endoreg-db 0.8.8.0__py3-none-any.whl → 0.8.8.9__py3-none-any.whl

endoreg_db/data/requirement/01_patient_data.yaml

@@ -0,0 +1,93 @@
+- model: endoreg_db.requirement
+  fields:
+    name: "patient_has_dob_information"
+    name_de: "Patient hat Geburtsdatum Information"
+    name_en: "Patient has date of birth information"
+    description: "Checks if the patient has date of birth information."
+    requirement_types:
+      - "patient"
+      - "patient_examination"
+    operator: model_attribute_set_any #TODO implement operator
+    operator_instructions: "dob;patient.dob"
+
+- model: endoreg_db.requirement
+  fields:
+    name: "patient_has_valid_dob_information"
+    name_de: "Patient hat gültige Geburtsdatum Information"
+    name_en: "Patient has valid date of birth information"
+    description: "Checks if the patient has valid date of birth information."
+    requirement_types:
+      - "patient"
+      - "patient_examination"
+    operator: model_attribute_numeric_in_range
+    operator_instructions: "?age;?patient.age"
+    numeric_value_min: 18
+    numeric_value_max: 110
+
+# Name related Requirements
+- model: endoreg_db.requirement
+  fields:
+    name: "patient_has_first_name_information"
+    name_de: "Patienten-Untersuchung hat Namensinformation"
+    name_en: "Patient Examination has names information"
+    description: "Checks if the patient has first and last name information."
+    requirement_types:
+      - "patient"
+      - "patient_examination"
+    operator: "model_attribute_set_any"
+    operator_instructions: "?first_name;?patient.first_name"
+
+- model: endoreg_db.requirement
+  fields:
+    name: "patient_has_last_name_information"
+    name_de: "Patienten-Untersuchung hat Nachnameninformation"
+    name_en: "Patient Examination has last name information"
+    description: "Checks if the patient has last name information."
+    requirement_types:
+      - "patient"
+      - "patient_examination"
+    operator: "model_attribute_set_any"
+    operator_instructions: "?last_name;?patient.last_name"
+
+############# Gender Related Requirements ################
+- model: endoreg_db.requirement
+  fields:
+    name: "patient_has_gender_information"
+    name_de: "Patient hat Geschlechtsinformation"
+    name_en: "Patient has gender information"
+    description: "Checks if the patient has gender information."
+    requirement_types:
+      - "patient"
+      - "patient_examination"
+    operator: model_attribute_set_any
+    operator_instructions: "?gender;?patient.gender"
+
+# model_attribute_is_among_values operator to be implemented
+# should resolve the target models defined in requirement types to
+# get at least one of the linked models (i.e. "patient_has_gender_information",
+# expects a patient as input and should fetch the gender attribute and check
+# if it is among the defined values [male, female])
+# operator_instructions must be provided for used operator;
+# we will parse the value as comma separated list;
+# it defines attributes the operator will try to fetch
+# from the input models defined in requirement_types.
+# at least one of the provided values must match at least one
+# valid field for each input model
+
+- model: endoreg_db.requirement
+  fields:
+    name: "patient_has_valid_gender_information"
+    name_de: "Patient hat Geschlechtsinformation"
+    name_en: "Patient has gender information"
+    description: "Checks if the patient has gender information."
+    requirement_types:
+      - "patient"
+      - "patient_examination"
+    operator: model_attribute_is_among_values #TODO implement operator; here,
+    # we add "entries leading with "!" to indicate the current
+    # requirements field we use to fetch  the list of values
+    # to check against
+    operator_instructions: "?gender;?patient.gender;!genders"
+    genders:
+      - "male"
+      - "female"

