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 _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 _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 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
