def testAnnotate(self):
"""
Annotate file in created RO
ro annotate file attribute-name [ attribute-value ]
"""
rodir = self.createTestRo("data/ro-test-1", "RO test annotation", "ro-testRoAnnotate")
args = [
"ro", "annotate", rodir+"/"+"subdir1/subdir1-file.txt", "title", "subdir1-file title",
"-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)
#self.assertRegexpMatches(outtxt, "annotation.*dc:title")
# Read manifest and check for annotation
manifestgraph = ro_manifest.readManifestGraph(rodir)
filesubj = ro_manifest.getComponentUri(rodir, "subdir1/subdir1-file.txt")
log.debug("filesubj %s"%filesubj)
filetitle = manifestgraph.value(filesubj, DCTERMS.title, None),
self.assertEqual(len(filetitle), 1, "Singleton result expected")
self.assertEqual(filetitle[0], "subdir1-file title")
self.deleteTestRo(rodir)
return
def _addSimpleAnnotation(ro_config, ro_dir, rofile, attrname, attrvalue):
"""
Add a simple annotation to a file in a research object.
ro_config is the research object manager configuration, supplied as a dictionary
ro_dir is the research object root directory
rofile names the file or resource to be annotated, possibly relative to the RO.
attrname names the attribute in a form recognized by getAnnotationByName
attrvalue is a value to be associated with the attribute
"""
annfile = createAnnotationBody(ro_config, ro_dir, rofile, { attrname: attrvalue} )
ro_graph = ro_manifest.readManifestGraph(ro_dir)
_addAnnotationBodyToRoGraph(ro_graph, ro_dir, rofile, annfile)
ro_manifest.writeManifestGraph(ro_dir, ro_graph)
return
def _getAnnotationValues(ro_config, ro_dir, rofile, attrname):
"""
Returns iterator over annotation values for given subject and attribute
"""
log.debug("getAnnotationValues: ro_dir %s, rofile %s, attrname %s"%(ro_dir, rofile, attrname))
ro_graph = ro_manifest.readManifestGraph(ro_dir)
subject = ro_manifest.getComponentUri(ro_dir, rofile)
(predicate,valtype) = getAnnotationByName(ro_config, attrname)
#@@TODO refactor common code with getRoAnnotations, etc.
for ann_node in ro_graph.subjects(predicate=RO.annotatesAggregatedResource, object=subject):
ann_uri = ro_graph.value(subject=ann_node, predicate=AO.body)
ann_graph = readAnnotationBody(ro_dir, ro_manifest.getComponentUriRel(ro_dir, ann_uri))
for v in ann_graph.objects(subject=subject, predicate=predicate):
#log.debug("Triple: %s %s %s"%(subject,p,v))
yield v
return
def _removeSimpleAnnotation(ro_config, ro_dir, rofile, attrname, attrvalue):
"""
Remove a simple annotation or multiple matching annotations a research object.
ro_config is the research object manager configuration, supplied as a dictionary
ro_dir is the research object root directory
rofile names the annotated file or resource, possibly relative to the RO.
attrname names the attribute in a form recognized by getAnnotationByName
attrvalue is the attribute value to be deleted, or Nomne to delete all vaues
"""
log.debug("removeSimpleAnnotation: ro_dir %s, rofile %s, attrname %s, attrvalue %s"%
(ro_dir, rofile, attrname, attrvalue))
# Enumerate annotations
# For each:
# if annotation is only one in graph then:
# remove aggregated annotation
# else:
# create new annotation graph witj annotation removed
# update aggregated annotation
ro_graph = ro_manifest.readManifestGraph(ro_dir)
subject = ro_manifest.getComponentUri(ro_dir, rofile)
(predicate,valtype) = getAnnotationByName(ro_config, attrname)
val = attrvalue and makeAnnotationValue(ro_config, attrvalue, valtype)
#@@TODO refactor common code with getRoAnnotations, etc.
