{variant_text["text"]}
') return section @@ -385,7 +385,7 @@ def get_ipr_analyst_comments( ipr_conn: IprConnection, matches: Sequence[KbMatch] | Sequence[Hashabledict], disease_name: str, - disease_match_names: [str], + disease_match_names: list[str], project_name: str, report_type: str, include_nonspecific_disease: bool = False, @@ -434,12 +434,13 @@ def get_ipr_analyst_comments( project_matches = [ item for item in itemlist - if 'project' in item.keys() and item['project']['name'] == project_name + if 'projects' in item.keys() + and project_name in [p['name'] for p in item['projects']] ] if project_matches: itemlist = project_matches elif include_nonspecific_project: - itemlist = [item for item in itemlist if 'project' not in item.keys()] + itemlist = [item for item in itemlist if 'projects' not in item.keys()] else: itemlist = [] @@ -463,7 +464,6 @@ def get_ipr_analyst_comments( ) > 0 ] - if disease_matches: itemlist = disease_matches elif include_nonspecific_disease: diff --git a/setup.cfg b/setup.cfg index 0cdeb341..8651f8a5 100644 --- a/setup.cfg +++ b/setup.cfg @@ -18,7 +18,7 @@ known_standard_library = requests [metadata] name = pori_python -version = 1.5.0 +version = 1.6.0 url = https://github.com/bcgsc/pori_python author_email = dat@bcgsc.ca maintainer_email = dat@bcgsc.ca @@ -36,6 +36,9 @@ install_requires = requests tqdm typing_extensions>=3.7.4.2,<5 + requests-cache>=1.3.0,<2.0 + requests-ratelimiter + pyrate-limiter [options.extras_require] deploy = twine; wheel; m2r @@ -62,3 +65,8 @@ pori_python = py.typed [options.entry_points] console_scripts = ipr = pori_python.ipr.main:command_interface + + +[tool:pytest] +log_cli = true +log_cli_level = INFO diff --git a/tests/test_graphkb/test_match.py b/tests/test_graphkb/test_match.py index 7a34b900..1e6b54d1 100644 --- a/tests/test_graphkb/test_match.py +++ b/tests/test_graphkb/test_match.py @@ -563,22 +563,6 @@ def test_structural_variants(self, conn): assert type not in expected.get('does_not_matches', {}).get('type', []) -class TestCacheMissingFeatures: - def test_filling_cache(self): - mock_conn = MagicMock( - query=MagicMock( - return_value=[ - {'name': 'bob', 'sourceId': 'alice'}, - {'name': 'KRAS', 'sourceId': '1234'}, - ] - ) - ) - match.cache_missing_features(mock_conn) - assert 'kras' in match.FEATURES_CACHE - assert 'alice' in match.FEATURES_CACHE - match.FEATURES_CACHE = None - - class TestTypeScreening: # Types as class variables default_type = DEFAULT_NON_STRUCTURAL_VARIANT_TYPE diff --git a/tests/test_graphkb/test_statement.py b/tests/test_graphkb/test_statement.py index 89faafdd..550191ed 100644 --- a/tests/test_graphkb/test_statement.py +++ b/tests/test_graphkb/test_statement.py @@ -17,11 +17,21 @@ def conn() -> GraphKBConnection: @pytest.fixture() def graphkb_conn(): + """ + Mocks the query functionality required by the calls made for the categorize_relevance function + + categorize_relevance calls query twice for each term in the values of the category_base_terms object + + - get_terms_set ([term, term, term...]) + - get_term_tree(term) + - query(query(term)) + """ + def make_rid_list(*values): return [{'@rid': v} for v in values] def term_tree_calls(*final_values): - # this function makes 2 calls to conn.query here + # this function makes 2 calls to conn.query here b/c the get_terms_set function will always call query twice sets = [['fake'], final_values] return [make_rid_list(*s) for s in sets] @@ -41,7 +51,7 @@ def term_tree_calls(*final_values): query_mock = Mock() query_mock.side_effect = return_values - return Mock(query=query_mock, cache={}) + return Mock(query=query_mock) class TestCategorizeRelevance: @@ -77,12 +87,13 @@ def test_no_match(self, graphkb_conn): category = statement.categorize_relevance(graphkb_conn, 'x') assert category == '' - def test_custom_categories(self, graphkb_conn): + def