def testChecklistEvalExcel(self):
"""
Test checklist evaluation with generated Minim file from Excel source
"""
self.setupConfig()
rodir = self.createTestRo(testbase, "testro", "RO for testMkMinim", "ro-testMkMinim")
self.populateTestRo(testbase, rodir)
self.annotateResource(testbase, rodir, "", "FileAnnotations.ttl")
rouri = ro_manifest.getRoUri(rodir)
# Create minim graph from CSV file
gridname = "TestMkMinim.xls"
griduri = ro_manifest.getComponentUri(rodir, gridname)
gridxls = os.path.join(rodir, gridname)
gridbase = "http://example.org/base/"
grid = GridExcel(gridxls, baseuri=gridbase)
(status, minimgr) = mkminim.mkminim(grid, baseuri=grid.resolveUri(""))
self.assertEquals(status, 0)
# Write Minim
minimname = "TestMkMinim_minim.ttl"
with open(rodir + "/" + minimname, "w") as minimfile:
minimgr.serialize(minimfile, format="turtle")
# Evaluate checklist
minimuri = ro_manifest.getComponentUri(rodir, minimname)
minimpurpose = "test1"
args = ["ro", "evaluate", "checklist", "-a", "-d", rodir + "/", minimname, minimpurpose, "."]
self.outstr.seek(0)
with StdoutContext.SwitchStdout(self.outstr):
status = ro.runCommand(
os.path.join(testbase, TestConfig.ro_test_config.CONFIGDIR),
os.path.join(testbase, TestConfig.ro_test_config.ROBASEDIR),
args,
)
outtxt = self.outstr.getvalue()
assert status == 0, "Status %d, outtxt: %s" % (status, outtxt)
log.debug("status %d, outtxt: %s" % (status, outtxt))
# Check response returned
# filelist = [ unicode(ro_manifest.getComponentUri(rodir, f))
# for f in ["File1.txt", "File2.txt", "File3.txt"] ]
filelist = ValueList(
[str(ro_manifest.getComponentUri(rodir, f)) for f in ["File1.txt", "File2.txt", "File3.txt"]]
)
expect = [
"Research Object file://%s/:" % (rodir),
"Fully complete for test1 of resource .",
"Satisfied requirements:",
" At least 3 file as part values are present",
" At most 3 file as part values are present",
" All part resource files %s are aggregated in RO" % (filelist),
" All file as part resources are accessible (live)",
" Python 2.7.x present",
" Files as part are partOf some indicated whole",
" File exists as a part",
"Research object URI: %s" % (rouri),
"Minimum information URI: %s" % (minimuri),
]
self.outstr.seek(0)
for line in self.outstr:
self.assertIn(str(line)[:-1], expect)
self.deleteTestRo(rodir)
return
def testGetRequirements(self):
def compare_reqs(req_expect, req_found):
for k in req_expect:
if not k in req_found:
log.debug("- not found: %s"%(k))
return False
elif isinstance(req_expect[k], dict) and isinstance(req_found[k], dict):
if not compare_reqs(req_expect[k], req_found[k]): return False
elif req_found[k] != req_expect[k]:
log.debug("- not found: %s: %s != %s "%(k,req_expect[k],req_found[k]))
return False
return True
self.setupConfig()
rodir = self.createTestRo(testbase, "test-data-1", "RO test minim", "ro-testMinim")
rouri = ro_manifest.getRoUri(rodir)
minimbase = ro_manifest.getComponentUri(rodir, "Minim-UserRequirements.rdf")
model = ro_minim.getElementUri(minimbase, "#runnableRequirementRO")
minimgraph = ro_minim.readMinimGraph(minimbase)
requirements = ro_minim.getRequirements(minimgraph, model)
expected_found = False
r1 = (
{ 'level': "MUST"
, 'label': rdflib.Literal("Python 2.7")
, 'softwarerule':
{ 'command': rdflib.Literal("python -V")
, 'response': rdflib.Literal("Python 2.7")
, 'derives': ro_minim.getElementUri(minimbase, "#environment-software/python-27")
}
, 'uri': ro_minim.getElementUri(minimbase, "#environment-software/python-27")
})
r2 = (
{ 'level': "MUST"
, 'label': rdflib.Literal("aggregates data/UserRequirements-astro.ods")
, 'datarule':
{ 'aggregates': ro_manifest.getComponentUri(rodir, "data/UserRequirements-astro.ods")
, 'derives': ro_minim.getElementUri(minimbase, "#isPresent/data/UserRequirements-astro.ods")
}
, 'uri': ro_minim.getElementUri(minimbase, "#isPresent/data/UserRequirements-astro.ods")
})
r3 = (
{ 'level': "SHOULD"
, 'label': rdflib.Literal("aggregates docs/reqs.css")
, 'datarule':
