adding lynch classes and utils

Andyg79 · Andyg79 · commit 445d5c50f884 · 2025-10-17T11:45:46.000+01:00
diff --git a/classes/data/data_creation.py b/classes/data/data_creation.py
@@ -5,7 +5,7 @@
 from classes.organisation.organisation_complex import Organisation
 from classes.subject.gender_type import GenderType
 from classes.address.address import Address
-from classes.person.person import Person
+from classes.person.person_data import Person
 from classes.screening.region_type import RegionType
 from classes.subject.pi_subject import PISubject
 from utils.nhs_number_tools import NHSNumberTools
@@ -113,17 +113,17 @@ def generate_random_subject(
         pi_subject = PISubject()
         pi_subject.nhs_number = NHSNumberTools.generate_random_nhs_number()
         person = self.generate_random_person(random_words_list, GenderType.NOT_KNOWN)
-        pi_subject.family_name = person.get_surname()
-        pi_subject.first_given_names = person.get_forename()
-        pi_subject.other_given_names = person.get_other_forenames()
-        pi_subject.previous_family_name = person.get_previous_surname()
-        pi_subject.name_prefix = person.get_title()
+        pi_subject.family_name = person.surname
+        pi_subject.first_given_names = person.forename
+        pi_subject.other_given_names = person.other_forenames
+        pi_subject.previous_family_name = person.previous_surname
+        pi_subject.name_prefix = person.title
         pi_subject.birth_date = datetime.date.today() - datetime.timedelta(
             days=60 * 365
         )
 
         pi_subject.death_date = None
-        gender = person.get_gender()
+        gender = person.gender
         if gender is not None:
             pi_subject.gender_code = gender.redefined_value
         else:
@@ -225,15 +225,15 @@ def generate_random_person(
             )
 
         person = Person()
-        person.set_title(self.generate_random_title(gender))
-        person.set_forename(random_words_list.get("forename", ""))
-        person.set_surname(random_words_list.get("surname", ""))
-        person.set_gender(gender)
+        person.title = self.generate_random_title(gender)
+        person.forename = random_words_list.get("forename", "")
+        person.surname = random_words_list.get("surname", "")
+        person.gender = gender
 
         if self.rand.randint(0, 100) < 5:
-            person.set_other_forenames(random_words_list.get("forename2", ""))
+            person.other_forenames = random_words_list.get("forename2", "")
         if self.rand.randint(0, 100) < 5:
-            person.set_previous_surname(random_words_list.get("surname2", ""))
+            person.previous_surname = random_words_list.get("surname2", "")
 
         logging.debug("generateRandomPerson: end")
         return person
diff --git a/classes/lynch/genetic_condition_type.py b/classes/lynch/genetic_condition_type.py
@@ -0,0 +1,51 @@
+from enum import Enum
+from typing import Optional
+
+
+class GeneticConditionType(Enum):
+    """
+    Enum representing genetic condition types with valid value ID, description, and lower age.
+    Provides lookup by description and valid value ID.
+    """
+
+    EPCAM = (307070, "EPCAM", 25)
+    MLH1 = (306443, "MLH1", 25)
+    MSH2 = (306444, "MSH2", 25)
+    MSH6 = (306445, "MSH6", 35)
+    PMS2 = (306446, "PMS2", 35)
+
+    def __init__(self, valid_value_id: int, description: str, lower_age: int):
+        self._valid_value_id = valid_value_id
+        self._description = description
+        self._lower_age = lower_age
+
+    @property
+    def valid_value_id(self) -> int:
+        """Return the valid value ID."""
+        return self._valid_value_id
+
+    @property
+    def description(self) -> str:
+        """Return the description."""
+        return self._description
+
+    @property
+    def lower_age(self) -> int:
+        """Return the lower age."""
+        return self._lower_age
+
+    @classmethod
+    def by_description(cls, description: str) -> Optional["GeneticConditionType"]:
+        """Return the GeneticConditionType instance for the given description."""
+        for member in cls:
+            if member.description == description:
+                return member
+        return None
+
+    @classmethod
+    def by_valid_value_id(cls, valid_value_id: int) -> Optional["GeneticConditionType"]:
+        """Return the GeneticConditionType instance for the given valid value ID."""
+        for member in cls:
+            if member.valid_value_id == valid_value_id:
+                return member
+        return None
diff --git a/classes/person/person_data.py b/classes/person/person_data.py
@@ -0,0 +1,30 @@
+from dataclasses import dataclass
+from typing import Optional
+from classes.subject.gender_type import GenderType
+
+
+@dataclass
+class Person:
+    """
+    Represents a person with name, title, previous surname, other forenames, and gender.
+    Provides methods to get full name and string representation.
+    """
+
+    surname: Optional[str] = None
+    forename: Optional[str] = None
+    title: Optional[str] = None
+    other_forenames: Optional[str] = None
+    previous_surname: Optional[str] = None
+    gender: Optional[GenderType] = None
+
+    def get_full_name(self) -> str:
+        """
+        Returns the full name of the person.
+        """
+        return f"{self.title or ''} {self.forename or ''} {self.surname or ''}".strip()
+
+    def __str__(self) -> str:
+        """
+        Returns a string representation of the person.
+        """
+        return f"{self.title or ''} {self.forename or ''} {self.surname or ''} (gender={self.gender})".strip()
diff --git a/classes/repositories/general_repository.py b/classes/repositories/general_repository.py
@@ -55,3 +55,15 @@ def run_database_transition(
             raise oracledb.DatabaseError(f"Error executing database transition: {e}")
         finally:
             self.oracle_db.disconnect_from_db(conn)
+
+    def process_new_lynch_patients(self):
+        logging.debug("[START] process_new_lynch_patients")
+        try:
+            self.oracle_db.execute_stored_procedure("pkg_lynch.p_process_patients")
+        except Exception as e:
+            logging.error("Error executing pkg_lynch.p_process_patients", exc_info=True)
+            raise oracledb.DatabaseError(
+                f"Error executing pkg_lynch.p_process_patients: {e}"
+            )
+
+        logging.debug("[END] process_new_lynch_patients")
diff --git a/tests/test_lynch_self_referral_seeking_further_data_flow.py b/tests/test_lynch_self_referral_seeking_further_data_flow.py
@@ -1,6 +1,7 @@
 import pytest
 import logging
 from playwright.sync_api import Page
+from streamlit import user
 from classes.user.user import User
 from classes.subject.subject import Subject
 from pages.logout.log_out_page import LogoutPage
@@ -11,6 +12,7 @@
 from utils.subject_assertion import subject_assertion
 from utils import screening_subject_page_searcher
 from utils.oracle.subject_selection_query_builder import SubjectSelectionQueryBuilder
+from utils.lynch_utils import insert_validated_lynch_patient_from_new_subject_with_age
 