test_custom_categories_not_found(self, graphkb_conn): category = statement.categorize_relevance( graphkb_conn, 'x', [('blargh', ['some', 'blargh'])] ) assert category == '' + def test_custom_categories_match(self, graphkb_conn): category = statement.categorize_relevance( graphkb_conn, '1', [('blargh', ['some', 'blargh'])] ) diff --git a/tests/test_graphkb/test_util.py b/tests/test_graphkb/test_util.py index dbbb2c2b..f7637bfe 100644 --- a/tests/test_graphkb/test_util.py +++ b/tests/test_graphkb/test_util.py @@ -1,12 +1,42 @@ +import io +import json import os -import pytest import re +import pytest +import requests +import urllib3 +from requests.adapters import HTTPAdapter +from requests_ratelimiter import LimiterAdapter + from pori_python.graphkb import GraphKBConnection, util EXCLUDE_BCGSC_TESTS = os.environ.get('EXCLUDE_BCGSC_TESTS') == '1' +class CountingAdapter(HTTPAdapter): + """Test transport adapter that returns a canned JSON response without any + real network I/O, and counts how many times it was actually invoked (i.e. + how many requests were NOT served from cache). + """ + + def __init__(self, *args, **kwargs): + self.calls = 0 + super().__init__(*args, **kwargs) + + def send(self, request, **kwargs): + self.calls += 1 + body = json.dumps({'call': self.calls}).encode('utf-8') + raw = urllib3.HTTPResponse( + body=io.BytesIO(body), + status=200, + preload_content=False, + headers={}, + request_url=request.url, + ) + return self.build_response(request, raw) + + class OntologyTerm: def __init__(self, name, sourceId, displayName): self.name = name @@ -16,7 +46,7 @@ def __init__(self, name, sourceId, displayName): @pytest.fixture(scope='module') def conn() -> GraphKBConnection: - conn = GraphKBConnection() + conn = GraphKBConnection(url=os.environ['GRAPHKB_URL']) conn.login(os.environ['GRAPHKB_USER'], os.environ['GRAPHKB_PASS']) return conn @@ -191,3 +221,173 @@ def test_get_related_terms(self, conn): subgraphType='parents', ) assert 'cancer' in disease_terms + + +class TestRateLimitingOptIn: + """Rate limiting is opt-in per-connection via the `limiter_kwargs` argument. + + Passing a truthy `limiter_kwargs` dict (e.g. `{'per_second': 3}`) mounts a + `LimiterAdapter`; leaving it unset (None/default) or empty leaves the plain + `HTTPAdapter` in place, i.e. rate limiting disabled. Regardless of + `limiter_kwargs`, rate limiting is always forced off while running under + pytest (`PYTEST_CURRENT_TEST` set) or when `only_if_cached=True`. + """ + + def test_default_has_no_rate_limiting(self): + conn = GraphKBConnection(url='http://localhost:8080') + assert isinstance(conn.http.adapters['https://'], HTTPAdapter) + assert not isinstance(conn.http.adapters['https://'], LimiterAdapter) + + def test_empty_limiter_kwargs_has_no_rate_limiting(self): + conn = GraphKBConnection(url='http://localhost:8080', limiter_kwargs={}) + assert not isinstance(conn.http.adapters['https://'], LimiterAdapter) + + def test_limiter_kwargs_forced_off_while_under_pytest(self, caplog): + # PYTEST_CURRENT_TEST is set while running under pytest, so rate + # limiting should stay disabled even when limiter_kwargs is provided. + assert 'PYTEST_CURRENT_TEST' in os.environ + conn = GraphKBConnection(url='http://localhost:8080', limiter_kwargs={'per_second': 3}) + assert not isinstance(conn.http.adapters['https://'], LimiterAdapter) + assert 'rate limiting is by default turned off' in caplog.text + + def test_limiter_kwargs_enables_rate_limiting_outside_pytest(self, monkeypatch): + monkeypatch.delenv('PYTEST_CURRENT_TEST', raising=False) + conn = GraphKBConnection(url='http://localhost:8080', limiter_kwargs={'per_second': 3}) + assert isinstance(conn.http.adapters['https://'], LimiterAdapter) + + def test_only_if_cached_forces_rate_limiting_off(self, monkeypatch, caplog): + monkeypatch.delenv('PYTEST_CURRENT_TEST', raising=False) + conn = GraphKBConnection( + url='http://localhost:8080', only_if_cached=True, limiter_kwargs={'per_second': 3} + ) + assert conn.only_if_cached is True + assert 'rate limiting is by default turned off' in caplog.text + + def test_limiter_kwargs_with_custom_session_raises(self): + with pytest.raises(NotImplementedError): + GraphKBConnection( + url='http://localhost:8080', + session=requests.Session(), + limiter_kwargs={'per_second': 3}, + ) + + +class TestCacheFilter: + """Unit tests for util.cache_filter, which decides which responses requests-cache + is allowed to store: all GETs, but only POSTs to the /query endpoint (other POSTs + create content and must never be cached). + """ + + class _FakeRequest: + def __init__(self, method, url): + self.method = method + self.url = url + + class _FakeResponse: + def __init__(self, method, url): + self.request = TestCacheFilter._FakeRequest(method, url) + + def test_get_requests_are_always_cacheable(self): + response = self._FakeResponse('GET', 'http://fake/api/statement') + assert util.cache_filter(response) is True + + @pytest.mark.parametrize('url', ['http://fake/api/query', 'http://fake/api/query/']) + def test_post_to_query_endpoint_is_cacheable(self, url): + response = self._FakeResponse('POST', url) + assert util.cache_filter(response) is True + + @pytest.mark.parametrize('url', ['http://fake/api/statement', 'http://fake/api/query/similar']) + def test_post_to_other_endpoints_is_not_cacheable(self, url): + response = self._FakeResponse('POST', url) + assert util.cache_filter(response) is False + + +class TestCachingBehavior: + """End-to-end tests that mount a counting fake adapter under GraphKBConnection's + session so we can assert whether a real request was made (adapter.calls + incremented) or the response was served from the requests-cache layer instead. + """ + + def test_repeated_get_is_served_from_cache(self): + conn = GraphKBConnection(url='http://fake-graphkb', use_global_cache=True) + adapter = CountingAdapter() + conn.http.mount('http://', adapter) + + first = conn.http.get('http://fake-graphkb/api/version') + second = conn.http.get('http://fake-graphkb/api/version') + + assert adapter.calls == 1 + assert first.json() == second.json() + assert getattr(second, 'from_cache', False) is True + + def test_no_cache_header_bypasses_cache(self): + conn = GraphKBConnection(url='http://fake-graphkb', use_global_cache=True) + adapter = CountingAdapter() + conn.http.mount('http://', adapter) + + conn.http.get('http://fake-graphkb/api/version') + conn.http.get('http://fake-graphkb/api/version', headers={'Cache-Control': 'no-cache'}) + + assert adapter.calls == 2 + + def test_only_if_cached_returns_504_when_not_cached(self): + conn = GraphKBConnection(url='http://fake-graphkb', use_global_cache=True) + adapter = CountingAdapter() + conn.http.mount('http://', adapter) + + resp = conn.http.get( + 'http://fake-graphkb/api/never-requested', + headers={'Cache-Control': 'only-if-cached'}, + ) + + assert resp.status_code == 504 + assert adapter.calls == 0 + + def test_only_if_cached_returns_cached_value_without_new_request(self): + conn = GraphKBConnection(url='http://fake-graphkb', use_global_cache=True) + adapter = CountingAdapter() + conn.http.mount('http://', adapter) + + conn.http.get('http://fake-graphkb/api/version') + resp = conn.http.get( + 'http://fake-graphkb/api/version', headers={'Cache-Control': 'only-if-cached'} + ) + + assert resp.status_code == 200 + assert adapter.calls == 1 + + def test_post_to_query_endpoint_is_cached(self): + conn = GraphKBConnection(url='http://fake-graphkb', use_global_cache=True) + adapter = CountingAdapter() + conn.http.mount('http://', adapter) + + conn.http.post('http://fake-graphkb/api/query', data='{}') + conn.http.post('http://fake-graphkb/api/query', data='{}') + + assert