diff --git a/poetry.lock b/poetry.lock index 1a16ec09..fac22e3d 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1,9 +1,10 @@ -# This file is automatically @generated by Poetry 1.8.2 and should not be changed by hand. +# This file is automatically @generated by Poetry 1.4.0 and should not be changed by hand. [[package]] name = "alabaster" version = "0.7.13" description = "A configurable sidebar-enabled Sphinx theme" +category = "main" optional = false python-versions = ">=3.6" files = [ @@ -15,6 +16,7 @@ files = [ name = "annotated-types" version = "0.6.0" description = "Reusable constraint types to use with typing.Annotated" +category = "main" optional = false python-versions = ">=3.8" files = [ @@ -26,6 +28,7 @@ files = [ name = "antlr4-python3-runtime" version = "4.9.3" description = "ANTLR 4.9.3 runtime for Python 3.7" +category = "main" optional = false python-versions = "*" files = [ @@ -36,6 +39,7 @@ files = [ name = "arrow" version = "1.3.0" description = "Better dates & times for Python" +category = "main" optional = false python-versions = ">=3.8" files = [ @@ -49,12 +53,13 @@ types-python-dateutil = ">=2.8.10" [package.extras] doc = ["doc8", "sphinx (>=7.0.0)", "sphinx-autobuild", "sphinx-autodoc-typehints", "sphinx_rtd_theme (>=1.3.0)"] -test = ["dateparser (==1.*)", "pre-commit", "pytest", "pytest-cov", "pytest-mock", "pytz (==2021.1)", "simplejson (==3.*)"] +test = ["dateparser (>=1.0.0,<2.0.0)", "pre-commit", "pytest", "pytest-cov", "pytest-mock", "pytz (==2021.1)", "simplejson (>=3.0.0,<4.0.0)"] [[package]] name = "attrs" version = "23.1.0" description = "Classes Without Boilerplate" +category = "main" optional = false python-versions = ">=3.7" files = [ @@ -73,6 +78,7 @@ tests-no-zope = ["cloudpickle", "hypothesis", "mypy (>=1.1.1)", "pympler", "pyte name = "babel" version = "2.13.1" description = "Internationalization utilities" +category = "main" optional = false python-versions = ">=3.7" files = [ @@ -88,24 +94,33 @@ dev = ["freezegun (>=1.0,<2.0)", "pytest (>=6.0)", "pytest-cov"] [[package]] name = "bmt" -version = "1.3.0" +version = "1.3.0.post4.dev0+d867edc" description = "Biolink Model Toolkit: A Python API for working with the Biolink Model" +category = "main" optional = false -python-versions = "<4.0,>=3.9" -files = [ - {file = "bmt-1.3.0-py3-none-any.whl", hash = "sha256:3518ae7afca94f2cd18122e37c20f1b079007c3445bc428dcb6e044270979406"}, - {file = "bmt-1.3.0.tar.gz", hash = "sha256:278b861d9e4b7c33437ae5135fa02d592a568bae5bf204a686111fa360b463a8"}, -] +python-versions = "^3.9" +files = [] +develop = false [package.dependencies] -deprecation = ">=2.1.0,<3.0.0" -linkml-runtime = ">=1.6.3,<2.0.0" -stringcase = ">=1.2.0,<2.0.0" +deprecation = "^2.1.0" +linkml-runtime = "^1.6.3" +stringcase = "^1.2.0" + +[package.extras] +docs = [] + +[package.source] +type = "git" +url = "https://github.com/biolink/biolink-model-toolkit.git" +reference = "1.4.0" +resolved_reference = "d867edc9c3eeaf3540fc9eaa1ef13e98c635ab72" [[package]] name = "cachetools" version = "5.3.2" description = "Extensible memoizing collections and decorators" +category = "main" optional = false python-versions = ">=3.7" files = [ @@ -117,6 +132,7 @@ files = [ name = "certifi" version = "2023.11.17" description = "Python package for providing Mozilla's CA Bundle." +category = "main" optional = false python-versions = ">=3.6" files = [ @@ -128,6 +144,7 @@ files = [ name = "cfgraph" version = "0.2.1" description = "rdflib collections flattening graph" +category = "main" optional = false python-versions = "*" files = [ @@ -141,6 +158,7 @@ rdflib = ">=0.4.2" name = "chardet" version = "5.2.0" description = "Universal encoding detector for Python 3" +category = "main" optional = false python-versions = ">=3.7" files = [ @@ -152,6 +170,7 @@ files = [ name = "charset-normalizer" version = "3.3.2" description = "The Real First Universal Charset Detector. 