{ 'aggregates': ro_manifest.getComponentUri(rodir, "docs/reqs.css")
, 'derives': ro_minim.getElementUri(minimbase, "#isPresent/docs/reqs.css")
}
, 'uri': ro_minim.getElementUri(minimbase, "#isPresent/docs/reqs.css")
})
r1_found = r2_found = r3_found = False
for r in requirements:
log.debug("requirement: %s"%(repr(r)))
if compare_reqs(r1, r): r1_found = True
if compare_reqs(r2, r): r2_found = True
if compare_reqs(r3, r): r3_found = True
self.assertTrue(r1_found, "Expected requirement(1) not found in minim")
self.assertTrue(r2_found, "Expected requirement(2) not found in minim")
self.assertTrue(r3_found, "Expected requirement(3) not found in minim")
return
def testGetConstraint(self):
self.setupConfig()
rodir = self.createTestRo(testbase, "test-data-1", "RO test minim", "ro-testMinim")
rouri = ro_manifest.getRoUri(rodir)
minimbase = ro_manifest.getComponentUri(rodir, "Minim-UserRequirements.rdf")
model = ro_minim.getElementUri(minimbase, "#runnableRequirementRO")
constraint = ro_minim.getElementUri(minimbase, "#create/docs/UserRequirements-astro.csv")
minimgraph = ro_minim.readMinimGraph(minimbase)
c = ro_minim.getConstraint(minimgraph, rodir,
"docs/UserRequirements-astro.csv",
r"create.*UserRequirements-astro\.csv")
self.assertEquals(c['target'], ro_manifest.getComponentUri(rodir, "docs/UserRequirements-astro.csv"))
self.assertEquals(c['purpose'], rdflib.Literal("create UserRequirements-astro.csv"))
self.assertEquals(c['model'], model)
self.assertEquals(c['uri'], constraint)
return
def testAnnotateMultiple(self):
rodir = self.createTestRo(testbase, "data/ro-test-1", "RO test annotation", "ro-testRoAnnotate")
rofile = rodir+"/"+"subdir1/subdir1-file.txt"
define_annotations = (
[ {"atypename": "type", "avalue":"atype", "atypeuri":DCTERMS.type, "aexpect":"atype" }
, {"atypename": "keywords", "avalue":"asubj", "atypeuri":DCTERMS.subject, "aexpect":"asubj" }
, {"atypename": "description", "avalue":"adesc", "atypeuri":DCTERMS.description, "aexpect":"adesc" }
, {"atypename": "format", "avalue":"aformat", "atypeuri":DCTERMS.format, "aexpect":"aformat" }
, {"atypename": "title", "avalue":"atitle", "atypeuri":DCTERMS.title, "aexpect":"atitle" }
, {"atypename": "created", "avalue":"acreated", "atypeuri":DCTERMS.created, "aexpect":"acreated" }
#, {"atypename": ..., "avalue":..., "atypeuri":..., "aexpect":... }
#, {"atypename": ..., "avalue":..., "atypeuri":..., "aexpect":... }
])
self.annotateMultiple(rodir, rofile, define_annotations)
# Read manifest and check for annotation
annotations = ro_annotation._getFileAnnotations(rodir, "subdir1/subdir1-file.txt")
resourceuri = ro_manifest.getComponentUri(rodir, "subdir1/subdir1-file.txt")
expected_annotations = (
[ (resourceuri, a["atypeuri"], rdflib.Literal(a["aexpect"]))
for a in define_annotations
])
for i in range(6):
next = annotations.next()
#log.debug("Next %s"%(repr(next)))
if ( next not in expected_annotations):
self.assertTrue(False, "Not expected (%d) %s"%(i, repr(next)))
self.assertRaises(StopIteration, annotations.next)
# Clean up
self.deleteTestRo(rodir)
return
def annotateTest(self, anntype, annvalue, anntypeuri, annexpect):
rodir = self.createTestRo(testbase, "data/ro-test-1", "RO test annotation", "ro-testRoAnnotate")
args = [
"ro", "annotate", rodir+"/"+"subdir1/subdir1-file.txt", anntype, annvalue,
"-v",
]
with SwitchStdout(self.outstr):
status = ro.runCommand(ro_test_config.CONFIGDIR, ro_test_config.ROBASEDIR, args)
outtxt = self.outstr.getvalue()
assert status == 0, outtxt
self.assertEqual(outtxt.count("ro annotate"), 1)
# Read manifest and check for annotation
annotations = ro_annotation._getFileAnnotations(rodir, "subdir1/subdir1-file.txt")
resourceuri = ro_manifest.getComponentUri(rodir, "subdir1/subdir1-file.txt")
expected_annotations = (
[ (resourceuri, anntypeuri, rdflib.Literal(annexpect))
])
for i in range(1):
next = annotations.next()
#log.debug("Next %s"%(repr(next)))
if ( next not in expected_annotations):