 
 @pytest.mark.wip
@@ -49,17 +51,14 @@ def debug_log_subject_db_row(nhs_no):
 
     # Given I log in to BCSS "England" as user role "Hub Manager"
     login_role = "Hub Manager at BCS01"
-    UserTools.user_login(page, login_role)
-
-    # Retrieve user details and user object
-    user_details = UserTools.retrieve_user(login_role)
-
+    user_role = UserTools.user_login(page, login_role, True)
+    if user_role is None:
+        raise ValueError(f"User role '{login_role}' could not be determined after login.")
+    
     # When I receive Lynch diagnosis "EPCAM" for a new subject in my hub aged "75" with diagnosis date "3 years ago" and last colonoscopy date "2 years ago"
-    # TODO: What is involved in receiving an "EPCAM" diagnosis? Is it covered by this code?
     # Get or create a subject suitable for Lynch self-referral
-    nhs_no = SubjectSelector.get_or_create_subject_for_lynch_self_referral(
-        screening_centre=user_details["hub_code"],
-        base_age=75,
+    nhs_no = insert_validated_lynch_patient_from_new_subject_with_age(
+        "75", "EPCAM", "3 years ago", "2 years ago", user_role
     )
 
     OracleDB().exec_bcss_timed_events(nhs_number=nhs_no)
@@ -82,14 +81,14 @@ def debug_log_subject_db_row(nhs_no):
 
     # Then my subject has been updated as follows:
     self_referral_criteria = {
-        # "calculated fobt due date": "Null",
-        # "calculated lynch due date": "Today",
+        "calculated fobt due date": "Null",
+        "calculated lynch due date": "Today",
         # "calculated surveillance due date": "Null",
         # "lynch due date": "Today",
         # "lynch due date date of change": "Null",
         # "lynch due date reason": "Self-referral",
         # "previous screening status": "Lynch Surveillance",
-        "screening due date": "Null",
+        # "screening due date": "Null",
         # "screening due date date of change": "Null",
         # "screening due date reason": "null",
         # "screening status": "Lynch Self-referral",
@@ -109,66 +108,66 @@ def debug_log_subject_db_row(nhs_no):
         "[ASSERTION PASSED] Subject details after self-referral are as expected"
     )
 
