Improves core tests

Author: sjoerdk

dicomtrolley/core.py

@@ -58,10 +58,10 @@ def download_study(self, study_instance_uid, output_dir):
             )
         )
         storage = DICOMStorageDir(output_dir)
-        for dataset in self.get_all_datasets(mint_objects=[study]):
+        for dataset in self.fetch_all_datasets(mint_objects=[study]):
             storage.save(dataset)
 
-    def get_all_datasets(self, mint_objects: List[MintObject]):
+    def fetch_all_datasets(self, mint_objects: List[MintObject]):
         """Get full DICOM dataset for each instance in study. Calls mint and wado
 
         Parameters
@@ -115,6 +115,7 @@ def __str__(self):
 
     def save(self, dataset):
         """Write dataset. Creates sub-folders if needed"""
+
         slice_path = Path(self.path) / self.generate_path(dataset)
         slice_path.parent.mkdir(parents=True, exist_ok=True)
         dataset.save_as(slice_path)

dicomtrolley/https.py

@@ -43,7 +43,11 @@ def get_session(self, user, password, realm):
         session = requests.Session()
         response = session.post(
             self.url,
-            headers={"X-Userid": user, "X-Password": password, "X-Realm": realm},
+            headers={
+                "X-Userid": user,
+                "X-Password": password,
+                "X-Realm": realm,
+            },
         )
         if response.status_code == 401:
             raise DICOMTrolleyException(

dicomtrolley/mint.py

@@ -30,7 +30,7 @@ def __repr__(self):
         return self.uid
 
     def all_instances(self):
-        pass
+        raise NotImplementedError()
 
 
 class MintInstance(MintObject):

tests/conftest.py

@@ -1,13 +1,15 @@
 import pytest
 import requests
 
-from dicomtrolley.mint import MintStudy, parse_mint_studies_response
+from dicomtrolley.mint import Mint, MintStudy, parse_mint_studies_response
+from dicomtrolley.wado import Wado
 from tests.mockresponses import (
     LOGIN_DENIED,
     LOGIN_SUCCESS,
     MINT_SEARCH_INSTANCE_LEVEL,
     MINT_SEARCH_SERIES_LEVEL,
     MINT_SEARCH_STUDY_LEVEL,
+    MockUrls,
 )
 
 
@@ -40,6 +42,16 @@ def mock_mint_responses(requests_mock):
         set_mock_response(requests_mock, mock)
 
 
+@pytest.fixture
+def a_mint(a_session):
+    return Mint(session=a_session, url=MockUrls.MINT_URL)
+
+
+@pytest.fixture
+def a_wado(a_session):
+    return Wado(session=a_session, url=MockUrls.WADO_URL)
+
+
 @pytest.fixture
 def a_study_with_instances() -> MintStudy:
     """An example MintStudy object"""
@@ -54,6 +66,11 @@ def a_study_without_instances() -> MintStudy:
     return studies[0]
 
 
+@pytest.fixture
+def some_studies(a_study_with_instances, a_study_without_instances):
+    return [a_study_with_instances, a_study_with_instances]
+
+
 def set_mock_response(requests_mock, response):
     """Register the given MockResponse with requests_mock"""
     requests_mock.register_uri(**response.as_dict())

tests/factories.py

@@ -22,6 +22,8 @@ def quick_dataset(*_, **kwargs) -> Dataset:
 
     """
     dataset = Dataset()
+    dataset.is_little_endian = True  # required common meta header choice
+    dataset.is_implicit_VR = False  # required common meta header choice
     for tag_name, value in kwargs.items():
         Tag(tag_name)  # assert valid dicom keyword. pydicom will not do this.
         dataset.__setattr__(tag_name, value)

tests/test_core.py

@@ -1,11 +1,19 @@
 from pathlib import Path
+from unittest.mock import Mock
 
 import pytest
 
-from dicomtrolley.core import DICOMStorageDir
+from dicomtrolley.core import DICOMStorageDir, Trolley
+from dicomtrolley.query import Query
 from tests.factories import quick_dataset
 