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test_validator_explicit_biolink_version(): subject="CHEMBL.COMPOUND:1222250", object="UBERON:0000001", category=["biolink:Association"], + knowledge_level="not_provided", + agent_type="not_provided", ) Validator.set_biolink_model(toolkit.get_model_version()) validator = Validator(verbose=True) diff --git a/tests/resources/chebi_kgx_tsv_edges.tsv b/tests/resources/chebi_kgx_tsv_edges.tsv index 83fa3f2e..47407187 100644 --- a/tests/resources/chebi_kgx_tsv_edges.tsv +++ b/tests/resources/chebi_kgx_tsv_edges.tsv @@ -1,10 +1,10 @@ -id subject predicate object category relation knowledge_source logical_interpretation -CHEBI:101257-biolink:subclass_of-CHEBI:22702 CHEBI:101257 biolink:subclass_of CHEBI:22702 rdfs:subClassOf chebiasc66dwf -CHEBI:101257-biolink:subclass_of-CHEBI:64459 CHEBI:101257 biolink:subclass_of CHEBI:64459 rdfs:subClassOf chebiasc66dwf -CHEBI:101257-biolink:subclass_of-CHEBI:50995 CHEBI:101257 biolink:subclass_of CHEBI:50995 rdfs:subClassOf chebiasc66dwf -CHEBI:101257-biolink:subclass_of-CHEBI:25018 CHEBI:101257 biolink:subclass_of CHEBI:25018 rdfs:subClassOf chebiasc66dwf -CHEBI:101257-biolink:subclass_of-CHEBI:48975 CHEBI:101257 biolink:subclass_of CHEBI:48975 rdfs:subClassOf chebiasc66dwf -CHEBI:101257-biolink:subclass_of-CHEBI:21644 CHEBI:101257 biolink:subclass_of CHEBI:21644 rdfs:subClassOf chebiasc66dwf -CHEBI:101257-biolink:subclass_of-CHEBI:25477 CHEBI:101257 biolink:subclass_of CHEBI:25477 rdfs:subClassOf chebiasc66dwf -CHEBI:101257-biolink:subclass_of-CHEBI:24780 CHEBI:101257 biolink:subclass_of CHEBI:24780 rdfs:subClassOf chebiasc66dwf -urn:uuid:6c0781c9-a64a-4750-be57-5c352a3b93fd CHEBI:101257 biolink:has_attribute CHEBI:67267 biolink:Association RO:0000087 chebiasc66dwf owlstar:AllSomeInterpretation +id subject predicate object category relation knowledge_source logical_interpretation knowledge_level agent_type +CHEBI:101257-biolink:subclass_of-CHEBI:22702 CHEBI:101257 biolink:subclass_of CHEBI:22702 rdfs:subClassOf chebiasc66dwf not_provided not_provided +CHEBI:101257-biolink:subclass_of-CHEBI:64459 CHEBI:101257 biolink:subclass_of CHEBI:64459 rdfs:subClassOf chebiasc66dwf not_provided not_provided +CHEBI:101257-biolink:subclass_of-CHEBI:50995 CHEBI:101257 biolink:subclass_of CHEBI:50995 rdfs:subClassOf chebiasc66dwf not_provided not_provided +CHEBI:101257-biolink:subclass_of-CHEBI:25018 CHEBI:101257 biolink:subclass_of CHEBI:25018 rdfs:subClassOf chebiasc66dwf not_provided not_provided +CHEBI:101257-biolink:subclass_of-CHEBI:48975 CHEBI:101257 biolink:subclass_of CHEBI:48975 rdfs:subClassOf chebiasc66dwf not_provided not_provided +CHEBI:101257-biolink:subclass_of-CHEBI:21644 CHEBI:101257 biolink:subclass_of CHEBI:21644 rdfs:subClassOf chebiasc66dwf not_provided not_provided +CHEBI:101257-biolink:subclass_of-CHEBI:25477 CHEBI:101257 biolink:subclass_of CHEBI:25477 rdfs:subClassOf chebiasc66dwf not_provided not_provided +CHEBI:101257-biolink:subclass_of-CHEBI:24780 CHEBI:101257 biolink:subclass_of CHEBI:24780 rdfs:subClassOf chebiasc66dwf not_provided not_provided +urn:uuid:6c0781c9-a64a-4750-be57-5c352a3b93fd CHEBI:101257 biolink:has_attribute CHEBI:67267 biolink:Association RO:0000087 chebiasc66dwf owlstar:AllSomeInterpretation not_provided not_provided diff --git a/tests/resources/cm_edges.csv b/tests/resources/cm_edges.csv index ec966bcb..8e442636 100644 --- a/tests/resources/cm_edges.csv +++ b/tests/resources/cm_edges.csv @@ -1,12 +1,12 @@ -subject,epredicate,object,relation,predicate,provided_by -HGNC:7670,http://www.w3.org/2002/07/owl#equivalentClass,OMIM:601937,owl:equivalentClass,biolink:same_as,hgnc.ttl -HGNC:7670,http://www.w3.org/2002/07/owl#equivalentClass,ENSEMBL:ENSG00000124151,owl:equivalentClass,biolink:same_as,hgnc.ttl -HGNC:7670,http://www.w3.org/2002/07/owl#equivalentClass,NCBIGene:8202,owl:equivalentClass,biolink:same_as,hgnc.ttl -HGNC:35302,http://www.w3.org/2002/07/owl#equivalentClass,ENSEMBL:ENSG00000284458,owl:equivalentClass,biolink:same_as,hgnc.ttl -HGNC:35302,http://www.w3.org/2002/07/owl#equivalentClass,NCBIGene:100302240,owl:equivalentClass,biolink:same_as,hgnc.ttl -OMIM:601937,http://www.w3.org/2000/01/rdf-schema#subClassOf,SO:0001217,rdfs:subClassOf,biolink:subclass_of,hgnc.ttl -ENSEMBL:ENSG00000124151,http://www.w3.org/2000/01/rdf-schema#subClassOf,SO:0001217,rdfs:subClassOf,biolink:subclass_of,hgnc.ttl -ENSEMBL:ENSG00000284458,http://www.w3.org/2000/01/rdf-schema#subClassOf,SO:0001265,rdfs:subClassOf,biolink:subclass_of,hgnc.ttl -NCBIGene:100302240,http://www.w3.org/2000/01/rdf-schema#subClassOf,SO:0001265,rdfs:subClassOf,biolink:subclass_of,hgnc.ttl -HGNC:3121,http://www.w3.org/2000/01/rdf-schema#subClassOf,SO:0001217,rdfs:subClassOf,biolink:subclass_of,hgnc.ttl -HGNC:35302,interacts_with,HGNC:3121,RO:00000000,biolink:interacts_with,test.ttl \ No newline at end of file +subject,epredicate,object,relation,predicate,provided_by,knowledge_level,agent_type +HGNC:7670,http://www.w3.org/2002/07/owl#equivalentClass,OMIM:601937,owl:equivalentClass,biolink:same_as,hgnc.ttl,not_provided,not_provided +HGNC:7670,http://www.w3.org/2002/07/owl#equivalentClass,ENSEMBL:ENSG00000124151,owl:equivalentClass,biolink:same_as,hgnc.ttl,not_provided,not_provided +HGNC:7670,http://www.w3.org/2002/07/owl#equivalentClass,NCBIGene:8202,owl:equivalentClass,biolink:same_as,hgnc.ttl,not_provided,not_provided +HGNC:35302,http://www.w3.org/2002/07/owl#equivalentClass,ENSEMBL:ENSG00000284458,owl:equivalentClass,biolink:same_as,hgnc.ttl,not_provided,not_provided +HGNC:35302,http://www.w3.org/2002/07/owl#equivalentClass,NCBIGene:100302240,owl:equivalentClass,biolink:same_as,hgnc.ttl,not_provided,not_provided +OMIM:601937,http://www.w3.org/2000/01/rdf-schema#subClassOf,SO:0001217,rdfs:subClassOf,biolink:subclass_of,hgnc.ttl,not_provided,not_provided +ENSEMBL:ENSG00000124151,http://www.w3.org/2000/01/rdf-schema#subClassOf,SO:0001217,rdfs:subClassOf,biolink:subclass_of,hgnc.ttl,not_provided,not_provided +ENSEMBL:ENSG00000284458,http://www.w3.org/2000/01/rdf-schema#subClassOf,SO:0001265,rdfs:subClassOf,biolink:subclass_of,hgnc.ttl,not_provided,not_provided +NCBIGene:100302240,http://www.w3.org/2000/01/rdf-schema#subClassOf,SO:0001265,rdfs:subClassOf,biolink:subclass_of,hgnc.ttl,not_provided,not_provided +HGNC:3121,http://www.w3.org/2000/01/rdf-schema#subClassOf,SO:0001217,rdfs:subClassOf,biolink:subclass_of,hgnc.ttl,not_provided,not_provided +HGNC:35302,interacts_with,HGNC:3121,RO:00000000,biolink:interacts_with,test.ttl,not_provided,not_provided \ No newline at end of file diff --git a/tests/resources/cm_test2_edges.tsv b/tests/resources/cm_test2_edges.tsv index d51f7352..eac845dc 100644 --- a/tests/resources/cm_test2_edges.tsv +++ b/tests/resources/cm_test2_edges.tsv @@ -1,19 +1,19 @@ -subject object relation predicate provided_by -HGNC:7670 OMIM:601937 owl:equivalentClass biolink:same_as Test -HGNC:7670 ENSEMBL:ENSG00000124151 owl:equivalentClass biolink:same_as Test -HGNC:7670 NCBIGene:8202 owl:equivalentClass biolink:same_as Test -HGNC:35302 ENSEMBL:ENSG00000284458 owl:equivalentClass biolink:same_as Test -HGNC:35302 NCBIGene:100302240 owl:equivalentClass biolink:same_as Test -OMIM:601937 SO:0001217 rdfs:subClassOf biolink:subclass_of Test -ENSEMBL:ENSG00000284458 SO:0001265 rdfs:subClassOf biolink:subclass_of Test -OMIM:601937 SO:0001217 rdfs:subClassOf biolink:subclass_of Test -OMIM:601937 UniProt:1 RO:0002434 biolink:interacts_with Test -OMIM:601937 UniProt:2 RO:0002434 biolink:interacts_with Test -OMIM:601937 UniProt:3 RO:0002434 biolink:interacts_with Test -OMIM:601937 UniProt:4 RO:0002434 biolink:interacts_with Test -PMID:1 NCBIGene:8202 RO:0000000 biolink:related_to Test -PMID:2 NCBIGene:8202 RO:0000000 biolink:related_to Test -PMID:3 NCBIGene:8202 RO:0000000 biolink:related_to Test -NCBIGene:100302240 SO:0001265 rdfs:subClassOf biolink:subclass_of Test -HGNC:3121 SO:0001217 