endoreg-db 0.5.2__py3-none-any.whl → 0.6.0__py3-none-any.whl

endoreg_db/models/case_template/case_template.py

@@ -1,81 +0,0 @@
-from django.db import models
-
-class CaseTemplateManager(models.Manager):
-    def get_by_natural_key(self, name):
-        return self.get(name=name)
-    
-class CaseTemplate(models.Model):
-    """
-    A class representing a case template.
-
-    Attributes:
-        name (str): The name of the case template. This is the natural key.
-        case_template_type (CaseTemplateType): The type of the case template.
-        description (str): A description of the case template.
-
-    """
-    name = models.CharField(max_length=255, unique=True)
-    template_type = models.ForeignKey("CaseTemplateType", on_delete=models.CASCADE, related_name="case_templates")
-    description = models.TextField(blank=True, null=True)
-
-    rules = models.ManyToManyField(
-        "CaseTemplateRule",
-    )
-
-    secondary_rules = models.ManyToManyField(
-        "CaseTemplateRule",
-        related_name="secondary_rules"
-    )
-
-    objects = CaseTemplateManager()
-
-    def natural_key(self):
-        return (self.name,)
-    
-    def __str__(self):
-        return self.name
-    
-    def get_rules(self):
-        rules = self.rules.all()
-        return rules
-    
-    def get_secondary_rules(self):
-        rules = self.secondary_rules.all()
-        return rules
-    
-    def _assert_max_one_create_patient_rule(self):
-        """Asserts that there is at most one rule with the rule_type__name "create-object" and target_model__name "Patient"."""
-        create_patient_rules = self.rules.filter(rule_type__name="create-object", target_model__name="Patient")
-        if len(create_patient_rules) > 1:
-            raise ValueError("There can be at most one rule with the rule_type__name 'create-object' and target_model__name 'Patient'.")
-
-    # custom save method which runs the _assert_max_one_create_patient_rule method and others
-    def save(self, *args, **kwargs):
-        # self._assert_max_one_create_patient_rule() #TODO Fails on first save since many to many can only be used if object has an id
-        super().save(*args, **kwargs)
-
-    def get_create_patient_rule(self):
-        """Filter the rules for the rule which has the rule_type__name "create-object" and target_model__name "Patient".
-        Also makes sure, that only 1 is returned. If there is no such rule, get default create patient rule.
-        """
-        from endoreg_db.models.case_template.case_template_rule import CaseTemplateRule
-        create_patient_rules = self.rules.filter(rule_type__name="create-object", target_model="Patient")
-        if len(create_patient_rules) > 1:
-            raise ValueError("There can be at most one rule with the rule_type__name 'create-object' and target_model__name 'Patient'.")
-        elif len(create_patient_rules) == 0:
-            create_patient_rules = CaseTemplateRule.objects.get_default_create_patient_rule()
-        return create_patient_rules[0]
-    
-    def get_create_patient_medication_schedule_rule(self):
-        """Filter the rules for the rule which has the rule_type__name "create-object" and target_model__name "PatientMedicationSchedule".
-        Also makes sure, that only 1 is returned. If there is no such rule, get default create patient medication schedule rule.
-        """
-        from endoreg_db.models.case_template.case_template_rule import CaseTemplateRule
-        create_patient_medication_schedule_rules = self.rules.filter(rule_type__name="create-object", target_model="PatientMedicationSchedule")
-        if len(create_patient_medication_schedule_rules) > 1:
-            raise ValueError("There can be at most one rule with the rule_type__name 'create-object' and target_model__name 'PatientMedicationSchedule'.")
-        elif len(create_patient_medication_schedule_rules) == 0:
-            from warnings import warn
-            warn("No create patient medication schedule rule found. Using default create patient medication schedule rule.")
-            create_patient_medication_schedule_rules = CaseTemplateRule.objects.get_default_create_patient_medication_schedule_rule()
-        return create_patient_medication_schedule_rules[0]