endoreg_db/data/requirement_operator/new_operators.yaml

@@ -0,0 +1,36 @@
+- model: endoreg_db.requirement_operator
+  fields:
+    name: "model_attribute_numeric_in_range"
+    name_de: "Modellattribut numerisch im Bereich"
+    name_en: "Model attribute numeric in range"
+    description: "
+      Checks if a numeric model attribute is within a specified range.
+      If this operator is used in a requirement, the requirement
+      must define 'target_attributes', 'numeric_value_min', and 'numeric_value_max' fields.
+      "
+
+- model: endoreg_db.requirement_operator
+  fields:
+    name: "model_attribute_set_any"
+    name_de: "Modellattribut Menge beliebig"
+    name_en: "Model attribute set any"
+    description: "
+      Checks if a model attribute is set to any value (not null or empty).
+      If this operator is used in a requirement, the requirement
+      must define 'target_attributes' field.
+      "
+
+- model: endoreg_db.requirement_operator
+  fields:
+    name: "model_attribute_is_among_values"
+    name_de: "Modellattribut ist unter Werten"
+    name_en: "Model attribute is among values"
+    description: "
+      Checks if a model attribute is among a specified set of values.
+      If this operator is used in a requirement, the requirement
+      must define 'target_attributes'. In this case,
+      target must contain a comma-separated list.
+      Entries without prefix are target fields to check against,
+      entries with prefix '?' define fields of the requirement to use
+      as reference during evaluation.
+      "

endoreg_db/data/requirement_set/01_endoscopy_generic.yaml

@@ -63,5 +63,3 @@
       - "patient_age_generic"
       - "patient_gender_generic"
       - "basic_lab_values_normal"
-
--

endoreg_db/data/requirement_set/90_coloreg.yaml

@@ -5,11 +5,12 @@
     name_en: "Coloreg Patient Data"
     description: "Coloreg Patient Data"
     requirement_set_type: "all"
-    requirements: []
+    requirements:
+      - "patient_has_gender_information" # Checks if any gender is set
+      # - "patient_has_valid_gender_information" # checks if gender is male or female
+      - "patient_has_dob_information" #TODO
+      - "patient_has_names_information" #TODO
     links_to_sets:
-      - "patient_gender_generic"
-      - "patient_names_generic"
-      - "patient_dob_generic"
       - "colonoscopy_basic_patient_history" # includes previous bowel_surgery_known and last_colonoscopy_known
     tags: [] # not tagged as report_mask_requirement_set, only used in top level requirement set
 
@@ -45,7 +46,7 @@
     name_en: "Coloreg Finding Colon Polyp Rectosigmoid Location"
     description: "Coloreg Finding Colon Polyp Rectosigmoid Location"
     requirement_set_type: "all"
-    depends_on_sets:
+    depends_on:
       - "coloreg_finding_colon_polyp_location_base"
     requirements:
       - "coloreg_finding_colon_polyp_rectosigmoid_has_location_cm" #TODO Rektosigmoid muss cm haben
@@ -105,7 +106,7 @@
     name_en: "Coloreg Finding Colon Polyp Morphology"
     description: "Coloreg Finding Colon Polyp Morphology"
     requirement_set_type: "any"
-    depends_on_sets:
+    depends_on:
       - "coloreg_finding_colon_polyp_size"
     links_to_sets:
       - "coloreg_polyp_small_morphology"
@@ -163,7 +164,18 @@
 
 - models: endoreg_db.requirement_set
   fields:
-    name: "colonoscopy_coloreg"
+    name: "coloreg_finding_data_complete"
+    name_de: "Coloreg Befund Kolon Polyp Komplett"
+    name_en: "Coloreg Finding Colon Polyp Complete"
+    description: "Coloreg Finding Colon Polyp Complete"
+    requirement_set_type: "all"
+    links_to_sets:
+      - "coloreg_finding_colon_polyp_base_description"
+    tags: []
+
+- models: endoreg_db.requirement_set
+  fields:
+    name: "coloreg_colonoscopy_report_complete"
     name_de: "Koloskopie Coloreg"
     name_en: "Colonoscopy Coloreg"
     description: "Colonoscopy Coloreg"
@@ -171,7 +183,7 @@
     links_to_sets:
       - "coloreg_patient_data"
       - "coloreg_examination_data"
-      - "coloreg_finding_colon_polyp_base_description"
+      - "coloreg_finding_data_complete"
     tags:
       - "report_mask_requirement_set"
     reqset_exam_links:

endoreg_db/exceptions.py

@@ -1,5 +1,4 @@
 import logging
-
 logger = logging.getLogger(__name__)
 
