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 add(progname, configbase, options, args):
"""
Add files to a research object manifest
ro add [ -d dir ] file
ro add [ -d dir ] [-a] [directory]
Use -a/--all to add subdirectories recursively
If no file or directory specified, defaults to current directory.
"""
ro_config = ro_utils.readconfig(configbase)
ro_options = {
"rodir": options.rodir or "",
"rofile": args[2] if len(args) == 3 else ".",
"recurse": options.all,
"recurseopt": "-a" if options.all else ""
}
log.debug("ro_options: " + repr(ro_options))
# Find RO root directory
ro_dir = ro_root_directory(progname + " add", ro_config, ro_options['rodir'])
if not ro_dir: return 1
# Read and update manifest
if options.verbose:
print "ro add -d %(rodir)s %(recurseopt)s %(rofile)s" % ro_options
rometa = ro_metadata(ro_config, ro_dir)
rometa.addAggregatedResources(ro_options['rofile'],
recurse=ro_options['recurse'], includeDirs=not ro_options['recurse'])
return 0
def status(progname, configbase, options, args):
"""
Display status of a designated research object
ro status [ -d dir ]
"""
# Check command arguments
ro_config = ro_utils.readconfig(configbase)
ro_options = {
"rodir": options.rodir or "",
}
log.debug("ro_options: " + repr(ro_options))
# Find RO root directory
ro_dir = ro_root_directory(progname + " status", ro_config, ro_options['rodir'])
if not ro_dir: return 1
# Read manifest and display status
if options.verbose:
print "ro status -d \"%(rodir)s\"" % ro_options
rometa = ro_metadata(ro_config, ro_dir)
rodict = rometa.getRoMetadataDict()
print "Research Object status"
print " identifier: %(roident)s, title: %(rotitle)s" % rodict
print " creator: %(rocreator)s, created: %(rocreated)s" % rodict
print " path: %(ropath)s" % rodict
if rodict['rouri']:
print " uri: %(rouri)s" % rodict
print " description: %(rodescription)s" % rodict
# @@TODO: add ROEVO information
return 0
def manifest(progname, configbase, options, args):
"""
Dump RDF of manifest
"""
log.debug("manifest: progname %s, configbase %s, args %s" %
(progname, configbase, repr(args)))
rouri = (args[2] if len(args) >= 3 else "")
ro_config = getroconfig(configbase, options, rouri)
ro_options = {
"rouri": rouri,
"rodir": options.rodir or ""
}
cmdname = progname + " manifest"
rouri = ro_root_reference(cmdname, ro_config, ro_options['rodir'], rouri)
if not rouri: return 1
if options.verbose:
if ro_options['rouri']:
print cmdname + (" \"%(rouri)s\" " % ro_options)
else:
print cmdname + (" -d \"%(rodir)s\" " % ro_options)
# Enumerate and display annotations
rometa = ro_metadata(ro_config, rouri)
format = "RDFXML"
if options.outformat and options.outformat.upper() in RDFTYPSERIALIZERMAP:
format = options.outformat.upper()
graph = rometa.getManifestGraph()
graph.serialize(destination=sys.stdout, format=RDFTYPSERIALIZERMAP[format])
return 0
def list(progname, configbase, options, args):
"""
List contents of a designated research object
-a displays files present in directory as well as aggregated resources
-h includes hidden files in display
ro list [ -a ] [ -h ] [ -d dir | uri ]
ro ls [ -a ] [ -h ] [ -d dir | uri ]
"""
# Check command arguments
rouri = (args[2] if len(args) >= 3 else "")
ro_config = getroconfig(configbase, options, rouri)
ro_options = {
"rouri": rouri,
"rodir": options.rodir or "",
"all": " -a" if options.all else "",
"hidden": " -h" if options.hidden else "",
}
log.debug("ro_options: " + repr(ro_options))
cmdname = progname + " list"
if rouri:
rouri = ro_root_reference(cmdname, ro_config, ro_options['rodir'], rouri)
if not rouri: return 1
if options.verbose:
print cmdname + (" \"%(rouri)s\" " % ro_options)
ro_dir = ""
else:
ro_dir = ro_root_directory(cmdname, ro_config, ro_options['rodir'], restricted=False)
if not ro_dir: return 1
if options.verbose:
print cmdname + ("%(all)s%(hidden)s -d \"%(rodir)s\" " % ro_options)
rouri = ro_dir
# Prepare to display aggregated resources
prep_f = ""
prep_a = ""
rofiles = []
if options.all:
if not ro_dir:
print ("%s: '--all' option is valid only with RO directory, not URI" % (cmdname))
return 1
prep_f = "f: "
prep_a = "a: "
rofiles = MiscUtils.ScanDirectories.CollectDirectoryContents(
ro_dir, baseDir=os.path.abspath(ro_dir),
listDirs=False, listFiles=True, recursive=True, appendSep=False)
if not options.hidden:
def notHidden(f):
return re.match("\.|.*/\.", f) == None
rofiles = filter(notHidden, rofiles)
# Scan RO and collect aggregated resources
try:
rometa = ro_metadata(ro_config, rouri)
except ROSRS_Error, e:
print str(e)
return 2
def evaluate(progname, configbase, options, args):
"""
Evaluate RO
ro evaluate checklist [ -d <dir> ] <minim> <purpose> [ <target> ]"
"""
log.debug("evaluate: progname %s, configbase %s, args %s" %
(progname, configbase, repr(args)))
ro_config = getroconfig(configbase, options)
ro_options = (
{ "rodir": options.rodir or ""
, "function": args[2]
})
log.debug("ro_options: " + repr(ro_options))
ro_ref = ro_root_reference(progname + " annotations", ro_config, None, ro_options['rodir'])
