diff options
| -rw-r--r-- | .guix-test | 2 | ||||
| -rw-r--r-- | test/data/regression/TN_UT2.rdf | 64 | ||||
| -rw-r--r-- | test/runner.py | 17 | ||||
| -rw-r--r-- | test/test_shex.py | 8 | ||||
| -rw-r--r-- | test/test_sparql.py | 11 |
5 files changed, 64 insertions, 38 deletions
@@ -8,4 +8,4 @@ export GUILE_LOAD_COMPILED_PATH=$GUIX_PROFILE/share/guile/site/3.0/ ls $GUILE_LOAD_PATH -env GUIX_PACKAGE_PATH=~/iwrk/opensource/guix/guix-bioinformatics/ $GUIX_PROFILE/bin/guix environment -C guix --ad-hoc git python python-flask python-pyyaml python-pycurl python-magic nss-certs python-pyshex python-pyyaml openssl python-pyshex python-pyshexc minimap2 python-schema-salad python-arvados-python-client -- python3 test/test_shex.py +env GUIX_PACKAGE_PATH=~/iwrk/opensource/guix/guix-bioinformatics/ $GUIX_PROFILE/bin/guix environment -C guix --ad-hoc git python python-flask python-pyyaml python-pycurl python-magic nss-certs python-pyshex python-pyyaml openssl python-pyshex python-pyshexc minimap2 python-schema-salad python-arvados-python-client -- python3 test/runner.py diff --git a/test/data/regression/TN_UT2.rdf b/test/data/regression/TN_UT2.rdf index 84353a5..28b7a2d 100644 --- a/test/data/regression/TN_UT2.rdf +++ b/test/data/regression/TN_UT2.rdf @@ -1,33 +1,33 @@ -_:N850430bbc537473e8fbab09c300daf2b <https://creativecommons.org/ns#License> <https://creativecommons.org/licenses/by/4.0/> . -_:Ncab40e8bd4b84431aa6782f7e7480ef3 <http://www.ebi.ac.uk/efo/EFO_0000532> <http://purl.obolibrary.org/obo/NCBITaxon_9606> . -_:N3c28bc8014134d77823451de114c6085 <http://purl.obolibrary.org/obo/NCIT_C42781> "Mariah Taylor" . -_:Ncab40e8bd4b84431aa6782f7e7480ef3 <http://semanticscience.org/resource/SIO_000115> "TN_UT2" . -<file:///export/local/home/wrk/iwrk/opensource/code/vg/bh20-seq-resource/test/data/input/placeholder> <http://biohackathon.org/bh20-seq-schema#MainSchema/license> _:N850430bbc537473e8fbab09c300daf2b . -_:N3c28bc8014134d77823451de114c6085 <http://purl.obolibrary.org/obo/NCIT_C42781> "TN_UT2" . -_:N850430bbc537473e8fbab09c300daf2b <https://creativecommons.org/ns#attributionURL> <https://www.uthsc.edu/medicine/molecular-sciences/faculty-directory/jonsson.php> . -_:N3c28bc8014134d77823451de114c6085 <http://semanticscience.org/resource/SIO_000172> "UTHSC, Memphis, Tennessee 38163, USA" . -_:Nebe62f68542a47d0936e953195cf25d7 <http://purl.obolibrary.org/obo/OBI_0001479> <http://purl.obolibrary.org/obo/NCIT_C155831> . -_:N3c28bc8014134d77823451de114c6085 <http://semanticscience.org/resource/SIO_000116> "Colleen B. Jonsson" . -_:N78bfdbe9d12745e99164d619cb125277 <http://edamontology.org/data_1875> <http://purl.obolibrary.org/obo/NCBITaxon_2697049> . -_:Nbf9e7b47381b4965926a47bf5b34e489 <http://semanticscience.org/resource/SIO_001167> "Oxford Nanopore MiniIon RNA long reads" . -<file:///export/local/home/wrk/iwrk/opensource/code/vg/bh20-seq-resource/test/data/input/placeholder> <http://biohackathon.org/bh20-seq-schema#MainSchema/host> _:Ncab40e8bd4b84431aa6782f7e7480ef3 . -_:Nbf9e7b47381b4965926a47bf5b34e489 <http://www.ebi.ac.uk/efo/EFO_0002699> "https://bio.tools/BWA#!" . -_:Nebe62f68542a47d0936e953195cf25d7 <http://semanticscience.org/resource/SIO_000115> "TN_UT2" . -<file:///export/local/home/wrk/iwrk/opensource/code/vg/bh20-seq-resource/test/data/input/placeholder> <http://biohackathon.org/bh20-seq-schema#MainSchema/sample> _:Nebe62f68542a47d0936e953195cf25d7 . -_:N850430bbc537473e8fbab09c300daf2b <https://creativecommons.org/ns#attributionName> "Mariah Taylor, Colleen