endoreg-db 0.3.6__py3-none-any.whl → 0.3.8__py3-none-any.whl

endoreg_db/models/persons/patient/patient_lab_sample.py

@@ -1,106 +1,106 @@
-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):
-        return f"{self.patient} - {self.sample_type} - {self.date} ()"
-    
-    def get_values(self):
-        return self.values
-    
-    @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
-
-
-    
-    
+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):
+        return f"{self.patient} - {self.sample_type} - {self.date} ()"
+    
+    def get_values(self):
+        return self.values
+    
+    @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
+
+
+    
+    

endoreg_db/models/persons/patient/patient_lab_value.py

@@ -1,176 +1,176 @@
-from django.db import models
-
-class PatientLabValue(models.Model):
-    """
-    A class representing a patient lab value.
-
-    Attributes:
-        patient (Patient): The patient.
-        lab_value (LabValue): The lab value.
-        value (float): The value of the lab value.
-        date (datetime): The date of the lab value.
-    """
-    patient = models.ForeignKey('Patient', on_delete=models.CASCADE,
-                                related_name="lab_values", blank=True, null=True
-    )
-    lab_value = models.ForeignKey('LabValue', on_delete=models.CASCADE)
-    value = models.FloatField(blank=True, null=True)
-    value_str = models.CharField(max_length=255, blank=True, null=True)
-    sample = models.ForeignKey(
-        'PatientLabSample', on_delete=models.CASCADE, 
-        blank=True, null=True,
-        related_name='values'
-    )
-    datetime = models.DateTimeField(# if not set, use now
-        auto_now_add=True        
-    )
-    normal_range = models.JSONField(
-        default = dict
-    )
-    unit = models.ForeignKey('Unit', on_delete=models.CASCADE, blank=True, null=True)
-
-    @classmethod
-    def create_lab_value_by_sample(cls, sample=None, lab_value_name=None, value=None, value_str=None, unit=None):
-        from endoreg_db.models import LabValue
-        patient = sample.patient
-        lab_value = LabValue.objects.get(name=lab_value_name)
-        value = value
-        value_str = value_str
-
-        pat_lab_val = cls.objects.create(
-            patient = patient,
-            lab_value = lab_value,
-            value = value,
-            value_str = value_str,
-            sample = sample,
-            unit = unit,
-        )
-
-        pat_lab_val.save()
-
-        return pat_lab_val
-
-    def __str__(self):
-        _str = f'{self.lab_value} - {self.value} {self.unit} ({self.datetime})'
-        print(_str)
-        return _str
-    
-    def set_min_norm_value(self, value, save = True):
-        self.normal_range["min"] = value
-        if save:
-            self.save()
-
-    def set_max_norm_value(self, value, save = True):
-        self.normal_range["max"] = value
-        if save:
-            self.save()
-
-    def set_norm_values_from_default(self):
-        age = self.patient.age()
-        gender = self.patient.gender
-        min_value, max_value = self.lab_value.get_normal_range(age=age, gender=gender)
-        self.set_min_norm_value(min_value, save = False)
-        self.set_max_norm_value(max_value, save = False)
-        self.save()
-
-
-    def set_unit_from_default(self):
-        self.unit = self.lab_value.default_unit
-        self.save()
-
-    def get_value(self):
-        if self.value:
-            return self.value
-        else:
-            return self.value_str
-        
-    def get_value_field_name(self):
-        if self.value:
-            return "value"
-        else:
-            return "value_str"
-        
-    # customize save method so that if a numeric value exists, we round it to the precision of the lab value
-    def save(self, *args, **kwargs):
-        if self.value:
-            precision = self.lab_value.numeric_precision
-            self.value = round(self.value, precision)
-        super().save(*args, **kwargs)
-
-    def set_value_by_distribution(self, distribution=None, save = True):
-        from endoreg_db.models import (
-            Patient, LabValue, Gender,
-            DateValueDistribution,
-            SingleCategoricalValueDistribution,
-            NumericValueDistribution,
-            MultipleCategoricalValueDistribution,
-        ) 
-        import warnings  
-
-        patient:Patient = self.patient
-
-        dob = patient.dob
-        gender:Gender = patient.gender
-        lab_value:LabValue = self.lab_value
-
-        assert self.lab_value, "Lab value must be set to set value by distribution"
-        self.unit = self.lab_value.default_unit
-
-        if not distribution:
-            distribution = lab_value.get_default_default_distribution()
-
-            if not distribution:
-                warnings.warn(
-                    "No distribution set for lab value, assuming uniform numeric distribution based on normal values"
-                )
-
-                if not self.normal_range.get("min", None) or not self.normal_range.get("max", None):
-                    self.set_norm_values_from_default()
-
-                self.normal_range:dict
-                _min = self.normal_range.get("min", 0.0001)
-                _max = self.normal_range.get("max", 100)
-                _name = "auto-" + self.lab_value.name + "-distribution-default-uniform" 
-                distribution = NumericValueDistribution(
-                    name = _name,
-                    min_value = _min,
-                    max_value = _max,
-                    distribution_type = "uniform"
-                )
-
-                value = distribution.generate_value()
-                self.value = value
-                if save:
-                    self.save()
-                
-                return value
-
-        if isinstance(distribution, SingleCategoricalValueDistribution):
-            value = distribution.generate_value()
-            self.value_str = value
-            if save:
-                self.save()
-            return value
-        
-        elif isinstance(distribution, NumericValueDistribution):
-            value = distribution.generate_value()
-            self.value = value
-            if save:
-                self.save()
-            return value
-        
-        elif isinstance(distribution, MultipleCategoricalValueDistribution):
-            value = distribution.generate_value()
