Make it clear when study already exported

pixl_dcmd/src/pixl_dcmd/_database.py

@@ -21,9 +21,10 @@
 from sqlalchemy.orm.session import Session
 
 from core.db.models import Image, Extract
-from sqlalchemy import URL, create_engine, exists
+from sqlalchemy import ColumnElement, URL, create_engine, exists
 from sqlalchemy.orm import sessionmaker, exc
 
+from core.exceptions import PixlDiscardError
 from pixl_dcmd.dicom_helpers import StudyInfo
 
 url = URL.create(
@@ -126,29 +127,33 @@ def get_unexported_image(
     Get an existing, non-exported (for this project) image record from the database
     identified by the study UID. If no result is found, retry with querying on
     MRN + accession number. If this fails as well, raise a NoResultFound.
+    If study has already been exported, raise a PixlDiscardError.
     """
     try:
-        existing_image: Image = (
-            pixl_session.query(Image)
-            .join(Extract)
-            .filter(
-                Extract.slug == project_slug,
-                Image.study_uid == study_info.study_uid,
-                Image.exported_at == None,  # noqa: E711
-            )
-            .one()
+        existing_image = _query_and_raise_if_exported(
+            pixl_session,
+            [Extract.slug == project_slug, Image.study_uid == study_info.study_uid],
         )
     # If no image is found by study UID, try MRN + accession number
     except exc.NoResultFound:
-        existing_image = (
-            pixl_session.query(Image)
-            .join(Extract)
-            .filter(
+        existing_image = _query_and_raise_if_exported(
+            pixl_session,
+            [
                 Extract.slug == project_slug,
                 Image.mrn == study_info.mrn,
                 Image.accession_number == study_info.accession_number,
-                Image.exported_at == None,  # noqa: E711
-            )
-            .one()
+            ],
         )
     return existing_image
+
+
+def _query_and_raise_if_exported(
+    pixl_session: Session, clause_list: list[ColumnElement[bool]]
+) -> Image:
+    existing_image: Image = (
+        pixl_session.query(Image).join(Extract).filter(*clause_list).one()
+    )
+    if existing_image.exported_at is not None:
+        msg = "Study already exported"
+        raise PixlDiscardError(msg)
+    return existing_image

pixl_dcmd/tests/test_database.py

@@ -14,9 +14,13 @@
 from __future__ import annotations
 
 import datetime
+from dataclasses import dataclass
 
 import pytest
+import sqlalchemy
+
 from core.db.models import Extract, Image
+from core.exceptions import PixlDiscardError
 from pixl_dcmd._database import (
     get_unexported_image,
     get_uniq_pseudo_study_uid_and_update_db,
@@ -26,13 +30,81 @@
 from sqlalchemy.orm import Session
 