self.assertTrue(False, "Not expected (%d) %s"%(i, repr(next)))
self.assertRaises(StopIteration, annotations.next)
self.deleteTestRo(rodir)
return
def testAddAggregatedResourcesCommand(self):
"""
Test function that adds aggregated resources to a research object manifest
"""
rodir = self.createTestRo(testbase, "data/ro-test-1", "RO test annotation", "ro-testRoAnnotate")
args = [
"ro", "add", "-v", "-a",
"-d", rodir,
rodir
]
with SwitchStdout(self.outstr):
status = ro.runCommand(ro_test_config.CONFIGDIR, ro_test_config.ROBASEDIR, args)
outtxt = self.outstr.getvalue()
assert status == 0, outtxt
log.debug("outtxt %s"%outtxt)
def URIRef(path):
return ro_manifest.getComponentUriAbs(rodir, path)
s = ro_manifest.getComponentUri(rodir, "")
g = rdflib.Graph()
g.add( (s, RDF.type, RO.ResearchObject ) )
g.add( (s, ORE.aggregates, URIRef("README-ro-test-1") ) )
g.add( (s, ORE.aggregates, URIRef("filename%20with%20spaces.txt") ) )
g.add( (s, ORE.aggregates, URIRef("filename%23with%23hashes.txt") ) )
g.add( (s, ORE.aggregates, URIRef("README-ro-test-1") ) )
g.add( (s, ORE.aggregates, URIRef("subdir1/subdir1-file.txt") ) )
g.add( (s, ORE.aggregates, URIRef("subdir2/subdir2-file.txt") ) )
self.checkManifestGraph(rodir, g)
self.deleteTestRo(rodir)
return
def testMkMinim(self):
self.setupConfig()
rodir = self.createTestRo(testbase, "testro", "RO for testMkMinim", "ro-testMkMinim")
rouri = ro_manifest.getRoUri(rodir)
# Create minim graph from CSV file
# NOTE: a base URI may be specoified when decoding the grid or when constructing the minim
# graph. The Minim graph uses its own relative references, so for consistency it may
# be necessary to pass the grid base URI to mkminim. The code below does this.
gridname = "TestMkMinim.csv"
griduri = ro_manifest.getComponentUri(rodir, gridname)
gridcsv = os.path.join(rodir, gridname)
gridbase = "http://example.org/base/"
with open(gridcsv, "rU") as gridfile:
grid = GridCSV(gridfile, baseuri=gridbase, dialect=csv.excel)
(status, minimgr) = mkminim.mkminim(grid, baseuri=grid.resolveUri(""))
self.assertEquals(status, 0)
# Read expected graph
graphname = os.path.join(rodir, "TestMkMinim.ttl")
expectgr = rdflib.Graph()
with open(graphname) as expectfile:
expectgr.parse(file=expectfile, publicID=gridbase, format="turtle")
# Check content of minim graph
###minimgr.serialize(sys.stdout, format="turtle")
self.checkTargetGraph(minimgr.graph(), expectgr, msg="Not found in constructed minim graph")
self.deleteTestRo(rodir)
return
def linkTest(self, anntype, annvalue, anntypeuri, annexpect):
rodir = self.createTestRo(testbase, "data/ro-test-1", "RO test annotation", "ro-testRoAnnotate")
args = [
"ro", "link", rodir+"/"+"subdir1/subdir1-file.txt", anntype, annvalue,
"-v",
]
with SwitchStdout(self.outstr):
status = ro.runCommand(ro_test_config.CONFIGDIR, ro_test_config.ROBASEDIR, args)
outtxt = self.outstr.getvalue()
assert status == 0, outtxt
self.assertEqual(outtxt.count("ro link"), 1)
# Read manifest and check for annotation
annotations = ro_annotation._getFileAnnotations(rodir, "subdir1/subdir1-file.txt")
resourceuri = ro_manifest.getComponentUri(rodir, "subdir1/subdir1-file.txt")
expected_annotations = (
[ (resourceuri, anntypeuri, annexpect)
])
count = 0
for next in list(annotations):
log.debug("- next %s"%(str(next[0])) )
log.debug(" - (%s, %s)"%(str(next[1]),str(next[2])) )
if next in expected_annotations:
count += 1
else:
self.assertTrue(False, "Not expected (%d) %s"%(count, repr(next)))
self.assertEqual(count,1)
self.deleteTestRo(rodir)
return
def testGetRequirements(self):
def compare_reqs(req_expect, req_found):
for k in req_expect:
if not k in req_found:
log.debug("- not found: %s"%(k))
return False
elif isinstance(req_expect[k], dict) and isinstance(req_found[k], dict):
if not compare_reqs(req_expect[k], req_found[k]): return False
elif req_found[k] != req_expect[k]:
log.debug("- not found: %s: %s != %s "%(k,req_expect[k],req_found[k]))
return False
return True
self.setupConfig()