rdfs:subClassOf biolink:subclass_of Test -HGNC:35302 HGNC:3121 RO:0002434 biolink:interacts_with Test \ No newline at end of file +subject object relation predicate provided_by knowledge_level agent_type +HGNC:7670 OMIM:601937 owl:equivalentClass biolink:same_as Test not_provided not_provided +HGNC:7670 ENSEMBL:ENSG00000124151 owl:equivalentClass biolink:same_as Test not_provided not_provided +HGNC:7670 NCBIGene:8202 owl:equivalentClass biolink:same_as Test not_provided not_provided +HGNC:35302 ENSEMBL:ENSG00000284458 owl:equivalentClass biolink:same_as Test not_provided not_provided +HGNC:35302 NCBIGene:100302240 owl:equivalentClass biolink:same_as Test not_provided not_provided +OMIM:601937 SO:0001217 rdfs:subClassOf biolink:subclass_of Test not_provided not_provided +ENSEMBL:ENSG00000284458 SO:0001265 rdfs:subClassOf biolink:subclass_of Test not_provided not_provided +OMIM:601937 SO:0001217 rdfs:subClassOf biolink:subclass_of Test not_provided not_provided +OMIM:601937 UniProt:1 RO:0002434 biolink:interacts_with Test not_provided not_provided +OMIM:601937 UniProt:2 RO:0002434 biolink:interacts_with Test not_provided not_provided +OMIM:601937 UniProt:3 RO:0002434 biolink:interacts_with Test not_provided not_provided +OMIM:601937 UniProt:4 RO:0002434 biolink:interacts_with Test not_provided not_provided +PMID:1 NCBIGene:8202 RO:0000000 biolink:related_to Test not_provided not_provided +PMID:2 NCBIGene:8202 RO:0000000 biolink:related_to Test not_provided not_provided +PMID:3 NCBIGene:8202 RO:0000000 biolink:related_to Test not_provided not_provided +NCBIGene:100302240 SO:0001265 rdfs:subClassOf biolink:subclass_of Test not_provided not_provided +HGNC:3121 SO:0001217 rdfs:subClassOf biolink:subclass_of Test not_provided not_provided +HGNC:35302 HGNC:3121 RO:0002434 biolink:interacts_with Test not_provided not_provided \ No newline at end of file diff --git a/tests/resources/complex_graph_edges.tsv b/tests/resources/complex_graph_edges.tsv index b41ad96d..b9e48066 100644 --- a/tests/resources/complex_graph_edges.tsv +++ b/tests/resources/complex_graph_edges.tsv @@ -1,8 +1,8 @@ -subject object predicate relation aggregator_knowledge_source -HGNC:10848 NCBIGene:6469 biolink:interacts_with RO:0002434 biogrid -HGNC:10848 HGNC:9398 biolink:interacts_with RO:0002434|RO:0002434|RO:0002434 string -HGNC:10848 HGNC:9399 biolink:interacts_with RO:0002434 string -HGNC:10848 HGNC:16265 biolink:interacts_with RO:0002434 string -HGNC:10848 HGNC:16787 biolink:interacts_with RO:0002434 biogrid -HGNC:10848 GO:0009986 biolink:part_of BFO:0000050 go -HGNC:10848 GO:0097190 biolink:related_to RO:0002331|RO:0002327 go \ No newline at end of file +subject object predicate relation aggregator_knowledge_source knowledge_level agent_type +HGNC:10848 NCBIGene:6469 biolink:interacts_with RO:0002434 biogrid not_provided not_provided +HGNC:10848 HGNC:9398 biolink:interacts_with RO:0002434|RO:0002434|RO:0002434 string not_provided not_provided +HGNC:10848 HGNC:9399 biolink:interacts_with RO:0002434 string not_provided not_provided +HGNC:10848 HGNC:16265 biolink:interacts_with RO:0002434 string not_provided not_provided +HGNC:10848 HGNC:16787 biolink:interacts_with RO:0002434 biogrid not_provided not_provided +HGNC:10848 GO:0009986 biolink:part_of BFO:0000050 go not_provided not_provided +HGNC:10848 GO:0097190 biolink:related_to RO:0002331|RO:0002327 go not_provided not_provided \ No newline at end of file diff --git a/tests/resources/graph_edges.tsv b/tests/resources/graph_edges.tsv index 01f8ccc8..265bd25c 100644 --- a/tests/resources/graph_edges.tsv +++ b/tests/resources/graph_edges.tsv @@ -1,540 +1,540 @@ -subject object predicate relation aggregator_knowledge_source -HGNC:10848 NCBIGene:6469 biolink:interacts_with RO:0002434 string|biogrid -HGNC:10848 HGNC:9398 biolink:interacts_with RO:0002434 string -HGNC:10848 HGNC:9399 biolink:interacts_with RO:0002434 string -HGNC:10848 HGNC:16265 biolink:interacts_with