 

endoreg_db/forms/examination_form.py

@@ -1,5 +1,5 @@
 from django import forms
-from endoreg_db.models.examination.examination import Examination
+from endoreg_db.models.medical import Examination
 
 class ExaminationForm(forms.ModelForm):
     class Meta:

endoreg_db/helpers/data_loader.py

@@ -1,183 +1,258 @@
 """
 Data Loader Helpers and others
 """
-from django.core.management import call_command
+
 from pathlib import Path
+
+from django.core.management import call_command
+
 ASSET_DIR = Path(__file__).resolve().parent.parent / "assets"
 
-def load_default_ai_model(): 
+
+def load_default_ai_model():
     """
     Loads the default AI model into the database using a predefined checkpoint file.
-    
+
     This function constructs the path to the default AI model checkpoint and invokes the
     Django management command `create_multilabel_model_meta` to register the model.
     """
     model_path = f"{ASSET_DIR.as_posix()}/colo_segmentation_RegNetX800MF_6.safetensors"
     # Pass arguments individually to call_command
-    call_command(
-        "create_multilabel_model_meta",
-        "--model_path",
-        model_path
-    )
+    call_command("create_multilabel_model_meta", "--model_path", model_path)
+
 
 def load_qualification_data():
     """
     Loads qualification data into the database using the corresponding Django management command.
     """
-    call_command("load_qualification_data", )
+    call_command(
+        "load_qualification_data",
+    )
+
 
 def load_shift_data():
     """
     Loads shift data into the database by invoking the corresponding Django management command.
     """
-    call_command("load_shift_data", )
+    call_command(
+        "load_shift_data",
+    )
+
 
 def load_base_db_data():
     """
     Loads the base database data by invoking the corresponding Django management command.
     """
-    call_command("load_base_db_data", )
+    call_command(
+        "load_base_db_data",
+    )
+
 
 def load_information_source():
     """
     Loads information source data into the database by invoking the corresponding Django management command.
     """
-    call_command("load_information_source", )
+    call_command(
+        "load_information_source",
+    )
+
 
 def load_risk_data():
     """
     Loads risk data into the database by invoking the corresponding Django management command.
     """
-    call_command("load_risk_data", )
+    call_command(
+        "load_risk_data",
+    )
+
 
 def load_center_data():
     """
     Loads center data into the database by invoking the corresponding Django management command.
     """
-    call_command("load_center_data", )
+    call_command(
+        "load_center_data",
+    )
+
 
 def load_endoscope_data():
     """
     Loads endoscope data into the database by invoking the corresponding Django management command.
     """
-    call_command("load_endoscope_data", )
+    call_command(
+        "load_endoscope_data",
+    )
+
 
 def load_distribution_data():
     """
     Loads distribution data into the database by invoking the corresponding Django management command.
     """
-    call_command("load_distribution_data", )
+    call_command(
+        "load_distribution_data",
+    )
+
 
 def load_gender_data():
     """
     Loads gender data into the database by invoking the corresponding Django management command.
     """
-    call_command("load_gender_data", )
+    call_command(
+        "load_gender_data",
+    )
+
 