rodir = self.createTestRo(testbase, "test-data-2", "RO test minim", "ro-testMinim")
rouri = ro_manifest.getRoUri(rodir)
minimbase = ro_manifest.getComponentUri(rodir, "Minim-UserRequirements2.rdf")
model = ro_minim.getElementUri(minimbase, "#runnableRO")
minimgraph = ro_minim.readMinimGraph(minimbase)
requirements = ro_minim.getRequirements(minimgraph, model)
r1 = (
{ 'level': "MUST"
, 'label': rdflib.Literal("aggregates data/UserRequirements-astro.ods")
, 'querytestrule':
{ 'query': rdflib.Literal("?ro a ro:ResearchObject")
, 'resultmod': None
, 'aggregates_t': rdflib.Literal("data/UserRequirements-astro.ods")
}
, 'uri': ro_minim.getElementUri(minimbase, "#isAggregated/data/UserRequirements-astro.ods")
})
r2 = (
{ 'level': "MUST"
, 'label': rdflib.Literal("accessible data/UserRequirements-astro.ods")
, 'querytestrule':
{ 'query': rdflib.Literal("?ro a ro:ResearchObject")
, 'resultmod': None
, 'islive_t': rdflib.Literal("data/UserRequirements-astro.ods")
}
, 'uri': ro_minim.getElementUri(minimbase, "#isAccessible/data/UserRequirements-astro.ods")
})
r3 = (
{ 'level': "MUST"
, 'label': rdflib.Literal("labeled data/UserRequirements-astro.ods")
, 'querytestrule':
{ 'query': rdflib.Literal("?ro a ro:ResearchObject")
, 'resultmod': rdflib.Literal("ORDER BY ?ro")
, 'exists': rdflib.Literal("<data/UserRequirements-astro.ods> rdfs:label ?label")
}
, 'uri': ro_minim.getElementUri(minimbase, "#isLabeled/data/UserRequirements-astro.ods")
})
r1_found = r2_found = r3_found = False
for r in requirements:
log.debug("requirement: %s"%(repr(r)))
if compare_reqs(r1, r): r1_found = True
if compare_reqs(r2, r): r2_found = True
if compare_reqs(r3, r): r3_found = True
self.assertTrue(r1_found, "Expected requirement(1) not found in minim")
self.assertTrue(r2_found, "Expected requirement(2) not found in minim")
self.assertTrue(r3_found, "Expected requirement(3) not found in minim")
return
def testGetConstraints(self):
self.setupConfig()
rodir = self.createTestRo(testbase, "test-data-2", "RO test minim", "ro-testMinim")
rouri = ro_manifest.getRoUri(rodir)
minimbase = ro_manifest.getComponentUri(rodir, "Minim-UserRequirements2.rdf")
model = ro_minim.getElementUri(minimbase, "#runnableRO")
constraint = ro_minim.getElementUri(minimbase, "#create/data/UserRequirements-astro.ods")
# Read Minim as graph, scan constraints and look for expected value
minimgraph = ro_minim.readMinimGraph(minimbase)
constraints = ro_minim.getConstraints(minimgraph)
expected_found = False
for c in constraints:
if ( c['target'] == ro_manifest.getComponentUri(rodir, "data/UserRequirements-astro.ods") and
c['purpose'] == rdflib.Literal("create UserRequirements-astro.ods") and
c['model'] == model and
c['uri'] == constraint ) :
expected_found = True
break
self.assertTrue(expected_found, "Expected constraint not found in minim")
return
def testGetModel(self):
self.setupConfig()
rodir = self.createTestRo(testbase, "test-data-2", "RO test minim", "ro-testMinim")
rouri = ro_manifest.getRoUri(rodir)
minimbase = ro_manifest.getComponentUri(rodir, "Minim-UserRequirements2.rdf")
model = ro_minim.getElementUri(minimbase, "#runnableRO")
minimgraph = ro_minim.readMinimGraph(minimbase)
m = ro_minim.getModel(minimgraph, model)
self.assertEquals(m['label'], rdflib.Literal("Runnable RO"))
self.assertEquals(m['uri'], model)
return
def testMinimRead(self):
"""
Basic test that Minim test file can be read
"""
self.setupConfig()
rodir = self.createTestRo(testbase, "test-data-2", "RO test minim", "ro-testMinim")
rouri = ro_manifest.getRoUri(rodir)
minimbase = ro_manifest.getComponentUri(rodir, "Minim-UserRequirements2.rdf")
target = ro_manifest.getComponentUri(rodir, "data/UserRequirements-astro.ods")
constraint = ro_minim.getElementUri(minimbase, "#create/data/UserRequirements-astro.ods")
model = ro_minim.getElementUri(minimbase, "#runnableRO")
g = ro_minim.readMinimGraph(minimbase)
expected_minim = (
[ (target, MINIM.hasChecklist, constraint )
