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 +++++++++++++++++++++++++++++++++
 1 file changed, 33 insertions(+)
 create mode 100644 test/data/regression/TN_UT2.rdf

(limited to 'test/data/regression/TN_UT2.rdf')

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" .
+
-- 
cgit v1.2.3


From 9709eca5c76aabe823ba34d976c5d11a9d150b76 Mon Sep 17 00:00:00 2001
From: Pjotr Prins
Date: Sat, 7 Nov 2020 10:06:30 +0000
Subject: RDF: use URIs

---
 bh20sequploader/bh20seq-schema.yml |  8 ++++-
 bh20sequploader/bh20seq-shex.rdf   |  5 +--
 test/data/input/TN_UT2.yaml        |  2 +-
 test/data/regression/TN_UT2.rdf    | 64 +++++++++++++++++++-------------------
 4 files changed, 43 insertions(+), 36 deletions(-)

(limited to 'test/data/regression/TN_UT2.rdf')

diff --git a/bh20sequploader/bh20seq-schema.yml b/bh20sequploader/bh20seq-schema.yml
index 861a5ca..645be5e 100644
--- a/bh20sequploader/bh20seq-schema.yml
+++ b/bh20sequploader/bh20seq-schema.yml
@@ -1,6 +1,6 @@
 $base: http://biohackathon.org/bh20-seq-schema
 $namespaces:
-  cc:  http://creativecommons.org/ns#
+  cc:  https://creativecommons.org/ns#
   dc:  http://purl.org/metadata/dublin_core_elements#
   sch: https://schema.org/
   efo: http://www.ebi.ac.uk/efo/
@@ -19,6 +19,8 @@ $graph:
       type: string
       jsonldPredicate:
           _id: https://creativecommons.org/ns#License
+          _type: "@id"
+          noLinkCheck: true
     title:
       doc: Attribution title related to data license
       type: string?
@@ -34,11 +36,15 @@ $graph:
       type: string?
       jsonldPredicate:
           _id: https://creativecommons.org/ns#attributionURL
+          _type: "@id"
+          noLinkCheck: true
     attribution_source:
       doc: Attribution source URL related to data license
       type: string?
       jsonldPredicate:
           _id: https://creativecommons.org/ns#attributionSource
+          _type: "@id"
+          noLinkCheck: true
 
 - name: hostSchema
   type: record
diff --git a/bh20sequploader/bh20seq-shex.rdf b/bh20sequploader/bh20seq-shex.rdf
index fa765dd..1b15c58 100644
--- a/bh20sequploader/bh20seq-shex.rdf
+++ b/bh20sequploader/bh20seq-shex.rdf
@@ -2,6 +2,7 @@ PREFIX : <https://raw.githubusercontent.com/arvados/bh20-seq-resource/master/bh2
 PREFIX MainSchema: <http://biohackathon.org/bh20-seq-schema#MainSchema/>
 PREFIX hostSchema: <http://biohackathon.org/bh20-seq-schema#hostSchema/>
 PREFIX cc:  <https://creativecommons.org/ns#>
+PREFIX cclicenses:  <https://creativecommons.org/licenses/>
 PREFIX dc:  <http://purl.org/metadata/dublin_core_elements#>
 PREFIX xsd: <http://www.w3.org/2001/XMLSchema#>
 PREFIX obo: <http://purl.obolibrary.org/obo/>
@@ -71,9 +72,9 @@ PREFIX wikidata: <http://www.wikidata.org/entity/>
 }
 
 :licenseShape{
-    cc:License xsd:string ;
+    cc:License [ cclicenses:~ ] ;
     dc:Title xsd:string ?;
     cc:attributionName xsd:string ?;
-    cc:attributionURL xsd:string ?;
+    cc:attributionURL /^http/ ;
     cc:attributionSource xsd:string ?;
 }
diff --git a/test/data/input/TN_UT2.yaml b/test/data/input/TN_UT2.yaml
index 2c5f987..9c4370d 100644
--- a/test/data/input/TN_UT2.yaml
+++ b/test/data/input/TN_UT2.yaml
@@ -1,7 +1,7 @@
 id: placeholder
 
 license:
-    license_type: http://creativecommons.org/licenses/by/4.0/
+    license_type: https://creativecommons.org/licenses/by/4.0/
     title: "TN_UT2 - Pegram, Tennessee, USA"
     attribution_name: "Mariah Taylor, Colleen Jonsson"
     attribution_url: https://www.uthsc.edu/medicine/molecular-sciences/faculty-directory/jonsson.php
diff --git a/test/data/regression/TN_UT2.rdf b/test/data/regression/TN_UT2.rdf
index aa1356a..84353a5 100644
--- a/test/data/regression/TN_UT2.rdf
+++ b/test/data/regression/TN_UT2.rdf
@@ -1,33 +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" .
+_: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 .
 