adapter.calls == 1 + + def test_post_to_non_query_endpoint_is_never_cached(self): + conn = GraphKBConnection(url='http://fake-graphkb', use_global_cache=True) + adapter = CountingAdapter() + conn.http.mount('http://', adapter) + + conn.http.post('http://fake-graphkb/api/statement', data='{}') + conn.http.post('http://fake-graphkb/api/statement', data='{}') + + assert adapter.calls == 2 + + def test_use_global_cache_false_hits_adapter_every_time(self): + conn = GraphKBConnection(url='http://fake-graphkb', use_global_cache=False) + adapter = CountingAdapter() + conn.http.mount('http://', adapter) + + conn.http.get('http://fake-graphkb/api/version') + conn.http.get('http://fake-graphkb/api/version') + + assert adapter.calls == 2 + + def test_use_global_cache_false_raises_with_cache_name(self): + with pytest.raises(NotImplementedError): + GraphKBConnection( + url='http://fake-graphkb', use_global_cache=False, cache_name='somewhere' + ) diff --git a/tests/test_ipr/test_annotate.py b/tests/test_ipr/test_annotate.py index 43de4216..79eb54c7 100644 --- a/tests/test_ipr/test_annotate.py +++ b/tests/test_ipr/test_annotate.py @@ -6,6 +6,7 @@ from pori_python.ipr.constants import ( COSMIC_SIGNATURE_VARIANT_TYPE, HLA_SIGNATURE_VARIANT_TYPE, + HRD_MAPPING, MSI_MAPPING, TMB_SIGNATURE, TMB_SIGNATURE_VARIANT_TYPE, @@ -13,7 +14,7 @@ from pori_python.ipr.inputs import preprocess_signature_variants from pori_python.types import IprSmallMutationVariant -from .test_ipr import DISEASE_RIDS +from .test_ipr import DISEASE_RIDS # dummy RIDs; will always result in matchedCancer == false EXCLUDE_BCGSC_TESTS = os.environ.get('EXCLUDE_BCGSC_TESTS') == '1' @@ -203,6 +204,29 @@ def test_annotate_signature_variants_msi(self, graphkb_conn): ) assert len(msi) != 0 + def test_annotate_signature_variants_hrd_strong(self, graphkb_conn): + """Test HRD strong signature""" + hrd = annotate_signature_variants( + graphkb_conn, + DISEASE_RIDS, + preprocess_signature_variants( + [HRD_MAPPING['homologous recombination deficiency strong signature']] + ), + ) + assert len(hrd) != 0 + + @pytest.mark.skip(reason='no GKB statement for HRD moderate Signature CVs yet') + def test_annotate_signature_variants_hrd_moderate(self, graphkb_conn): + """Test HRD moderate signature""" + hrd = annotate_signature_variants( + graphkb_conn, + DISEASE_RIDS, + preprocess_signature_variants( + [HRD_MAPPING['homologous recombination deficiency moderate signature']] + ), + ) + assert len(hrd) != 0 + def test_annotate_structural_variants_tp53(self, graphkb_conn): """Verify alternate TP53 variants match.""" ref_key = 'prot_only' diff --git a/tests/test_ipr/test_ipr.py b/tests/test_ipr/test_ipr.py index 687c14b4..ba270153 100644 --- a/tests/test_ipr/test_ipr.py +++ b/tests/test_ipr/test_ipr.py @@ -1034,3 +1034,9 @@ def test_create_key_alterations_includes_only_pruned_kbmatches(self): # partial matches is false assert len(key_alts1) == 3 assert len(key_alts2) == 4 + assert {(alt['variantType'], alt['variant']) for alt in key_alts1} == { + (variant['variantType'], variant['key']) for variant in ALL_VARIANTS[:3] + } + assert {(alt['variantType'], alt['variant']) for alt in key_alts2} == { + (variant['variantType'], variant['key']) for variant in ALL_VARIANTS[:4] + } diff --git a/tests/test_ipr/test_ipr_integration.py b/tests/test_ipr/test_ipr_integration.py new file mode 100644 index 00000000..af9c5793 --- /dev/null +++ b/tests/test_ipr/test_ipr_integration.py @@ -0,0 +1,102 @@ +import os +import json +import jsonschema +import pytest + +from pori_python.ipr.connection import IprConnection + +from .constants import EXCLUDE_INTEGRATION_TESTS + + +mock_ipr_results = [ + [ + { + 'text': 'no cancerType
', + 'variantName': 'ERBB2 amplification', + 'cancerType': [], + 'template': {'name': 'test3'}, + 'projects': [{'name': 'test2'}], + }, + { + 'text': 'normal
