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

endoreg_db/models/quiz/quiz_answer.py

@@ -1,41 +0,0 @@
-from django.db import models
-
-class QuizAnswerTypeManager(models.Manager):
-    def get_by_natural_key(self, name):
-        return self.get(name=name)
-
-class QuizAnswerType(models.Model):
-    objects = QuizAnswerTypeManager()
-
-    name = models.CharField(max_length=255)
-    description = models.TextField(blank=True, null=True)
-
-    def natural_key(self):
-        return (self.name,)
-
-    def __str__(self):
-        return self.name
-
-class QuizAnswerManager(models.Manager):
-    def get_by_natural_key(self, text):
-        return self.get(text=text)
-    
-class QuizAnswer(models.Model):
-    objects = QuizAnswerManager()
-
-    text_value = models.CharField(max_length=255, null=True, blank=True)
-    number_value = models.FloatField(null=True, blank=True)
-    answer_type = models.ForeignKey("QuizAnswerType", on_delete=models.CASCADE)
-    question = models.ForeignKey("QuizQuestion", on_delete=models.CASCADE)
-
-    last_updated = models.DateTimeField(auto_now=True)
-
-    #TODO add user as foreign key
-
-    def natural_key(self):
-        return (self.text,)
-    
-    def __str__(self):
-        return self.text
-    
-

endoreg_db/models/quiz/quiz_question.py

@@ -1,54 +0,0 @@
-from django.db import models
-
-class QuizQuestionTypeManager(models.Manager):
-    def get_by_natural_key(self, name):
-        return self.get(name=name)
-    
-class QuizQuestionType(models.Model):
-    """
-    A class representing a quiz question type.
-
-    Attributes:
-        name (str): The name of the quiz question type.
-        description (str): A description of the quiz question type.
-
-    """
-    name = models.CharField(max_length=255)
-    description = models.TextField(blank=True, null=True)
-
-    objects = QuizQuestionTypeManager()
-
-    def natural_key(self):
-        return (self.name,)
-
-    def __str__(self):
-        return self.name
-    
-class QuizQuestionManager(models.Manager):
-    def get_by_natural_key(self, text):
-        return self.get(text=text)
-    
-class QuizQuestion(models.Model):
-    """
-    A class representing a quiz question.
-
-    Attributes:
-        text (str): The text of the quiz question.
-        question_type (QuizQuestionType): The type of the quiz question.
-        description (str): A description of the quiz question.
-
-    """
-    text = models.TextField()
-    description = models.TextField(blank=True, null=True)
-    question_type = models.ForeignKey("QuizQuestionType", on_delete=models.CASCADE)
-
-    objects = QuizQuestionManager()
-
-    def natural_key(self):
-        return (self.text,)
-    
-    def __str__(self):
-        return self.text
-    
-    def get_question_type(self):
-        return self.question_type.name

endoreg_db/models/report_reader/__init__.py

@@ -1,2 +0,0 @@
-from .report_reader_config import ReportReaderConfig
-from .report_reader_flag import ReportReaderFlag