Jonsson" . -_:N78bfdbe9d12745e99164d619cb125277 <http://semanticscience.org/resource/SIO_010055> "SARS-CoV-2/human/USA/TN_UT2/2020" . -_:N3c28bc8014134d77823451de114c6085 <http://purl.obolibrary.org/obo/NCIT_C42781> "Colleen Jonsson" . -_:N3c28bc8014134d77823451de114c6085 <http://semanticscience.org/resource/SIO_000115> <https://orcid.org/0000-0002-2640-7672> . -_:Nebe62f68542a47d0936e953195cf25d7 <http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C25164> "2020-04-26" . -_:Nebe62f68542a47d0936e953195cf25d7 <http://purl.obolibrary.org/obo/GAZ_00000448> <http://www.wikidata.org/entity/Q3289517> . -_:N850430bbc537473e8fbab09c300daf2b <http://purl.org/metadata/dublin_core_elements#Title> "TN_UT2 - Pegram, Tennessee, USA" . -_:Nbf9e7b47381b4965926a47bf5b34e489 <http://purl.obolibrary.org/obo/OBI_0600047> <http://www.ebi.ac.uk/efo/EFO_0008632> . -_:N3c28bc8014134d77823451de114c6085 <http://semanticscience.org/resource/SIO_000116> "Mariah Taylor" . -_:N3c28bc8014134d77823451de114c6085 <http://www.ebi.ac.uk/efo/EFO_0001741> "TN_UT2" . -_:N3c28bc8014134d77823451de114c6085 <http://semanticscience.org/resource/SIO_000116> "Pjotr Prins" . -<file:///export/local/home/wrk/iwrk/opensource/code/vg/bh20-seq-resource/test/data/input/placeholder> <http://biohackathon.org/bh20-seq-schema#MainSchema/submitter> _:N3c28bc8014134d77823451de114c6085 . -_:N3c28bc8014134d77823451de114c6085 <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> _:N78bfdbe9d12745e99164d619cb125277 . -_:N3c28bc8014134d77823451de114c6085 <http://purl.obolibrary.org/obo/NCIT_C37984> "Regional Biocontainment Laboratory, Memphis, TN" . -<file:///export/local/home/wrk/iwrk/opensource/code/vg/bh20-seq-resource/test/data/input/placeholder> <http://biohackathon.org/bh20-seq-schema#MainSchema/technology> _:Nbf9e7b47381b4965926a47bf5b34e489 . +_:N76e90938195c463c9dd2af9dadcf3d56 <http://semanticscience.org/resource/SIO_000115> <https://orcid.org/0000-0002-8021-9162> . +_:N14a259ceba1446a389be1076f7090540 <http://www.ebi.ac.uk/efo/EFO_0000532> <http://purl.obolibrary.org/obo/NCBITaxon_9606> . +<file:///export/local/home/wrk/iwrk/opensource/code/vg/bh20-seq-resource/test/data/input/placeholder> <http://biohackathon.org/bh20-seq-schema#MainSchema/host> _:N14a259ceba1446a389be1076f7090540 . +<file:///export/local/home/wrk/iwrk/opensource/code/vg/bh20-seq-resource/test/data/input/placeholder> <http://biohackathon.org/bh20-seq-schema#MainSchema/license> _:N1421ab28904c425faf6c308f77800e08 . +_:N76e90938195c463c9dd2af9dadcf3d56 <http://purl.obolibrary.org/obo/NCIT_C42781> "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> _:Na3153e61734c4cd1b7c4a11bb64b76cc . +_:N1421ab28904c425faf6c308f77800e08 <https://creativecommons.org/ns#attributionURL> <https://www.uthsc.edu/medicine/molecular-sciences/faculty-directory/jonsson.php> . +_:N17d644aee0054862ab8beb6cdf5cb4d6 <http://www.ebi.ac.uk/efo/EFO_0002699> "https://bio.tools/BWA#!" . +_:N76e90938195c463c9dd2af9dadcf3d56 <http://purl.obolibrary.org/obo/NCIT_C42781> "TN_UT2" . +_:N69368ab7984c4659bcfa493bdca2d5f1 <http://semanticscience.org/resource/SIO_010055> "SARS-CoV-2/human/USA/TN_UT2/2020" . +_:Na3153e61734c4cd1b7c4a11bb64b76cc <http://purl.obolibrary.org/obo/OBI_0001479> <http://purl.obolibrary.org/obo/NCIT_C155831> . +_:N76e90938195c463c9dd2af9dadcf3d56 <http://semanticscience.org/resource/SIO_000116> "Colleen B. Jonsson" . +_:N76e90938195c463c9dd2af9dadcf3d56 <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> _:N76e90938195c463c9dd2af9dadcf3d56 . +_:N1421ab28904c425faf6c308f77800e08 <http://purl.org/metadata/dublin_core_elements#Title> "TN_UT2 - Pegram, Tennessee, USA" . +_:N1421ab28904c425faf6c308f77800e08 <https://creativecommons.org/ns#attributionName> "Mariah Taylor, Colleen Jonsson" . +_:N76e90938195c463c9dd2af9dadcf3d56 <http://purl.obolibrary.org/obo/NCIT_C42781> "Mariah Taylor" . +_:N76e90938195c463c9dd2af9dadcf3d56 <http://semanticscience.org/resource/SIO_000116> "Mariah Taylor" . +_:N76e90938195c463c9dd2af9dadcf3d56 <http://purl.obolibrary.org/obo/NCIT_C37984> "Regional Biocontainment Laboratory, Memphis, TN" . +_:N14a259ceba1446a389be1076f7090540 <http://semanticscience.org/resource/SIO_000115> "TN_UT2" . +_:Na3153e61734c4cd1b7c4a11bb64b76cc <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/technology> _:N17d644aee0054862ab8beb6cdf5cb4d6 . +_:N1421ab28904c425faf6c308f77800e08 <https://creativecommons.org/ns#License> <https://creativecommons.org/licenses/by/4.0/> . +_:N76e90938195c463c9dd2af9dadcf3d56 <http://semanticscience.org/resource/SIO_000116> "Pjotr Prins" . +_:N76e90938195c463c9dd2af9dadcf3d56 <http://semanticscience.org/resource/SIO_000172> "UTHSC, Memphis, Tennessee 38163, USA" . +_:N17d644aee0054862ab8beb6cdf5cb4d6 <http://semanticscience.org/resource/SIO_001167> "Oxford Nanopore MiniIon RNA long reads" . +_:N69368ab7984c4659bcfa493bdca2d5f1 <http://edamontology.org/data_1875> <http://purl.obolibrary.org/obo/NCBITaxon_2697049> . +_:Na3153e61734c4cd1b7c4a11bb64b76cc <http://semanticscience.org/resource/SIO_000115> "TN_UT2" . +_:N76e90938195c463c9dd2af9dadcf3d56 <http://www.ebi.ac.uk/efo/EFO_0001741> "TN_UT2" . +<file:///export/local/home/wrk/iwrk/opensource/code/vg/bh20-seq-resource/test/data/input/placeholder> <http://biohackathon.org/bh20-seq-schema#MainSchema/virus> _:N69368ab7984c4659bcfa493bdca2d5f1 . +_:N17d644aee0054862ab8beb6cdf5cb4d6 <http://purl.obolibrary.org/obo/OBI_0600047> <http://www.ebi.ac.uk/efo/EFO_0008632> . +_:Na3153e61734c4cd1b7c4a11bb64b76cc <http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C25164> "2020-04-26" . diff --git a/test/runner.py b/test/runner.py new file mode 100644 index 0000000..3cfe042 --- /dev/null +++ b/test/runner.py @@ -0,0 +1,17 @@ +# Run tests. python3 test/runner.py + +import unittest + +# initialize the test suite +loader = unittest.TestLoader() +suite = unittest.TestSuite() + +import test_shex +import test_sparql + +suite.addTests(loader.loadTestsFromModule(test_shex)) +suite.addTests(loader.loadTestsFromModule(test_sparql)) + +# initialize a runner, pass it your suite and run it +runner = unittest.TextTestRunner(verbosity=3) +result = runner.run(suite) diff --git a/test/test_shex.py b/test/test_shex.py index e5d97cc..728bfdc 100644 --- a/test/test_shex.py +++ b/test/test_shex.py @@ -1,14 +1,12 @@ +# Run with python3 test/test_shex.py + import schema_salad.schema import schema_salad.ref_resolver import schema_salad.jsonld_context -# import pkg_resources -import logging -# import traceback -# from rdflib import Graph, Namespace from pyshex.evaluate import evaluate import unittest -class TestStringMethods(unittest.TestCase): +class TestShexMethods(unittest.TestCase): def test_schema(self): with open("bh20sequploader/bh20seq-schema.yml") as schema_resource: diff --git a/test/test_sparql.py b/test/test_sparql.py new file mode 100644 index 0000000..00bb3ed --- /dev/null +++ b/test/test_sparql.py @@ -0,0 +1,11 @@ +# Run with python3 test/test_sparql.py + +import unittest + +class TestSPARQL(unittest.TestCase): + + def test_sparql(self): + pass + +if __name__ == '__main__': + unittest.main() |