', + 'variantName': 'ERBB2 amplification', + 'cancerType': ['test1', 'test'], + 'template': {'name': 'test3'}, + 'projects': [{'name': 'test2'}], + }, + { + 'text': 'no project
', + 'variantName': 'ERBB2 amplification', + 'cancerType': ['test1', 'test'], + 'template': {'name': 'test3'}, + }, + { + 'text': 'no template
', + 'variantName': 'ERBB2 amplification', + 'cancerType': ['test1', 'test'], + 'projects': [{'name': 'test2'}], + }, + ], + [ + { + 'text': 'normal, second variant
', + 'variantName': 'second variant', + 'cancerType': ['test1', 'test'], + 'template': {'name': 'test3'}, + 'projects': [{'name': 'test2'}], + }, + ], +] + + +def validate_mock_ipr_results_against_schema(schema, results): + # Since the IPR generated schema has required fields, but the purpose of the test is to prevent + # schema drift and not to validate POST payloads to variant-text, we create a custom validator + # that ignores the required fields and only validates the properties that are defined in the schema. + custom_validators = dict(jsonschema.Draft7Validator.VALIDATORS) + custom_validators.pop('required', None) + non_required_validator = jsonschema.validators.create( + meta_schema=jsonschema.Draft7Validator.META_SCHEMA, + validators=custom_validators, + version='draft7-lazy', + ) + validator = non_required_validator(schema) + declared_properties = set(schema.get('properties', {})) + + for group_index, group in enumerate(results): + for record_index, record in enumerate(group): + location = f'group {group_index} record {record_index}' + unknown = sorted(set(record) - declared_properties) + assert not unknown, ( + f'{location}: properties {unknown} are not defined in the IPR variant-text schema' + ) + errors = sorted(validator.iter_errors(record), key=lambda err: list(err.path)) + assert not errors, f'{location}: ' + '; '.join( + f'{list(err.path)}: {err.message}' for err in errors + ) + + +def make_ipr_connection(): + return IprConnection( + username=os.environ.get('IPR_USER', os.environ['USER']), + password=os.environ['IPR_PASS'], + url=os.environ['IPR_INTEGRATION_TEST_URL'], + ) + + +# DEVSU-3011 adding IPR integration test to validate variant text schema from the IPR API side to prevent schema drift +@pytest.mark.skipif(EXCLUDE_INTEGRATION_TESTS, reason='excluding long running integration tests') +class TestVariantTextSchema: + def test_mock_ipr_results_match_variant_text_schema(self): + ipr_conn = make_ipr_connection() + schema = ipr_conn.request( + 'variant-text/schema', + method='GET', + headers=json.dumps( + { + 'Content-Length': '0', + 'Accept': 'application/json', + } + ), + ) + validate_mock_ipr_results_against_schema(schema, mock_ipr_results) diff --git a/tests/test_ipr/test_main.py b/tests/test_ipr/test_main.py index 3dbd0aa5..1dc20ab2 100644 --- a/tests/test_ipr/test_main.py +++ b/tests/test_ipr/test_main.py @@ -151,7 +151,6 @@ def side_effect_function(*args, **kwargs): return report_content -@pytest.mark.skip(reason='KBDEV-1308; taking too long, getting canceled after reaching max delay') @pytest.mark.skipif(EXCLUDE_INTEGRATION_TESTS, reason='excluding long running integration tests') class TestCreateReport: def test_main_sections_present(self, report_upload_content: Dict) -> None: diff --git a/tests/test_ipr/test_summary.py b/tests/test_ipr/test_summary.py index 248a99f2..c3e128f6 100644 --- a/tests/test_ipr/test_summary.py +++ b/tests/test_ipr/test_summary.py @@ -166,14 +166,14 @@ def test_multiple_diseases_only_matches(self): 'variantName': 'ERBB2 amplification', 'cancerType': [], 'template': {'name': 'test3'}, - 'project': {'name': 'test2'}, + 'projects': [{'name': 'test2'}], }, { 'text': 'normal
', 'variantName': 'ERBB2 amplification', 'cancerType': ['test1', 'test'], 'template': {'name': 'test3'}, - 'project': {'name': 'test2'}, + 'projects': [{'name': 'test2'}], }, { 'text': 'no project