endoreg_db/models/report_reader/report_reader_config.py

@@ -1,53 +0,0 @@
-# ReportReaderConfig Class
-# Description: This class is used to store the configuration of the ReportReader
-
-# PATIENT_INFO_LINE_FLAG = "Patient: "
-# ENDOSCOPE_INFO_LINE_FLAG = "Gerät: "
-# EXAMINER_INFO_LINE_FLAG = "1. Unters.:"
-# CUT_OFF_BELOW_LINE_FLAG = "________________"
-
-
-# CUT_OFF_ABOVE_LINE_FLAGS = [
-#     ENDOSCOPE_INFO_LINE_FLAG,
-#     EXAMINER_INFO_LINE_FLAG,
-# ]
-
-# CUT_OFF_BELOW_LINE_FLAGS = [
-#         CUT_OFF_BELOW_LINE_FLAG
-#     ]
-
-from django.db import models
-from .report_reader_flag import ReportReaderFlag
-from ..center import Center
-from ..data_file import PdfType
-
-class ReportReaderConfig(models.Model):
-
-    locale = models.CharField(default="de_DE", max_length=10)
-    first_names = models.ManyToManyField('FirstName', related_name='report_reader_configs')
-    last_names = models.ManyToManyField('LastName', related_name='report_reader_configs')
-    text_date_format = models.CharField(default = "%d.%m.%Y", max_length=10)
-    patient_info_line_flag = models.ForeignKey(ReportReaderFlag, related_name='report_reader_configs_patient_info_line', on_delete=models.CASCADE)
-    endoscope_info_line_flag = models.ForeignKey(ReportReaderFlag, related_name='report_reader_configs_endoscope_info_line', on_delete=models.CASCADE)
-    examiner_info_line_flag = models.ForeignKey(ReportReaderFlag, related_name='report_reader_configs_examiner_info_line', on_delete=models.CASCADE)
-    cut_off_below = models.ManyToManyField(ReportReaderFlag, related_name='report_reader_configs_cut_off_below')
-    cut_off_above = models.ManyToManyField(ReportReaderFlag, related_name='report_reader_configs_cut_off_above')
-    
-    def __str__(self):
-        return self.locale
-    
-    def update_names_by_center(self, center:Center, save = True):
-        self.first_names.set(center.first_names.all())
-        self.last_names.set(center.last_names.all())
-        if save:
-            self.save()
-
-    def update_flags_by_pdf_type(self, pdf_type:PdfType, save = True):
-        self.patient_info_line_flag = pdf_type.patient_info_line_flag
-        self.endoscope_info_line_flag = pdf_type.endoscope_info_line_flag
-        self.examiner_info_line_flag = pdf_type.examiner_info_line_flag
-        self.cut_off_below.set(pdf_type.cut_off_below.all())
-        self.cut_off_above.set(pdf_type.cut_off_above.all())
-        if save:
-            self.save()
-

endoreg_db/models/report_reader/report_reader_flag.py

@@ -1,20 +0,0 @@
-# Django model for the report reader flag
-# have name and value
-# name is natural key
-
-from django.db import models
-
-class ReportReaderFlagManager(models.Manager):
-    def get_by_natural_key(self, name):
-        return self.get(name=name)
-    
-class ReportReaderFlag(models.Model):
-    objects = ReportReaderFlagManager()
-    name = models.CharField(max_length=255, unique=True)
-    value = models.CharField(max_length=255)
-    
-    def natural_key(self):
-        return (self.name,)
-    
-    def __str__(self):
-        return self.name

endoreg_db/models/rules/__init__.py

@@ -1,5 +0,0 @@
-from .rule_type import RuleType
-from .rule import Rule
-from .ruleset import Ruleset
-from .rule_attribute_dtype import RuleAttributeDType
-from .rule_applicator import RuleApplicator

endoreg_db/models/rules/rule.py

@@ -1,24 +0,0 @@
-from django.db import models
-
-class RuleManager(models.Manager):
-    def get_by_natural_key(self, name):
-        return self.get(name=name)
-
-class Rule(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)
-    description = models.TextField(blank=True, null=True)
-    attribute_key = models.CharField(max_length=255)
-    rule_type = models.ForeignKey("RuleType", on_delete=models.CASCADE)
-    attribute_dtype = models.ForeignKey("RuleAttributeDType", on_delete=models.CASCADE)
-
-    objects = RuleManager()
-
-    class Meta:
-        verbose_name = 'Rule'
-        verbose_name_plural = 'Rules'
-
-    def natural_key(self):
-        return (self.name,)
-    