, (constraint, MINIM.forPurpose, rdflib.Literal('create UserRequirements-astro.ods') )
, (constraint, MINIM.toModel, model )
, (model, RDF.type, MINIM.Model )
])
self.checkTargetGraph(g, expected_minim, msg="Not found in Minim")
self.deleteTestRo(rodir)
return
def testGridRead(self):
"""
Basic test that Minim test file can be read
"""
self.setupConfig()
rodir = self.createTestRo(testbase, "testro", "RO for Minim creation test", "ro-testMkMinim")
rouri = ro_manifest.getRoUri(rodir)
gridname = "TestMkMinim.csv"
griduri = ro_manifest.getComponentUri(rodir, gridname)
gridcsv = os.path.join(rodir, gridname)
with open(gridcsv, "rU") as gridfile:
grid = GridCSV(gridfile, baseuri=griduri, dialect=csv.excel)
self.assertEqual(grid[0][0], "Minim definition for MkMinim testing")
self.deleteTestRo(rodir)
return
def testGetModels(self):
self.setupConfig()
rodir = self.createTestRo(testbase, "test-data-2", "RO test minim", "ro-testMinim")
rouri = ro_manifest.getRoUri(rodir)
minimbase = ro_manifest.getComponentUri(rodir, "Minim-UserRequirements2.rdf")
model = ro_minim.getElementUri(minimbase, "#runnableRO")
minimgraph = ro_minim.readMinimGraph(minimbase)
models = ro_minim.getModels(minimgraph)
expected_found = False
for m in models:
if ( m['label'] == rdflib.Literal("Runnable RO") and
m['uri'] == model ) :
expected_found = True
break
self.assertTrue(expected_found, "Expected model not found in minim")
return
def testGetComponentUri(self):
self.assertEquals(ro_manifest.getComponentUri("/example/ro/dir", "a/b.txt"),
rdflib.URIRef("file:///example/ro/dir/a/b.txt"))
self.assertEquals(ro_manifest.getComponentUri("/example/ro/dir/", "a/b.txt"),
rdflib.URIRef("file:///example/ro/dir/a/b.txt"))
self.assertEquals(ro_manifest.getComponentUri("ro/dir", "a/b.txt"),
rdflib.URIRef("file://%s/ro/dir/a/b.txt"%(cwd)))
self.assertEquals(ro_manifest.getComponentUri("ro/dir/", "a/b.txt"),
rdflib.URIRef("file://%s/ro/dir/a/b.txt"%(cwd)))
self.assertEquals(ro_manifest.getComponentUri("/example/ro/dir", "a/b/d/"),
rdflib.URIRef("file:///example/ro/dir/a/b/d/"))
self.assertEquals(ro_manifest.getComponentUri("/example/ro/dir/", "a/b/d/"),
rdflib.URIRef("file:///example/ro/dir/a/b/d/"))
self.assertEquals(ro_manifest.getComponentUri("ro/dir", "a/b/d/"),
rdflib.URIRef("file://%s/ro/dir/a/b/d/"%(cwd)))
self.assertEquals(ro_manifest.getComponentUri("ro/dir/", "a/b/d/"),
rdflib.URIRef("file://%s/ro/dir/a/b/d/"%(cwd)))
return
def testManifestContent(self):
"""
Test content of newly created manifest
"""
rodir = self.createTestRo(testbase, "data/ro-test-1", "RO test annotation", "ro-testRoAnnotate")
ro_graph = ro_manifest.readManifestGraph(rodir)
self.checkManifestGraph(rodir, ro_graph)
s = ro_manifest.getComponentUri(rodir, "")
g = rdflib.Graph()
g.add( (s, RDF.type, RO.ResearchObject ) )
g.add( (s, DCTERMS.creator, rdflib.Literal(ro_test_config.ROBOXUSERNAME) ) )
g.add( (s, DCTERMS.description, rdflib.Literal("RO test annotation") ) )
g.add( (s, DCTERMS.title, rdflib.Literal("RO test annotation") ) )
g.add( (s, DCTERMS.identifier, rdflib.Literal("ro-testRoAnnotate") ) )
self.checkManifestGraph(rodir, g)
self.deleteTestRo(rodir)
return
def testAddAggregatedResources(self):
"""
Test function that adds aggregated resources to a research object manifest
"""
rodir = self.createTestRo(testbase, "data/ro-test-1", "RO test annotation", "ro-testRoAnnotate")
ro_manifest.addAggregatedResources(rodir, rodir, recurse=True)
def URIRef(path):
return ro_manifest.getComponentUri(rodir, path)
s = ro_manifest.getComponentUri(rodir, "")
g = rdflib.Graph()
g.add( (s, RDF.type, RO.ResearchObject ) )
g.add( (s, ORE.aggregates, URIRef("README-ro-test-1") ) )
g.add( (s, ORE.aggregates, URIRef("subdir1/subdir1-file.txt") ) )
g.add( (s, ORE.aggregates, URIRef("subdir2/subdir2-file.txt") ) )
self.checkManifestGraph(rodir, g)
self.deleteTestRo(rodir)
return
def testAddGetAllAnnotations(self):
rodir = self.createTestRo(testbase, "data/ro-test-1", "Test get all annotations", "ro-testRoAnnotate")
