def showAnnotations(ro_config, ro_dir, annotations, outstr):
sname_prev = None
for (asubj,apred,aval) in annotations:
# log.debug("Annotations: asubj %s, apred %s, aval %s"%
# (repr(asubj), repr(apred), repr(aval)))
if apred != ORE.aggregates:
(aname, atype) = getAnnotationByUri(ro_config, apred)
sname = ro_manifest.getComponentUriRel(ro_dir, str(asubj))
log.debug("Annotations: sname %s, aname %s"%(sname, aname))
if sname == "":
sname = ro_manifest.getRoUri(ro_dir)
if sname != sname_prev:
print "\n<"+str(sname)+">"
sname_prev = sname
outstr.write(" %s %s\n"%(aname, formatAnnotationValue(aval, atype)))
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 _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 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