endoreg_db/models/rules/rule_applicator.py

@@ -1,224 +0,0 @@
-from .rule import Rule
-import random
-from django.core.exceptions import ValidationError
-
-class RuleApplicator:
-    """
-    A class to apply different types of rules to a Django model instance based on the Rule configuration.
-    """
-
-    def get_rule_by_name(self, rule_name):
-        """
-        A helper method to fetch a rule by name. This can be further customized.
-        """
-        # get rule by name which is natural key
-        rule = Rule.objects.get_by_natural_key(rule_name)
-        return rule
-
-
-    def apply(self, obj, rule):
-        """
-        Applies a specified rule to an object based on the rule type and attributes.
-
-        Parameters:
-        obj (Django model instance): The object to which the rule is applied.
-        rule (Rule): The rule instance containing the rule_type and attribute details.
-        """
-        rule_type_method = self.get_rule_type_method(rule.rule_type.name)
-        if rule_type_method:
-            rule_type_method(obj, rule)
-
-        else:
-            raise ValueError(f"Unsupported rule type: {rule.rule_type.name}")
-        
-    def apply_rule_by_name(self, obj, rule_name):
-        """
-        A helper method to apply a rule and get a value. This can be further customized.
-        """
-        rule = self.get_rule_by_name(rule_name)
-        self.apply(obj, rule)
-
-    def apply_rules_by_name(self, obj, rule_names):
-        """
-        A helper method to apply multiple rules and get values. This can be further customized.
-        """
-        rules = [self.get_rule_by_name(rule_name) for rule_name in rule_names]
-        for rule in rules:
-            self.apply(obj, rule)
-            
-
-    def get_rule_type_method(self, rule_type_name):
-        """
-        Maps rule type name to the corresponding method.
-        """
-        return getattr(self, f"handle_{rule_type_name}", None)
-
-    def parse_attribute_path(self, obj, attribute_key):
-        """
-        Parses the attribute path and applies the value to the correct attribute of a nested object.
-        """
-        parts = attribute_key.split('.')
-        model_name = parts[0]
-        if model_name.lower() != obj.__class__.__name__.lower():
-            raise ValidationError(f"Model type mismatch: expected {model_name}, got {obj.__class__.__name__}")
-
-        # Navigate through the nested attributes
-        target = obj
-        for part in parts[1:-1]:
-            target = getattr(target, part)
-
-        return target, parts[-1]
-
-    def set_attribute_value(self, obj, rule):
-        """
-        Generic method to set attribute value considering nested paths.
-        """
-        target, attribute = self.parse_attribute_path(obj, rule.attribute_key)
-        setattr(target, attribute, rule.attribute_dict['value'])
-        target.save()
-
-    #####
-
-    def handle_case_attribute_set_value(self, obj, rule):
-        """
-        Sets a specific attribute to a given value.
-        """
-        self.set_attribute_value(obj, rule.attribute_key, rule.attribute_dict["value"])
-
-    def handle_case_attribute_set_value_range_uniform(self, obj, rule):
-        """
-        Sets an attribute to a value within a specified range, selected uniformly.
-        """
-        if not hasattr(rule, 'attribute_dtype') or rule.attribute_dtype.name not in ['numeric', 'ordered_categorical']:
-            raise ValidationError("Attribute dtype must be numeric or ordered_categorical")
-        min_val = rule.attribute_dict["value_min"]
-        max_val = rule.attribute_dict["value_max"]
-        value = random.uniform(min_val, max_val)
-        self.set_attribute_value(obj, rule.attribute_key, value)
-
-    def handle_case_attribute_set_value_range_norm_dist(self, obj, rule):
-        """
-        Sets an attribute to a value within a specified range, based on a normal distribution.
-        """
-        if rule.attribute_dtype.name in ['float', "integer"]:
-            raise ValidationError("Attribute dtype must be float or integer")
-        mean = rule.attribute_dict["value_mean"]
-        std_dev = rule.attribute_dict["value_sd"]
-        value = random.normalvariate(mean, std_dev)
-        self.set_attribute_value(obj, rule.attribute_key, value)
-        
-
-    def handle_case_attribute_set_from_list_uniform(self, obj, rule):
-        """
-        Selects an attribute value uniformly from a list of choices.
-        """
-        choices = rule.attribute_dict["value_choices"]
-        value = random.choice(choices)
-        self.set_attribute_value(obj, rule.attribute_key, value)
-
-    def handle_case_attribute_set_from_prop_tuple_list(self, obj, rule):
-        """
-        Selects an attribute value based on a list of value-probability tuples.