RO:0002434 string -HGNC:10848 HGNC:16262 biolink:interacts_with RO:0002434 string -HGNC:10848 HGNC:16466 biolink:interacts_with RO:0002434 string -HGNC:10848 HGNC:16787 biolink:interacts_with RO:0002434 biogrid -HGNC:10848 HGNC:16889 biolink:interacts_with RO:0002434 string -HGNC:10848 HGNC:16809 biolink:interacts_with RO:0002434 string -HGNC:10848 HGNC:16807 biolink:interacts_with RO:0002434 string -HGNC:10848 HGNC:16994 biolink:interacts_with RO:0002434 string -HGNC:10848 HGNC:9530 biolink:interacts_with RO:0002434 string -HGNC:10848 HGNC:9531 biolink:interacts_with RO:0002434 string -HGNC:10848 HGNC:9532 biolink:interacts_with RO:0002434 string -HGNC:10848 HGNC:9533 biolink:interacts_with RO:0002434 string -HGNC:10848 HGNC:9534 biolink:interacts_with RO:0002434 string -HGNC:10848 HGNC:9540 biolink:interacts_with RO:0002434 string -HGNC:10848 HGNC:9541 biolink:interacts_with RO:0002434 string -HGNC:10848 HGNC:9542 biolink:interacts_with RO:0002434 string -HGNC:10848 HGNC:9543 biolink:interacts_with RO:0002434 string -HGNC:10848 HGNC:9544 biolink:interacts_with RO:0002434 string -HGNC:10848 HGNC:9545 biolink:interacts_with RO:0002434 string -HGNC:10848 HGNC:9535 biolink:interacts_with RO:0002434 string -HGNC:10848 HGNC:9536 biolink:interacts_with RO:0002434 string -HGNC:10848 HGNC:9537 biolink:interacts_with RO:0002434 string -HGNC:10848 HGNC:9538 biolink:interacts_with RO:0002434 string -HGNC:10848 HGNC:9539 biolink:interacts_with RO:0002434 string -HGNC:10848 HGNC:9571 biolink:interacts_with RO:0002434 string -HGNC:10848 HGNC:9570 biolink:interacts_with RO:0002434 string -HGNC:10848 HGNC:9568 biolink:interacts_with RO:0002434 string -HGNC:10848 HGNC:9569 biolink:interacts_with RO:0002434 string -HGNC:10848 HGNC:9585 biolink:interacts_with RO:0002434 string -HGNC:10848 HGNC:9586 biolink:interacts_with RO:0002434 string -HGNC:10848 HGNC:9552 biolink:interacts_with RO:0002434 string -HGNC:10848 HGNC:9553 biolink:interacts_with RO:0002434 string -HGNC:10848 HGNC:9554 biolink:interacts_with RO:0002434 string -HGNC:10848 HGNC:9555 biolink:interacts_with RO:0002434 string -HGNC:10848 HGNC:9556 biolink:interacts_with RO:0002434 string -HGNC:10848 HGNC:9546 biolink:interacts_with RO:0002434 string -HGNC:10848 HGNC:9547 biolink:interacts_with RO:0002434 string -HGNC:10848 HGNC:9548 biolink:interacts_with RO:0002434 string -HGNC:10848 HGNC:9549 biolink:interacts_with RO:0002434 string -HGNC:10848 HGNC:9560 biolink:interacts_with RO:0002434 string -HGNC:10848 HGNC:9561 biolink:interacts_with RO:0002434 string -HGNC:10848 HGNC:9565 biolink:interacts_with RO:0002434 string -HGNC:10848 HGNC:9566 biolink:interacts_with RO:0002434 string -HGNC:10848 HGNC:9567 biolink:interacts_with RO:0002434 string -HGNC:10848 HGNC:9551 biolink:interacts_with RO:0002434 string -HGNC:10848 HGNC:9557 biolink:interacts_with RO:0002434 string -HGNC:10848 HGNC:9559 biolink:interacts_with RO:0002434 string -HGNC:10848 HGNC:9563 biolink:interacts_with RO:0002434 string -HGNC:10848 HGNC:20635 biolink:interacts_with RO:0002434 string -HGNC:10848 HGNC:20738 biolink:interacts_with RO:0002434 string|biogrid -HGNC:10848 HGNC:15877 biolink:interacts_with RO:0002434 biogrid -HGNC:10848 HGNC:15983 biolink:interacts_with RO:0002434 string -HGNC:10848 HGNC:8548 biolink:interacts_with RO:0002434 string -HGNC:10848 HGNC:8522 biolink:interacts_with RO:0002434 string -HGNC:10848 HGNC:8620 biolink:interacts_with RO:0002434 string -HGNC:10848 HGNC:8621 biolink:interacts_with RO:0002434 string -HGNC:10848 HGNC:8615 biolink:interacts_with RO:0002434 string -HGNC:10848 HGNC:8616 biolink:interacts_with RO:0002434 string -HGNC:10848 HGNC:8617 biolink:interacts_with RO:0002434 string -HGNC:10848 HGNC:23734 biolink:interacts_with RO:0002434 string -HGNC:10848 HGNC:2865 biolink:interacts_with RO:0002434 string -HGNC:10848 HGNC:2895 biolink:interacts_with RO:0002434 string -HGNC:10848 HGNC:2914 biolink:interacts_with RO:0002434 