def setUp(self):
# Initialization
self.login(*self.create_user("*****@*****.**", "password"))
encoded_file = b64encode(self.data.encode('utf8')).decode('ascii')
print("XML length:", len(encoded_file))
upload = self.upload_template % (encoded_file)
response = self.client.post("/pub",
data=upload,
content_type="text/turtle",
follow_redirects=True)
self.assertEquals(response.status, '201 CREATED')
response = self.client.post(
"/pub",
data=open('/apps/nanomine-graph/setl/xml_ingest.setl.ttl',
'rb').read(),
content_type="text/turtle",
follow_redirects=True)
self.assertEquals(response.status, '201 CREATED')
setlmaker = autonomic.SETLMaker()
setlmaker.dry_run = False
results = self.run_agent(setlmaker)
# confirm this is creating a SETL script for the XML file.
self.assertTrue(len(results) > 0)
setlr = autonomic.SETLr()
setlr.dry_run = False
print(len(self.app.db))
for setlr_np in results:
setlr_results = self.run_agent(setlr, nanopublication=setlr_np)
def test_L102_S3_Hu_2007(self):
self.login(*self.create_user("*****@*****.**","password"))
upload = files['L102_S3_Hu_2007']
response = self.client.post("/pub", data=upload, content_type="text/turtle",follow_redirects=True)
self.assertEquals(response.status,'201 CREATED')
response = self.client.post("/pub", data=open('/apps/nanomine-graph/setl/xml_ingest.setl.ttl','rb').read(),
content_type="text/turtle", follow_redirects=True)
self.assertEquals(response.status,'201 CREATED')
setlmaker = autonomic.SETLMaker()
results = self.run_agent(setlmaker)
# confirm this is creating a SETL script for the XML file.
self.assertTrue(len(results) > 0)
setlr = autonomic.SETLr()
print(len(self.app.db))
for setlr_np in results:
setlr_results = self.run_agent(setlr, nanopublication=setlr_np)
nanocomposites = list(self.app.db.subjects(RDF.type,URIRef("http://nanomine.org/ns/PolymerNanocomposite")))
print(nanocomposites, len(self.app.db))
self.assertEquals(len(nanocomposites),1)
def test_L102_S3_Hu_2007(self):
self.login(*self.create_user("*****@*****.**", "password"))
text = "Hello, World!"
b64text = b64encode(text)
nanopub = files['L102_S3_Hu_2007']
response = self.client.post("/pub",
data=nanopub,
content_type="application/ld+json",
follow_redirects=True)
self.assertEquals(response.status, '201 CREATED')
content = self.client.get(
"/about",
query_string={"uri": "http://example.com/testdatab64"},
follow_redirects=True)
self.assertEquals(content.mimetype, "text/plain")
self.assertEquals(content.data, text)
np = nanopub.Nanopublication()
np.assertion.parse(data=open('../setl/xml_ingest.setl.ttl'),
format="turtle")
setlmaker = autonomic.SETLMaker()
results = self.run_agent(setlmaker, nanopublication=np)
# confirm this is creating a SETL script for the XML file.
setlr = autonomic.SETLr()
for nanopub in results:
setlr_results = self.run_agent(setlr, nanopublication=nanopub)
def setUp(self):
self.maxDiff = 10000
self.login(*self.create_user("*****@*****.**", "password"))
upload = '''<{}> a <http://nanomine.org/ns/NanomineJSONFile>,
<https://www.iana.org/assignments/media-types/application/json> ,
<http://schema.org/DataDownload> ;
<http://vocab.rpi.edu/whyis/hasContent> "data:application/json;charset=UTF-8;base64,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" .
'''.format(
"/apps/nanomine-graph/ChemDatabase/chemprops_example.json")
response = self.client.post("/pub",
data=upload,
content_type="text/turtle",
follow_redirects=True)
self.assertEquals(response.status, "201 CREATED")
response = self.client.post(
"/pub",
data=open("/apps/nanomine-graph/setl/chem_props.setl.ttl",
"rb").read(),
content_type="text/turtle",
follow_redirects=True)
self.assertEquals(response.status, "201 CREATED")
setlmaker = autonomic.SETLMaker()
results = self.run_agent(setlmaker)
self.assertTrue(len(results) > 0)
setlr = autonomic.SETLr()
print(len(self.app.db))
for setlr_np in results:
setlr_results = self.run_agent(setlr, nanopublication=setlr_np)
def setUp(runner, file_under_test):
# Skip setting up disabled tests
if os.getenv("CI") is not None:
if runner._testMethodName in disabled:
print("Skipping test", str(runner._testMethodName),
"in CI since it is disabled")
return
# Initialization
runner.login(*runner.create_user("*****@*****.**", "password"))
xml_str = get_xml(file_under_test)
encoded_file = b64encode(xml_str.encode('utf8'))
print("XML length:", len(encoded_file))
files[file_under_test] = files["template"] % (file_under_test,
encoded_file)
upload = files[file_under_test]
response = runner.client.post("/pub",
data=upload,
content_type="text/turtle",
follow_redirects=True)
runner.assertEquals(response.status, '201 CREATED')
response = runner.client.post(
"/pub",
data=open('/apps/nanomine-graph/setl/xml_ingest.setl.ttl',
'rb').read(),
content_type="text/turtle",
follow_redirects=True)
runner.assertEquals(response.status, '201 CREATED')
fileid = runner.app.db.value(
rdflib.URIRef('https://materialsmine.org/nmr/xml/' + file_under_test),
rdflib.URIRef('http://vocab.rpi.edu/whyis/hasFileID'))
runner.assertNotEquals(fileid, None)
setlmaker = autonomic.SETLMaker()
results = runner.run_agent(setlmaker)