-            self.value_str = value
-            if save:
-                self.save()
-            return value
-
-        elif isinstance(distribution, DateValueDistribution):
-            # raise not implemented error
-            value = distribution.generate_value()
-            self.value = value
-            if save:
-                self.save()
-
-
+from django.db import models
+
+class PatientLabValue(models.Model):
+    """
+    A class representing a patient lab value.
+
+    Attributes:
+        patient (Patient): The patient.
+        lab_value (LabValue): The lab value.
+        value (float): The value of the lab value.
+        date (datetime): The date of the lab value.
+    """
+    patient = models.ForeignKey('Patient', on_delete=models.CASCADE,
+                                related_name="lab_values", blank=True, null=True
+    )
+    lab_value = models.ForeignKey('LabValue', on_delete=models.CASCADE)
+    value = models.FloatField(blank=True, null=True)
+    value_str = models.CharField(max_length=255, blank=True, null=True)
+    sample = models.ForeignKey(
+        'PatientLabSample', on_delete=models.CASCADE, 
+        blank=True, null=True,
+        related_name='values'
+    )
+    datetime = models.DateTimeField(# if not set, use now
+        auto_now_add=True        
+    )
+    normal_range = models.JSONField(
+        default = dict
+    )
+    unit = models.ForeignKey('Unit', on_delete=models.CASCADE, blank=True, null=True)
+
+    @classmethod
+    def create_lab_value_by_sample(cls, sample=None, lab_value_name=None, value=None, value_str=None, unit=None):
+        from endoreg_db.models import LabValue
+        patient = sample.patient
+        lab_value = LabValue.objects.get(name=lab_value_name)
+        value = value
+        value_str = value_str
+
+        pat_lab_val = cls.objects.create(
+            patient = patient,
+            lab_value = lab_value,
+            value = value,
+            value_str = value_str,
+            sample = sample,
+            unit = unit,
+        )
+
+        pat_lab_val.save()
+
+        return pat_lab_val
+
+    def __str__(self):
+        _str = f'{self.lab_value} - {self.value} {self.unit} ({self.datetime})'
+        print(_str)
+        return _str
+    
+    def set_min_norm_value(self, value, save = True):
+        self.normal_range["min"] = value
+        if save:
+            self.save()
+
+    def set_max_norm_value(self, value, save = True):
+        self.normal_range["max"] = value
+        if save:
+            self.save()
+
+    def set_norm_values_from_default(self):
+        age = self.patient.age()
+        gender = self.patient.gender
+        min_value, max_value = self.lab_value.get_normal_range(age=age, gender=gender)
+        self.set_min_norm_value(min_value, save = False)
+        self.set_max_norm_value(max_value, save = False)
+        self.save()
+
+
+    def set_unit_from_default(self):
+        self.unit = self.lab_value.default_unit
+        self.save()
+
+    def get_value(self):
+        if self.value:
+            return self.value
+        else:
+            return self.value_str
+        
+    def get_value_field_name(self):
+        if self.value:
+            return "value"
+        else:
+            return "value_str"
+        
+    # customize save method so that if a numeric value exists, we round it to the precision of the lab value
+    def save(self, *args, **kwargs):
+        if self.value:
+            precision = self.lab_value.numeric_precision
+            self.value = round(self.value, precision)
+        super().save(*args, **kwargs)
+
+    def set_value_by_distribution(self, distribution=None, save = True):
+        from endoreg_db.models import (
+            Patient, LabValue, Gender,
+            DateValueDistribution,
+            SingleCategoricalValueDistribution,
+            NumericValueDistribution,
+            MultipleCategoricalValueDistribution,
+        ) 
+        import warnings  
+
+        patient:Patient = self.patient
+
+        dob = patient.dob
+        gender:Gender = patient.gender
+        lab_value:LabValue = self.lab_value
+
+        assert self.lab_value, "Lab value must be set to set value by distribution"
+        self.unit = self.lab_value.default_unit
+
+        if not distribution:
+            distribution = lab_value.get_default_default_distribution()
+
+            if not distribution:
+                warnings.warn(
+                    "No distribution set for lab value, assuming uniform numeric distribution based on normal values"
+                )
+
+                if not self.normal_range.get("min", None) or not self.normal_range.get("max", None):
+                    self.set_norm_values_from_default()
+
+                self.normal_range:dict
+                _min = self.normal_range.get("min", 0.0001)
+                _max = self.normal_range.get("max", 100)
+                _name = "auto-" + self.lab_value.name + "-distribution-default-uniform" 
+                distribution = NumericValueDistribution(
+                    name = _name,
+                    min_value = _min,
+                    max_value = _max,
+                    distribution_type = "uniform"
+                )
+
+                value = distribution.generate_value()
+                self.value = value
+                if save:
+                    self.save()
+                
+                return value
+
+        if isinstance(distribution, SingleCategoricalValueDistribution):
+            value = distribution.generate_value()
+            self.value_str = value
+            if save:
+                self.save()
+            return value
+        
+        elif isinstance(distribution, NumericValueDistribution):
+            value = distribution.generate_value()
+            self.value = value
+            if save:
+                self.save()
+            return value
+        
+        elif isinstance(distribution, MultipleCategoricalValueDistribution):
+            value = distribution.generate_value()
+            self.value_str = value
+            if save:
+                self.save()
+            return value
+
+        elif isinstance(distribution, DateValueDistribution):
+            # raise not implemented error
+            value = distribution.generate_value()
+            self.value = value
+            if save:
+                self.save()
+
+

