diff --git a/CHANGELOG.md b/CHANGELOG.md index 66ca6a4..f351b48 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -2,6 +2,11 @@ The Reasoner Validator package is evolving along with progress in TRAPI and Biolink Model standards within the NCATS Biomedical Knowledge Translator. +## 4.1.4 + +- Added more fine-grained validation reporting inside case_input_found_in_response() TRAPI Response validation method, also injecting externalized "missing edge" validation message into method(); added/refactored validation codes accordingly +- Full TRAPI 1.5.0 unit tests still skipped (need rework) + ## 4.1.3 - Generalize trapi_1.4 testing predicate to trapi_1.4 or later diff --git a/DEVELOPER_NOTES.md b/DEVELOPER_NOTES.md index 41e598c..4e2105d 100644 --- a/DEVELOPER_NOTES.md +++ b/DEVELOPER_NOTES.md @@ -28,12 +28,12 @@ Steps to properly issue a new project release: 2. If the **codes.yaml** were revised, regenerated the associate code documentation by running the reasoner_validator/validation_codes.py module as a script from the CLI. 3. Run the unit test suite to ensure that nothing fails. Iterate to fix failures (in the code or in terms of revised unit tests to reflect fresh code designs) 4. Document release changes in the **CHANGELOG.md** -5. Update the **`[Tool Poetry]version =`** field in the **pyprojects.yaml**, e.g. "4.1.3" +5. Update the **`[Tool Poetry]version =`** field in the **pyprojects.yaml**, e.g. "4.1.4" 6. Run **`poetry update`** (preferably within **`poetry shell`**) 7. The project pip **requirements.txt** file snapshot of dependencies should also be updated at this point (type **`$ poetry export --output requirements.txt`**, assuming that the [proper poetry export plugin is installed](https://python-poetry.org/docs/pre-commit-hooks#poetry-export)). This may facilitate module deployment within environments that prefer to use pip rather than poetry to manage their deployments. 8. Commit or pull request merge all files (including the **poetry.lock** file) to **master** -9. Add the equivalent Git **tag** to **master**. This should be the Semantic Version string from step 4 with an added 'v' prefix, i.e. "v4.1.3". +9. Add the equivalent Git **tag** to **master**. This should be the Semantic Version string from step 4 with an added 'v' prefix, i.e. "v4.1.4". 10. Push **master** to remote. 11. Check if Git Actions for testing and documentation complete successfully. -12. Create the release using the same release tag, i.e. "v4.1.3". -13. Check if Git Action for package deployment is successful and check if the new version (i.e. "4.1.3") is now visible on **[pypy.org](https://pypi.org/search/?q=reasoner-validator)** +12. Create the release using the same release tag, i.e. "v4.1.4". +13. Check if Git Action for package deployment is successful and check if the new version (i.e. "4.1.4") is now visible on **[pypy.org](https://pypi.org/search/?q=reasoner-validator)** diff --git a/docs/validation_codes_dictionary.md b/docs/validation_codes_dictionary.md index 2854258..d1b3e6e 100644 --- a/docs/validation_codes_dictionary.md +++ b/docs/validation_codes_dictionary.md @@ -66,14 +66,6 @@ **Description:** TRAPI Response should generally have a TRAPI request message Knowledge Graph key value in its reply. -### error.trapi.response.knowledge_graph.missing_expected_edge - -**Message:** Knowledge Graph of TRAPI Response Message is missing expected Edge - -**Context:** identifier - -**Description:** The given TRAPI Response is expected to return specific edge(s) relating to the original (test edge?) data used to prepare the TRAPI Request! - ### error.trapi.response.knowledge_graph.empty **Message:** Response returned an empty Message Knowledge Graph, which is an error in this context! @@ -100,6 +92,30 @@ **Description:** TRAPI Message.Results cannot resolve its reported identifier mappings to the original query. +### error.trapi.response.missing_expected.knowledge_graph.node + +**Message:** Knowledge Graph of TRAPI Response Message