# confirm this is creating a SETL script for the XML file.
runner.assertTrue(len(results) > 0)
setlr = autonomic.SETLr()
print(len(runner.app.db))
for setlr_np in results:
print(setlr_np.serialize(format="trig").decode('utf8'))
setlr_results = runner.run_agent(setlr, nanopublication=setlr_np)
def test_L168_S3_Luo_2013(self):
self.login(*self.create_user("*****@*****.**", "password"))
upload = files['L168_S3_Luo_2013']
response = self.client.post("/pub",
data=upload,
content_type="text/turtle",
follow_redirects=True)
self.assertEquals(response.status, '201 CREATED')
xml_content = self.client.get(
"/about",
query_string={
'uri': 'http://nanomine.org/nmr/xml/L163_S4_Luo_2013.xml'
}).data
print("the xml content ", xml_content)
response = self.client.post(
"/pub",
data=open('/apps/nanomine-graph/setl/xml_ingest.setl.ttl',
'rb').read(),
content_type="text/turtle",
follow_redirects=True)
self.assertEquals(response.status, '201 CREATED')
# xml_content = self.client.get("/about",query_string={'uri':'http://nanomine.org/nmr/xml/L102_S3_Hu_2007.xml'}).data
# print("the xml content ", xml_content)
setlmaker = autonomic.SETLMaker()
results = self.run_agent(setlmaker)
self.assertTrue(len(results) > 0)
setlr = autonomic.SETLr()
print(len(self.app.db))
for setlr_np in results:
print("\nThe setlr_np is : ", setlr_np)
setlr_results = self.run_agent(setlr, nanopublication=setlr_np)
nanocomposites = list(
self.app.db.subjects(
RDF.type,
URIRef("http://nanomine.org/ns/PolymerNanocomposite")))
print(nanocomposites, len(self.app.db))
self.assertEquals(len(nanocomposites), 1)
def setUp(runner, file_under_test):
# Initialization
runner.login(*runner.create_user("*****@*****.**", "password"))
r = requests.get('http://nanomine.org/nmr/xml/' + file_under_test + '.xml')
j = json.loads(r.text)
xml_str = j["data"][0]["xml_str"]
temp = tempfile.NamedTemporaryFile()
temp.write(xml_str.encode("utf-8"))
temp.seek(0)
files[file_under_test] = files["template"].format(temp.name)
upload = files[file_under_test]
response = runner.client.post("/pub",
data=upload,
content_type="text/turtle",
follow_redirects=True)
runner.assertEquals(response.status, '201 CREATED')
response = runner.client.post(
"/pub",
data=open('/apps/nanomine-graph/setl/xml_ingest.setl.ttl',
'rb').read(),
content_type="text/turtle",
follow_redirects=True)
runner.assertEquals(response.status, '201 CREATED')
setlmaker = autonomic.SETLMaker()
results = runner.run_agent(setlmaker)
# confirm this is creating a SETL script for the XML file.
runner.assertTrue(len(results) > 0)
setlr = autonomic.SETLr()
print(len(runner.app.db))
for setlr_np in results:
setlr_results = runner.run_agent(setlr, nanopublication=setlr_np)
temp.close()
importer.LinkedData(
prefix=LOD_PREFIX + '/dbpedia/ontolgy/',
url='http://dbpedia.org/ontology/%s',
headers={'Accept': 'text/turtle'},
format='turtle',
),
# importer.LinkedData(
# prefix = LOD_PREFIX+'/dbpedia/class/',
# url = 'http://dbpedia.org/class/%s',
# access_url = 'http://dbpedia.org/sparql?default-graph-uri=http://dbpedia.org&query=DESCRIBE+<%s>&format=application/json-ld',
# format='json-ld',
# )
],
inferencers={
"SETLr":
autonomic.SETLr(),
"Class Subsumption Closure":
autonomic.Deductor(
resource="?resource",
prefixes="",
where=
"\t?resource rdfs:subClassOf ?class .\n\t?class rdfs:subClassOf+ ?superClass .",
construct="?resource rdfs:subClassOf ?superClass .",
explanation=
"Since {{class}} is a subclass of {{superClass}}, any class that is a subclass of {{class}} is also a subclass of {{superClass}}. Therefore, {{resource}} is a subclass of {{superClass}}."
),
"Instance Subsumbtion Closure":
autonomic.Deductor(
resource="?resource",
prefixes="",
where=
headers={'Accept': 'text/turtle'},
format='turtle',
postprocess_update='''insert {
graph ?g {
?article <http://purl.org/dc/terms/abstract> ?abstract.
}
} where {
graph ?g {
?article <http://dbpedia.org/ontology/abstract> ?abstract.
}
}
''')
],
inferencers={
"SDDAgent": autonomic.SDDAgent(),
"SETLr": autonomic.SETLr(),
"SETLMaker": autonomic.SETLMaker(),
"CacheUpdater": autonomic.CacheUpdater(),
"UnitConverter": converter.UnitConverter(),
# "HTML2Text" : nlp.HTML2Text(),
"EntityExtractor": nlp.EntityExtractor(),
"EntityResolver": nlp.EntityResolver(),
# "TF-IDF Calculator" : nlp.TFIDFCalculator(),
# "SKOS Crawler" : autonomic.Crawler(predicates=[skos.broader, skos.narrower, skos.related])
},
inference_tasks=[
# dict ( name="SKOS Crawler",
# service=autonomic.Crawler(predicates=[skos.broader, skos.narrower, skos.related]),
# schedule=dict(hour="1")
# )
])