-        """
-        prop_list = rule.attribute_dict["value_prop_tuple_list"]
-        total = sum(prop for _, prop in prop_list)
-        pick = random.uniform(0, total)
-        current = 0
-        for value, prop in prop_list:
-            current += prop
-            if current > pick:
-                self.set_attribute_value(obj, rule.attribute_key, value)
-                break
-
-
-    #####
-
-    def handle_case_add_patient(self, obj, rule):
-        """Function to add a patient to a case. If the patient already exists, raise an error. Requires the following
-        rules in the rule_dict:
-        - gender_rule
-        - dob_rule
-        - event_rules
-        - disease_rules
-        """
-        from endoreg_db.models import Patient, PatientEvent, PatientDisease, Case
-
-        # Check if the 
-        obj:Case = obj
-        if obj.patient:
-            raise ValueError("Patient already exists in the case")
-        
-        patient = Patient()
-        self.apply_rule_by_name(patient, rule.attribute_dict["patient_gender_rule"])
-        self.apply_rule_by_name(patient, rule.attribute_dict["patient_dob_rule"])
-        self.apply_rules_by_name(patient, rule.attribute_dict["patient_event_rules"])
-        self.apply_rules_by_name(patient, rule.attribute_dict["patient_disease_rules"])
-
-    def handle_case_add_polyp(self, obj, rule):
-        """
-        Adds a polyp to the case, processing various polyp characteristics. Requires Rules for each attribute:
-        - polyp_location_organ_rule (single rule)
-        - polyp_location_organ_part_rule (single rule)
-        - polyp_morphology_classification_shape_choices_rule (list of rules)
-        - polyp_morphology_classification_chromo_choices_rule (list of rules)
-        - polyp_intervention_type_rule (single rule)
-        - polyp_intervention_instrument_rule (single rule)
-        - polyp_size_mm_rule (single rule)
-
-        """
-        # Example: create and add a polyp instance based on the rules
-        from endoreg_db.models import Polyp  # Ensure you have a Polyp model and adjust the import
-        from endoreg_db.models import Location
-        from endoreg_db.models import EndoscopicIntervention
-        from endoreg_db.models import PolypMorphology
-
-        assert obj.examination.type != None, "Examination type is required"
-
-        location = Location()
-        location.organ = self.apply_rule_by_name(location, rule.attribute_dict["polyp_location_organ_rule"])
-        location.organ_part = self.apply_rule_by_name(location, rule.attribute_dict["polyp_location_organ_part_rule"])
-        location.save()
-
-        morphology = PolypMorphology()
-        # M2M to ClassificationChoice (linked to Classification which has name as natural key)
-        morphology.shape_classification_choices = self.apply_rules_by_name(morphology, rule.attribute_dict["polyp_morphology_classification_shape_choices_rules"])
-        # M2M to ClassificationChoice (linked to Classification which has name as natural key)
-        morphology.chromo_classification_choices = self.apply_rules_by_name(morphology, rule.attribute_dict["polyp_morphology_classification_chromo_choices_rules"])
-        morphology.save()
-
-        intervention = EndoscopicIntervention()
-        intervention.type = self.apply_rule_by_name(intervention, rule.attribute_dict["polyp_intervention_type_rule"])
-        intervention.instrument = self.apply_rule_by_name(intervention, rule.attribute_dict["polyp_intervention_instrument_rule"])
-        intervention.save()
-
-        polyp = Polyp()
-        polyp.size_mm = self.apply_rule_by_name(polyp, rule.attribute_dict["polyp_size_mm_rule"])
-        polyp.location = location
-        polyp.morphology = morphology
-        polyp.intervention = intervention
-        
-        polyp.save()
-
-        obj.polyps.add(polyp)
-        obj.save()
-
-
-    # def handle_case_add_esophageal_varices(self, obj, rule):
-    #     """
-    #     Handles adding esophageal varices to a case based on the rule.
-    #     """
-    #     # Similar to the polyp case, create and add esophageal varices based on the attributes
-    #     from endoreg_db.models import EsophagealVarices  # Ensure this model exists
-    #     varices = EsophagealVarices()
-    #     varices.origin = self.apply_rule_by_name(obj, rule.attribute_dict["esophageal_varices_origin_rule"])
-    #     varices.classification = self.apply_rule_by_name(obj, rule.attribute_dict["esophageal_varices_classification_rule"])
-    #     varices.location_extent = self.apply_rule_by_name(obj, rule.attribute_dict["esophageal_varices_location_extent_rule"])
-    #     varices.save()
-    #     # Assuming a relationship setup
-    #     obj.esophageal_varices.add(varices)
-    #     obj.save()
-
-
-    
-    
-        

