Merge branch 'main' into feature/BCSS-21765-repo-documentation

Author: adrianoaru-nhs

classes/date/date_description_utils.py

@@ -1,4 +1,5 @@
 from datetime import datetime, timedelta, date
+from dateutil.relativedelta import relativedelta
 from typing import Optional
 import logging
 from classes.date.date_description import DateDescription
@@ -235,12 +236,129 @@ def is_valid_date(date_str: str, date_format: str) -> bool:
     @staticmethod
     def oracle_to_date_function(date_str: str, oracle_format: str) -> str:
         """
-        Constructs an Oracle TO_DATE function to convert a string to a date.
-        This method formats the date string according to the specified format.
+        Constructs a safe Oracle TO_DATE() expression from a Python date string.
         Args:
-            date_str (str): The date string to be converted.
-            oracle_format (str): The format in which the date string is provided.
+            date_str (str): The date string to be converted (e.g., '06/10/1950').
+            oracle_format (str): The Oracle format mask (e.g., 'dd/mm/yyyy').
         Returns:
-            str: The SQL expression for the Oracle TO_DATE function.
+            str: The SQL-safe TO_DATE(...) expression, or 'NULL' if date_str is None/empty.
         """
-        return f" TO_DATE( '{date_str}', '{oracle_format}') "
+        if not date_str or str(date_str).strip().lower() == "none":
+            return "NULL"
+
+        clean = str(date_str).strip().replace("\u00a0", "")
+        py_fmt = (
+            oracle_format.lower()
+            .replace("dd", "%d")
+            .replace("mm", "%m")
+            .replace("yyyy", "%Y")
+        )
+
+        # Validate in Python before sending to Oracle
+        datetime.strptime(clean, py_fmt)
+
+        return f"TO_DATE('{clean}', '{oracle_format}')"
+
+    @staticmethod
+    def convert_description_to_python_date(
+        which_date: str, date_description: str
+    ) -> Optional[date]:
+        """
+        Converts a date description (e.g. '2 years ago', '15/08/2020', 'NULL')
+        into a Python datetime.date object or None.
+        Args:
+            which_date (str): Label for logging.
+            date_description (str): Human-readable or exact date description.
+        Returns:
+            Optional[date]: The corresponding date object, or None if not applicable.
+        """
+        logging.debug(
+            f"convert_description_to_python_date: {which_date}, {date_description}"
+        )
+
+        if not date_description or date_description.strip().upper() in (
+            DateDescriptionUtils.NULL_STRING,
+            "NONE",
+        ):
+            return None
+
+        date_description = date_description.strip()
+        today = datetime.today().date()
+
+        # Try direct date formats
+        abs_date = _parse_absolute_date(date_description)
+        if abs_date:
+            return abs_date
+
+        # Try relative phrases like "3 years ago"
+        rel_date = _parse_relative_date(date_description, today)
+        if rel_date:
+            return rel_date
+
+        # Try enum-based descriptions
+        enum_date = _parse_enum_date(date_description, today)
+        if enum_date is not None:
+            return enum_date
+
+        return None
+
+
+def _parse_absolute_date(date_description: str) -> Optional[date]:
+    """
+    Tries to parse an absolute date from the description.
+    Args:
+        date_description (str): The date description to parse.
+    Returns:
+        Optional[date]: The parsed absolute date or None if parsing failed.
+    """
+    for fmt in (
+        DateDescriptionUtils.DATE_FORMAT_DD_MM_YYYY,
+        DateDescriptionUtils.DATE_FORMAT_YYYY_MM_DD,
+    ):
+        if DateDescriptionUtils.is_valid_date(date_description, fmt):
+            return datetime.strptime(date_description, fmt).date()
+    return None
+
+
+def _parse_relative_date(date_description: str, today: date) -> Optional[date]:
+    """
+    Tries to parse a relative date from the description (e.g., "3 years ago").
+    Args:
+        date_description (str): The date description to parse.
+        today (date): The reference date for relative calculations.
+    Returns:
+        Optional[date]: The parsed relative date or None if parsing failed.
+    """
+    words = date_description.split(" ")
+    if date_description.endswith(" ago") and len(words) == 3:
+        try:
+            number = int(words[0])
+            unit = words[1]
+            if "year" in unit:
+                return today - relativedelta(years=number)
+            if "month" in unit:
+                return today - relativedelta(months=number)
+            if "day" in unit:
+                return today - timedelta(days=number)
+        except Exception as e:
+            logging.warning(f"Could not parse relative date '{date_description}': {e}")
+    return None
+
+
+def _parse_enum_date(date_description: str, today: date) -> Optional[date]:
+    """
+    Tries to parse a date from the DateDescription enum.
+    Args:
+        date_description (str): The date description to parse.
+        today (date): The reference date for special cases.
+    Returns:
+        Optional[date]: The parsed enum date or None if parsing failed.
+    """
+    enum_val = DateDescription.by_description_case_insensitive(date_description)
+    if enum_val is not None:
+        if enum_val.name == DateDescriptionUtils.NULL_STRING:
+            return None
+        if enum_val.name == DateDescriptionUtils.NOT_NULL_STRING_UNDERSCORE:
+            return today
+        return enum_val.suitable_date
+    return None

