def ro_root_reference(cmdname, ro_config, rodir, roref=None):
"""
Find research object root directory. If the supplied rodir is not a local file
reference, it is returned as-is, otherwise ro_root_directory is used to locate
the RO root directory containing the indicated file.
cmdname name of ro command, used in diagnostic messages
ro_config RO configuration details, used when resolving supplied directory
rodir RO directory supplied via -d option. Must be in configured work area.
roref RO reference, supplied by other means, or None. May be any URI reference,
resolved against base of file URI for current directory.
Returns directory path string, or None if not found, in which
case an error message is displayed.
"""
if not roref:
# Process supplied directory option
roref = ro_uriutils.resolveFileAsUri(rodir)
if ro_uriutils.isFileUri(roref):
roref = ro_root_directory(cmdname, ro_config, rodir, restricted=False)
else:
if rodir:
print ("%s: specify either RO directory or URI, not both" % (cmdname))
return 1
roref = ro_uriutils.resolveFileAsUri(roref)
return roref
def annotations(progname, configbase, options, args):
"""
Display annotations
ro annotations [ file | -d dir ]
"""
log.debug("annotations: progname %s, configbase %s, args %s" %
(progname, configbase, repr(args)))
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
# Enumerate and display annotations
rometa = ro_metadata(ro_config, ro_dir)
if ro_options['rofile']:
rofile = ro_uriutils.resolveFileAsUri(ro_options['rofile']) # Relative to CWD
log.debug("Annotations for %s" % str(rofile))
annotations = rometa.getFileAnnotations(rofile)
else:
annotations = rometa.getAllAnnotations()
if options.debug:
log.debug("---- Annotations:")
for a in annotations:
log.debug(" %s" % repr(a))
log.debug("----")
rometa.showAnnotations(annotations, sys.stdout)
return 0
def __init__(self, roconfig, roref, dummysetupfortest=False):
"""
Initialize: read manifest from object at given directory into local RDF graph
roconfig is the research object manager configuration, supplied as a dictionary
roref a URI reference that refers to the Research Object to be accessed, or
relative path name (see ro_uriutils.resolveFileAsUri for interpretation)
dummysetupfortest is an optional parameter that, if True, suppresses some aspects of
the setup (does not attempt to read a RO manifest) for isolated testing.
"""
self.roconfig = roconfig
self.roref = roref
self.dummyfortest = dummysetupfortest
self.manifestgraph = None
self.roannotations = None
self.registries = None
uri = resolveFileAsUri(roref)
if not uri.endswith("/"): uri += "/"
self.rouri = rdflib.URIRef(uri)
if self._isLocal():
self.rosrs = None
else:
self.rosrs = ROSRS_Session(
self.roconfig["rosrs_uri"],
self.roconfig["rosrs_access_token"]
)
self._loadManifest()
# Get RO URI from manifest
# May be different from computed value if manifest has absolute URI
self.rouri = self.manifestgraph.value(None, RDF.type, RO.ResearchObject)
# Check that the manifest contained at least one RO URI
assert self.rouri is not None
return
def getResourceNameString(ro_config, rname, base=None):
"""
Returns a string value corresoponding to a URI indicated by the supplied parameter.
Relative references are assumed to be paths relative to the supplied base URI or,
if no rbase is supplied, relative to the current directory.
"""
rsplit = rname.split(":")
if len(rsplit) == 2:
# Try to interpret name as CURIE
for rpref in ro_config["annotationPrefixes"]:
if rsplit[0] == rpref:
rname = ro_config["annotationPrefixes"][rpref]+rsplit[1]
if urlparse.urlsplit(rname).scheme == "":
if base:
rname = resolveUri(rname, base)
else:
rname = resolveFileAsUri(rname)
return rname
def annotations(progname, configbase, options, args):
"""
Display annotations
ro annotations [ file | -d dir ]
"""