roresource = "subdir1/subdir1-file.txt"
# Add anotations for file
ro_annotation._addSimpleAnnotation(ro_config, rodir, roresource,
"type", "Test file")
ro_annotation._addSimpleAnnotation(ro_config, rodir, roresource,
"description", "File in test research object")
ro_annotation._addSimpleAnnotation(ro_config, rodir, roresource,
"note", "Research object file created for annotation testing")
ro_annotation._addSimpleAnnotation(ro_config, rodir, roresource,
"title", "Test file in RO")
ro_annotation._addSimpleAnnotation(ro_config, rodir, roresource,
"created", "2011-12-07")
ro_annotation._addSimpleAnnotation(ro_config, rodir, roresource,
"rdf:type", ROTERMS.resource)
# Retrieve the file anotations
annotations = ro_annotation.getAllAnnotations(rodir)
rouri = ro_manifest.getRoUri(rodir)
resourceuri = ro_manifest.getComponentUri(rodir, roresource)
log.debug("resourceuri: %s"%(resourceuri))
expected_annotations = (
[ (rouri, DCTERMS.description, rdflib.Literal('Test get all annotations'))
, (rouri, DCTERMS.title, rdflib.Literal('Test get all annotations'))
, (rouri, DCTERMS.created, rdflib.Literal('unknown'))
, (rouri, DCTERMS.creator, rdflib.Literal('Test User'))
, (rouri, DCTERMS.identifier, rdflib.Literal('ro-testRoAnnotate'))
, (rouri, RDF.type, RO.ResearchObject)
, (resourceuri, DCTERMS.type, rdflib.Literal('Test file'))
, (resourceuri, DCTERMS.description, rdflib.Literal('File in test research object'))
, (resourceuri, ROTERMS.note, rdflib.Literal('Research object file created for annotation testing'))
, (resourceuri, DCTERMS.title, rdflib.Literal('Test file in RO'))
, (resourceuri, DCTERMS.created, rdflib.Literal('2011-12-07'))
, (resourceuri, RDF.type, ROTERMS.resource)
])
for i in range(12+1+6): # Annotations + aggregations
next = annotations.next()
#log.debug("Next %s"%(repr(next)))
if ( next not in expected_annotations and
next[1] != DCTERMS.created and
next[1] != ORE.aggregates ):
self.assertTrue(False, "Not expected (%d) %s"%(i, repr(next)))
self.assertRaises(StopIteration, annotations.next)
self.deleteTestRo(rodir)
return
def testCreateReadRoAnnotationBody(self):
"""
Test function to create simple annotation body
"""
rodir = self.createTestRo(testbase, "data/ro-test-1", "RO test annotation", "ro-testRoAnnotate")
roresource = "."
attrdict = {
"type": rdflib.Literal("Research Object"),
# @@TODO: handle lists "keywords": ["test", "research", "object"],
"description": rdflib.Literal("Test research object"),
"format": rdflib.Literal("application/vnd.wf4ever.ro"),
"note": rdflib.Literal("Research object created for annotation testing"),
"title": rdflib.Literal("Test research object"),
"created": rdflib.Literal("2011-12-07")
}
annotationfilebase = ro_annotation.createAnnotationBody(
ro_config, rodir, roresource, attrdict)
# Ann-%04d%02d%02d-%04d-%s.rdf
self.assertRegexpMatches(annotationfilebase,
r"Ann-\d\d\d\d\d\d\d\d-\d+-RO_test_annotation\.rdf",
msg="Unexpected filename form for annotation: "+annotationfilebase)
annotationfilename = ro_annotation.makeAnnotationFilename(rodir, annotationfilebase)
annotationgraph = ro_annotation.readAnnotationBody(rodir, annotationfilename)
attrpropdict = {
"type": DCTERMS.type,
# @@TODO "keywords": DCTERMS.subject,
"description": DCTERMS.description,
"format": DCTERMS.format,
"note": ROTERMS.note,
"title": DCTERMS.title,
"created": DCTERMS.created
}
s = ro_manifest.getComponentUri(rodir, roresource)
log.debug("annotation subject %s"%repr(s))
for k in attrpropdict:
p = attrpropdict[k]
log.debug("annotation predicate %s"%repr(p))
v = attrdict[k]
a = annotationgraph.value(s, p, None)
log.debug("annotation value %s"%repr(a))
#self.assertEqual(len(a), 1, "Singleton result expected")
self.assertEqual(a, v)
self.deleteTestRo(rodir)
return
def testLinkWithGraph(self):
rodir = self.createTestRo(testbase, "data/ro-test-1", "RO test annotation", "ro-testRoAnnotate")
rofile = rodir+"/"+"subdir1/subdir1-file.txt"
define_annotations = (