string -HGNC:10848 HGNC:18081 biolink:interacts_with RO:0002434 string -HGNC:10848 HGNC:18270 biolink:interacts_with RO:0002434 string -HGNC:10848 HGNC:18967 biolink:interacts_with RO:0002434 biogrid -HGNC:10848 HGNC:2514 biolink:interacts_with RO:0002434 string -HGNC:10848 HGNC:1582 biolink:interacts_with RO:0002434 string -HGNC:10848 HGNC:1579 biolink:interacts_with RO:0002434 string -HGNC:10848 HGNC:1722 biolink:interacts_with RO:0002434 string -HGNC:10848 HGNC:22985 biolink:interacts_with RO:0002434 string -HGNC:10848 HGNC:17173 biolink:interacts_with RO:0002434 string -HGNC:10848 HGNC:1033 biolink:interacts_with RO:0002434 string -HGNC:10848 HGNC:17104 biolink:interacts_with RO:0002434 string -HGNC:10848 HGNC:1074 biolink:interacts_with RO:0002434 string -HGNC:10848 HGNC:1071 biolink:interacts_with RO:0002434 string -HGNC:10848 HGNC:1069 biolink:interacts_with RO:0002434 string -HGNC:10848 HGNC:17943 biolink:interacts_with RO:0002434 string|biogrid -HGNC:10848 HGNC:11782 biolink:interacts_with RO:0002434 string -HGNC:10848 HGNC:11825 biolink:interacts_with RO:0002434 string -HGNC:10848 HGNC:11998 biolink:interacts_with RO:0002434 string -HGNC:10848 HGNC:4808 biolink:interacts_with RO:0002434 string -HGNC:10848 HGNC:31963 biolink:interacts_with RO:0002434 string -HGNC:10848 HGNC:5173 biolink:interacts_with RO:0002434 string -HGNC:10848 HGNC:5136 biolink:interacts_with RO:0002434 string -HGNC:10848 HGNC:5273 biolink:interacts_with RO:0002434 string -HGNC:10848 HGNC:12463 biolink:interacts_with RO:0002434 string -HGNC:10848 HGNC:12468 biolink:interacts_with RO:0002434 string -HGNC:10848 HGNC:12458 biolink:interacts_with RO:0002434 string -HGNC:10848 HGNC:12666 biolink:interacts_with RO:0002434 string -HGNC:10848 HGNC:12680 biolink:interacts_with RO:0002434 string -HGNC:10848 HGNC:12780 biolink:interacts_with RO:0002434 string -HGNC:10848 HGNC:12784 biolink:interacts_with RO:0002434 string -HGNC:10848 HGNC:12779 biolink:interacts_with RO:0002434 string -HGNC:10848 HGNC:12774 biolink:interacts_with RO:0002434 string -HGNC:10848 HGNC:12778 biolink:interacts_with RO:0002434 string -HGNC:10848 HGNC:5022 biolink:interacts_with RO:0002434 string -HGNC:10848 HGNC:12872 biolink:interacts_with RO:0002434 string -HGNC:10848 HGNC:12873 biolink:interacts_with RO:0002434 string -HGNC:10848 HGNC:10417 biolink:interacts_with RO:0002434 string -HGNC:10848 HGNC:10472 biolink:interacts_with RO:0002434 string -HGNC:10848 HGNC:10776 biolink:interacts_with RO:0002434 string -HGNC:10848 HGNC:10717 biolink:interacts_with RO:0002434 string|biogrid -HGNC:10848 HGNC:10889 biolink:interacts_with RO:0002434 string -HGNC:10848 HGNC:19221 biolink:interacts_with RO:0002434 string -HGNC:10848 HGNC:10879 biolink:interacts_with RO:0002434 string -HGNC:10848 HGNC:10845 biolink:interacts_with RO:0002434 string -HGNC:10848 HGNC:3670 biolink:interacts_with RO:0002434 string -HGNC:10848 HGNC:3666 biolink:interacts_with RO:0002434 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RO:0002434 string -HGNC:10848 HGNC:4453 biolink:interacts_with RO:0002434 string -HGNC:10848 HGNC:4454 biolink:interacts_with RO:0002434 string -HGNC:10848 HGNC:25222 biolink:interacts_with RO:0002434 string -HGNC:10848 HGNC:738 biolink:interacts_with RO:0002434 string -HGNC:10848 HGNC:4317 biolink:interacts_with RO:0002434 string -HGNC:10848 HGNC:4318 biolink:interacts_with RO:0002434 string -HGNC:10848 HGNC:4319 biolink:interacts_with RO:0002434 string -HGNC:10848 HGNC:797 biolink:interacts_with RO:0002434 string -HGNC:10848 HGNC:195 biolink:interacts_with RO:0002434 string -HGNC:10848 HGNC:11195 biolink:interacts_with RO:0002434 string -HGNC:10848 HGNC:11119 biolink:interacts_with RO:0002434 string -HGNC:10848 HGNC:391 biolink:interacts_with RO:0002434 string -HGNC:10848 HGNC:11204 biolink:interacts_with RO:0002434 string -HGNC:10848 HGNC:28454 biolink:interacts_with RO:0002434 biogrid -HGNC:10848 HGNC:7764 biolink:interacts_with