def remove(dir, file_uri_or_pattern, verbose=False, regexp=False):
"""
Remove a specified research object component or components
remove [ -d <dir> ] <file-or-uri>
remove -d <dir> -w <pattern>
"""
#Get the manifest file for this ro
manifest_file_path = manifest_file(dir)
manifest = Manifest(filename=manifest_file_path)
if regexp:
try:
pattern = re.compile(file_uri_or_pattern)
except re.error as e:
#print('''%(rocmd)s remove -w "%(rofile)s" <...> : %(err)s''' % ro_options)
return 1
for aggregate in [ aggregate for aggregate in manifest.aggregates if pattern.search(str(aggregate.uri)) ]:
manifest.remove_aggregate(aggregate)
for annotation in [ annotation for annotation in manifest.annotations if pattern.search(str(annotation.uri)) ]:
manifest.remove_annotation(annotation)
else:
aggregate = manifest.get_aggregate(file_uri_or_pattern)
if aggregate:
manifest.remove_aggregate(aggregate)
annotation = manifest.get_annotation(file_uri_or_pattern)
if annotation:
manifest.remove_annotation(annotation)
with open(manifest_file_path, 'w') as manifest_filehandle:
manifest_filehandle.write(manifest.to_json())
return 0
def init(name, dir, id=None, creator=None, verbose=False, force=False):
"""
Create a new Research Object.
ro init name [-f] [ -d dir ] [ -i id ]
"""
id = id or sanitize_name_for_identifier(name)
timestamp = datetime.datetime.now().replace(microsecond=0)
if verbose:
print("ro create \{}\" -d \"{}\" -i \"{}\"".format(name,dir,id))
manifestdir = manifest_directory(dir)
log.debug("manifestdir: " + manifestdir)
manifestfilepath = manifest_file(dir)
log.debug("manifestfilepath: " + manifestfilepath)
try:
os.makedirs(manifestdir)
except OSError:
if os.path.isdir(manifestdir):
# Someone else created it...
if force:
pass
else:
print(".ro folder already exists, use --force to init an existing ro.")
return 1
else:
# There was an error on creation, so make sure we know about it
raise
#Create the manifest
manifest = Manifest(id=id)
manifest.createdBy = creator
manifest.createdOn = timestamp
manifest.title = name
manifest.description = name
log.debug("manifest: " + manifest.to_json())
with open(manifestfilepath, 'w') as manifest_filehandle:
manifest_filehandle.write(manifest.to_json())
return 0
def add(dir, file_or_directory, createdBy=None, createdOn=None, mediatype=None, recursive=False, verbose=False, force=False):
"""
Add files to a research object manifest
ro add [ -d dir ] file
ro add [ -d dir ] [-r] [directory]
Use -r/--recursive to add subdirectories recursively
If no file or directory specified, defaults to current directory.
"""
#TODO check for file_or_directory = '.'
#TODO work out what root directory of ro is and make all files relative to that
#os.path.relpath
if not in_directory(file_or_directory, dir):
print("Error: Can't add files outside the ro directory")
return 1
files = []
if os.path.isdir(file_or_directory):
if recursive:
for dirpath, dirnames, filenames in os.walk(file_or_directory):
#make the path relative to the top dir of the ro
dirpath = os.path.relpath(dirpath, dir)
files += [os.path.join(dirpath, filename) for filename in filenames]
else:
files = [os.path.join(file_or_directory, filename) for filename in os.listdir(file_or_directory) if os.path.isfile(os.path.join(file_or_directory, filename))]
else:
if os.path.isfile(file_or_directory):
files = [file_or_directory]
else:
print("Error - File does not exist: {}".format(file_or_directory))
# Read and update manifest
if verbose:
print("ro add -d ") #TODO fix print
manifest_file_path = manifest_file(dir)
manifest = Manifest(filename=manifest_file_path)
for file in files:
file = sanitize_filename_for_identifier(file, dir)
manifest.add_aggregate(file, createdBy=createdBy, createdOn=createdOn, mediatype=mediatype)
with open(manifest_file_path, 'w') as manifest_filehandle:
manifest_filehandle.write(manifest.to_json())
return 0
def annotate(dir, file_uri_or_pattern, attributename=None, attributevalue=None, annotation_file_or_uri=None, regexp=False):
"""
Annotate a specified research object component
ro annotate file attribute-name [ attribute-value ]
ro annotation file -f file_or_uri
"""
manifestfilepath = manifest_file(dir)
if not directory_and_manifest_exist(dir):
print("Could not find manifest file: {}".format(manifestfilepath))
return 1
manifest = Manifest(filename=manifestfilepath)
files = []
if regexp:
try:
pattern = re.compile(file_uri_or_pattern)
except re.error as e:
#print('''%(rocmd)s remove -w "%(rofile)s" <...> : %(err)s''' % ro_options)
return 1
files = [ aggregate for aggregate in manifest.aggregates if pattern.search(str(aggregate.uri)) ]
else:
files = [file_uri_or_pattern]
if annotation_file_or_uri:
#we are adding an annotation about file_uri_or_pattern using annotation_file_or_uri as the contents of the annotation
for file in files:
if os.path.isfile(annotation_file_or_uri):
if not annotation_file_or_uri.startswith(".ro/annotations/"):
annotation_file_or_uri = sanitize_filename_for_identifier(annotation_file_or_uri, dir)
manifest.add_annotation(about=file, contents=annotation_file_or_uri)
with open(manifestfilepath, 'w') as manifest_filehandle:
manifest_filehandle.write(manifest.to_json())
return 0