', @@ -185,7 +185,7 @@ def test_multiple_diseases_only_matches(self): 'text': 'no template
', 'variantName': 'ERBB2 amplification', 'cancerType': ['test1', 'test'], - 'project': {'name': 'test2'}, + 'projects': [{'name': 'test2'}], }, ], [ @@ -194,7 +194,7 @@ def test_multiple_diseases_only_matches(self): 'variantName': 'second variant', 'cancerType': ['test1', 'test'], 'template': {'name': 'test3'}, - 'project': {'name': 'test2'}, + 'projects': [{'name': 'test2'}], }, ], ] @@ -204,10 +204,10 @@ def test_multiple_diseases_only_matches(self): class TestVariantTextFromIPR: def test_gets_fully_matched_output_when_possible(self): - ipr_conn = MagicMock(get=MagicMock(side_effect=copy(mock_ipr_results))) matches = [{'kbVariant': 'ERBB2 amplification'}] + mock_ipr_conn = MagicMock(get=MagicMock(side_effect=copy(mock_ipr_results))) ipr_summary = get_ipr_analyst_comments( - ipr_conn, + mock_ipr_conn, matches=matches, disease_name='test1', disease_match_names=[], @@ -218,15 +218,15 @@ def test_gets_fully_matched_output_when_possible(self): include_nonspecific_template=True, ) summary_lines = ipr_summary.split('\n') - assert summary_lines[1] == 'normal
' assert len(summary_lines) == 3 def test_omits_nonspecific_project_matches_when_specified(self): - ipr_conn = MagicMock(get=MagicMock(side_effect=copy(mock_ipr_results))) matches = [{'kbVariant': 'ERBB2 amplification'}] + mock_ipr_conn = MagicMock(get=MagicMock(side_effect=copy(mock_ipr_results))) ipr_summary = get_ipr_analyst_comments( - ipr_conn, + mock_ipr_conn, matches=matches, disease_name='test1', disease_match_names=[], @@ -239,10 +239,10 @@ def test_omits_nonspecific_project_matches_when_specified(self): assert ipr_summary == no_comments_found_output def test_omits_nonspecific_template_matches_when_specified(self): - ipr_conn = MagicMock(get=MagicMock(side_effect=copy(mock_ipr_results))) matches = [{'kbVariant': 'ERBB2 amplification'}] + mock_ipr_conn = MagicMock(get=MagicMock(side_effect=copy(mock_ipr_results))) ipr_summary = get_ipr_analyst_comments( - ipr_conn, + mock_ipr_conn, matches=matches, disease_name='test1', disease_match_names=[], @@ -255,10 +255,10 @@ def test_omits_nonspecific_template_matches_when_specified(self): assert ipr_summary == no_comments_found_output def test_omits_nonspecific_disease_matches_when_specified(self): - ipr_conn = MagicMock(get=MagicMock(side_effect=copy(mock_ipr_results))) matches = [{'kbVariant': 'ERBB2 amplification'}] + mock_ipr_conn = MagicMock(get=MagicMock(side_effect=copy(mock_ipr_results))) ipr_summary = get_ipr_analyst_comments( - ipr_conn, + mock_ipr_conn, matches=matches, disease_name='notfound', disease_match_names=[], @@ -271,10 +271,10 @@ def test_omits_nonspecific_disease_matches_when_specified(self): assert ipr_summary == no_comments_found_output def test_includes_nonspecific_project_matches_when_specified(self): - ipr_conn = MagicMock(get=MagicMock(side_effect=copy(mock_ipr_results))) matches = [{'kbVariant': 'ERBB2 amplification'}] + mock_ipr_conn = MagicMock(get=MagicMock(side_effect=copy(mock_ipr_results))) ipr_summary = get_ipr_analyst_comments( - ipr_conn, + mock_ipr_conn, matches=matches, disease_name='test1', disease_match_names=[], @@ -289,10 +289,10 @@ def test_includes_nonspecific_project_matches_when_specified(self): assert len(summary_lines) == 3 def test_includes_nonspecific_template_matches_when_specified(self): - ipr_conn = MagicMock(get=MagicMock(side_effect=copy(mock_ipr_results))) matches = [{'kbVariant': 'ERBB2 amplification'}] + mock_ipr_conn = MagicMock(get=MagicMock(side_effect=copy(mock_ipr_results))) ipr_summary = get_ipr_analyst_comments( - ipr_conn, + mock_ipr_conn, matches=matches, disease_name='test1', disease_match_names=[], @@ -307,10 +307,10 @@ def test_includes_nonspecific_template_matches_when_specified(self): assert