RO:0002434 string -HGNC:10848 HGNC:7835 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RO:0002200 hpoa not_provided manual_agent +MONDO:0010011 HP:0010636 biolink:has_phenotype RO:0002200 hpoa not_provided manual_agent +MONDO:0010011 HP:0007370 biolink:has_phenotype RO:0002200 hpoa not_provided manual_agent +MONDO:0010011 HP:0001250 biolink:has_phenotype RO:0002200 hpoa not_provided manual_agent +MONDO:0010011 HP:0001269 biolink:has_phenotype RO:0002200 hpoa not_provided manual_agent +MONDO:0010011 HP:0001263 biolink:has_phenotype RO:0002200 hpoa not_provided manual_agent +MONDO:0010011 HP:0001257 biolink:has_phenotype RO:0002200 hpoa not_provided manual_agent +MONDO:0010011 HP:0001249 biolink:has_phenotype RO:0002200 hpoa not_provided manual_agent +MONDO:0010011 HP:0001274 biolink:has_phenotype RO:0002200 hpoa not_provided manual_agent +MONDO:0010011 HP:0002353 biolink:has_phenotype RO:0002200 hpoa not_provided manual_agent \ No newline at end of file diff --git a/tests/resources/graph_edges_small.tsv b/tests/resources/graph_edges_small.tsv index 7d3fb9db..7e509d47 100644 --- a/tests/resources/graph_edges_small.tsv +++ b/tests/resources/graph_edges_small.tsv @@ -1,3 +1,3 @@ -subject,object,predicate,relation,aggregator_knowledge_source -HGNC:20635,biolink:interacts_with,RO:0002434,string -HGNC:10848,HGNC:20738,biolink:interacts_with,RO:0002434,string|biogrid \ No newline at end of file +subject,object,predicate,relation,aggregator_knowledge_source,knowledge_level,agent_type +HGNC:20635,biolink:interacts_with,RO:0002434,string,not_provided,not_provided +HGNC:10848,HGNC:20738,biolink:interacts_with,RO:0002434,string|biogrid,not_provided,not_provided \ No newline at end of file diff --git a/tests/resources/graph_multi_category_edges.tsv b/tests/resources/graph_multi_category_edges.tsv index 5da29fc0..b4aa530b 100644 --- a/tests/resources/graph_multi_category_edges.tsv +++ b/tests/resources/graph_multi_category_edges.tsv @@ -1,10 +1,10 @@ -subject object predicate relation provided_by -HGNC:10848 NCBIGene:6469 biolink:interacts_with RO:0002434 biogrid -HGNC:10848 HGNC:9398 biolink:interacts_with RO:0002434 string -HGNC:10848 HGNC:9399 biolink:interacts_with RO:0002434 string -HGNC:10848 HGNC:16265 biolink:interacts_with RO:0002434 string -MONDO:0010011 HP:0002510 biolink:has_phenotype RO:0002200 hpoa -MONDO:0010011 HP:0002132 biolink:has_phenotype RO:0002200 hpoa -MONDO:0010011 HP:0002120 biolink:has_phenotype RO:0002200 hpoa -MONDO:0010011 HP:0000486 biolink:has_phenotype RO:0002200 hpoa -MONDO:0010011 HP:0010636 biolink:has_phenotype RO:0002200 hpoa +subject object predicate relation provided_by knowledge_level agent_type +HGNC:10848 NCBIGene:6469 biolink:interacts_with RO:0002434 biogrid not_provided manual_agent +HGNC:10848 HGNC:9398 biolink:interacts_with RO:0002434 string not_provided manual_agent +HGNC:10848 HGNC:9399 biolink:interacts_with RO:0002434 string not_provided manual_agent +HGNC:10848 HGNC:16265 biolink:interacts_with RO:0002434 string not_provided manual_agent +MONDO:0010011 HP:0002510 biolink:has_phenotype RO:0002200 hpoa not_provided manual_agent +MONDO:0010011 HP:0002132 biolink:has_phenotype RO:0002200 hpoa not_provided manual_agent +MONDO:0010011 HP:0002120 biolink:has_phenotype RO:0002200 hpoa not_provided manual_agent +MONDO:0010011 HP:0000486 biolink:has_phenotype RO:0002200 hpoa not_provided manual_agent +MONDO:0010011 HP:0010636 biolink:has_phenotype RO:0002200 hpoa not_provided manual_agent diff --git a/tests/resources/graph_tiny_edges.tsv b/tests/resources/graph_tiny_edges.tsv index f9dfcc28..10e9fc31 100644 --- a/tests/resources/graph_tiny_edges.tsv +++ b/tests/resources/graph_tiny_edges.tsv @@ -1,11 +1,11 @@ -subject object predicate relation aggregator_knowledge_source -HGNC:10848 GO:0005576 biolink:part_of BFO:0000050 go -HGNC:20635 GO:0005576 biolink:part_of BFO:0000050 go|string -HGNC:20738 GO:0005576 biolink:part_of