[ {"atypename": "type", "avalue":"atype", "atypeuri":DCTERMS.type, "aexpect":"atype" }
, {"atypename": "keywords", "avalue":"asubj", "atypeuri":DCTERMS.subject, "aexpect":"asubj" }
, {"atypename": "description", "avalue":"adesc", "atypeuri":DCTERMS.description, "aexpect":"adesc" }
, {"atypename": "format", "avalue":"aformat", "atypeuri":DCTERMS.format, "aexpect":"aformat" }
, {"atypename": "title", "avalue":"atitle", "atypeuri":DCTERMS.title, "aexpect":"atitle" }
, {"atypename": "created", "avalue":"acreated", "atypeuri":DCTERMS.created, "aexpect":"acreated" }
])
# Create annotation graph file and apply annotations
annotation_graph = rdflib.Graph()
resourceuri = ro_manifest.getComponentUri(rodir, "subdir1/subdir1-file.txt")
for ann in define_annotations:
annotation_graph.add( (resourceuri, ann["atypeuri"], rdflib.Literal(ann["aexpect"])) )
annotation_graph_filename = os.path.join(os.path.abspath(rodir), "annotate-subdir1-file.txt.rdf")
annotation_graph.serialize(annotation_graph_filename,
format='xml', base=ro_manifest.getRoUri(rodir), xml_base="")
args = ["ro", "annotate", rofile, "-g", annotation_graph_filename ]
with SwitchStdout(self.outstr):
status = ro.runCommand(ro_test_config.CONFIGDIR, ro_test_config.ROBASEDIR, args)
outtxt = self.outstr.getvalue()
assert status == 0, outtxt
# Read manifest and check for annotation
annotations = ro_annotation._getFileAnnotations(rodir, "subdir1/subdir1-file.txt")
expected_annotations = (
[ (resourceuri, a["atypeuri"], rdflib.Literal(a["aexpect"]))
for a in define_annotations
])
count = 0
for next in list(annotations):
log.debug("- next %s"%(str(next[0])) )
log.debug(" - (%s, %s)"%(str(next[1]),str(next[2])) )
if next in expected_annotations:
count += 1
else:
self.assertTrue(False, "Not expected (%d) %s"%(count, repr(next)))
self.assertEqual(count,6)
# Clean up
self.deleteTestRo(rodir)
return
def getConstraint(minimgraph, rouri, target_ref, purpose_regex_string):
"""
Find constraint matching supplied RO, target and purpose regex
Constraint is returned with:
targetro_actual -> URI of resource
targetres_actual -> URI of target if supplied, else subject of minium:hasConstraint
"""
def mkstr(u):
return u and str(u)
log.debug("getConstraint: rouri %s, target_ref %s"%(rouri, target_ref))
target = target_ref and ro_manifest.getComponentUri(rouri, target_ref)
log.debug(" target_uri %s"%(target))
purpose = purpose_regex_string and re.compile(purpose_regex_string)
templatedict = {'targetro': urllib.unquote(str(rouri))}
if target:
# Allow use of {+targetres} in checklist target template:
templatedict['targetres'] = urllib.unquote(str(target))
for c in getConstraints(minimgraph):
log.debug("- test: target %s purpose %s"%(c['target'],c['purpose']))
log.debug("- purpose %s, c['purpose'] %s"%(purpose_regex_string, c['purpose']))
if not purpose or purpose.match(c['purpose']):
c['targetro_actual'] = rouri
c['targetres_actual'] = target or c['target']
if not target:
# No target specified in request, match any (first) constraint
return c
if c['target'] == target:
# Match explicit target specification (subject of minim:hasConstraint)
return c
log.debug("- target: %s, c['target_t']: %s"%(target, repr(c['target_t'])))
if c['target_t'] and c['target_t'].value == "*":
# Special case: wilcard ("*") template matches any target
return c
if target and c['target_t']:
log.debug("- expand %s"%(uritemplate.expand(c['target_t'], templatedict)))
if str(target) == uritemplate.expand(c['target_t'], templatedict):
# Target matches expanded template from constraint description
return c
return None
def testCreateReadFileAnnotationBody(self):
"""
Test function to create simple annotation body
"""
rodir = self.createTestRo(testbase, "data/ro-test-1", "RO test annotation", "ro-testRoAnnotate")
roresource = "subdir1/subdir1-file.txt"
attrdict = {
"type": "Test file",
"description": "File in test research object",
"note": "File in research object created for annotation testing",
