def _get_by_pid(self, pid, sysmeta=None, mn_client=None, cn_client=None):
""" Return DataObject
"""
if pid is None:
raise Exception("Missing pid")
fname = utils.get_object_by_pid(pid, resolve=True, mn_client=mn_client, cn_client=cn_client)
if fname:
meta = sysmeta
if not meta:
meta = utils.get_sysmeta_by_pid(pid, True)
url = utils.create_get_url_for_pid(mn_client.base_url, pid)
return DataObject(pid, False, fname, url, meta, meta.formatId, None)
else:
return None
def scimeta_add(self, pid, file_name=None, format_id=None, **kwargs):
""" Add a scimeta object.
"""
if not pid:
raise Exception("Missing the pid")
# if (self.scimeta and not
# cli_util.confirm('Do you wish to delete the existing science metadata object?')):
# return
else:
self.scimeta = None
if not file_name:
new_meta = utils.get_sysmeta_by_pid(pid, True)
if not new_meta:
raise Exception("Couldn't find scimeta in DataONE, and there was no file specified.")
if not self._is_metadata_format(new_meta.formatId):
raise Exception('"%s" is not an allowable science metadata type.' % new_meta.formatId)
new_pid = new_meta.identifier.value()
if new_pid != pid:
pid = new_pid
self.scimeta = self._get_by_pid(pid, new_meta)
authMN = new_meta.authoritativeMemberNode
if authMN:
baseURL = utils.get_baseUrl(authMN.value())
if baseURL:
self.scimeta.url = utils.create_get_url_for_pid(baseURL, pid)
else:
complex_path = utils.create_complex_path(file_name)
if not os.path.exists(complex_path.path):
raise Exception("%s: file not found" % complex_path.path)
if not format_id:
format_id = complex_path.formatId
if not format_id and configuration.check("format"):
format_id = configuration.format
if not format_id:
raise Exception("The object format could not be determined and was not defined.")
if not self._is_metadata_format(format_id):
raise Exception('"%s" is not an allowable science metadata type.' % new_meta.formatId)
return
#
sysmeta = utils.create_sysmeta_from_path(pid, complex_path.path, format_id=format_id, **kwargs)
self.scimeta = DataObject(pid, True, complex_path.path, None, sysmeta, format_id)
scidata_list = self._find_scidata(self.scimeta)
if scidata_list:
for scidata in scidata_list:
self.scidata_add(scidata.pid, scidata.fname)
def scidata_add(self, pid, file_name=None, format_id=None, **kwargs):
""" Add a science data object to the list.
"""
if not pid:
raise Exception("Missing the pid")
if file_name:
# if utils.get_sysmeta_by_pid(pid):
# if not cli_util.confirm('That pid (%s) already exists in DataONE. Continue?' % pid):
# return
# raise Exception("The identifer (%s) already exists in DataONE." % pid)
complex_path = utils.create_complex_path(file_name)
if not format_id:
format_id = complex_path.formatId
if not format_id and configuration.check("format"):
format_id = configuration.format
if not format_id:
raise Exception("The object format could not be determined and was not defined.")
meta = utils.create_sysmeta_from_path(pid, complex_path.path, format_id=format_id, **kwargs)
self.scidata_dict[pid] = DataObject(pid, True, complex_path.path, None, meta, format_id)
else:
sysmeta = utils.get_sysmeta_by_pid(pid, True)
if not sysmeta:
raise Exception("The identifier (%s) was not found in DataONE." % pid)
else:
pid = sysmeta.identifier.value()
# if pid in self.scidata_dict:
# if not cli_util.confirm('That science data object (%s) is already in the package. Replace?' % pid):
# return
# Get the scidata object.
scidata = self._get_by_pid(pid, sysmeta)
authMN = sysmeta.authoritativeMemberNode
if authMN:
baseURL = utils.get_baseUrl(authMN.value())
if baseURL:
scidata.url = utils.create_get_url_for_pid(baseURL, pid)
self.scidata_dict[pid] = scidata
def _generate_resmap(self, mn_client_base_url):
""" Create a package.
"""
# Create the aggregation
foresite.utils.namespaces["cito"] = Namespace("http://purl.org/spar/cito/")
aggr = foresite.Aggregation(self.pid)
aggr._dcterms.title = "Simple aggregation of science metadata and data."
# Create a reference to the science metadata
uri_scimeta = URIRef(self.scimeta.url)
res_scimeta = foresite.AggregatedResource(uri_scimeta)
res_scimeta._dcterms.identifier = self.scimeta.pid
res_scimeta._dcterms.description = "Science metadata object."
# Create references to the science data
resource_list = []
for scidata in self.scidata_dict.values():
uri_scidata = URIRef(scidata.url)
res_scidata = foresite.AggregatedResource(uri_scidata)
res_scidata._dcterms.identifier = scidata.pid
res_scidata._dcterms.description = "Science data object"
res_scidata._cito.isDocumentedBy = uri_scimeta
res_scimeta._cito.documents = uri_scidata
resource_list.append(res_scidata)
# Add all the resources.
aggr.add_resource(res_scimeta)
for resource in resource_list:
aggr.add_resource(resource)
# Create the resource map
resmap_url = utils.create_get_url_for_pid(mn_client_base_url, format(self.pid))
self.resmap = foresite.ResourceMap(resmap_url)
self.resmap._dcterms.identifier = self.pid
self.resmap.set_aggregation(aggr)
return self.resmap