endoreg_db/models/rules/rule_attribute_dtype.py

@@ -1,19 +0,0 @@
-from django.db import models
-
-
-class RuleAttributeDtypeManager(models.Manager):
-    def get_by_natural_key(self, name):
-        return self.get(name=name)
-
-class RuleAttributeDType(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 = RuleAttributeDtypeManager()
-
-    def natural_key(self):
-        return (self.name,)
-
-    def __str__(self):
-        return self.name

endoreg_db/models/rules/rule_type.py

@@ -1,22 +0,0 @@
-from django.db import models
-
-class RuleTypeManager(models.Manager):
-    def get_by_natural_key(self, name):
-        return self.get(name=name)
-
-class RuleType(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 = RuleTypeManager()
-
-    def natural_key(self):
-        return (self.name,)
-
-    def __str__(self):
-        return self.name
-
-    class Meta:
-        verbose_name = 'Rule Type'
-        verbose_name_plural = 'Rule Types'

endoreg_db/models/rules/ruleset.py

@@ -1,19 +0,0 @@
-from django.db import models
-
-class RulesetManager(models.Manager):
-    def get_by_natural_key(self, name):
-        return self.get(name=name)
-
-class Ruleset(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)
-    rules = models.ManyToManyField('Rule')
-
-    objects = RulesetManager()
-
-    def natural_key(self):
-        return (self.name,)
-
-    def __str__(self):
-        return self.name

endoreg_db/models/unit.py

@@ -1,22 +0,0 @@
-from django.db import models
-
-class UnitManager(models.Manager):
-    def get_by_natural_key(self, name):
-        return self.get(name=name)
-
-class Unit(models.Model):
-    objects = UnitManager()
-
-    name = models.CharField(max_length=100) # e.g. "Centimeter"
-    name_de = models.CharField(max_length=100, blank=True, null=True) # e.g. "Zentimeter"
-    name_en = models.CharField(max_length=100, blank=True, null=True) # e.g. "Centimeter"
-    description = models.CharField(max_length=100, blank=True, null=True) # e.g. "centimeters", "milimeters", "inches"
-    abbreviation = models.CharField(max_length=25, blank=True, null=True) # e.g. "cm", "mm", "in"
-    
-    def __str__(self):
-        if self.abbreviation:
-            return self.abbreviation
-        return self.name
-    
-    def natural_key(self):
-        return (self.name,)

endoreg_db/queries/__init__.py

@@ -1,5 +0,0 @@
-from .annotations import (
-    generate_legacy_dataset_output
-)
-
-from .get import *

endoreg_db/queries/annotations/__init__.py

@@ -1,3 +0,0 @@
-from .legacy import (
-    get_legacy_annotations_for_labelset, generate_legacy_dataset_output
-)