"title": "Test file in RO",
"created": "2011-12-07"
}
annotationfilebase = ro_annotation.createAnnotationBody(
ro_config, rodir, roresource, attrdict)
# Ann-%04d%02d%02d-%04d-%s.rdf
self.assertRegexpMatches(annotationfilebase,
r"Ann-\d\d\d\d\d\d\d\d-\d+-subdir1-file\.txt\.rdf",
msg="Unexpected filename form for annotation: "+annotationfilebase)
annotationfilename = ro_annotation.makeAnnotationFilename(rodir, annotationfilebase)
annotationgraph = ro_annotation.readAnnotationBody(rodir, annotationfilename)
attrpropdict = {
"type": DCTERMS.type,
"description": DCTERMS.description,
"note": ROTERMS.note,
"title": DCTERMS.title,
"created": DCTERMS.created
}
s = ro_manifest.getComponentUri(rodir, roresource)
log.debug("annotation subject %s"%repr(s))
for k in attrpropdict:
p = attrpropdict[k]
log.debug("annotation predicate %s"%repr(p))
v = attrdict[k]
a = annotationgraph.value(s, p, None)
log.debug("annotation value %s"%repr(a))
#self.assertEqual(len(a), 1, "Singleton result expected")
self.assertEqual(a, v)
self.deleteTestRo(rodir)
return
def testAnnotateFileWithEscapes(self):
rodir = self.createTestRo(testbase, "data/ro-test-1", "RO test annotation", "ro-testRoAnnotate")
rofile1 = rodir+"/"+"filename with spaces.txt"
rofile2 = rodir+"/"+"filename#with#hashes.txt"
with SwitchStdout(self.outstr):
for rofile in [rofile1,rofile2]:
args = ["ro", "annotate", rofile, "type", "atype"]
status = ro.runCommand(ro_test_config.CONFIGDIR, ro_test_config.ROBASEDIR, args)
outtxt = self.outstr.getvalue()
assert status == 0, outtxt
# Reset output stream buffer closed
self.outstr = StringIO.StringIO()
# Read manifest and check for annotation
for rofile in [rofile1,rofile2]:
resourceuri = ro_manifest.getComponentUri(rodir, rofile)
annotations = ro_annotation._getFileAnnotations(rodir, rofile)
next = annotations.next()
self.assertEqual(next, (resourceuri, DCTERMS.type, rdflib.Literal("atype")))
self.assertRaises(StopIteration, annotations.next)
# Clean up
self.deleteTestRo(rodir)
return
def testRemoveGetFileAnnotations(self):
rodir = self.createTestRo(testbase, "data/ro-test-1", "Test remove file annotation", "ro-testRoAnnotate")
roresource = "subdir1/subdir1-file.txt"
# Add anotations for file
ro_annotation._addSimpleAnnotation(ro_config, rodir, roresource,
"type", "Test file")
ro_annotation._addSimpleAnnotation(ro_config, rodir, roresource,
"description", "File in test research object")
ro_annotation._addSimpleAnnotation(ro_config, rodir, roresource,
"note", "Research object file created for annotation testing")
ro_annotation._addSimpleAnnotation(ro_config, rodir, roresource,
"title", "Test file in RO")
ro_annotation._addSimpleAnnotation(ro_config, rodir, roresource,
"created", "2011-12-07")
ro_annotation._addSimpleAnnotation(ro_config, rodir, roresource,
"rdf:type", ROTERMS.resource)
# Remove annotations
ro_annotation._removeSimpleAnnotation(ro_config, rodir, roresource,
"description", "File in test research object")
ro_annotation._removeSimpleAnnotation(ro_config, rodir, roresource,
"note", None)
# Retrieve the file anotations
annotations = ro_annotation._getFileAnnotations(rodir, roresource)
resourceuri = ro_manifest.getComponentUri(rodir, roresource)
log.debug("resourceuri: %s"%(resourceuri))
expected_annotations = (
[ (resourceuri, DCTERMS.type, rdflib.Literal('Test file'))
, (resourceuri, DCTERMS.title, rdflib.Literal('Test file in RO'))
, (resourceuri, DCTERMS.created, rdflib.Literal('2011-12-07'))
, (resourceuri, RDF.type, ROTERMS.resource)
])
for i in range(4):
next = annotations.next()
#log.debug("Next %s"%(repr(next)))
if ( next not in expected_annotations):
self.assertTrue(False, "Not expected (%d) %s"%(i, repr(next)))
self.assertRaises(StopIteration, annotations.next)
self.deleteTestRo(rodir)
return
def testUri(rodir, path, uristring):
self.assertEquals(ro_manifest.getComponentUri(rodir, path), rdflib.URIRef(uristring))
return
def URIRef(path):
return ro_manifest.getComponentUri(rodir, path)