 STUDY_DATE = datetime.date.fromisoformat("2023-01-01")
+
+
+@dataclass
+class StudyData:
+    """Database setup of study data."""
+
+    mrn: str
+    accession_number: str
+    study_uid: str | None
+    study_date: datetime.date | sqlalchemy.Date = STUDY_DATE
+    pseudo_patient_id: str | None = None
+    pseudo_study_uid: str | None = None
+    exported_at: datetime.datetime | sqlalchemy.DateTime | None = None
+
+
+@dataclass
+class TestData:
+    """All test data, separated so that the input values can be overriden and different to db data."""
+
+    db: StudyData
+    input: StudyInfo
+
+
+def _create_test_data(study_data: StudyData) -> TestData:
+    return TestData(
+        study_data,
+        StudyInfo(
+            mrn=study_data.mrn,
+            accession_number=study_data.accession_number,
+            study_uid=study_data.study_uid,
+        ),
+    )
+
+
 TEST_PROJECT_SLUG = "test-extract-uclh-omop-cdm"
-TEST_STUDY_INFO = StudyInfo(
-    mrn="123456", accession_number="abcde", study_uid="1.2.3.4.5"
+UNPROCESSED_STUDY = _create_test_data(
+    StudyData(mrn="123456", accession_number="abcde", study_uid="1.2.3.4.5")
 )
-TEST_STUDY_INFO_WITH_PSEUDO_PATIENT_ID = StudyInfo(
-    mrn="234567", accession_number="bcdef", study_uid="2.3.4.5.6"
+PSEUDO_IDS_STUDY = _create_test_data(
+    StudyData(
+        mrn="234567",
+        accession_number="bcdef",
+        study_uid="2.3.4.5.6",
+        pseudo_patient_id="garbled",
+        pseudo_study_uid="0.0.0.0.0.0",
+    )
+)
+
+EXPORTED_STUDY = _create_test_data(
+    StudyData(
+        mrn="exported_mrn",
+        accession_number="exported_accession",
+        study_uid="6.6.6",
+        pseudo_study_uid="1.1.1",
+        exported_at=datetime.datetime.fromisoformat("2024-01-01"),
+    )
+)
+
+# For duplicates, the database should have no UIDs
+DUPLICATE_ACCESSION_BUT_HAS_UID = _create_test_data(
+    StudyData(
+        mrn="duplicate_mrn",
+        accession_number="duplicate_accession",
+        study_uid="7.7.7",
+    )
+)
+
+DUPLICATE_ACCESSION_NO_UID = _create_test_data(
+    StudyData(
+        mrn="duplicate_mrn",
+        accession_number="duplicate_accession",
+        study_uid="8.8.8",
+    )
 )
+DUPLICATE_ACCESSION_NO_UID.db.study_uid = None
 
 
 @pytest.fixture()
@@ -42,46 +114,45 @@ def rows_for_database_testing(db_session) -> Session:
     pytest_pixl.dicom.generate_dicom_dataset.
     """
     extract = Extract(slug=TEST_PROJECT_SLUG)
-
-    existing_image = Image(
-        mrn=TEST_STUDY_INFO.mrn,
-        accession_number=TEST_STUDY_INFO.accession_number,
-        study_uid=TEST_STUDY_INFO.study_uid,
-        study_date=STUDY_DATE,
-        extract=extract,
-    )
-
-    existing_image_with_pseudo_study_uid = Image(
-        mrn=TEST_STUDY_INFO_WITH_PSEUDO_PATIENT_ID.mrn,
-        accession_number=TEST_STUDY_INFO_WITH_PSEUDO_PATIENT_ID.accession_number,
-        study_uid=TEST_STUDY_INFO_WITH_PSEUDO_PATIENT_ID.study_uid,
-        study_date=STUDY_DATE,
-        extract=extract,
-        # This should be a valid VR UI value!
-        # https://dicom.nema.org/medical/dicom/current/output/html/part05.html#table_6.2-1
-        pseudo_study_uid="0.0.0.0.0.0",
-        pseudo_patient_id=TEST_STUDY_INFO_WITH_PSEUDO_PATIENT_ID.mrn,
-    )
-
     with db_session:
         db_session.add_all(
-            [extract, existing_image, existing_image_with_pseudo_study_uid]
+            [
+                extract,
+                _image_from_study_data(UNPROCESSED_STUDY.db, extract),
+                _image_from_study_data(PSEUDO_IDS_STUDY.db, extract),
+                _image_from_study_data(EXPORTED_STUDY.db, extract),
+                _image_from_study_data(DUPLICATE_ACCESSION_BUT_HAS_UID.db, extract),
+                _image_from_study_data(DUPLICATE_ACCESSION_NO_UID.db, extract),
+            ]
         )
         db_session.commit()
 
     return db_session
 
 
+def _image_from_study_data(study_data: StudyData, extract: Extract) -> Image:
+    return Image(
+        mrn=study_data.mrn,
+        accession_number=study_data.accession_number,
+        study_uid=study_data.study_uid,
+        study_date=study_data.study_date,
+        pseudo_study_uid=study_data.pseudo_study_uid,
+        pseudo_patient_id=study_data.pseudo_patient_id,
+        exported_at=study_data.exported_at,
+        extract=extract,
+    )
+
+
 def test_get_uniq_pseudo_study_uid_and_update_db(rows_for_database_testing, db_session):
     """
     GIVEN an existing image that already has a pseudo_study_uid
     WHEN we query the database for that image
     THEN the function should return the existing pseudo_study_uid.
     """
     pseudo_study_uid = get_uniq_pseudo_study_uid_and_update_db(
-        TEST_PROJECT_SLUG, TEST_STUDY_INFO_WITH_PSEUDO_PATIENT_ID
+        TEST_PROJECT_SLUG, PSEUDO_IDS_STUDY.input
     )
-    assert pseudo_study_uid == "0.0.0.0.0.0"
+    assert pseudo_study_uid == PSEUDO_IDS_STUDY.db.pseudo_study_uid
 