if not ro_ref: return 1
# Evaluate...
if ro_options["function"] == "checklist":
if len(args) not in [5, 6]:
print ("%s evaluate checklist: wrong number of arguments provided" % (progname))
print ("Usage: %s evaluate checklist [ -d <dir> ] [ -a | -l <level> ] <minim> <purpose> [ <target> ]" % (progname))
return 1
levels = ["summary", "must", "should", "may", "full"]
if options.level not in ["summary", "must", "should", "may", "full"]:
print ("%s evaluate checklist: invalid reporting level %s, must be one of %s" %
(progname, options.level, repr(levels)))
return 1
ro_options["minim"] = ((len(args) > 3) and args[3]) or "minim.rdf"
ro_options["purpose"] = ((len(args) > 4) and args[4]) or "create"
ro_options["target"] = ((len(args) > 5) and args[5]) or "."
if options.verbose:
print "ro evaluate %(function)s -d \"%(rodir)s\" %(minim)s %(purpose)s %(target)s" % ro_options
rometa = ro_metadata(ro_config, ro_ref)
(minimgraph, evalresult) = ro_eval_minim.evaluate(rometa,
ro_options["minim"], ro_options["target"], ro_options["purpose"])
if options.verbose:
print "== Evaluation result =="
print json.dumps(evalresult, indent=2)
if options.outformat and options.outformat.upper() in RDFTYPSERIALIZERMAP:
# RDF output
graph = ro_eval_minim.evalResultGraph(minimgraph, evalresult)
graph.serialize(destination=sys.stdout,
format=RDFTYPSERIALIZERMAP[options.outformat.upper()])
else:
ro_eval_minim.format(evalresult,
{ "detail" : "full" if options.all else options.level },
sys.stdout)
# elif ... other functions here
else:
print ("%s evaluate: unrecognized function provided (%s)" % (progname, ro_options["function"]))
print ("Usage:")
print (" %s evaluate checklist [ -d <dir> ] [ -a | -l <level> ] <minim> <purpose> [ <target> ]" % (progname))
return 1
return 0
def list(progname, configbase, options, args):
"""
List contents of a designated research object
-a displays files present as well as aggregated resources
-h includes hidden files in display
ro list [ -a ] [ -h ] [ -d dir ]
ro ls [ -a ] [ -h ] [ -d dir ]
"""
# Check command arguments
ro_config = ro_utils.readconfig(configbase)
ro_options = {
"rodir": options.rodir or "",
"all": " -a" if options.all else "",
"hidden": " -h" if options.hidden else "",
}
log.debug("ro_options: " + repr(ro_options))
# Find RO root directory
ro_dir = ro_root_directory(progname + " list", ro_config, ro_options['rodir'])
if not ro_dir: return 1
# Scan directory tree and collect filenames
if options.verbose:
print "ro list%(all)s%(hidden)s -d \"%(rodir)s\"" % ro_options
prep_f = ""
prep_a = ""
rofiles = []
if options.all:
prep_f = "f: "
prep_a = "a: "
rofiles = MiscLib.ScanDirectories.CollectDirectoryContents(
ro_dir, baseDir=os.path.abspath(ro_dir),
listDirs=False, listFiles=True, recursive=True, appendSep=False)
if not options.hidden:
def notHidden(f):
return re.match("\.|.*/\.", f) == None
rofiles = filter(notHidden, rofiles)
# Scan RO and collect aggregated resources
rometa = ro_metadata(ro_config, ro_dir)
roaggs = [ str(rometa.getComponentUriRel(a)) for a in rometa.getAggregatedResources() ]
# Assemble and output listing
print "\n".join(mapmerge(prepend_f(prep_a), roaggs, prepend_f(prep_f), rofiles))
return 0
def remove(progname, configbase, options, args):
"""
Remove a specified research object component or components
remove [ -d <dir> ] <file-or-uri>
remove -d <dir> -w <pattern>
"""
ro_config = ro_utils.readconfig(configbase)
rodir = options.rodir or (not options.wildcard and os.path.dirname(args[2]))
ro_options = {
# Usding graph annotation form
"rofile": args[2],
"rodir": rodir,
"wildcard": options.wildcard,
"wild": "-w " if options.wildcard else "",
"rocmd": progname,
}
log.debug("remove: 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:
print "%(rocmd)s remove -d %(rodir)s %(wild)s%(rofile)s" % (ro_options)
