def _serialize(self, fmt="xml", mn_client=None):
assert fmt in ALLOWABLE_PACKAGE_SERIALIZATIONS
if mn_client is None:
mn_client = utils.get_d1_mn_client()
if not self._prepare_urls(mn_client):
return
self._generate_resmap(mn_client.base_url)
if self.resmap.serializer is not None:
self.resmap.serializer = None
serializer = foresite.RdfLibSerializer(fmt)
self.resmap.register_serialization(serializer)
doc = self.resmap.get_serialization()
return doc.data
def _create_object(self, item, mn_client=None, **kwargs):
""" Create an object in DataONE. """
path = utils.expand_path(item.fname)
# cli_util.assert_file_exists(path)
assert os.path.exists(path)
if "format_id" in kwargs:
del kwargs["format_id"]
sysmeta = utils.create_sysmeta_from_path(item.pid, path, format_id=item.format_id, **kwargs)
if mn_client is None:
mn_client = utils.get_d1_mn_client()
with open(path, "r") as f:
try:
result = mn_client.create(item.pid, f, sysmeta)
print 'Created object "%s"' % item.pid
return result
except DataONEException as e:
raise Exception("Unable to create Science Object on Member Node\n{0}".format(e.friendly_format()))
def _prepare_urls(self, mn_client=None):
""" Walk through the objects make sure that everything can be
serialized.
"""
if mn_client is None:
mn_client = utils.get_d1_mn_client()
if self.scimeta and not self.scimeta.url:
if not self._check_item(self.scimeta):
return False
elif not self.scimeta.url:
self.scimeta.url = utils.create_resolve_url_for_pid(mn_client.base_url, self.scimeta.pid)
if self.scidata_dict:
for scidata in self.scidata_dict.values():
if not self._check_item(scidata):
return False
elif not scidata.url:
scidata.url = utils.create_resolve_url_for_pid(mn_client.base_url, scidata.pid)
return True
def save(self, mn_client=None, cn_client=None, **kwargs):
""" Save this object referred to by this pid.
"""
if self.pid is None:
raise Exception("Missing pid")
if mn_client is None:
mn_client = utils.get_d1_mn_client()
if cn_client is None:
cn_client = utils.get_d1_cn_client()
pkg_xml = self._serialize("xml", mn_client)
if not pkg_xml:
raise Exception("Couldn't serialize object.")
algorithm = configuration.checksum_alg
hash_fcn = util.get_checksum_calculator_by_dataone_designator(algorithm)
hash_fcn.update(pkg_xml)
checksum = hash_fcn.hexdigest()
sysmeta = utils.create_system_metadata(self.pid, len(pkg_xml), checksum, algorithm, RDFXML_FORMATID, **kwargs)
flo = StringIO.StringIO(pkg_xml)
# Save all the objects.
if self.scimeta and self.scimeta.dirty:
self._create_or_update(mn_client, cn_client, self.scimeta)
for scidata_pid in self.scidata_dict.keys():
scidata = self.scidata_dict.get(scidata_pid)
if scidata and scidata.dirty:
self._create_or_update(mn_client, cn_client, scidata)
response = mn_client.create(pid=self.pid, obj=flo, sysmeta=sysmeta)
if response is None:
return None
else:
self.original_pid = self.pid
if self.scimeta:
self.scimeta.dirty = False
if self.scidata_dict:
for scidata in self.scidata_dict.values():
scidata.dirty = False
return response.value()
def run_pkg_test():
configuration.mn_url = "https://mn-demo-9.test.dataone.org/knb/d1/mn"
configuration.cn_url = "https://cn-stage-2.test.dataone.org/cn"
cn_client = utils.get_d1_cn_client()
mn_client = utils.get_d1_mn_client()
pid = "dakoop_test_pkg603"
meta_pid = "dakoop_cadwsap003"
meta_fname = "/vistrails/local_packages/dataone/package_data/cadwsap-s2910001-001.xml"
meta_format = "FGDC-STD-001-1998"
data_list = [
(
"dakoop_cadwsap_main003",
"/vistrails/local_packages/dataone/package_data/cadwsap-s2910001-001-main.csv",
"text/csv",
),
(
"dakoop_cadwsap_vuln003",
"/vistrails/local_packages/dataone/package_data/cadwsap-s2910001-001-vuln.csv",
"text/csv",
),
]
pkg = DataPackage(pid)
sysmeta_kwargs = {
"format_id": meta_format,
"submitter": "dakoop",
"owner": "dakoop",
"orig_mn": configuration.mn_url,
"auth_mn": configuration.mn_url,
}
pkg.scimeta_add(meta_pid, meta_fname, **sysmeta_kwargs)
for (data_pid, data_fname, data_format) in data_list:
sysmeta_kwargs["format_id"] = data_format
pkg.scidata_add(data_pid, data_fname, **sysmeta_kwargs)
del sysmeta_kwargs["format_id"]
pkg.save(mn_client, cn_client, **sysmeta_kwargs)