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