        patient_examination_indication = PatientExaminationIndication.objects.create(
+            patient_examination=patient_examination, examination_indication=indication
+        )
+        patient_examination_indication.save()
+
+        return patient_examination, patient_examination_indication
+
+    def create_event(
+        self,
+        event_name_str: str,
+        date_start: datetime = None,
+        date_end: datetime = None,
+        description: str = None,
+    ):
+        from endoreg_db.models import Event, PatientEvent
+
+        event = Event.objects.get(name=event_name_str)
+
+        if not date_start:
+            date_start = datetime.now()
+
+        patient_event = PatientEvent.objects.create(
+            patient=self,
+            event=event,
+            date_start=date_start,
+        )
+
+        return patient_event
+
+    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(cls, 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 = [p_male, p_female]
+
+        # 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(
+        cls, 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(cls, 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(cls, 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(cls, 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,
+            gender=gender,
+        )
+        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 +1,22 @@
+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)
+    numerical_descriptors = models.JSONField(default=dict)
+    subcategories = models.JSONField(default=dict)
+
+    last_update = models.DateTimeField(auto_now=True)
+
+    def __str__(self):
+        return f"{self.patient} - {self.disease}"
+    
+    class Meta:
+        # unique_together = ('patient', 'disease', 'start_date')
+        verbose_name = 'Patient Disease'
+        verbose_name_plural = 'Patient Diseases'

endoreg_db/models/persons/patient/patient_event.py

@@ -0,0 +1,52 @@
+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)
+    classification_choice = models.ForeignKey(
+        "EventClassificationChoice", on_delete=models.CASCADE, blank=True, null=True
+    )
+
+    subcategories = models.JSONField(default=dict)
+    numerical_descriptors = models.JSONField(default=dict)
+
+    last_update = models.DateTimeField(auto_now=True)
+    
+    def __str__(self):
+        return str(self.date_start) + ": " + self.event.name
+    
+    def set_subcategories_from_classification_choice(self):
+        """
+        Sets the subcategories for this event from the classification choice.
+        """
+        from endoreg_db.models import EventClassificationChoice
+        if self.classification_choice:
+            self.classification_choice:EventClassificationChoice
+            self.subcategories = self.classification_choice.subcategories
+            self.save()
+        
+        return self.subcategories
+    
+    def set_numerical_descriptors_from_classification_choice(self):
+        """
+        Sets the numerical descriptors for this event from the classification choice.
+        """
+        from endoreg_db.models import EventClassificationChoice
+        if self.classification_choice:
+            self.classification_choice:EventClassificationChoice
+            self.numerical_descriptors = self.classification_choice.numerical_descriptors
+            self.save()
+        
+        return self.numerical_descriptors

endoreg_db/models/persons/patient/patient_examination_indication.py

@@ -0,0 +1,32 @@
+from django.db import models
+
+class PatientExaminationIndication(models.Model):
+    '''A model to store the indication for a patient examination.'''
+    patient_examination = models.ForeignKey('PatientExamination', on_delete=models.CASCADE, related_name='indications')
+    examination_indication = models.ForeignKey('ExaminationIndication', on_delete=models.CASCADE)
+    indication_choice = models.ForeignKey('ExaminationIndicationClassificationChoice', on_delete=models.CASCADE, blank=True, null=True)
+
+    def __str__(self):
+        return f"{self.patient_examination} - {self.examination_indication}"
+
+    def get_examination(self):
+        from endoreg_db.models import Examination
+        pe = self.get_patient_examination()
+        e: Examination = pe.examination
+
+        return e
+    
+    def get_patient_examination(self):
+        from endoreg_db.models import PatientExamination
+        pe: PatientExamination = self.patient_examination
+        return pe
+    
+    def get_choices(self):
+        from endoreg_db.models import (
+            ExaminationIndicationClassificationChoice,
+            ExaminationIndication
+        )
+        examination_indication:ExaminationIndication = self.examination_indication
+        choices = [_ for _ in examination_indication.get_choices()]
+        return choices
+    

endoreg_db/models/persons/patient/patient_lab_sample.py

@@ -0,0 +1,108 @@
+from django.db import models
+
+DEFAULT_PATIENT_LAB_SAMPLE_TYPE_NAME = "generic"
+
+class PatientLabSampleTypeManager(models.Manager):
+    def get_by_natural_key(self, name):
+        return self.get(name=name)
+    
+class PatientLabSampleType(models.Model):
+    """
+    A class representing a patient lab sample type.
+
+    Attributes:
+        name (str): The name of the patient lab sample type.
+        description (str): A description of the patient lab sample type.
+
+    """
+    name = models.CharField(max_length=255)
+    name_de = models.CharField(max_length=255, null=True)
+    name_en = models.CharField(max_length=255, null=True)
+    description = models.TextField(blank=True, null=True)
+
+    objects = PatientLabSampleTypeManager()
+
+    def natural_key(self):
+        return (self.name,)
+
+    def __str__(self):
+        return self.name
+    
+    @classmethod
+    def get_default_sample_type(cls):
+        """
+        Get the default patient lab sample type.
+
+        Returns:
+            PatientLabSampleType: The default patient lab sample type.
+
+        """
+        return cls.objects.get_or_create(name="default")[0]
+    
+from datetime import datetime as dt    
+from datetime import timezone
+class PatientLabSample(models.Model):
+    """
+    A class representing a patient lab sample.
+
+    Attributes:
+        patient (Patient): The patient to which the lab sample belongs.
+        sample_type (PatientLabSampleType): The type of the lab sample.
+        date (datetime): The date of the lab sample.
+        values (PatientLabValue; One2Many): The value of the lab sample.
+        unit (Unit): The unit of the lab sample.
+
+    """
+    patient = models.ForeignKey("Patient", on_delete=models.CASCADE, related_name="lab_samples")
+    sample_type = models.ForeignKey("PatientLabSampleType", on_delete=models.CASCADE)
+    date = models.DateTimeField()
+
+    def __str__(self):
+
+        formatted_datetime = self.date.strftime('%Y-%m-%d %H:%M')
+        return f"{self.patient} - {self.sample_type} - {formatted_datetime} ()"
+    
+    def get_values(self):
+        return self.values.all()
+    
+    @classmethod
+    def create_by_patient(cls, patient=None, sample_type=None, date=None, save = True):
+        """
+        Create a new patient lab sample by patient.
+
+        Args:
+            patient (Patient): The patient to which the lab sample belongs.
+            sample_type (PatientLabSampleType): The type of the lab sample.
+            date (datetime): The date of the lab sample.
+
+        Returns:
+            PatientLabSample: The new patient lab sample.
+
+        """
+        from endoreg_db.models.persons.patient import Patient, PatientLabSampleType
+        from warnings import warn
+
+        if not patient:
+            warn("No patient given. Cannot create patient lab sample.")
+            return None
+        if not sample_type:
+            sample_type = PatientLabSampleType.get_default_sample_type()
+        else:
+            sample_type = PatientLabSampleType.objects.get(name=sample_type)
+        if not date:
+            date = dt.now(timezone.utc)
+
+        patient_lab_sample = cls.objects.create(
+            patient=patient,
+            sample_type=sample_type,
+            date=date
+        )
+
+        if save:
+            patient_lab_sample.save()
+
+        return patient_lab_sample
+
+
+    
+