BFO:0000050 biogrid|go|string -HGNC:20635 HGNC:20635 biolink:interacts_with RO:0002434 string -HGNC:10848 HGNC:20735 biolink:interacts_with RO:0002434 string|biogrid -HGNC:20635 HGNC:20735 biolink:interacts_with RO:0002434 string -HGNC:20635 HGNC:10848 biolink:interacts_with RO:0002434 biogrid -HGNC:20634 HGNC:10848 biolink:interacts_with RO:0002434 string|biogrid -HGNC:20634 HGNC:20738 biolink:interacts_with RO:0002434 biogrid|string -HGNC:20634 HGNC:20738 biolink:interacts_with RO:0002434 new_thing_source \ No newline at end of file +subject object predicate relation aggregator_knowledge_source knowledge_level agent_type +HGNC:10848 GO:0005576 biolink:part_of BFO:0000050 go not_provided manual_agent +HGNC:20635 GO:0005576 biolink:part_of BFO:0000050 go|string not_provided manual_agent +HGNC:20738 GO:0005576 biolink:part_of BFO:0000050 biogrid|go|string not_provided manual_agent +HGNC:20635 HGNC:20635 biolink:interacts_with RO:0002434 string not_provided manual_agent +HGNC:10848 HGNC:20735 biolink:interacts_with RO:0002434 string|biogrid not_provided manual_agent +HGNC:20635 HGNC:20735 biolink:interacts_with RO:0002434 string not_provided manual_agent +HGNC:20635 HGNC:10848 biolink:interacts_with RO:0002434 biogrid not_provided manual_agent +HGNC:20634 HGNC:10848 biolink:interacts_with RO:0002434 string|biogrid not_provided manual_agent +HGNC:20634 HGNC:20738 biolink:interacts_with RO:0002434 biogrid|string not_provided manual_agent +HGNC:20634 HGNC:20738 biolink:interacts_with RO:0002434 new_thing_source not_provided manual_agent \ No newline at end of file diff --git a/tests/resources/json_edges.json b/tests/resources/json_edges.json index e85dc9e7..b8316f77 100644 --- a/tests/resources/json_edges.json +++ b/tests/resources/json_edges.json @@ -41,6 +41,8 @@ "object": "NCIT:C138901", "biolink:original_knowledge_source": "infores:icees-kg", "test1": "test1", + "knowledge_level": "not_provided", + "agent_type": "not_provided", "crappy_list_of_objects": [ { "feature_matrix": 0.0 diff --git a/tests/resources/test.db b/tests/resources/test.db index 34dd59b3..75f04b29 100644 Binary files a/tests/resources/test.db and b/tests/resources/test.db differ diff --git a/tests/resources/valid.json b/tests/resources/valid.json index 73a3155f..f4726321 100644 --- a/tests/resources/valid.json +++ b/tests/resources/valid.json @@ -117,6 +117,8 @@ "object": "MONDO:0005002", "predicate": "biolink:related_to", "relation": "RO:0003304", + "knowledge_level": "knowledge_assertion", + "agent_type": "manual_agent", "category": [ "biolink:Association" ] @@ -127,6 +129,8 @@ "object": "MONDO:0013238", "predicate": "biolink:related_to", "relation": "RO:0003304", + "knowledge_level": "knowledge_assertion", + "agent_type": "manual_agent", "category": [ "biolink:Association" ] @@ -137,6 +141,8 @@ "object": "MONDO:0013329", "predicate": "biolink:related_to", "relation": "RO:0003304", + "knowledge_level": "knowledge_assertion", + "agent_type": "manual_agent", "category": [ "biolink:Association" ] @@ -147,6 +153,8 @@ "object": "MONDO:0017148", "predicate": "biolink:related_to", "relation": "RO:0004013", + "knowledge_level": "knowledge_assertion", + "agent_type": "manual_agent", "category": [ "biolink:Association" ] @@ -157,6 +165,8 @@ "object": "MONDO:0007841", "predicate": "biolink:related_to", "relation": "RO:0004013", + "knowledge_level": "knowledge_assertion", + "agent_type": "manual_agent", "category": [ "biolink:Association" ] diff --git a/tests/unit/test_cli_utils.py b/tests/unit/test_cli_utils.py index 47279fea..08158d08 100644 --- a/tests/unit/test_cli_utils.py +++ b/tests/unit/test_cli_utils.py @@ -170,7 +170,8 @@ def test_transform_uncompressed_tsv_to_tsv(): csv_headings = next(edges) assert "aggregator_knowledge_source" in csv_headings for row in edges: - assert len(row) == 10 + print(row) + assert len(row) == 12 assert "someks" in row assert "someotherks" in row assert "newknowledge" not in row