# @@TODO: although a URI is accepted on the command line, the actual display logic assumes
# a local file when displaying annotations.
log.debug("annotations: progname %s, configbase %s, args %s" %
(progname, configbase, repr(args)))
ro_config = getroconfig(configbase, options)
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))
cmdname = progname + " annotations"
rouri = ro_root_reference(cmdname, ro_config, ro_options['rodir'])
if not rouri: return 1
if options.verbose:
print cmdname + " -d \"%(rodir)s\" %(rofile)s " % ro_options
# Enumerate and display annotations
log.debug("- displaying annotations for %s"%(rouri))
rometa = ro_metadata(ro_config, rouri)
if ro_options['rofile']:
rofile = ro_uriutils.resolveFileAsUri(ro_options['rofile']) # Relative to CWD
log.debug("Annotations for %s" % str(rofile))
annotations = rometa.getFileAnnotations(rofile)
else:
annotations = rometa.getAllAnnotations()
if options.debug:
log.debug("---- Annotations:")
for a in annotations:
log.debug(" %s" % repr(a))
log.debug("----")
rometa.showAnnotations(annotations, sys.stdout)
return 0
def __init__(self, roconfig, roref, dummysetupfortest=False):
"""
Initialize: read manifest from object at given directory into local RDF graph
roconfig is the research object manager configuration, supplied as a dictionary
roref a URI reference that refers to the Research Object to be accessed, or
relative path name (see ro_uriutils.resolveFileAsUri for interpretation)
dummysetupfortest is an optional parameter that, if True, suppresses some aspects of
the setup (does not attempt to read a RO manifest) for isolated testing.
"""
self.roconfig = roconfig
self.roref = roref
self.dummyfortest = dummysetupfortest
self.manifestgraph = None
self.roannotations = None
self.registries = None
uri = resolveFileAsUri(roref)
if not uri.endswith("/"): uri += "/"
self.rouri = rdflib.URIRef(uri)
if self._isLocal():
self.rosrs = None
else:
self.rosrs = ROSRS_Session(self.roconfig["rosrs_uri"],
self.roconfig["rosrs_access_token"])
self._loadManifest()
# Get RO URI from manifest
# May be different from computed value if manifest has absolute URI
# Nested URIs may be present; ours is the one described by the manifest URI,
# which is determined by the _loadManifest() method.
for s in self.manifestgraph.subjects(RDF.type, RO.ResearchObject):
if self.manifestgraph.value(s,
ORE.isDescribedBy) == self.manifesturi:
self.rouri = s
# Check that the manifest contained at least one RO URI
assert self.rouri is not None
return
def annotate(progname, configbase, options, args):
"""
Annotate a specified research object component
ro annotate file attribute-name [ attribute-value ]
ro link file attribute-name [ attribute-value ]
"""
ro_config = ro_utils.readconfig(configbase)
rodir = options.rodir or (not options.wildcard and os.path.dirname(args[2]))
if len(args) == 3:
# Using graph form
ro_options = {
# Usding graph annotation form
"rofile": args[2],
"rodir": rodir,
"wildcard": options.wildcard,
"wild": "-w " if options.wildcard else "",
"graph": options.graph or None,
"defaultType": "resource" if args[1] == "link" else "string",
"rocmd": progname,
"anncmd": args[1]
}
else:
ro_options = {
# Usding explicit annotation form
"rofile": args[2],
"rodir": rodir,
"wildcard": options.wildcard,
"wild": "-w " if options.wildcard else "",
"roattribute": args[3],
"rovalue": args[4] if len(args) == 5 else None,
"defaultType": "resource" if args[1] == "link" else "string",
"rocmd": progname,
"anncmd": args[1]
}
log.debug("ro_options: " + repr(ro_options))
# Find RO root directory
ro_dir = ro_root_directory("%s %s" % (progname, args[1]), ro_config, ro_options['rodir'])
if not ro_dir: return 1
if options.verbose:
if len(args) == 3:
print "%(rocmd)s %(anncmd)s -d %(rodir)s %(wild)s%(rofile)s -g %(graph)s " % (ro_options)
else:
print "%(rocmd)s %(anncmd)s -d %(rodir)s %(wild)s%(rofile)s %(roattribute)s \"%(rovalue)s\"" % ro_options
# Read and update manifest and annotations
# ---- local function to annotate a single entry ----
def annotate_single(rofile):
if len(args) == 3:
# Add existing graph as annotation
rometa.addGraphAnnotation(rofile, ro_options['graph'])
else:
# Create new annotation graph
rometa.addSimpleAnnotation(rofile,
ro_options['roattribute'], ro_options['rovalue'],
ro_options['defaultType'])
# ----
rometa = ro_metadata(ro_config, ro_dir)
if options.wildcard:
try:
rofilepattern = re.compile(ro_options['rofile'])
except re.error as e:
ro_options["err"] = str(e)
print '''%(rocmd)s %(anncmd)s -w "%(rofile)s" <...> : %(err)s''' % ro_options
return 1
for rofile in [ str(r) for r in rometa.getAggregatedResources() if rofilepattern.search(str(r)) ]:
annotate_single(rofile)
else:
rofile = ro_uriutils.resolveFileAsUri(ro_options['rofile']) # Relative to CWD
annotate_single(rofile)
return 0