diff options
| -rw-r--r-- | test/data/regression/TN_UT2.rdf | 33 | ||||
| -rw-r--r-- | test/test_shex.py | 14 |
2 files changed, 41 insertions, 6 deletions
diff --git a/test/data/regression/TN_UT2.rdf b/test/data/regression/TN_UT2.rdf new file mode 100644 index 0000000..aa1356a --- /dev/null +++ b/test/data/regression/TN_UT2.rdf @@ -0,0 +1,33 @@ +_:Nc519408f538a4bb39ea09f56ce9bb88e <http://semanticscience.org/resource/SIO_000115> "TN_UT2" . +_:N299826fb66794f11991cebc5f8d8b24a <http://www.ebi.ac.uk/efo/EFO_0002699> "https://bio.tools/BWA#!" . +_:N982774a13a39474aae39272447a09574 <https://creativecommons.org/ns#attributionURL> "https://www.uthsc.edu/medicine/molecular-sciences/faculty-directory/jonsson.php" . +_:N7857c4718ab741169bae9fafa9b47c75 <http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C25164> "2020-04-26" . +_:N708d19e87323455c9f9bb317538f742d <http://semanticscience.org/resource/SIO_000116> "Pjotr Prins" . +_:N95d4a000e14d4bd99b46d6ec84989aaf <http://semanticscience.org/resource/SIO_010055> "SARS-CoV-2/human/USA/TN_UT2/2020" . +<file:///export/local/home/wrk/iwrk/opensource/code/vg/bh20-seq-resource/test/data/input/placeholder> <http://biohackathon.org/bh20-seq-schema#MainSchema/license> _:N982774a13a39474aae39272447a09574 . +_:N95d4a000e14d4bd99b46d6ec84989aaf <http://edamontology.org/data_1875> <http://purl.obolibrary.org/obo/NCBITaxon_2697049> . +_:Nc519408f538a4bb39ea09f56ce9bb88e <http://www.ebi.ac.uk/efo/EFO_0000532> <http://purl.obolibrary.org/obo/NCBITaxon_9606> . +_:N708d19e87323455c9f9bb317538f742d <http://purl.obolibrary.org/obo/NCIT_C42781> "Colleen Jonsson" . +_:N982774a13a39474aae39272447a09574 <https://creativecommons.org/ns#attributionName> "Mariah Taylor, Colleen Jonsson" . +<file:///export/local/home/wrk/iwrk/opensource/code/vg/bh20-seq-resource/test/data/input/placeholder> <http://biohackathon.org/bh20-seq-schema#MainSchema/sample> _:N7857c4718ab741169bae9fafa9b47c75 . +_:N708d19e87323455c9f9bb317538f742d <http://purl.obolibrary.org/obo/NCIT_C37984> "Regional Biocontainment Laboratory, Memphis, TN" . +_:N299826fb66794f11991cebc5f8d8b24a <http://purl.obolibrary.org/obo/OBI_0600047> <http://www.ebi.ac.uk/efo/EFO_0008632> . +_:N708d19e87323455c9f9bb317538f742d <http://semanticscience.org/resource/SIO_000172> "UTHSC, Memphis, Tennessee 38163, USA" . +_:N7857c4718ab741169bae9fafa9b47c75 <http://purl.obolibrary.org/obo/OBI_0001479> <http://purl.obolibrary.org/obo/NCIT_C155831> . +_:N708d19e87323455c9f9bb317538f742d <http://purl.obolibrary.org/obo/NCIT_C42781> "TN_UT2" . +_:N7857c4718ab741169bae9fafa9b47c75 <http://semanticscience.org/resource/SIO_000115> "TN_UT2" . +_:N708d19e87323455c9f9bb317538f742d <http://semanticscience.org/resource/SIO_000115> <https://orcid.org/0000-0002-2640-7672> . +<file:///export/local/home/wrk/iwrk/opensource/code/vg/bh20-seq-resource/test/data/input/placeholder> <http://biohackathon.org/bh20-seq-schema#MainSchema/submitter> _:N708d19e87323455c9f9bb317538f742d . +<file:///export/local/home/wrk/iwrk/opensource/code/vg/bh20-seq-resource/test/data/input/placeholder> <http://biohackathon.org/bh20-seq-schema#MainSchema/technology> _:N299826fb66794f11991cebc5f8d8b24a . +_:N982774a13a39474aae39272447a09574 <http://purl.org/metadata/dublin_core_elements#Title> "TN_UT2 - Pegram, Tennessee, USA" . +_:N299826fb66794f11991cebc5f8d8b24a <http://semanticscience.org/resource/SIO_001167> "Oxford Nanopore MiniIon RNA long reads" . +_:N7857c4718ab741169bae9fafa9b47c75 <http://purl.obolibrary.org/obo/GAZ_00000448> <http://www.wikidata.org/entity/Q3289517> . +<file:///export/local/home/wrk/iwrk/opensource/code/vg/bh20-seq-resource/test/data/input/placeholder> <http://biohackathon.org/bh20-seq-schema#MainSchema/host> _:Nc519408f538a4bb39ea09f56ce9bb88e . +_:N708d19e87323455c9f9bb317538f742d <http://purl.obolibrary.org/obo/NCIT_C42781> "Mariah Taylor" . +_:N708d19e87323455c9f9bb317538f742d <http://semanticscience.org/resource/SIO_000115> <https://orcid.org/0000-0002-8021-9162> . +<file:///export/local/home/wrk/iwrk/opensource/code/vg/bh20-seq-resource/test/data/input/placeholder> <http://biohackathon.org/bh20-seq-schema#MainSchema/virus> _:N95d4a000e14d4bd99b46d6ec84989aaf . +_:N708d19e87323455c9f9bb317538f742d <http://semanticscience.org/resource/SIO_000116> "Colleen B. Jonsson" . +_:N708d19e87323455c9f9bb317538f742d <http://www.ebi.ac.uk/efo/EFO_0001741> "TN_UT2" . +_:N982774a13a39474aae39272447a09574 <https://creativecommons.org/ns#License> "http://creativecommons.org/licenses/by/4.0/" . +_:N708d19e87323455c9f9bb317538f742d <http://semanticscience.org/resource/SIO_000116> "Mariah Taylor" . + diff --git a/test/test_shex.py b/test/test_shex.py index 50ce723..e5d97cc 100644 --- a/test/test_shex.py +++ b/test/test_shex.py @@ -1,9 +1,9 @@ import schema_salad.schema import schema_salad.ref_resolver import schema_salad.jsonld_context -import pkg_resources +# import pkg_resources import logging -import traceback +# import traceback # from rdflib import Graph, Namespace from pyshex.evaluate import evaluate import unittest @@ -17,17 +17,19 @@ class TestStringMethods(unittest.TestCase): avsc_names, schema_metadata, metaschema_loader) = metadata_schema - print(metadata_schema) - assert(isinstance(avsc_names, schema_salad.avro.schema.Names)) + # print(metadata_schema) + self.assertTrue(isinstance(avsc_names, schema_salad.avro.schema.Names)) metadatafile = "test/data/input/TN_UT2.yaml" doc, metadata = schema_salad.schema.load_and_validate(document_loader, avsc_names, metadatafile, True) print(doc) g = schema_salad.jsonld_context.makerdf("workflow", doc, document_loader.ctx) - shex = pkg_resources.resource_stream(__name__, "../bh20sequploader/bh20seq-shex.rdf").read().decode("utf-8") + with open("bh20sequploader/bh20seq-shex.rdf") as f: + shex = f.read() # Note the https link simply acts as a URI descriptor (it does not fetch) rslt, reason = evaluate(g, shex, doc["id"], "https://raw.githubusercontent.com/arvados/bh20-seq-resource/master/bh20sequploader/bh20seq-shex.rdf#submissionShape") - g.serialize(format="ntriples") + with open("test/data/regression/TN_UT2.rdf","w") as f: + f.write(g.serialize(format="ntriples").decode("utf-8")) if not rslt: raise Exception(reason) |