From 7eea5e99222166731c7e55a95f6c00928289b4b9 Mon Sep 17 00:00:00 2001 From: Pjotr Prins Date: Sat, 7 Nov 2020 08:48:38 +0000 Subject: Added failing unit test: No matching triples found for predicate cc:License --- .guix-test | 11 +++++++++++ 1 file changed, 11 insertions(+) create mode 100644 .guix-test (limited to '.guix-test') diff --git a/.guix-test b/.guix-test new file mode 100644 index 0000000..b7b9ab3 --- /dev/null +++ b/.guix-test @@ -0,0 +1,11 @@ +#! /bin/sh +# +# This script runs the tests in a Guix container + +GUIX_PROFILE=~/.config/guix/current +export GUILE_LOAD_PATH=$GUIX_PROFILE/share/guile/site/3.0/ +export GUILE_LOAD_COMPILED_PATH=$GUIX_PROFILE/share/guile/site/3.0/ + +ls $GUILE_LOAD_PATH + +env GUIX_PACKAGE_PATH=~/iwrk/opensource/guix/guix-bioinformatics/ $GUIX_PROFILE/bin/guix environment -C guix --ad-hoc git python python-flask python-pyyaml python-pycurl python-magic nss-certs python-pyshex python-pyyaml --network openssl python-pyshex python-pyshexc minimap2 python-schema-salad python-arvados-python-client -- python3 test/test_shex.py -- cgit v1.2.3 From 8aae577137f7614dc0889d0527cc25d6d078b68e Mon Sep 17 00:00:00 2001 From: Pjotr Prins Date: Sat, 7 Nov 2020 08:50:25 +0000 Subject: Running tests without network --- .guix-test | 2 +- test/test_shex.py | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) (limited to '.guix-test') diff --git a/.guix-test b/.guix-test index b7b9ab3..362fe8b 100644 --- a/.guix-test +++ b/.guix-test @@ -8,4 +8,4 @@ export GUILE_LOAD_COMPILED_PATH=$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 --network 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/ $GUIX_PROFILE/bin/guix environment -C guix --ad-hoc git python python-flask python-pyyaml python-pycurl python-magic nss-certs python-pyshex python-pyyaml openssl python-pyshex python-pyshexc minimap2 python-schema-salad python-arvados-python-client -- python3 test/test_shex.py diff --git a/test/test_shex.py b/test/test_shex.py index ead2396..e094184 100644 --- a/test/test_shex.py +++ b/test/test_shex.py @@ -12,7 +12,7 @@ class TestStringMethods(unittest.TestCase): def test_schema(self): with open("bh20sequploader/bh20seq-schema.yml") as schema_resource: - metadata_schema = schema_salad.schema.load_schema("https://raw.githubusercontent.com/arvados/bh20-seq-resource/master/bh20sequploader/bh20seq-schema.yml") + metadata_schema = schema_salad.schema.load_schema("bh20sequploader/bh20seq-schema.yml") (document_loader, avsc_names, schema_metadata, -- cgit v1.2.3 From 8a02280c4bd05a7f8df598a75a1ea2d3caaddd7d Mon Sep 17 00:00:00 2001 From: Pjotr Prins Date: Sat, 7 Nov 2020 10:21:48 +0000 Subject: Tests: add runner and frame for SPARQL --- .guix-test | 2 +- test/data/regression/TN_UT2.rdf | 64 ++++++++++++++++++++--------------------- test/runner.py | 17 +++++++++++ test/test_shex.py | 8 ++---- test/test_sparql.py | 11 +++++++ 5 files changed, 64 insertions(+), 38 deletions(-) create mode 100644 