add_annotations = []
remove_annotations = []
for ann_node in ro_graph.subjects(predicate=RO.annotatesAggregatedResource, object=subject):
ann_uri = ro_graph.value(subject=ann_node, predicate=AO.body)
ann_graph = readAnnotationBody(ro_dir, ro_manifest.getComponentUriRel(ro_dir, ann_uri))
if (subject, predicate, val) in ann_graph:
ann_graph.remove((subject, predicate, val))
if (subject, None, None) in ann_graph:
# Triples remain in annotation body: write new body and update RO graph
ann_name = createAnnotationGraphBody(ro_config, ro_dir, rofile, ann_graph)
remove_annotations.append(ann_node)
add_annotations.append(ann_name)
else:
# Remove annotation from RO graph
remove_annotations.append(ann_node)
# Update RO graph if needed
if add_annotations or remove_annotations:
for a in remove_annotations:
_removeAnnotationBodyFromRoGraph(ro_graph, a)
for a in add_annotations:
_addAnnotationBodyToRoGraph(ro_graph, ro_dir, rofile, a)
ro_manifest.writeManifestGraph(ro_dir, ro_graph)
return
def _getRoAnnotations(ro_dir):
"""
Returns iterator over annotations applied to the RO as an entity.
Each value returned by the iterator is a (subject,predicate,object) triple.
"""
ro_graph = ro_manifest.readManifestGraph(ro_dir)
subject = ro_manifest.getRoUri(ro_dir)
log.debug("getRoAnnotations %s"%str(subject))
for ann_node in ro_graph.subjects(predicate=RO.annotatesAggregatedResource, object=subject):
ann_uri = ro_graph.value(subject=ann_node, predicate=AO.body)
ann_graph = readAnnotationBody(ro_dir, ro_manifest.getComponentUriRel(ro_dir, ann_uri))
if ann_graph:
for (p, v) in ann_graph.predicate_objects(subject=subject):
#log.debug("Triple: %s %s %s"%(subject,p,v))
yield (subject, p, v)
return
def _replaceSimpleAnnotation(ro_config, ro_dir, rofile, attrname, attrvalue):
"""
Replace a simple annotation in a research object.
ro_config is the research object manager configuration, supplied as a dictionary
ro_dir is the research object root directory
rofile names the file or resource to be annotated, possibly relative to the RO.
attrname names the attribute in a form recognized by getAnnotationByName
attrvalue is a new value to be associated with the attribute
"""
ro_graph = ro_manifest.readManifestGraph(ro_dir)
subject = ro_manifest.getComponentUri(ro_dir, rofile)
(predicate,valtype) = getAnnotationByName(ro_config, attrname)
log.debug("Replace annotation: subject %s, predicate %s, value %s"%(repr(subject), repr(predicate), repr(attrvalue)))
ro_graph.remove((subject, predicate, None))
ro_graph.add((subject, predicate, makeAnnotationValue(ro_config, attrvalue, valtype)))
ro_manifest.writeManifestGraph(ro_dir, ro_graph)
return
def _getFileAnnotations(ro_dir, rofile):
"""
Returns iterator over annotations applied to a specified component in the RO
Each value returned by the iterator is a (subject,predicate,object) triple.
"""
log.debug("getFileAnnotations: ro_dir %s, rofile %s"%(ro_dir, rofile))
ro_graph = ro_manifest.readManifestGraph(ro_dir)
subject = ro_manifest.getComponentUri(ro_dir, rofile)
log.debug("getFileAnnotations: %s"%str(subject))
#@@TODO refactor common code with getRoAnnotations, etc.
for ann_node in ro_graph.subjects(predicate=RO.annotatesAggregatedResource, object=subject):
ann_uri = ro_graph.value(subject=ann_node, predicate=AO.body)
ann_graph = readAnnotationBody(ro_dir, ro_manifest.getComponentUriRel(ro_dir, ann_uri))
if ann_graph:
for (p, v) in ann_graph.predicate_objects(subject=subject):
#log.debug("Triple: %s %s %s"%(subject,p,v))
yield (subject, p, v)
return
def annotationTest(self, anntype, annvalue, anntypeuri, annexpect):
rodir = self.createTestRo("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
manifestgraph = ro_manifest.readManifestGraph(rodir)
filesubj = ro_manifest.getComponentUri(rodir, "subdir1/subdir1-file.txt")
fileann = manifestgraph.value(filesubj, anntypeuri, None),
#@@TODO: deal with case that expected result is a list
self.assertEqual(len(fileann), 1, "Singleton result expected")
self.assertEqual(fileann[0], annexpect)
self.deleteTestRo(rodir)
return
def getAllAnnotations(ro_dir):
"""
Returns iterator over all annotations associated with the RO
Each value returned by the iterator is a (subject,predicate,object) triple.