 def load_report_reader_flag_data():
     """
     Loads the report reader flag data into the database using the corresponding management command.
     """
-    call_command("load_report_reader_flag_data", )
-    
+    call_command(
+        "load_report_reader_flag_data",
+    )
+
+
 def load_pdf_type_data():
     """
-    Loads PDF type data into the database by invoking the corresponding Django management command.
+    Loads report type data into the database by invoking the corresponding Django management command.
     """
-    call_command("load_pdf_type_data", )
-    
+    call_command(
+        "load_pdf_type_data",
+    )
+
+
 def load_unit_data():
     """
     Loads unit data into the database by invoking the corresponding Django management command.
     """
-    call_command("load_unit_data", )
-    
+    call_command(
+        "load_unit_data",
+    )
+
+
 def load_disease_data():
     """
     Loads disease data into the database using the corresponding Django management command.
     """
-    call_command("load_disease_data", )
-    
+    call_command(
+        "load_disease_data",
+    )
+
+
 def load_event_data():
     """
     Loads event data into the database by invoking the corresponding Django management command.
     """
-    call_command("load_event_data", )
-    
+    call_command(
+        "load_event_data",
+    )
+
+
 def load_organ_data():
     """
     Loads organ data into the database by invoking the corresponding Django management command.
     """
-    call_command("load_organ_data", )
-    
+    call_command(
+        "load_organ_data",
+    )
+
+
 def load_contraindication_data():
     """
     Loads contraindication data into the database using the corresponding management command.
     """
-    call_command("load_contraindication_data", )
-    
+    call_command(
+        "load_contraindication_data",
+    )
+
+
 def load_examination_data():
     """
     Loads examination data into the database using the corresponding Django management command.
     """
-    call_command("load_examination_data", )
-    
+    call_command(
+        "load_examination_data",
+    )
+
+
 def load_lab_value_data():
     """
     Loads laboratory value data into the database using the corresponding Django management command.
     """
-    call_command("load_lab_value_data", )
-    
+    call_command(
+        "load_lab_value_data",
+    )
+
+
 def load_finding_data():
     """
     Loads finding data into the database by invoking the corresponding Django management command.
     """
-    call_command("load_finding_data", )
-    
+    call_command(
+        "load_finding_data",
+    )
+
+
 def load_examination_indication_data():
     """
     Loads examination indication data into the database using the corresponding Django management command.
     """
-    call_command("load_examination_indication_data", )
-    
+    call_command(
+        "load_examination_indication_data",
+    )
+
+
 def load_medication_data():
     """
     Loads medication data into the database using the corresponding Django management command.
     """
-    call_command("load_medication_data", )
+    call_command(
+        "load_medication_data",
+    )
 
-def load_requirement_data():
 
+def load_requirement_data():
     """
     Loads requirement data into the database by invoking the corresponding Django management command.
     """
-    call_command("load_requirement_data", )
+    call_command(
+        "load_requirement_data",
+    )
+
 
 def load_ai_model_label_data():
     """
     Loads AI model label data into the database by invoking the corresponding Django management command.
     """
-    call_command("load_ai_model_label_data", )
+    call_command(
+        "load_ai_model_label_data",
+    )
+
 
-def load_ai_model_data():    
+def load_ai_model_data():
     """
     Loads AI model data into the database by invoking the corresponding Django management command.
     """
-    call_command("load_ai_model_data", )
+    call_command(
+        "load_ai_model_data",
+    )
+
 
 def load_green_endoscopy_wuerzburg_data():
     """
     Loads the Green Endoscopy Wuerzburg dataset into the database using the corresponding Django management command.
     """
-    call_command("load_green_endoscopy_wuerzburg_data", )
+    call_command(
+        "load_green_endoscopy_wuerzburg_data",
+    )
+
 
 def load_data():
     """
     Loads all predefined data sets into the database in the required sequence.
-    
+
     Calls individual data loading functions in a specific order to ensure that dependencies between data sets are respected.
     """
-    
+
     load_information_source()
     load_risk_data()
     load_center_data()
@@ -203,6 +278,3 @@ def load_data():
     load_ai_model_data()
 
     load_green_endoscopy_wuerzburg_data()
-
-    
-