endoreg_db/models/persons/patient/patient_medication.py

@@ -1,44 +1,44 @@
-from django.db import models
-from django.utils.translation import gettext_lazy as _
-
-class PatientMedication(models.Model):
-    patient = models.ForeignKey("Patient", on_delete= models.CASCADE)
-    medication_indication = models.ForeignKey(
-        "MedicationIndication", on_delete=models.CASCADE,
-        related_name="patient_medications", null=True
-    )
-
-    medication_schedules = models.ManyToManyField(
-        'MedicationSchedule'
-    )
-    unit = models.ForeignKey('Unit', on_delete=models.CASCADE)
-    dosage = models.JSONField()
-    active = models.BooleanField(default=True)
-
-    objects = models.Manager()
-
-    class Meta:
-        verbose_name = _('Patient Medication')
-        verbose_name_plural = _('Patient Medications')
-
-    @classmethod
-    def create_by_patient_and_indication(cls, patient, medication_indication):
-        from endoreg_db.models import MedicationIndication
-        medication_indication: MedicationIndication
-        patient_medication = cls.objects.create(patient=patient, medication_indication=medication_indication)
-        patient_medication.save()
-        patient_medication.set_schedules_from_indication()
-        
-        return patient_medication
-
-    def set_schedules_from_indication(self):
-        schedules = self.medication_indication.medication_schedules.all()
-        self.medication_schedules.set(schedules)
-        self.save()
-
-    def __str__(self):
-        indication = self.medication_indication
-        schedules = self.medication_schedules.all()
-        return f'{indication} - {schedules}'
-    
+from django.db import models
+from django.utils.translation import gettext_lazy as _
+
+class PatientMedication(models.Model):
+    patient = models.ForeignKey("Patient", on_delete= models.CASCADE)
+    medication_indication = models.ForeignKey(
+        "MedicationIndication", on_delete=models.CASCADE,
+        related_name="patient_medications", null=True
+    )
+
+    medication_schedules = models.ManyToManyField(
+        'MedicationSchedule'
+    )
+    unit = models.ForeignKey('Unit', on_delete=models.CASCADE)
+    dosage = models.JSONField()
+    active = models.BooleanField(default=True)
+
+    objects = models.Manager()
+
+    class Meta:
+        verbose_name = _('Patient Medication')
+        verbose_name_plural = _('Patient Medications')
+
+    @classmethod
+    def create_by_patient_and_indication(cls, patient, medication_indication):
+        from endoreg_db.models import MedicationIndication
+        medication_indication: MedicationIndication
+        patient_medication = cls.objects.create(patient=patient, medication_indication=medication_indication)
+        patient_medication.save()
+        patient_medication.set_schedules_from_indication()
+        
+        return patient_medication
+
+    def set_schedules_from_indication(self):
+        schedules = self.medication_indication.medication_schedules.all()
+        self.medication_schedules.set(schedules)
+        self.save()
+
+    def __str__(self):
+        indication = self.medication_indication
+        schedules = self.medication_schedules.all()
+        return f'{indication} - {schedules}'
+