"""
log.debug("getAllAnnotations %s"%str(ro_dir))
ro_graph = ro_manifest.readManifestGraph(ro_dir)
#@@TODO refactor common code with getRoAnnotations, etc.
for (ann_node, subject) in ro_graph.subject_objects(predicate=RO.annotatesAggregatedResource):
ann_uri = ro_graph.value(subject=ann_node, predicate=AO.body)
log.debug("- ann_uri %s"%(str(ann_uri)))
ann_graph = readAnnotationBody(ro_dir, ro_manifest.getComponentUriRel(ro_dir, ann_uri))
if ann_graph == None:
log.debug("No annotation graph: ann_uri: "+str(ann_uri))
else:
for (p, v) in ann_graph.predicate_objects(subject=subject):
#log.debug("Triple: %s %s %s"%(subject,p,v))
yield (subject, p, v)
return
def annotations(progname, configbase, options, args):
"""
Dusplay annotations
ro annotations [ file | -d dir ]
"""
# Check command arguments
if len(args) not in [2,3]:
print ("%s annotations: wrong number of arguments provided"%
(progname))
print ("Usage: %s annotations [ file | -d dir ]"%
(progname))
return 1
ro_config = ro_utils.readconfig(configbase)
ro_file = (args[2] if len(args) >= 3 else "")
ro_options = {
"rofile": ro_file,
"rodir": options.rodir or os.path.dirname(ro_file)
}
log.debug("ro_options: "+repr(ro_options))
if options.verbose:
print "ro annotations -d \"%(rodir)s\" %(rofile)s "%ro_options
ro_dir= ro_root_directory(progname+" annotations", ro_config, ro_options['rodir'])
if not ro_dir: return 1
ro_graph = ro_manifest.readManifestGraph(ro_dir)
if ro_options['rofile']:
ro_file = ro_manifest.getComponentUri(ro_dir, os.path.abspath(ro_options['rofile']))
annotations = ro_graph.predicate_objects(subject=ro_file)
print str(ro_file) # @@TODO figure relativization
log.debug("annotations for %s"%str(ro_file))
for (atyp,aval) in annotations:
aname = getAnnotationNameByUri(ro_config, atyp)
log.debug("Annotations atyp %s, aname %s, aval %s"%(repr(atyp), aname, repr(aval)))
print " %s: %s"%(aname,str(aval))
else:
# list all annotations
assert False, "@@TODO - show annotations for all RO components"
return 0
def testAnnotateMultiple(self):
rodir = self.createTestRo("data/ro-test-1", "RO test annotation", "ro-testRoAnnotate")
rofile = rodir+"/"+"subdir1/subdir1-file.txt"
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, annotations)
# Read manifest and check for annotation
manifestgraph = ro_manifest.readManifestGraph(rodir)
filesubj = ro_manifest.getComponentUri(rodir, "subdir1/subdir1-file.txt")
for a in annotations:
fileann = manifestgraph.value(filesubj, a["atypeuri"], None),
self.assertEqual(len(fileann), 1, "Singleton result expected")
self.assertEqual(fileann[0], a["aexpect"])
self.deleteTestRo(rodir)
return
def annotate(progname, configbase, options, args):
"""
Annotate a specified research object component
ro annotate file attribute-name [ attribute-value ]
"""
# Check command arguments
if len(args) not in [4,5]:
print ("%s annotate: wrong number of arguments provided"%
(progname))
print ("Usage: %s annotate file attribute-name [ attribute-value ]"%
(progname))
return 1
ro_config = ro_utils.readconfig(configbase)
ro_options = {
"rofile": args[2],
"rodir": os.path.dirname(args[2]),
"roattribute": args[3],
"rovalue": args[4] or None
}
log.debug("ro_options: "+repr(ro_options))
# Find RO root directory
ro_dir = ro_root_directory(progname+" attribute", ro_config, ro_options['rodir'])
if not ro_dir: return 1
# Read and update manifest
if options.verbose:
print "ro annotate %(rofile)s %(roattribute)s \"%(rovalue)s\""%ro_options
ro_graph = ro_manifest.readManifestGraph(ro_dir)
(predicate,valtype) = getAnnotationByName(ro_config, ro_options['roattribute'])
log.debug("Adding annotation predicate: %s, value %s"%(repr(predicate),repr(ro_options['rovalue'])))
ro_graph.add(
( ro_manifest.getComponentUri(ro_dir, os.path.abspath(ro_options['rofile'])),
predicate,
rdflib.Literal(ro_options['rovalue'])
) )
ro_manifest.writeManifestGraph(ro_dir, ro_graph)
return 0