Knowledge Graph is missing expected Node + +**Context:** identifier, context + +**Description:** The given TRAPI Response is expected to return specific nodes(s) relating to the original input data used to prepare the TRAPI Request! + +### error.trapi.response.missing_expected.knowledge_graph.edge + +**Message:** Knowledge Graph of TRAPI Response Message Knowledge Graph is missing expected Edge + +**Context:** identifier + +**Description:** The given TRAPI Response is expected to return specific edge(s) relating to the original input data used to prepare the TRAPI Request! + +### error.trapi.response.missing_expected.result + +**Message:** Knowledge Graph of TRAPI Response Message is missing expected Result + +**Context:** identifier + +**Description:** The given TRAPI Response is expected to return specific result(s) relating to the original input data used to prepare the TRAPI Request! + ### error.input_edge.node.category.missing **Message:** Category missing for node diff --git a/poetry.lock b/poetry.lock index 2e829b1..1594b5a 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1,4 +1,4 @@ -# This file is automatically @generated by Poetry 1.8.2 and should not be changed by hand. +# This file is automatically @generated by Poetry 1.5.1 and should not be changed by hand. 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a/reasoner_validator/codes.yaml +++ b/reasoner_validator/codes.yaml @@ -60,11 +60,6 @@ error: missing: $message: "TRAPI Message is missing its Knowledge Graph component!" $description: "TRAPI Response should generally have a TRAPI request message Knowledge Graph key value in its reply." - missing_expected_edge: - $message: "Knowledge Graph of TRAPI Response Message is missing expected Edge" - $context: - - identifier - $description: "The given TRAPI Response is expected to return specific edge(s) relating to the original (test edge?) data used to prepare the TRAPI Request!" empty: $message: "Response returned an empty Message Knowledge Graph, which is an error in this context!" $description: "An empty Knowledge Graph is considered an error in this validation context!" @@ -81,6 +76,24 @@ error: - identifier - output_node_binding $description: "TRAPI Message.Results cannot resolve its reported identifier mappings to the original query." + missing_expected: + knowledge_graph: + node: + $message: "Knowledge Graph of TRAPI Response Message Knowledge Graph is missing expected Node" + $context: + - identifier + - context # 'subject' or 'object' + $description: "The given TRAPI Response is expected to return specific nodes(s) relating to the original input data used to prepare the TRAPI Request!" + edge: + $message: "Knowledge Graph of TRAPI Response Message Knowledge Graph is missing expected Edge" + $context: + - identifier + $description: "The given TRAPI Response is expected to return specific edge(s) relating to the original input data used to prepare the TRAPI Request!" + result: + $message: "Knowledge Graph of TRAPI Response Message is missing expected Result" + $context: + - identifier + $description: "The given TRAPI Response is expected to return specific result(s) relating to the original input data used to prepare the TRAPI Request!" input_edge: node: category: diff --git a/reasoner_validator/validator.py b/reasoner_validator/validator.py index 187f3a4..1cf0a49 100644 --- a/reasoner_validator/validator.py +++ b/reasoner_validator/validator.py @@ -444,6 +444,9 @@ def case_node_found(target: str, identifiers: List[str], case: Dict, nodes: Dict node_details = nodes[identifier] if "categories" in node_details: category = case[f"{target}_category"] + # TODO: it may be helpful here to also try to match + # any parent classes of the specified 'category' + # to the node_details["categories"], using BMT if category in node_details["categories"]: return True @@ -644,11 +647,6 @@ def case_input_found_in_response( # this, input test data edge is automatically deemed missing return False - # TODO: We need to check **here*** whether or not the - # TRAPI response returned the original test case edge!!?!! - # Not totally sure if we should first search the Results then - # the Knowledge Graph, or go directly to the Knowledge Graph... - # The Message Query Graph could be something like: # "query_graph": { # "nodes": { @@ -686,13 +684,21 @@ def case_input_found_in_response( subject_id = case["subject_id"] if "subject_id" in case else case["subject"] subject_aliases = get_aliases(subject_id) if not self.case_node_found("subject", subject_aliases, case, nodes): - # 'subject' node identifier not found? + self.report( + code="error.trapi.response.missing_expected.knowledge_graph.node", + identifier=subject_id, + context="subject" + ) return False object_id = case["object_id"] if "object_id" in case else case["object"] object_aliases = get_aliases(object_id) if not self.case_node_found("object", object_aliases, case, nodes): - # 'object' node identifier not found? + self.report( + code="error.trapi.response.missing_expected.knowledge_graph.node", + identifier=object_id, + context="object" + ) return False # In the Knowledge Graph: @@ -746,14 +752,25 @@ def case_input_found_in_response( edge_id_match = edge_id break + edge_id: str = \ + f"{case['idx']}|" +\ + f"({case['subject_id']}#{case['subject_category']})" + \ + f"-[{case['predicate_id']}]->" + \ + f"({case['object_id']}#{case['object_category']})" + if edge_id_match is None: - # Test case S--P->O edge not found? + self.report( + code="error.trapi.response.missing_expected.knowledge_graph.edge", + identifier=edge_id + ) return False results: List = message["results"] if not self.case_result_found(subject_match, object_match, edge_id_match, results, trapi_version): - # Some components of test case S--P->O edge - # NOT bound within any Results? + self.report( + code="error.trapi.response.missing_expected.result", + identifier=edge_id + ) return False # By this point, the case data assumed to be diff --git a/requirements.txt b/requirements.txt index ed97157..f0458ea 100644 --- a/requirements.txt +++ b/requirements.txt @@ -4,9 +4,9 @@ annotated-types==0.6.0 ; python_version >= "3.9" and python_version < "3.12" \ attrs==23.2.0 ; python_version >= "3.9" and python_version < "3.12" \ --hash=sha256:935dc3b529c262f6cf76e50877d35a4bd3c1de194fd41f47a2b7ae8f19971f30 \ --hash=sha256:99b87a485a5820b23b879f04c2305b44b951b502fd64be915879d77a7e8fc6f1 -bioregistry==0.11.2 ; python_version >= "3.9" and python_version < "3.12" \ - --hash=sha256:8ecb782505d729e6338946b3af6a2b297dfe281114381961d5acc4fdf1af9033 \ - --hash=sha256:e2a33c6afdac19bcd76230a87750cac84eb99bebea1fd55ef9d595c033269b86 +bioregistry==0.11.3 ; python_version >= "3.9" and python_version < "3.12" \ + --hash=sha256:7e04e926ee0068b7623b2ec1984e1872e0b152c203b71542a4edfe26985044f1 \ + --hash=sha256:ea23736b41f2e7e7f26f544d19f5a3ab4ba41343a0a10d3162507922adc3ebfd bmt==1.4.0 ; python_version >= "3.9" and python_version < "3.12" \ --hash=sha256:26a831eda3d64405d849f49ee579b44412e3e6b9c2e6587e2240a7605b28fc55 \ --hash=sha256:ca81f3e91b3a0312bed01692a93d343d828e556ae14fc00fb016f5a3f38f44c3 @@ -294,9 +294,7 @@ pytest==7.4.4 ; python_version >= "3.9" and python_version < "3.12" \ pytrie==0.4.0 ; python_version >= "3.9" and python_version < "3.12" \ --hash=sha256:8f4488f402d3465993fb6b6efa09866849ed8cda7903b50647b7d0342b805379 pyyaml==6.0.1 ; python_version >= "3.9" and python_version < "3.12" \ - --hash=sha256:04ac92ad1925b2cff1db0cfebffb6ffc43457495c9b3c39d3fcae417d7125dc5 \ --hash=sha256:062582fca9fabdd2c8b54a3ef1c978d786e0f6b3a1510e0ac93ef59e0ddae2bc \ - --hash=sha256:0d3304d8c0adc42be59c5f8a4d9e3d7379e6955ad754aa9d6ab7a398b59dd1df \ --hash=sha256:1635fd110e8d85d55237ab316b5b011de701ea0f29d07611174a1b42f1444741 \ --hash=sha256:184c5108a2aca3c5b3d3bf9395d50893a7ab82a38004c8f61c258d4428e80206 \ --hash=sha256:18aeb1bf9a78867dc38b259769503436b7c72f7a1f1f4c93ff9a17de54319b27 \ @@ -304,10 +302,7 @@ pyyaml==6.0.1 ; python_version >= "3.9" and python_version < "3.12" \ --hash=sha256:1e2722cc9fbb45d9b87631ac70924c11d3a401b2d7f410cc0e3bbf249f2dca62 \ --hash=sha256:1fe35611261b29bd1de0070f0b2f47cb6ff71fa6595c077e42bd0c419fa27b98 \ --hash=sha256:28c119d996beec18c05208a8bd78cbe4007878c6dd15091efb73a30e90539696 \ - --hash=sha256:326c013efe8048858a6d312ddd31d56e468118ad4cdeda36c719bf5bb6192290 \ - --hash=sha256:40df9b996c2b73138957fe23a16a4f0ba614f4c0efce1e9406a184b6d07fa3a9 \ --hash=sha256:42f8152b8dbc4fe7d96729ec2b99c7097d656dc1213a3229ca5383f973a5ed6d \ - --hash=sha256:49a183be227561de579b4a36efbb21b3eab9651dd81b1858589f796549873dd6 \ --hash=sha256:4fb147e7a67ef577a588a0e2c17b6db51dda102c71de36f8549b6816a96e1867 \ --hash=sha256:50550eb667afee136e9a77d6dc71ae76a44df8b3e51e41b77f6de2932bfe0f47 \ --hash=sha256:510c9deebc5c0225e8c96813043e62b680ba2f9c50a08d3724c7f28a747d1486 \ @@ -315,12 +310,9 @@ pyyaml==6.0.1 ; python_version >= "3.9" and python_version < "3.12" \ --hash=sha256:596106435fa6ad000c2991a98fa58eeb8656ef2325d7e158344fb33864ed87e3 \ --hash=sha256:6965a7bc3cf88e5a1c3bd2e0b5c22f8d677dc88a455344035f03399034eb3007 \ --hash=sha256:69b023b2b4daa7548bcfbd4aa3da05b3a74b772db9e23b982788168117739938 \ - --hash=sha256:6c22bec3fbe2524cde73d7ada88f6566758a8f7227bfbf93a408a9d86bcc12a0 \ --hash=sha256:704219a11b772aea0d8ecd7058d0082713c3562b4e271b849ad7dc4a5c90c13c \ --hash=sha256:7e07cbde391ba96ab58e532ff4803f79c4129397514e1413a7dc761ccd755735 \ --hash=sha256:81e0b275a9ecc9c0c0c07b4b90ba548307583c125f54d5b6946cfee6360c733d \ - --hash=sha256:855fb52b0dc35af121542a76b9a84f8d1cd886ea97c84703eaa6d88e37a2ad28 \ - --hash=sha256:8d4e9c88387b0f5c7d5f281e55304de64cf7f9c0021a3525bd3b1c542da3b0e4 \ --hash=sha256:9046c58c4395dff28dd494285c82ba00b546adfc7ef001486fbf0324bc174fba \ --hash=sha256:9eb6caa9a297fc2c2fb8862bc5370d0303ddba53ba97e71f08023b6cd73d16a8 \ --hash=sha256:a0cd17c15d3bb3fa06978b4e8958dcdc6e0174ccea823003a106c7d4d7899ac5 \ @@ -335,9 +327,7 @@ pyyaml==6.0.1 ; python_version >= "3.9" and python_version < "3.12" \ --hash=sha256:bfdf460b1736c775f2ba9f6a92bca30bc2095067b8a9d77876d1fad6cc3b4a43 \ --hash=sha256:c8098ddcc2a85b61647b2590f825f3db38891662cfc2fc776415143f599bb859 \ --hash=sha256:d2b04aac4d386b172d5b9692e2d2da8de7bfb6c387fa4f801fbf6fb2e6ba4673 \ - --hash=sha256:d483d2cdf104e7c9fa60c544d92981f12ad66a457afae824d146093b8c294c54 \ --hash=sha256:d858aa552c999bc8a8d57426ed01e40bef403cd8ccdd0fc5f6f04a00414cac2a \ - --hash=sha256:e7d73685e87afe9f3b36c799222440d6cf362062f78be1013661b00c5c6f678b \ --hash=sha256:f003ed9ad21d6a4713f0a9b5a7a0a79e08dd0f221aff4525a2be4c346ee60aab \ --hash=sha256:f22ac1c3cac4dbc50079e965eba2c1058622631e526bd9afd45fedd49ba781fa \ --hash=sha256:faca3bdcf85b2fc05d06ff3fbc1f83e1391b3e724afa3feba7d13eeab355484c \ diff --git a/tests/test_response_validator.py b/tests/test_response_validator.py index 449483d..a11a3f5 100644 --- a/tests/test_response_validator.py +++ b/tests/test_response_validator.py @@ -204,6 +204,35 @@ "edges": _TEST_EDGES_4 } +_TEST_KG_EDGE_SOURCES = [ + { + "resource_id": "infores:chebi", + "resource_role": "primary_knowledge_source", + "upstream_resource_ids": [] + }, + { + "resource_id": "infores:biothings-explorer", + "resource_role": "aggregator_knowledge_source", + "upstream_resource_ids": [ + "infores:chebi" + ] + }, + { + "resource_id": "infores:molepro", + "resource_role": "aggregator_knowledge_source", + "upstream_resource_ids": [ + "infores:biothings-explorer" + ] + }, + { + "resource_id": "infores:arax", + "resource_role": "aggregator_knowledge_source", + "upstream_resource_ids": [ + "infores:molepro" + ] + } +] + # From Implementation Guidelines circa June 2023 _TEST_TRAPI_1_4_2_FULL_SAMPLE = { "message": { @@ -227,34 +256,7 @@ "subject": "ncats.drug:9100L32L2N", "predicate": "biolink:ameliorates_condition", "object": "MONDO:0005148", - "sources": [ - { - "resource_id": "infores:chebi", - "resource_role": "primary_knowledge_source", - "upstream_resource_ids": [] - }, - { - "resource_id": "infores:biothings-explorer", - "resource_role": "aggregator_knowledge_source", - "upstream_resource_ids": [ - "infores:chebi" - ] - }, - { - "resource_id": "infores:molepro", - "resource_role": "aggregator_knowledge_source", - "upstream_resource_ids": [ - "infores:biothings-explorer" - ] - }, - { - "resource_id": "infores:arax", - "resource_role": "aggregator_knowledge_source", - "upstream_resource_ids": [ - "infores:molepro" - ] - } - ] + "sources": _TEST_KG_EDGE_SOURCES } } }, @@ -327,34 +329,7 @@ "subject": "MONDO:0005148", "predicate": "biolink:treated_by", "object": "ncats.drug:9100L32L2N", - "sources": [ - { - "resource_id": "infores:chebi", - "resource_role": "primary_knowledge_source", - "upstream_resource_ids": [] - }, - { - "resource_id": "infores:biothings-explorer", - "resource_role": "aggregator_knowledge_source", - "upstream_resource_ids": [ - "infores:chebi" - ] - }, - { - "resource_id": "infores:molepro", - "resource_role": "aggregator_knowledge_source", - "upstream_resource_ids": [ - "infores:biothings-explorer" - ] - }, - { - "resource_id": "infores:arax", - "resource_role": "aggregator_knowledge_source", - "upstream_resource_ids": [ - "infores:molepro" - ] - } - ] + "sources": _TEST_KG_EDGE_SOURCES } } }, diff --git a/tests/test_validate.py b/tests/test_validate.py index 6a0c887..6f4b833 100644 --- a/tests/test_validate.py +++ b/tests/test_validate.py @@ -144,7 +144,7 @@ def test_trapi_pre_1_5_edgebinding(trapi_version: str): }, "EdgeBinding") -@pytest.mark.skip("Test inputs are not yet TRAPI 1.5 compliant") +@pytest.mark.skip(reason="Not updated to work correctly with TRAPI 1.5.0") @pytest.mark.parametrize("trapi_version", LATEST_TEST_RELEASES) def test_trapi_1_5_edgebinding(trapi_version: str): """Test TRAPIValidator(trapi_version=query).validate_EdgeBinding().""" @@ -323,7 +323,7 @@ def test_pre_1_5_query_latest_trapi_workflow_properties(trapi_version: str): validator.validate(faulty_query_wf, "Query") -@pytest.mark.skip("Test inputs are not yet TRAPI 1.5 compliant") +@pytest.mark.skip(reason="Not updated to work correctly with TRAPI 1.5.0") @pytest.mark.parametrize("trapi_version", LATEST_TEST_RELEASES) def test_1_5_query_latest_trapi_workflow_properties(trapi_version: str): """Test flawed TRAPI Query workflow properties.""" @@ -592,7 +592,7 @@ def test_trapi_1_4_message_results_component_validation(trapi_version: str): }, "Result") -@pytest.mark.skip("Test inputs are not yet TRAPI 1.5 compliant") +@pytest.mark.skip(reason="Not updated to work correctly with TRAPI 1.5.0") @pytest.mark.parametrize("trapi_version", LATEST_TEST_RELEASES) def test_latest_trapi_message_results_component_validation(trapi_version: str): """Test Message.Results component in TRAPIValidator(trapi_version=query).validate().""" @@ -758,7 +758,8 @@ def test_message_pre_1_5_node_binding_component_validation(trapi_version: str): "bar": {}, }, "NodeBinding") -@pytest.mark.skip("Test inputs are not yet TRAPI 1.5 compliant") + +@pytest.mark.skip(reason="Not updated to work correctly with TRAPI 1.5.0") @pytest.mark.parametrize("trapi_version", LATEST_TEST_RELEASES) def test_latest_trapi_message_node_binding_component_validation(trapi_version: str): """Test NodeBinding component in TRAPIValidator(trapi_version=query).validate().""" diff --git a/tests/test_workflows.py b/tests/test_workflows.py index fa7c763..382daa0 100644 --- a/tests/test_workflows.py +++ b/tests/test_workflows.py @@ -84,7 +84,7 @@ def test_trapi_1_4_query_trapi_workflow_properties(trapi_version: str, query: Di TRAPI_LATEST_TRAPI_QUERY_VERSION = [qv for qv in product(LATEST_TEST_RELEASES, (SAMPLE_QUERY_1, SAMPLE_QUERY_2))] -@pytest.mark.skip("Test inputs are not yet TRAPI 1.5 compliant") +@pytest.mark.skip(reason="Not updated to work correctly with TRAPI 1.5.0") @pytest.mark.parametrize("trapi_version,query", TRAPI_LATEST_TRAPI_QUERY_VERSION) def test_query_latest_trapi_workflow_properties(trapi_version: str, query: Dict): """Test flawed TRAPI Query workflow properties."""