From 9887e427d4e0beb29af14e554a3508126f0d505a Mon Sep 17 00:00:00 2001 From: Pjotr Prins Date: Sat, 7 Nov 2020 09:24:17 +0000 Subject: Test: simplify and add regression test --- test/data/regression/TN_UT2.rdf | 33 +++++++++++++++++++++++++++++++++ test/test_shex.py | 14 ++++++++------ 2 files changed, 41 insertions(+), 6 deletions(-) create mode 100644 test/data/regression/TN_UT2.rdf (limited to 'test') 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 "TN_UT2" . +_:N299826fb66794f11991cebc5f8d8b24a "https://bio.tools/BWA#!" . +_:N982774a13a39474aae39272447a09574 "https://www.uthsc.edu/medicine/molecular-sciences/faculty-directory/jonsson.php" . +_:N7857c4718ab741169bae9fafa9b47c75 "2020-04-26" . +_:N708d19e87323455c9f9bb317538f742d "Pjotr Prins" . +_:N95d4a000e14d4bd99b46d6ec84989aaf "SARS-CoV-2/human/USA/TN_UT2/2020" . + _:N982774a13a39474aae39272447a09574 . +_:N95d4a000e14d4bd99b46d6ec84989aaf . +_:Nc519408f538a4bb39ea09f56ce9bb88e . +_:N708d19e87323455c9f9bb317538f742d "Colleen Jonsson" . +_:N982774a13a39474aae39272447a09574 "Mariah Taylor, Colleen Jonsson" . + _:N7857c4718ab741169bae9fafa9b47c75 . +_:N708d19e87323455c9f9bb317538f742d "Regional Biocontainment Laboratory, Memphis, TN" . +_:N299826fb66794f11991cebc5f8d8b24a . +_:N708d19e87323455c9f9bb317538f742d "UTHSC, Memphis, Tennessee 38163, USA" . +_:N7857c4718ab741169bae9fafa9b47c75 . +_:N708d19e87323455c9f9bb317538f742d "TN_UT2" . +_:N7857c4718ab741169bae9fafa9b47c75 "TN_UT2" . +_:N708d19e87323455c9f9bb317538f742d . + _:N708d19e87323455c9f9bb317538f742d . + _:N299826fb66794f11991cebc5f8d8b24a . +_:N982774a13a39474aae39272447a09574 "TN_UT2 - Pegram, Tennessee, USA" . +_:N299826fb66794f11991cebc5f8d8b24a "Oxford Nanopore MiniIon RNA long reads" . +_:N7857c4718ab741169bae9fafa9b47c75 . + _:Nc519408f538a4bb39ea09f56ce9bb88e . +_:N708d19e87323455c9f9bb317538f742d "Mariah Taylor" . +_:N708d19e87323455c9f9bb317538f742d . + _:N95d4a000e14d4bd99b46d6ec84989aaf . +_:N708d19e87323455c9f9bb317538f742d "Colleen B. Jonsson" . +_:N708d19e87323455c9f9bb317538f742d "TN_UT2" . +_:N982774a13a39474aae39272447a09574 "http://creativecommons.org/licenses/by/4.0/" . +_:N708d19e87323455c9f9bb317538f742d "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) -- cgit v1.2.3