-    # When I view the subject
-    screening_subject_page_searcher.navigate_to_subject_summary_page(page, nhs_no)
-
-    # And I set the subject to Seeking Further Data
-    subject_page.set_seeking_further_data()
-
-    # Then my subject has been updated as follows:
-    seeking_further_data_criteria = {
-        "calculated fobt due date": "Null",
-        "calculated lynch due date": "today",
-        "calculated surveillance due date": "Null",
-        "lynch due date": "today",
-        "lynch due date date of change": "Null",
-        "lynch due date reason": "Self-referral",
-        "previous screening status": "Lynch Self-referral",
-        "screening due date": "Null",
-        "screening due date date of change": "Null",
-        "screening due date reason": "Null",
-        "subject has lynch diagnosis": "Yes",
-        "subject lower fobt age": "Default",
-        "subject lower lynch age": "25",
-        "screening status": "Seeking Further Data",
-        "screening status date of change": "Today",
-        "screening status reason": "Uncertified Death",
-        "surveillance due date": "Null",
-        "surveillance due date date of change": "Null",
-        "surveillance due date reason": "Null",
-    }
-    debug_log_subject_db_row(nhs_no)  # For debug purposes - can be removed later
-
-    subject_assertion(nhs_no, seeking_further_data_criteria)
-
-    # When I set the subject from Seeking Further Data back to "Lynch Self-referral"
-    subject_page.set_self_referral_screening_status()
-
-    # Then my subject has been updated as follows:
-    reverted_criteria = {
-        "calculated fobt due date": "Null",
-        "calculated lynch due date": "today",
-        "calculated surveillance due date": "Null",
-        "lynch due date": "today",
-        "lynch due date date of change": "Null",
-        "lynch due date reason": "Self-referral",
-        "previous screening status": "Lynch Self-referral",
-        "screening due date": "Null",
-        "screening due date date of change": "Null",
-        "screening due date reason": "Null",
-        "subject has lynch diagnosis": "Yes",
-        "subject lower fobt age": "Default",
-        "subject lower lynch age": "25",
-        "screening status": "Lynch Self-referral",
-        "screening status date of change": "Today",
-        "screening status reason": "Reset seeking further data to Lynch Self-referral",
-        "surveillance due date": "Null",
-        "surveillance due date date of change": "Null",
-        "surveillance due date reason": "Null",
-    }
-    debug_log_subject_db_row(nhs_no)  # For debug purposes - can be removed later
-
-    subject_assertion(nhs_no, reverted_criteria)
-
-    LogoutPage(page).log_out()
-    logging.info("[TEST END] test_lynch_self_referral_seeking_further_data_flow")
+    # # When I view the subject
+    # screening_subject_page_searcher.navigate_to_subject_summary_page(page, nhs_no)
+
+    # # And I set the subject to Seeking Further Data
+    # subject_page.set_seeking_further_data()
+
+    # # Then my subject has been updated as follows:
+    # seeking_further_data_criteria = {
+    #     "calculated fobt due date": "Null",
+    #     "calculated lynch due date": "today",
+    #     "calculated surveillance due date": "Null",
+    #     "lynch due date": "today",
+    #     "lynch due date date of change": "Null",
+    #     "lynch due date reason": "Self-referral",
+    #     "previous screening status": "Lynch Self-referral",
+    #     "screening due date": "Null",
+    #     "screening due date date of change": "Null",
+    #     "screening due date reason": "Null",
+    #     "subject has lynch diagnosis": "Yes",
+    #     "subject lower fobt age": "Default",
+    #     "subject lower lynch age": "25",
+    #     "screening status": "Seeking Further Data",
+    #     "screening status date of change": "Today",
+    #     "screening status reason": "Uncertified Death",
+    #     "surveillance due date": "Null",
+    #     "surveillance due date date of change": "Null",
+    #     "surveillance due date reason": "Null",
+    # }
+    # debug_log_subject_db_row(nhs_no)  # For debug purposes - can be removed later
+
+    # subject_assertion(nhs_no, seeking_further_data_criteria)
+
+    # # When I set the subject from Seeking Further Data back to "Lynch Self-referral"
+    # subject_page.set_self_referral_screening_status()
+
+    # # Then my subject has been updated as follows:
+    # reverted_criteria = {
+    #     "calculated fobt due date": "Null",
+    #     "calculated lynch due date": "today",
+    #     "calculated surveillance due date": "Null",
+    #     "lynch due date": "today",
+    #     "lynch due date date of change": "Null",
+    #     "lynch due date reason": "Self-referral",
+    #     "previous screening status": "Lynch Self-referral",
+    #     "screening due date": "Null",
+    #     "screening due date date of change": "Null",
+    #     "screening due date reason": "Null",
+    #     "subject has lynch diagnosis": "Yes",
+    #     "subject lower fobt age": "Default",
+    #     "subject lower lynch age": "25",
+    #     "screening status": "Lynch Self-referral",
+    #     "screening status date of change": "Today",
+    #     "screening status reason": "Reset seeking further data to Lynch Self-referral",
+    #     "surveillance due date": "Null",
+    #     "surveillance due date date of change": "Null",
+    #     "surveillance due date reason": "Null",
+    # }
+    # debug_log_subject_db_row(nhs_no)  # For debug purposes - can be removed later
+
+    # subject_assertion(nhs_no, reverted_criteria)
+
+    # LogoutPage(page).log_out()
+    # logging.info("[TEST END] test_lynch_self_referral_seeking_further_data_flow")
diff --git a/utils/lynch_utils.py b/utils/lynch_utils.py
diff --git a/utils/oracle/subject_selection_query_builder.py b/utils/oracle/subject_selection_query_builder.py