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

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")

pages/screening_subject_search/subject_screening_summary_page.py

@@ -1,7 +1,7 @@
 import re
 from playwright.sync_api import Page, expect, Locator
 from pages.base_page import BasePage
-from enum import Enum
+from enum import StrEnum
 import logging
 import pytest
 from typing import List
@@ -39,8 +39,10 @@ def __init__(self, page: Page):
         )
         self.patient_contacts = self.page.get_by_role("link", name="Patient Contacts")
         self.more = self.page.get_by_role("link", name="more")
-        self.change_screening_status = self.page.get_by_label("Change Screening Status")
-        self.reason = self.page.get_by_label("Reason", exact=True)
+        self.change_screening_status_dropdown = self.page.get_by_label(
+            "Change Screening Status"
+        )
+        self.reason_dropdown = self.page.get_by_label("Reason", exact=True)
         self.update_subject_data = self.page.get_by_role(
             "button", name="Update Subject Data"
         )
@@ -89,6 +91,9 @@ def __init__(self, page: Page):
         self.reopen_for_correction_button = self.page.get_by_role(
             "button", name="Reopen episode for correction"
         )
+        self.self_refer_lynch_surveillance_button = self.page.get_by_role(
+            "button", name="Self-refer Lynch Surveillance"
+        )
 
     def wait_for_page_title(self) -> None:
         """Waits for the page to be the Subject Screening Summary"""
@@ -188,7 +193,7 @@ def click_more(self) -> None:
 
     def click_update_subject_data(self) -> None:
         """Click on the 'Update Subject Data' button."""
-        self.click(self.update_subject_data)
+        self.safe_accept_dialog(self.update_subject_data)
 
     def click_close_fobt_screening_episode(self) -> None:
         """Click on the 'Close FOBT Screening Episode' button."""
@@ -204,11 +209,11 @@ def go_to_a_page_to_close_the_episode(self) -> None:
 
     def select_change_screening_status(self, option: str) -> None:
         """Select the given 'change screening status' option."""
-        self.change_screening_status.select_option(option)
+        self.change_screening_status_dropdown.select_option(option)
 
     def select_reason(self, option: str) -> None:
         """Select the given 'reason' option."""
-        self.reason.select_option(option)
+        self.reason_dropdown.select_option(option)
 
     def expand_episodes_list(self) -> None:
         """Click on the episodes list expander icon."""
@@ -422,14 +427,35 @@ def reopen_fobt_screening_episode(self) -> None:
         # Step 2: Safely accept the confirmation dialog triggered by the correction button
         self.safe_accept_dialog(self.reopen_for_correction_button)
 
+    def click_self_refer_lynch_surveillance_button(self) -> None:
+        """Click on the 'Self-refer Lynch Surveillance' button"""
+        self.safe_accept_dialog(self.self_refer_lynch_surveillance_button)
+        self.page.wait_for_timeout(1000)
+
+    def change_screening_status(self, status_option: str, reason_option: str) -> None:
+        """
+        Change the screening status of the subject by selecting the given status and reason options,
+        then clicking the 'Update Subject Data' button.
+
+        Args:
+            status_option (str): The option value to select for the screening status.
+            reason_option (str): The option value to select for the reason.
+        """
+        self.select_change_screening_status(status_option)
+        self.select_reason(reason_option)
+        self.click_update_subject_data()
+        self.page.wait_for_timeout(1000)
+
 
-class ChangeScreeningStatusOptions(Enum):
+class ChangeScreeningStatusOptions(StrEnum):
     """Enum for Change Screening Status options."""
 
     SEEKING_FURTHER_DATA = "4007"
+    LYNCH_SELF_REFERRAL = "307129"
 
 
-class ReasonOptions(Enum):
+class ReasonOptions(StrEnum):
     """Enum for Reason options."""
 
     UNCERTIFIED_DEATH = "11314"
+    RESET_SEEKING_FURTHER_DATA_TO_LYNCH_SELF_REFERRAL = "307135"

pytest.ini

@@ -55,3 +55,4 @@ markers =
     spine_retrieval_search_tests: tests that are part of subject spine retrieval demographics
     hub_user_tests: tests that are part of the hub user test suite
     fobt_regression_tests: tests that are part of the fobt regression test suite
+    lynch_self_referral_tests: tests that are part of the lynch self referral test suite