test/runner.py create mode 100644 test/test_sparql.py (limited to '.guix-test') diff --git a/.guix-test b/.guix-test index 362fe8b..b8e92a0 100644 --- a/.guix-test +++ b/.guix-test @@ -8,4 +8,4 @@ export GUILE_LOAD_COMPILED_PATH=$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 . -_:Ncab40e8bd4b84431aa6782f7e7480ef3 . -_:N3c28bc8014134d77823451de114c6085 "Mariah Taylor" . -_:Ncab40e8bd4b84431aa6782f7e7480ef3 "TN_UT2" . - _:N850430bbc537473e8fbab09c300daf2b . -_:N3c28bc8014134d77823451de114c6085 "TN_UT2" . -_:N850430bbc537473e8fbab09c300daf2b . -_:N3c28bc8014134d77823451de114c6085 "UTHSC, Memphis, Tennessee 38163, USA" . -_:Nebe62f68542a47d0936e953195cf25d7 . -_:N3c28bc8014134d77823451de114c6085 "Colleen B. Jonsson" . -_:N78bfdbe9d12745e99164d619cb125277 . -_:Nbf9e7b47381b4965926a47bf5b34e489 "Oxford Nanopore MiniIon RNA long reads" . - _:Ncab40e8bd4b84431aa6782f7e7480ef3 . -_:Nbf9e7b47381b4965926a47bf5b34e489 "https://bio.tools/BWA#!" . -_:Nebe62f68542a47d0936e953195cf25d7 "TN_UT2" . - _:Nebe62f68542a47d0936e953195cf25d7 . -_:N850430bbc537473e8fbab09c300daf2b "Mariah Taylor, Colleen Jonsson" . -_:N78bfdbe9d12745e99164d619cb125277 "SARS-CoV-2/human/USA/TN_UT2/2020" . -_:N3c28bc8014134d77823451de114c6085 "Colleen Jonsson" . -_:N3c28bc8014134d77823451de114c6085 . -_:Nebe62f68542a47d0936e953195cf25d7 "2020-04-26" . -_:Nebe62f68542a47d0936e953195cf25d7 . -_:N850430bbc537473e8fbab09c300daf2b "TN_UT2 - Pegram, Tennessee, USA" . -_:Nbf9e7b47381b4965926a47bf5b34e489 . -_:N3c28bc8014134d77823451de114c6085 "Mariah Taylor" . -_:N3c28bc8014134d77823451de114c6085 "TN_UT2" . -_:N3c28bc8014134d77823451de114c6085 "Pjotr Prins" . - _:N3c28bc8014134d77823451de114c6085 . -_:N3c28bc8014134d77823451de114c6085 . - _:N78bfdbe9d12745e99164d619cb125277 . -_:N3c28bc8014134d77823451de114c6085 "Regional Biocontainment Laboratory, Memphis, TN" . - _:Nbf9e7b47381b4965926a47bf5b34e489 . +_:N76e90938195c463c9dd2af9dadcf3d56 . +_:N14a259ceba1446a389be1076f7090540 . + _:N14a259ceba1446a389be1076f7090540 . + _:N1421ab28904c425faf6c308f77800e08 . +_:N76e90938195c463c9dd2af9dadcf3d56 "Colleen Jonsson" . + _:Na3153e61734c4cd1b7c4a11bb64b76cc . +_:N1421ab28904c425faf6c308f77800e08 . +_:N17d644aee0054862ab8beb6cdf5cb4d6 "https://bio.tools/BWA#!" . +_:N76e90938195c463c9dd2af9dadcf3d56 "TN_UT2" . +_:N69368ab7984c4659bcfa493bdca2d5f1 "SARS-CoV-2/human/USA/TN_UT2/2020" . +_:Na3153e61734c4cd1b7c4a11bb64b76cc . +_:N76e90938195c463c9dd2af9dadcf3d56 "Colleen B. Jonsson" . +_:N76e90938195c463c9dd2af9dadcf3d56 . + _:N76e90938195c463c9dd2af9dadcf3d56 . +_:N1421ab28904c425faf6c308f77800e08 "TN_UT2 - Pegram, Tennessee, USA" . +_:N1421ab28904c425faf6c308f77800e08 "Mariah Taylor, Colleen Jonsson" . +_:N76e90938195c463c9dd2af9dadcf3d56 "Mariah Taylor" . +_:N76e90938195c463c9dd2af9dadcf3d56 "Mariah Taylor" . +_:N76e90938195c463c9dd2af9dadcf3d56 "Regional Biocontainment Laboratory, Memphis, TN" . +_:N14a259ceba1446a389be1076f7090540 "TN_UT2" . +_:Na3153e61734c4cd1b7c4a11bb64b76cc . + _:N17d644aee0054862ab8beb6cdf5cb4d6 . +_:N1421ab28904c425faf6c308f77800e08 . +_:N76e90938195c463c9dd2af9dadcf3d56 "Pjotr Prins" . +_:N76e90938195c463c9dd2af9dadcf3d56 "UTHSC, Memphis, Tennessee 38163, USA" . +_:N17d644aee0054862ab8beb6cdf5cb4d6 "Oxford Nanopore MiniIon RNA long reads" . +_:N69368ab7984c4659bcfa493bdca2d5f1 . +_:Na3153e61734c4cd1b7c4a11bb64b76cc "TN_UT2" . +_:N76e90938195c463c9dd2af9dadcf3d56 "TN_UT2" . + _:N69368ab7984c4659bcfa493bdca2d5f1 . +_:N17d644aee0054862ab8beb6cdf5cb4d6 . +_:Na3153e61734c4cd1b7c4a11bb64b76cc "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() -- cgit v1.2.3 From f9c64353ac87b1fe05e0cad68e358a7f69b3bcdc Mon Sep 17 00:00:00 2001 From: Pjotr Prins Date: Sat, 7 Nov 2020 10:31:27 +0000 Subject: Tests: added SPARQL test --- .guix-test | 2 +- test/data/regression/TN_UT2.rdf | 64 ++++++++++++++++++++--------------------- test/test_sparql.py | 30 ++++++++++++++++++- 3 files changed, 62 insertions(+), 34 deletions(-) (limited to '.guix-test') diff --git a/.guix-test b/.guix-test index b8e92a0..26d2548 100644 --- a/.guix-test +++ b/.guix-test @@ -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/runner.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 --network 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 28b7a2d..05492d2 100644 --- a/test/data/regression/TN_UT2.rdf +++ b/test/data/regression/TN_UT2.rdf @@ -1,33 +1,33 @@ -_:N76e90938195c463c9dd2af9dadcf3d56 . -_:N14a259ceba1446a389be1076f7090540 . - _:N14a259ceba1446a389be1076f7090540 . - _:N1421ab28904c425faf6c308f77800e08 . -_:N76e90938195c463c9dd2af9dadcf3d56 "Colleen Jonsson" . - _:Na3153e61734c4cd1b7c4a11bb64b76cc . -_:N1421ab28904c425faf6c308f77800e08 . -_:N17d644aee0054862ab8beb6cdf5cb4d6 "https://bio.tools/BWA#!" . -_:N76e90938195c463c9dd2af9dadcf3d56 "TN_UT2" . -_:N69368ab7984c4659bcfa493bdca2d5f1 "SARS-CoV-2/human/USA/TN_UT2/2020" . -_:Na3153e61734c4cd1b7c4a11bb64b76cc . -_:N76e90938195c463c9dd2af9dadcf3d56 "Colleen B. Jonsson" . -_:N76e90938195c463c9dd2af9dadcf3d56 . - _:N76e90938195c463c9dd2af9dadcf3d56 . -_:N1421ab28904c425faf6c308f77800e08 "TN_UT2 - Pegram, Tennessee, USA" . -_:N1421ab28904c425faf6c308f77800e08 "Mariah Taylor, Colleen Jonsson" . -_:N76e90938195c463c9dd2af9dadcf3d56 "Mariah Taylor" . -_:N76e90938195c463c9dd2af9dadcf3d56 "Mariah Taylor" . -_:N76e90938195c463c9dd2af9dadcf3d56 "Regional Biocontainment Laboratory, Memphis, TN" . -_:N14a259ceba1446a389be1076f7090540 "TN_UT2" . -_:Na3153e61734c4cd1b7c4a11bb64b76cc . - _:N17d644aee0054862ab8beb6cdf5cb4d6 . -_:N1421ab28904c425faf6c308f77800e08 . -_:N76e90938195c463c9dd2af9dadcf3d56 "Pjotr Prins" . -_:N76e90938195c463c9dd2af9dadcf3d56 "UTHSC, Memphis, Tennessee 38163, USA" . -_:N17d644aee0054862ab8beb6cdf5cb4d6 "Oxford Nanopore MiniIon RNA long reads" . -_:N69368ab7984c4659bcfa493bdca2d5f1 . -_:Na3153e61734c4cd1b7c4a11bb64b76cc "TN_UT2" . -_:N76e90938195c463c9dd2af9dadcf3d56 "TN_UT2" . - _:N69368ab7984c4659bcfa493bdca2d5f1 . -_:N17d644aee0054862ab8beb6cdf5cb4d6 . -_:Na3153e61734c4cd1b7c4a11bb64b76cc "2020-04-26" . +_:N2db9cee579dd43f1b726d25af29c234e "TN_UT2" . +_:N2db9cee579dd43f1b726d25af29c234e . + _:Nd4901846018d495bb053138baa027814 . +_:N2db9cee579dd43f1b726d25af29c234e "Pjotr Prins" . +_:N2db9cee579dd43f1b726d25af29c234e "UTHSC, Memphis, Tennessee 38163, USA" . +_:Nd4901846018d495bb053138baa027814 "TN_UT2 - Pegram, Tennessee, USA" . + _:N7e96da40d73c4c2dbf05111f468abae3 . +_:N2db9cee579dd43f1b726d25af29c234e . +_:N98ebfff2566041cda89444d4cfe03752 "SARS-CoV-2/human/USA/TN_UT2/2020" . +_:N2db9cee579dd43f1b726d25af29c234e "Colleen Jonsson" . + _:N2db9cee579dd43f1b726d25af29c234e . +_:N572d266882144945822657d869333da9 "Oxford Nanopore MiniIon RNA long reads" . +_:N7e96da40d73c4c2dbf05111f468abae3 "TN_UT2" . +_:N2db9cee579dd43f1b726d25af29c234e "Mariah Taylor" . +_:Nd4901846018d495bb053138baa027814 . +_:N98ebfff2566041cda89444d4cfe03752 . +_:N7e96da40d73c4c2dbf05111f468abae3 "2020-04-26" . + _:N98ebfff2566041cda89444d4cfe03752 . +_:N572d266882144945822657d869333da9 . + _:N572d266882144945822657d869333da9 . +_:N2db9cee579dd43f1b726d25af29c234e "Mariah Taylor" . +_:N2db9cee579dd43f1b726d25af29c234e "TN_UT2" . +_:N572d266882144945822657d869333da9 "https://bio.tools/BWA#!" . +_:Nc89d151473da47de943e512a926416a8 . +_:Nd4901846018d495bb053138baa027814 . +_:N2db9cee579dd43f1b726d25af29c234e "Regional Biocontainment Laboratory, Memphis, TN" . +_:Nd4901846018d495bb053138baa027814 "Mariah Taylor, Colleen Jonsson" . +_:N7e96da40d73c4c2dbf05111f468abae3 . +_:N2db9cee579dd43f1b726d25af29c234e "Colleen B. Jonsson" . +_:Nc89d151473da47de943e512a926416a8 "TN_UT2" . +_:N7e96da40d73c4c2dbf05111f468abae3 . + _:Nc89d151473da47de943e512a926416a8 . diff --git a/test/test_sparql.py b/test/test_sparql.py index 00bb3ed..41cf717 100644 --- a/test/test_sparql.py +++ b/test/test_sparql.py @@ -1,11 +1,39 @@ # Run with python3 test/test_sparql.py import unittest +import requests +import logging + + class TestSPARQL(unittest.TestCase): def test_sparql(self): - pass + sparqlURL='http://sparql.genenetwork.org/sparql/' + id = "http://collections.lugli.arvadosapi.com/c=0002e93b86ad77824620bf938b97e134+126/sequence.fasta" + id = "MT800005.1" + query=f""" +PREFIX pubseq: +PREFIX sio: +select distinct ?sample ?geoname ?date ?source ?geo ?sampletype ?institute ?sequenceuri +{{ + ?sample sio:SIO_000115 "{id}" . + ?sequenceuri pubseq:sample ?sample . + ?sample ?geo . + ?geo rdfs:label ?geoname . + ?sample ?date . + OPTIONAL {{ ?sample ?source }} + OPTIONAL {{ ?sample ?sampletype }} + OPTIONAL {{ ?sample ?institute }} +}} + """ + print(query) + payload = {'query': query, 'format': 'json'} + r = requests.get(sparqlURL, params=payload) + result = r.json()['results']['bindings'] + # for now we just take the first one + print(result) + self.assertEqual(result[0]['geoname']['value'],'Mahuva') if __name__ == '__main__': unittest.main() -- cgit v1.2.3