endoreg_db/models/case_template/case_template_rule.py

@@ -1,276 +0,0 @@
-from django.db import models
-
-class CaseTemplateRuleTypeManager(models.Manager):
-    def get_by_natural_key(self, name):
-        return self.get(name=name)
-    
-class CaseTemplateRuleType(models.Model):
-    """
-    A class representing a case template rule type.
-
-    Attributes:
-        name (str): The name of the case template rule type.
-        description (str): A description of the case template rule 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 = CaseTemplateRuleTypeManager()
-
-    def natural_key(self):
-        return (self.name,)
-    
-    def __str__(self):
-        return self.name
-
-class CaseTemplateRuleManager(models.Manager):
-    def get_by_natural_key(self, name):
-        return self.get(name=name)
-    
-    def get_default_create_patient_rule(self):
-        """Get the default create patient rule."""
-        return self.get(name="create-patient-default")
-    
-    def get_default_create_patient_lab_sample_rules(self):
-        """Get the default create patient lab sample rules."""
-        return self.get(name="create-patient_lab_sample-default")
-    
-    def get_default_create_patient_medication_schedule_rule(self):
-        """Get the create patient medication schedule rule."""
-        r = self.get(name="create-patient_medication_schedule")
-        assert r, "No create patient medication schedule rule found"
-        return r
-    
-class CaseTemplateRule(models.Model):
-    """
-    A class representing a case template rule.
-
-    Attributes:
-        name (str): The name of the case template rule.
-        case_template (CaseTemplate): The case template to which the rule belongs.
-        description (str): A description of the case template rule.
-        name_de (str): The name of the case template rule in German.
-        name_en (str): The name of the case template rule in English.
-        rule_type (CaseTemplateRuleType): The type of the rule.
-        parent_model (str): The model on which the rule is applied.
-        target_field (str): The field of the parent model on which the rule is applied.
-        target_model (str): The model to which the foreign key points (used for foreign key and many-to-many rules).
-        rule_values (list): A list of string values for the rule.
-        extra_parameters (dict): A dictionary of extra parameters for the rule.
-        value_type (CaseTemplateRuleValueType): The type of the rule value.
-        chained_rules (QuerySet): The chained rules associated with the current rule.
-        single_categorical_value_distribution (SingleCategoricalValueDistribution): The single categorical value distribution for the rule.
-        numerical_value_distribution (NumericValueDistribution): The numerical value distribution for the rule.
-        multiple_categorical_value_distribution (MultipleCategoricalValueDistribution): The multiple categorical value distribution for the rule.
-        date_value_distribution (DateValueDistribution): The date value distribution for the rule.
-        objects (CaseTemplateRuleManager): The manager for the CaseTemplateRule model.
-
-    Methods:
-        natural_key(): Returns the natural key of the rule.
-        __str__(): Returns a string representation of the rule.
-        get_rule_type(): Returns the name of the rule type.
-        get_chained_rules(): Returns all the chained rules associated with the current rule.
-        get_all_downward_chained_rules(): Returns all the chained rules of the current rule, including indirectly chained rules.
-        chained_rules_has_self_reference(): Checks if any directly or indirectly chained rules reference this rule, creating a non-terminating loop.
-        save(*args, **kwargs): Customizes the save method to check for self-references.
-
-    """
-    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)
-    rule_type = models.ForeignKey(
-        "CaseTemplateRuleType", on_delete=models.CASCADE
-    )
-    parent_model = models.CharField(max_length=255, blank=True, null=True)
-    parent_field = models.CharField(max_length=255, blank=True, null=True)
-    target_field = models.CharField(max_length=255, blank=True, null=True)
-    target_model = models.CharField(max_length=255, blank=True, null=True)
-    rule_values = models.JSONField(blank=True, null=True)
-    extra_parameters = models.JSONField(blank=True, null=True)
-    value_type = models.ForeignKey("CaseTemplateRuleValueType", on_delete=models.SET_NULL, null=True)
-    chained_rules = models.ManyToManyField(
-        "CaseTemplateRule",
-        related_name="calling_rules"
-    )
-    single_categorical_value_distribution = models.ForeignKey(
-        "SingleCategoricalValueDistribution", on_delete=models.SET_NULL, null=True
-    )
-    numerical_value_distribution = models.ForeignKey(
-        "NumericValueDistribution", on_delete=models.SET_NULL, null=True
-    )
-    multiple_categorical_value_distribution = models.ForeignKey(
-        "MultipleCategoricalValueDistribution", on_delete=models.SET_NULL, null=True
-    )
-    date_value_distribution = models.ForeignKey(
-        "DateValueDistribution", on_delete=models.SET_NULL, null=True
-    )
-    objects = CaseTemplateRuleManager()
-
-    def natural_key(self):
-        """
-        Returns the natural key of the rule.
-
-        :return: A tuple representing the natural key of the rule.
-        """
-        return (self.name,)
-
-    def __str__(self):
-        """
-        Returns a string representation of the rule.
-
-        :return: A string representation of the rule.
-        """
-        return self.name
-