len(summary_lines) == 3 def test_includes_nonspecific_disease_matches_when_specified(self): - ipr_conn = MagicMock(get=MagicMock(side_effect=copy(mock_ipr_results))) matches = [{'kbVariant': 'ERBB2 amplification'}] + mock_ipr_conn = MagicMock(get=MagicMock(side_effect=copy(mock_ipr_results))) ipr_summary = get_ipr_analyst_comments( - ipr_conn, + mock_ipr_conn, matches=matches, disease_name='notfound', disease_match_names=[], @@ -321,15 +321,15 @@ def test_includes_nonspecific_disease_matches_when_specified(self): include_nonspecific_template=False, ) summary_lines = ipr_summary.split('\n') - assert summary_lines[1] == 'no cancerType
' assert len(summary_lines) == 3 def test_includes_all_graphkb_disease_matches(self): - ipr_conn = MagicMock(get=MagicMock(side_effect=copy(mock_ipr_results))) matches = [{'kbVariant': 'ERBB2 amplification'}] + mock_ipr_conn = MagicMock(get=MagicMock(side_effect=copy(mock_ipr_results))) ipr_summary = get_ipr_analyst_comments( - ipr_conn, + mock_ipr_conn, matches=matches, disease_name='notfound', disease_match_names=['TEST1'], @@ -340,19 +340,19 @@ def test_includes_all_graphkb_disease_matches(self): include_nonspecific_template=False, ) summary_lines = ipr_summary.split('\n') - assert summary_lines[1] == 'normal
' assert len(summary_lines) == 3 def test_prepare_section_for_multiple_variants(self): - ipr_conn = MagicMock(get=MagicMock(side_effect=copy(mock_ipr_results))) # NB this test relies on matches being processed in this order matches = [{'kbVariant': 'ERBB2 amplification'}, {'kbVariant': 'second variant'}] + mock_ipr_conn = MagicMock(get=MagicMock(side_effect=copy(mock_ipr_results))) ipr_summary = get_ipr_analyst_comments( - ipr_conn, + mock_ipr_conn, matches=matches, - disease_name='test1', - disease_match_names=[], + disease_name='notfound', + disease_match_names=['TEST1'], project_name='test2', report_type='test3', include_nonspecific_project=False, @@ -363,17 +363,17 @@ def test_prepare_section_for_multiple_variants(self): assert len(summary_lines) == 5 assert ( '\n'.join(summary_lines[1:]) - == 'normal
\nnormal, second variant
' + == 'normal
\nnormal, second variant
' ) def test_empty_section_when_no_variant_match(self): - ipr_conn = MagicMock(get=MagicMock(side_effect=[[], []])) matches = [{'kbVariant': 'notfound1'}, {'kbVariant': 'notfound2'}] + mock_ipr_conn = MagicMock(get=MagicMock(side_effect=[[], []])) ipr_summary = get_ipr_analyst_comments( - ipr_conn, + mock_ipr_conn, matches=matches, - disease_name='test1', - disease_match_names=[], + disease_name='notfound', + disease_match_names=['TEST1'], project_name='test2', report_type='test3', include_nonspecific_project=False, diff --git a/tests/test_ipr/test_upload.py b/tests/test_ipr/test_upload.py index 6e7f9b05..4445b9c4 100644 --- a/tests/test_ipr/test_upload.py +++ b/tests/test_ipr/test_upload.py @@ -189,7 +189,7 @@ def loaded_reports(tmp_path_factory) -> Generator: '--graphkb_password', os.environ.get('GRAPHKB_PASS', os.environ['IPR_PASS']), '--ipr_url', - os.environ['IPR_TEST_URL'], + os.environ['IPR_URL'], '--graphkb_url', os.environ.get('GRAPHKB_URL', False), '--therapeutics', @@ -213,7 +213,7 @@ def loaded_reports(tmp_path_factory) -> Generator: ipr_conn = IprConnection( username=os.environ.get('IPR_USER', os.environ['USER']), password=os.environ['IPR_PASS'], - url=os.environ['IPR_TEST_URL'], + url=os.environ['IPR_URL'], ) loaded_report = ipr_conn.get(uri=f'reports?searchText={patient_id}') async_loaded_report = ipr_conn.get(uri=f'reports?searchText={async_patient_id}') @@ -233,7 +233,7 @@ def get_section(loaded_report, section_name): ipr_conn = IprConnection( username=os.environ.get('IPR_USER', os.environ['USER']), password=os.environ['IPR_PASS'], - url=os.environ['IPR_TEST_URL'], + url=os.environ['IPR_URL'], ) return ipr_conn.get(uri=f'reports/{ident}/{section_name}')