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 <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)
-- 
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