-    def get_rule_type(self):
-        """
-        Returns the name of the rule type.
-
-        :return: The name of the rule type.
-        """
-        return self.rule_type.name
-
-    def get_chained_rules(self):
-        """
-        Returns all the chained rules associated with the current rule.
-
-        :return: A queryset of all the chained rules associated with the current rule.
-        """
-        return self.chained_rules.all()
-    
-    def get_distribution(self):
-        """
-        Returns the value distribution of the rule.
-
-        :return: The value distribution of the rule.
-        """
-        DEBUG = True
-        if DEBUG:
-            print("Rule: ", self.name)
-            print(f"single_categorical_value_distribution: {self.single_categorical_value_distribution}")
-            print(f"numerical_value_distribution: {self.numerical_value_distribution}")
-            print(f"multiple_categorical_value_distribution: {self.multiple_categorical_value_distribution}")
-            print(f"date_value_distribution: {self.date_value_distribution}")
-
-
-        if self.single_categorical_value_distribution:
-            return self.single_categorical_value_distribution
-        elif self.numerical_value_distribution:
-            return self.numerical_value_distribution
-        elif self.multiple_categorical_value_distribution:
-            return self.multiple_categorical_value_distribution
-        elif self.date_value_distribution:
-            return self.date_value_distribution
-        return None
-
-    def get_all_downward_chained_rules(self):
-        """
-        Get all chained rules of the current rule, including indirectly chained rules.
-
-        :return: A set of all chained rules of the current rule.
-        """
-        all_chained_rules = set()
-
-        def traverse_chained_rules(rule):
-            """
-            Helper function to recursively traverse chained rules.
-
-            :param rule: The current CaseTemplateRule being checked.
-            :return: None
-            """
-            for chained_rule in rule.chained_rules.all():
-                if chained_rule not in all_chained_rules:
-                    all_chained_rules.add(chained_rule)
-                    traverse_chained_rules(chained_rule)
-
-        # Initialize the traversal starting with the current rule
-        traverse_chained_rules(self)
-        return all_chained_rules
-
-    def chained_rules_has_self_reference(self):
-        """
-        Check if any directly or indirectly chained rules reference this rule, creating a non-terminating loop.
-        Return a list containing a tuple (first_rule, self_referencing_rule) for each self-reference.
-        first_rule is the most upward rule in the chain that references the rule.
-        self_referencing_rule is the rule that references the current rule itself.
-
-        :return: A list of tuples representing the self-referencing rules.
-        """
-        result_list = []
-
-        def traverse_chained_rules(rule, visited_rules):
-            """
-            Helper function to recursively traverse chained rules and check for self-references.
-
-            :param rule: The current CaseTemplateRule being checked.
-            :param visited_rules: A list of tuples representing the path of rules visited so far.
-            :return: None
-            """
-            for chained_rule in rule.chained_rules.all():
-                if chained_rule == self:
-                    # A self-reference is detected
-                    first_rule = visited_rules[0][0]
-                    self_referencing_rule = visited_rules[-1][1]
-                    result_list.append((first_rule, self_referencing_rule))
-                elif chained_rule not in [r[1] for r in visited_rules]:
-                    # Continue to check chained rules of the current chained rule
-                    traverse_chained_rules(chained_rule, visited_rules + [(rule, chained_rule)])
-
-        # Initialize the traversal starting with the current rule
-        traverse_chained_rules(self, [(self, self)])
-        return result_list
-    
-    def get_target_model(self):
-        """
-        Returns the target model of the rule.
-
-        :return: The target model of the rule.
-        """
-        from django.apps import apps
-
-        if not self.target_model:
-            return None
-
-        try:
-            target_model = apps.get_model("endoreg_db", self.target_model)
-        except LookupError:
-            raise ValueError(f"Model {self.target_model} not found.")
-        return target_model
-    
-    def get_target_field(self):
-        """
-        Returns the target field of the rule.
-
-        :return: The target field of the rule.
-        """
-        return self.target_field
-    
-    def get_parent_model(self):
-        """
-        Returns the parent model of the rule.
-
-        :return: The parent model of the rule.
-        """
-        from django.apps import apps
-
-        if not self.parent_model:
-            return None
-
-        try:
-            self.parent_model = apps.get_model("endoreg_db", self.parent_model)
-        except LookupError:
-            raise ValueError(f"Model {self.parent_model} not found.")
-        return self.parent_model
-
-    # customize the save method to check for self-references
-    # def save(self, *args, **kwargs):
-    #     # Check for self-references
-    #     self_referencing_rules = self.chained_rules_has_self_reference()
-    #     if self_referencing_rules:
-    #         raise ValueError(f"Self-references detected: {self_referencing_rules}")
-    #     super().save(*args, **kwargs)
-