 
 def test_get_pseudo_patient_id_and_update_db(rows_for_database_testing, db_session):
@@ -92,13 +163,11 @@ def test_get_pseudo_patient_id_and_update_db(rows_for_database_testing, db_sessi
     """
     get_pseudo_patient_id_and_update_db(
         TEST_PROJECT_SLUG,
-        TEST_STUDY_INFO_WITH_PSEUDO_PATIENT_ID,
-        TEST_STUDY_INFO_WITH_PSEUDO_PATIENT_ID.mrn,
-    )
-    result = get_unexported_image(
-        TEST_PROJECT_SLUG, TEST_STUDY_INFO_WITH_PSEUDO_PATIENT_ID, db_session
+        PSEUDO_IDS_STUDY.input,
+        PSEUDO_IDS_STUDY.input.mrn,
     )
-    assert result.pseudo_patient_id == TEST_STUDY_INFO_WITH_PSEUDO_PATIENT_ID.mrn
+    result = get_unexported_image(TEST_PROJECT_SLUG, PSEUDO_IDS_STUDY.input, db_session)
+    assert result.pseudo_patient_id == PSEUDO_IDS_STUDY.db.pseudo_patient_id
 
 
 def test_get_unexported_image_fallback(rows_for_database_testing, db_session):
@@ -113,4 +182,27 @@ def test_get_unexported_image_fallback(rows_for_database_testing, db_session):
         study_uid="nope",
     )
     result = get_unexported_image(TEST_PROJECT_SLUG, wrong_uid_info, db_session)
-    assert result.study_uid == TEST_STUDY_INFO.study_uid
+    assert result.study_uid == UNPROCESSED_STUDY.input.study_uid
+
+
+def test_exported_image_throws(rows_for_database_testing, db_session):
+    """
+    GIVEN a database entry with the image exported
+    WHEN we query for the image
+    THEN a NoRowFound exception should be thrown
+    """
+    with pytest.raises(PixlDiscardError) as exception:
+        get_unexported_image(TEST_PROJECT_SLUG, EXPORTED_STUDY.input, db_session)
+    assert str(exception.value) == "Study already exported"
+
+
+def test_duplicate_image_throws(rows_for_database_testing, db_session):
+    """
+    GIVEN the database has two entries for the same accession number, one with a study uid
+    WHEN the input without the study uid is processed
+    THEN a MultipleResultsFound exception should be thrown
+    """
+    with pytest.raises(sqlalchemy.exc.MultipleResultsFound):
+        get_unexported_image(
+            TEST_PROJECT_SLUG, DUPLICATE_ACCESSION_NO_UID.input, db_session
+        )

pixl_dcmd/tests/test_main.py

@@ -23,14 +23,14 @@
 import numpy as np
 import pydicom
 import pytest
-import sqlalchemy
 from pytest_check import check
 from core.db.models import Image
 from core.dicom_tags import (
     PrivateDicomTag,
     add_private_tag,
     create_private_tag,
 )
+from core.exceptions import PixlDiscardError
 from core.project_config import load_project_config, load_tag_operations
 from core.project_config.pixl_config_model import load_config_and_validate
 from decouple import config
@@ -251,7 +251,7 @@ def test_image_already_exported_throws(test_project_config, exported_dicom_datas
     WHEN the dicom tag scheme is applied
     THEN an exception will be thrown as
     """
-    with pytest.raises(sqlalchemy.exc.NoResultFound):
+    with pytest.raises(PixlDiscardError):
         anonymise_dicom_and_update_db(
             exported_dicom_dataset,
             config=test_project_config,