# Read and update manifest and annotations
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 remove -w "%(rofile)s" <...> : %(err)s''' % ro_options
return 1
for rofile in [ r for r in rometa.getAggregatedResources() if rofilepattern.search(str(r)) ]:
rometa.removeAggregatedResource(rofile)
else:
rofile = rometa.getComponentUri(ro_options['rofile'])
rometa.removeAggregatedResource(rofile)
return 0
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 push(progname, configbase, options, args):
"""
Push all or selected ROs and their resources to ROSRS
ro push <zip> | -d <dir> [ -f ] [ -r <rosrs_uri> ] [ -t <access_token> ]
"""
ro_config = ro_utils.readconfig(configbase)
ro_options = {
"rodir": options.rodir,
"rosrs_uri": options.rosrs_uri or getoptionvalue(ro_config['rosrs_uri'], "URI for ROSRS service: "),
"rosrs_access_token": options.rosrs_access_token or getoptionvalue(ro_config['rosrs_access_token'],
"Access token for ROSRS service: "),
"force": options.force
}
log.debug("ro_options: " + repr(ro_options))
if len(args) == 3:
return push_zip(progname, configbase, options, args)
if options.verbose:
print "ro push -d %(rodir)s -r %(rosrs_uri)s -t %(rosrs_access_token)s" % ro_options
ro_dir = ro_root_directory(progname + " push", ro_config, ro_options['rodir'])
if not ro_dir: return 1
localRo = ro_metadata(ro_config, ro_dir)
roId = ro_dir.replace(ro_config["robase"], "", 1)
if roId.startswith("/"):
roId = roId.replace("/", "", 1)
rosrs = ROSRS_Session(ro_options["rosrs_uri"], ro_options["rosrs_access_token"])
(status, _, rouri, _) = ro_remote_metadata.createRO(rosrs, roId)
if status == 201:
print "Created RO: %s" % (rouri)
elif status == 409:
rouri = urlparse.urljoin(ro_options["rosrs_uri"], roId + "/")
print "RO already exists: %s" % (rouri)
remoteRo = ro_remote_metadata.ro_remote_metadata(ro_config, rosrs, rouri)
pushedResCnt = 0
pushedAnnCnt = 0
deletedResCnt = 0
deletedAnnCnt = 0
for (action, resuri) in ro_rosrs_sync.pushResearchObject(localRo, remoteRo):
if action == ro_rosrs_sync.ACTION_AGGREGATE_INTERNAL:
print "Resource uploaded: %s" % (resuri)
log.debug("Resource uploaded: %s" % (resuri))
pushedResCnt += 1
elif action == ro_rosrs_sync.ACTION_AGGREGATE_EXTERNAL:
print "External resource pushed: %s" % (resuri)
log.debug("External resource pushed: %s" % (resuri))
pushedResCnt += 1
elif action == ro_rosrs_sync.ACTION_AGGREGATE_ANNOTATION:
if options.verbose:
print "Annotation pushed: %s" % (resuri)
log.debug("Annotation pushed: %s" % (resuri))
pushedAnnCnt += 1
elif action == ro_rosrs_sync.ACTION_UPDATE_OVERWRITE:
# TODO ask user for confirmation
print "Resource uploaded (WARNING: it has overwritten changes in RODL): %s" % (resuri)
log.debug("Resource uploaded (WARNING: it has overwritten changes in RODL): %s" % (resuri))
pushedResCnt += 1
elif action == ro_rosrs_sync.ACTION_UPDATE:
print "Resource uploaded: %s" % (resuri)
log.debug("Resource uploaded: %s" % (resuri))
pushedResCnt += 1
elif action == ro_rosrs_sync.ACTION_UPDATE_ANNOTATION:
if options.verbose:
print "Annotation updated: %s" % (resuri)
log.debug("Annotation updated: %s" % (resuri))
pushedAnnCnt += 1
elif action == ro_rosrs_sync.ACTION_SKIP:
print "Resource skipped: %s" % (resuri)
log.debug("Resource skipped: %s" % (resuri))
elif action == ro_rosrs_sync.ACTION_DELETE:
# TODO ask user for confirmation
print "Resource deleted in ROSRS: %s" % (resuri)
log.debug("Resource deleted in ROSRS: %s" % (resuri))
deletedResCnt += 1
elif action == ro_rosrs_sync.ACTION_DELETE_ANNOTATION:
if options.verbose:
print "Annotation deleted in ROSRS: %s" % (resuri)
log.debug("Annotation deleted in ROSRS: %s" % (resuri))
deletedAnnCnt += 1
elif action == ro_rosrs_sync.ACTION_ERROR:
print resuri
print "%d resources pushed, %d annotations pushed, %d resources deleted, %d annotations deleted" \
% (pushedResCnt, pushedAnnCnt, deletedResCnt, deletedAnnCnt)
return 0
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