endoreg_db/models/case_template/case_template_rule_value.py

@@ -1,73 +0,0 @@
-from django.db import models
-
-class CaseTemplateRuleValueTypeManager(models.Manager):
-    def get_by_natural_key(self, name):
-        return self.get(name=name)
-
-class CaseTemplateRuleValueType(models.Model):
-    """
-    A class representing a case template rule value type.
-
-    Attributes:
-        name (str): The name of the case template rule value type.
-        distribution_type: One of "single_categorical", "multiple_categorical", "numeric"
-        description (str): A description of the case template rule value type.
-    """
-    DISTRIBUTION_TYPES = [
-        ("single_categorical", "single_categorical"),
-        ("multiple_categorical", "multiple_categorical"),
-        ("numeric", "numeric")
-    ]
-    objects = CaseTemplateRuleValueTypeManager()
-
-    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)
-
-    distribution_type = models.CharField(max_length=255, choices=DISTRIBUTION_TYPES)
-
-
-    def natural_key(self):
-        return (self.name,)
-
-    def __str__(self):
-        return self.name
-
-class CaseTemplateRuleValueManager(models.Manager):
-    def get_by_natural_key(self, name):
-        return self.get(name=name)
-    
-class CaseTemplateRuleValue(models.Model):
-    """
-    A class representing a case template rule value.
-
-    Attributes:
-        value (str): The value of the case template rule value.
-        case_template_rule (CaseTemplateRule): The case template rule of the case template rule value.
-        case_template (CaseTemplate): The case template of the case template rule value.
-    """
-    objects = CaseTemplateRuleValueManager()
-
-    name = models.CharField(max_length=255)
-    description = models.TextField(blank=True, null=True)
-
-    fk_value = models.CharField(max_length=255, null=True, blank=True)
-    numeric_value = models.FloatField(null=True, blank=True)
-    text_value = models.CharField(max_length=255, null=True, blank=True)
-
-    def natural_key(self):
-        return (self.name,)
-    
-    def __str__(self):
-        return self.name
-    
-    def get_value(self):
-        if self.fk_value:
-            return self.fk_value
-        elif self.numeric_value:
-            return self.numeric_value
-        elif self.text_value:
-            return self.text_value
-        else:
-            return None

endoreg_db/models/case_template/case_template_type.py

@@ -1,28 +0,0 @@
-from django.db import models
-
-
-class CaseTemplateTypeManager(models.Manager):
-    def get_by_natural_key(self, name):
-        return self.get(name=name)
-    
-class CaseTemplateType(models.Model):
-    """
-    A class representing a case template type.
-
-    Attributes:
-        name (str): The name of the case template type.
-        description (str): A description of the case template 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 = CaseTemplateTypeManager()
-
-    def natural_key(self):
-        return (self.name,)
-
-    def __str__(self):
-        return self.name

endoreg_db/models/center/__init__.py

@@ -1,4 +0,0 @@
-from .center import Center
-from .center_product import CenterProduct
-from .center_resource import CenterResource
-from .center_waste import CenterWaste

endoreg_db/models/center/center.py

@@ -1,25 +0,0 @@
-from django.db import models
-
-class CenterManager(models.Manager):
-    def get_by_natural_key(self, name):
-        return self.get(name=name)
-
-class Center(models.Model):
-    objects = CenterManager()
-
-    # import_id = models.IntegerField(primary_key=True)
-    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)
-
-    first_names = models.ManyToManyField(
-        'FirstName',
-        related_name='centers',
-    )
-    last_names = models.ManyToManyField('LastName', related_name='centers')
-
-    def natural_key(self):
-        return (self.name,)
-    
-    def __str__(self):
-        return self.name

endoreg_db/models/center/center_product.py

@@ -1,34 +0,0 @@
-from itertools import product
-from django.db import models
-
-class CenterProduct(models.Model):
-    product = models.ForeignKey("Product", on_delete=models.CASCADE)
-    date_used = models.DateField()
-    center = models.ForeignKey("Center", on_delete=models.CASCADE)
-
-
-    def get_product_group(self):
-        product = self.product
-        product_group = product.product_group
-
-        return product_group
-    
-    def get_reference_product(self):
-        product_group = self.get_product_group()
-        reference_product = product_group.reference_product
-
-        return reference_product
-    
-    def get_product_weight(self):
-        product = self.product
-        weight, unit = product.get_product_weight()
-
-        return weight, unit
-    
-    def get_package_weight(self):
-        product = self.product
-        weight, unit = product.get_package_weight()
-
-        return weight, unit
-    
-    