 
+@pytest.fixture
+def a_trolley(a_mint, a_wado) -> Trolley:
+    """Trolley instance that will not hit any server"""
+    return Trolley(mint=a_mint, wado=a_wado)
+
+
 @pytest.mark.parametrize(
     "dataset, expected_path",
     [
@@ -22,6 +30,50 @@
         (quick_dataset(), "/tmp/unknown/unknown/unknown"),
     ],
 )
-def test_storage_dir(dataset, expected_path):
+def test_storage_dir_generate_path(dataset, expected_path):
     storage = DICOMStorageDir("/tmp")
     assert storage.generate_path(dataset) == Path("/tmp") / expected_path
+
+
+def test_storage_dir_write(tmpdir):
+    """Make sure writing to disk works. Seems slight overkill. But coverage."""
+    expected_path = Path(str(tmpdir)) / "unknown/unknown/unknown"
+    assert not expected_path.exists()
+    DICOMStorageDir(str(tmpdir)).save(quick_dataset())
+    assert expected_path.exists()
+
+
+def test_trolley_find(a_trolley, some_studies):
+    a_trolley.mint.find_studies = Mock(return_value=some_studies)
+    assert a_trolley.find_studies(query=Query()) == some_studies
+
+
+def test_trolley_download_study(a_trolley, some_studies, tmpdir):
+    a_trolley.mint.find_studies = Mock(return_value=some_studies[:1])
+    a_trolley.wado.get_dataset = Mock(
+        return_value=quick_dataset(
+            StudyInstanceUID="foo",
+            SeriesInstanceUID="baz",
+            SOPInstanceUID="bimini",
+        )
+    )
+
+    expected_path = Path(str(tmpdir)) / "foo/baz/bimini"
+    assert not expected_path.exists()
+    a_trolley.download_study(study_instance_uid="1", output_dir=tmpdir)
+    assert expected_path.exists()
+
+
+def test_trolley_get_dataset(a_trolley, some_studies, tmpdir):
+    a_trolley.mint.find_studies = Mock(return_value=some_studies)
+    a_trolley.wado.get_dataset = Mock(
+        return_value=quick_dataset(
+            StudyInstanceUID="foo",
+            SeriesInstanceUID="baz",
+            SOPInstanceUID="bimini",
+        )
+    )
+
+    datasets = list(a_trolley.fetch_all_datasets(some_studies))
+    assert len(datasets) == 28
+    assert datasets[0].SOPInstanceUID == "bimini"

tests/test_mint.py

@@ -1,21 +1,16 @@
 from datetime import date, datetime
+from unittest.mock import Mock
 from xml.etree.ElementTree import Element
 
 import pytest
 
+from dicomtrolley.exceptions import DICOMTrolleyException
 from dicomtrolley.mint import (
-    Mint,
     MintAttribute,
     MintSeries,
     parse_attribs,
 )
 from dicomtrolley.query import Query, QueryLevels
-from tests.mockresponses import MockUrls
-
-
-@pytest.fixture
-def a_mint(a_session):
-    return Mint(session=a_session, url=MockUrls.MINT_URL)
 
 
 def test_search_study_level(a_mint, mock_mint_responses):
@@ -40,6 +35,13 @@ def test_search_instance_level(a_mint, mock_mint_responses):
     assert len(response[0].series[1].instances) == 13
 
 
+def test_find_study_exception(a_mint, some_studies):
+    """Using a find_study query that returns multiple studies is not allowed"""
+    a_mint.find_studies = Mock(return_value=some_studies)
+    with pytest.raises(DICOMTrolleyException):
+        a_mint.find_study(Query())
+
+
 @pytest.mark.parametrize(
     "query_params",
     (
@@ -114,3 +116,9 @@ def test_study_instance_iterator(
 
     assert len([x for x in a_study_with_instances.all_instances()]) == 14
     assert len([x for x in a_study_without_instances.all_instances()]) == 0
+
+
+def test_study_dump(a_study_with_instances):
+    dump = a_study_with_instances.dump_content()
+    assert "BEELDENZORG" in dump
+    assert "85551.608" in dump

tests/test_wado.py

@@ -1,19 +1,12 @@
 import pytest
 
-from dicomtrolley.wado import Wado
 from tests.conftest import set_mock_response
 from tests.mockresponses import (
-    MockUrls,
     MockWadoParameters,
     WADO_RESPONSE_DICOM,
 )
 
 
-@pytest.fixture
-def a_wado(a_session):
-    return Wado(session=a_session, url=MockUrls.WADO_URL)
-
-
 @pytest.fixture
 def mock_wado_response(requests_mock):
     set_mock_response(requests_mock, WADO_RESPONSE_DICOM)