-- 
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 'test/data/regression/TN_UT2.rdf')

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 <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()
-- 
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 'test/data/regression/TN_UT2.rdf')

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 <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" .
+_:N2db9cee579dd43f1b726d25af29c234e <http://www.ebi.ac.uk/efo/EFO_0001741> "TN_UT2" .
+_:N2db9cee579dd43f1b726d25af29c234e <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/license> _:Nd4901846018d495bb053138baa027814 .
+_:N2db9cee579dd43f1b726d25af29c234e <http://semanticscience.org/resource/SIO_000116> "Pjotr Prins" .
+_:N2db9cee579dd43f1b726d25af29c234e <http://semanticscience.org/resource/SIO_000172> "UTHSC, Memphis, Tennessee 38163, USA" .
+_:Nd4901846018d495bb053138baa027814 <http://purl.org/metadata/dublin_core_elements#Title> "TN_UT2 - Pegram, Tennessee, USA" .
+<file:///export/local/home/wrk/iwrk/opensource/code/vg/bh20-seq-resource/test/data/input/placeholder> <http://biohackathon.org/bh20-seq-schema#MainSchema/sample> _:N7e96da40d73c4c2dbf05111f468abae3 .
+_:N2db9cee579dd43f1b726d25af29c234e <http://semanticscience.org/resource/SIO_000115> <https://orcid.org/0000-0002-2640-7672> .
+_:N98ebfff2566041cda89444d4cfe03752 <http://semanticscience.org/resource/SIO_010055> "SARS-CoV-2/human/USA/TN_UT2/2020" .
+_:N2db9cee579dd43f1b726d25af29c234e <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/submitter> _:N2db9cee579dd43f1b726d25af29c234e .
+_:N572d266882144945822657d869333da9 <http://semanticscience.org/resource/SIO_001167> "Oxford Nanopore MiniIon RNA long reads" .
+_:N7e96da40d73c4c2dbf05111f468abae3 <http://semanticscience.org/resource/SIO_000115> "TN_UT2" .
+_:N2db9cee579dd43f1b726d25af29c234e <http://semanticscience.org/resource/SIO_000116> "Mariah Taylor" .
+_:Nd4901846018d495bb053138baa027814 <https://creativecommons.org/ns#attributionURL> <https://www.uthsc.edu/medicine/molecular-sciences/faculty-directory/jonsson.php> .
+_:N98ebfff2566041cda89444d4cfe03752 <http://edamontology.org/data_1875> <http://purl.obolibrary.org/obo/NCBITaxon_2697049> .
+_:N7e96da40d73c4c2dbf05111f468abae3 <http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C25164> "2020-04-26" .
+<file:///export/local/home/wrk/iwrk/opensource/code/vg/bh20-seq-resource/test/data/input/placeholder> <http://biohackathon.org/bh20-seq-schema#MainSchema/virus> _:N98ebfff2566041cda89444d4cfe03752 .
+_:N572d266882144945822657d869333da9 <http://purl.obolibrary.org/obo/OBI_0600047> <http://www.ebi.ac.uk/efo/EFO_0008632> .
+<file:///export/local/home/wrk/iwrk/opensource/code/vg/bh20-seq-resource/test/data/input/placeholder> <http://biohackathon.org/bh20-seq-schema#MainSchema/technology> _:N572d266882144945822657d869333da9 .
+_:N2db9cee579dd43f1b726d25af29c234e <http://purl.obolibrary.org/obo/NCIT_C42781> "Mariah Taylor" .
+_:N2db9cee579dd43f1b726d25af29c234e <http://purl.obolibrary.org/obo/NCIT_C42781> "TN_UT2" .
+_:N572d266882144945822657d869333da9 <http://www.ebi.ac.uk/efo/EFO_0002699> "https://bio.tools/BWA#!" .
+_:Nc89d151473da47de943e512a926416a8 <http://www.ebi.ac.uk/efo/EFO_0000532> <http://purl.obolibrary.org/obo/NCBITaxon_9606> .
+_:Nd4901846018d495bb053138baa027814 <https://creativecommons.org/ns#License> <https://creativecommons.org/licenses/by/4.0/> .
+_:N2db9cee579dd43f1b726d25af29c234e <http://purl.obolibrary.org/obo/NCIT_C37984> "Regional Biocontainment Laboratory, Memphis, TN" .
+_:Nd4901846018d495bb053138baa027814 <https://creativecommons.org/ns#attributionName> "Mariah Taylor, Colleen Jonsson" .
+_:N7e96da40d73c4c2dbf05111f468abae3 <http://purl.obolibrary.org/obo/GAZ_00000448> <http://www.wikidata.org/entity/Q3289517> .
+_:N2db9cee579dd43f1b726d25af29c234e <http://semanticscience.org/resource/SIO_000116> "Colleen B. Jonsson" .
+_:Nc89d151473da47de943e512a926416a8 <http://semanticscience.org/resource/SIO_000115> "TN_UT2" .
+_:N7e96da40d73c4c2dbf05111f468abae3 <http://purl.obolibrary.org/obo/OBI_0001479> <http://purl.obolibrary.org/obo/NCIT_C155831> .
+<file:///export/local/home/wrk/iwrk/opensource/code/vg/bh20-seq-resource/test/data/input/placeholder> <http://biohackathon.org/bh20-seq-schema#MainSchema/host> _: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: <http://biohackathon.org/bh20-seq-schema#MainSchema/>
+PREFIX sio: <http://semanticscience.org/resource/>
+select distinct ?sample ?geoname ?date ?source ?geo ?sampletype ?institute ?sequenceuri
+{{
+   ?sample sio:SIO_000115 "{id}" .
+   ?sequenceuri pubseq:sample ?sample .
+   ?sample <http://purl.obolibrary.org/obo/GAZ_00000448> ?geo .
+   ?geo rdfs:label ?geoname .
+   ?sample <http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C25164> ?date .
+   OPTIONAL {{ ?sample <http://edamontology.org/data_2091> ?source }}
+   OPTIONAL {{ ?sample <http://purl.obolibrary.org/obo/OBI_0001479> ?sampletype }}
+   OPTIONAL {{ ?sample <http://purl.obolibrary.org/obo/NCIT_C41206> ?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()
-- 
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