endoreg_db/models/center/center_resource.py

@@ -1,19 +0,0 @@
-from os import name
-from django.db import models
-
-class CenterResource(models.Model):
-    name = models.CharField(max_length=255, null=True)
-    center = models.ForeignKey("Center", on_delete=models.CASCADE)
-    name_de = models.CharField(max_length=255, null=True)
-    name_en = models.CharField(max_length=255, null=True)
-    quantity = models.FloatField()
-    resource = models.ForeignKey("Resource", on_delete=models.CASCADE)
-    transport_emission_factor = models.ForeignKey("EmissionFactor", on_delete=models.SET_NULL, null=True,
-                                                  related_name="center_resource_transport_emission_factor")
-    use_emission_factor = models.ForeignKey("EmissionFactor", on_delete=models.SET_NULL, null=True,
-                                            related_name="center_resource_use_emission_factor")
-    year = models.IntegerField()
-    unit = models.ForeignKey("Unit", on_delete=models.SET_NULL, null=True)
-    
-    def __str__(self):
-        return self.center.name + " - " + self.resource.name + " (" + str(self.year) + ")"

endoreg_db/models/center/center_waste.py

@@ -1,11 +0,0 @@
-from django.db import models
-    
-class CenterWaste(models.Model):
-    center = models.ForeignKey("Center", on_delete=models.CASCADE)
-    year = models.IntegerField()
-    waste = models.ForeignKey("Waste", on_delete=models.CASCADE)
-    quantity = models.FloatField()
-    unit = models.ForeignKey("Unit", on_delete=models.SET_NULL, null=True)
-    emission_factor = models.ForeignKey("EmissionFactor", on_delete=models.SET_NULL, null=True)
-
-    

endoreg_db/models/data_file/__init__.py

@@ -1,6 +0,0 @@
-from .frame import Frame, LegacyFrame
-from .report_file import ReportFile
-from .video import Video, LegacyVideo, VideoImportMeta
-from .video_segment import LegacyLabelVideoSegment, LabelVideoSegment
-from .metadata import *
-from .import_classes import *

endoreg_db/models/data_file/base_classes/__init__.py

@@ -1,2 +0,0 @@
-from .abstract_frame import AbstractFrame
-from .abstract_video import AbstractVideo

endoreg_db/models/data_file/base_classes/abstract_frame.py

@@ -1,51 +0,0 @@
-from endoreg_db.models.annotation.image_classification import ImageClassificationAnnotation
-from endoreg_db.models.label.label import Label
-
-from django.db import models
-
-
-class AbstractFrame(models.Model):
-    video = None # Placeholder for the video field, to be defined in derived classes
-    frame_number = models.IntegerField()
-    # Add any other fields you need to store frame-related information
-    image = models.ImageField(upload_to="frames")  # Or some other field type, depending on how you're storing the frame
-    suffix = models.CharField(max_length=255)
-    # ImageClassificationAnnotation has a foreign key to this model (related name: image_classification_annotations)
-
-    class Meta:
-        # Ensure that for each video, the frame_number is unique
-        abstract = True
-        unique_together = ('video', 'frame_number')
-        # Optimize for retrieval in frame_number order
-        indexes = [models.Index(fields=['video', 'frame_number'])]
-
-
-    def __str__(self):
-        return self.video.file.path + " - " + str(self.frame_number)
-
-    def get_frame_model(self):
-        assert 1 == 2, "This method should be overridden in derived classes"
-
-    def get_classification_annotations(self):
-        """
-        Get all image classification annotations for this frame.
-        """
-        return ImageClassificationAnnotation.objects.filter(frame=self)
-
-    def get_classification_annotations_by_label(self, label:Label):
-        """
-        Get all image classification annotations for this frame with the given label.
-        """
-        return ImageClassificationAnnotation.objects.filter(frame=self, label=label)
-
-    def get_classification_annotations_by_value(self, value:bool):
-        """
-        Get all image classification annotations for this frame with the given value.
-        """
-        return ImageClassificationAnnotation.objects.filter(frame=self, value=value)
-
-    def get_classification_annotations_by_label_and_value(self, label:Label, value:bool):
-        """
-        Get all image classification annotations for this frame with the given label and value.
-        """
-        return ImageClassificationAnnotation.objects.filter(frame=self, label=label, value=value)