def real_evaluate(request):
# From: http://tools.ietf.org/html/rfc3986#section-2.1
# gen-delims = ":" / "/" / "?" / "#" / "[" / "]" / "@"
# sub-delims = "!" / "$" / "&" / "'" / "(" / ")"
# / "*" / "+" / "," / ";" / "="
quotesafe = ":/?#[]@!$&'()*+,;=" + "%"
# isolate parameters (keep invalid URI characters %-encoded)
RO = urllib.quote(request.params["RO"], quotesafe)
minim = urllib.quote(request.params["minim"], quotesafe)
target = urllib.quote(request.params.get("target","."), quotesafe)
purpose = request.params["purpose"]
log.info("Evaluate RO %s, minim %s, target %s, purpose %s"%(RO,minim,target,purpose))
# create rometa object
# @@TODO: use proper configuration and credentials
ROparse = urlparse.urlparse(RO)
rosrs_uri = (ROparse.scheme or "http") + "://" + (ROparse.netloc or "localhost:8000") + "/"
ro_config = {
"annotationTypes": annotationTypes,
"annotationPrefixes": annotationPrefixes,
"rosrs_uri": rosrs_uri,
#"rosrs_uri": target,
#"rosrs_uri": "http://sandbox.wf4ever-project.org/rodl/ROs/",
#"rosrs_access_token": "ac14dd1a-ab59-40ec-b510-ffdb01a85473",
"rosrs_access_token": None,
}
rometa = ro_metadata(ro_config, RO)
log.info("rometa.rouri: %s"%(rometa.rouri) )
# invoke evaluation service
(graph, evalresult) = ro_eval_minim.evaluate(rometa, minim, target, purpose)
log.debug("evaluate:results: \n"+json.dumps(evalresult, indent=2))
# Assemble graph of results
graph = ro_eval_minim.evalResultGraph(graph, evalresult)
return graph
def evaluate(progname, configbase, options, args):
"""
Evaluate RO
ro evaluate checklist [ -d <dir> ] <minim> <purpose> [ <target> ]"
"""
log.debug("evaluate: progname %s, configbase %s, args %s" %
(progname, configbase, repr(args)))
ro_config = getroconfig(configbase, options)
ro_options = (
{ "rodir": options.rodir or ""
, "function": args[2]
})
log.debug("ro_options: " + repr(ro_options))
ro_ref = ro_root_reference(progname + " annotations", ro_config, None, ro_options['rodir'])
if not ro_ref: return 1
# Evaluate...
if ro_options["function"] == "checklist":
if len(args) not in [5, 6]:
print ("%s evaluate checklist: wrong number of arguments provided" % (progname))
print ("Usage: %s evaluate checklist [ -d <dir> ] [ -a | -l <level> ] <minim> <purpose> [ <target> ]" % (progname))
return 1
levels = ["summary", "must", "should", "may", "full"]
if options.level not in ["summary", "must", "should", "may", "full"]:
print ("%s evaluate checklist: invalid reporting level %s, must be one of %s" %
(progname, options.level, repr(levels)))
return 1
ro_options["minim"] = ((len(args) > 3) and args[3]) or "minim.rdf"
ro_options["purpose"] = ((len(args) > 4) and args[4]) or "create"
ro_options["target"] = ((len(args) > 5) and args[5]) or "."
if options.verbose:
print "ro evaluate %(function)s -d \"%(rodir)s\" %(minim)s %(purpose)s %(target)s" % ro_options
rometa = ro_metadata(ro_config, ro_ref)
(minimgraph, evalresult) = ro_eval_minim.evaluate(rometa,
ro_options["minim"], ro_options["target"], ro_options["purpose"])
if options.verbose:
print "== Evaluation result =="
print json.dumps(evalresult, indent=2)
if options.outformat and options.outformat.upper() in RDFTYPSERIALIZERMAP:
# RDF output
graph = ro_eval_minim.evalResultGraph(minimgraph, evalresult)
graph.serialize(destination=sys.stdout,
format=RDFTYPSERIALIZERMAP[options.outformat.upper()])
else:
ro_eval_minim.format(evalresult,
{ "detail" : "full" if options.all else options.level },
sys.stdout)
# elif ... other functions here
else:
print ("%s evaluate: unrecognized function provided (%s)" % (progname, ro_options["function"]))
print ("Usage:")
print (" %s evaluate checklist [ -d <dir> ] [ -a | -l <level> ] <minim> <purpose> [ <target> ]" % (progname))
return 1
return 0
def testEvaluateRDF(self):
self.setupConfig()
rodir = self.createTestRo(testbase, "test-chembox", "RO test minim", "ro-testMinim")
rouri = ro_manifest.getRoUri(rodir)
self.populateTestRo(testbase, rodir)
rometa = ro_metadata(ro_config, rodir)
resuri = rometa.getComponentUriAbs("http://purl.org/net/chembox/Ethane")
reslabel = "Ethane"
rometa.addGraphAnnotation(resuri, "Ethane.ttl")
# Now run evaluation against test RO
(minimgr, evalresult) = ro_eval_minim.evaluate(rometa,
"Minim-chembox.ttl", # Minim file
resuri, # Target resource
"complete") # Purpose
resultgr = ro_eval_minim.evalResultGraph(minimgr, evalresult)
log.debug("------ resultgr:\n%s\n----"%(resultgr.serialize(format='turtle'))) # pretty-xml
## print "------ resultgr:\n%s\n----"%(resultgr.serialize(format='turtle'))
# Check response returned
modeluri = rdflib.URIRef('http://example.com/chembox-samples/minim_model')
prefixes = make_sparql_prefixes()
probequeries = (
[ '''ASK { _:r minim:testedRO <%s> ; minim:minimUri <%s> }'''%
(rouri, rometa.getComponentUri("Minim-chembox.ttl"))
, '''ASK { _:r minim:testedRO <%s> ; minim:testedModel <%s> }'''%
(rouri, modeluri)
, '''ASK { _:r minim:testedTarget <%s> ; minim:satisfied [ minim:tryMessage "%s" ] }'''%
(resuri, "InChI identifier is present")
, '''ASK { _:r minim:testedTarget <%s> ; minim:satisfied [ minim:tryMessage "%s" ] }'''%
(resuri, "ChemSpider identifier is present")
, '''ASK { _:r minim:testedTarget <%s> ; minim:missingMay [ minim:tryMessage "%s" ] }'''%
(resuri, "No synomym is present")
, '''ASK { _:r minim:testedTarget <%s> ; minim:nominallySatisfies <%s> }'''%
(resuri, modeluri)
, '''ASK { _:r minim:testedTarget <%s> ; minim:minimallySatisfies <%s> }'''%
(resuri, modeluri)
, '''ASK { <%s> rdfs:label "%s" }'''%
(resuri, reslabel)
])
for q in probequeries:
r = resultgr.query(prefixes+q)
self.assertEqual(r.type, 'ASK', "Result type %s for: %s"%(r.type, q))
self.assertTrue(r.askAnswer, "Failed query: %s"%(q))
self.deleteTestRo(rodir)
return
