def generate_ro_manifest(bag_path,
overwrite=False,
config_file=DEFAULT_CONFIG_FILE):
bag = bdbagit.BDBag(bag_path)
bag_ro_metadata_path = os.path.abspath(
os.path.join(bag_path, "metadata", "manifest.json"))
exists = os.path.isfile(bag_ro_metadata_path)
if exists and not overwrite:
logger.info("Auto-generating RO manifest: update existing file.")
ro_metadata = bdbro.read_bag_ro_metadata(bag_path)
else:
logger.info(
"Auto-generating RO manifest: %s." %
"creating new file" if not exists else "overwrite existing file")
ro_metadata = bdbro.init_ro_manifest(
author_name=bag.info.get("Contact-Name"),
author_orcid=bag.info.get("Contact-Orcid"),
creator_name=bdbro.BAG_CREATOR_NAME,
creator_uri=bdbro.BAG_CREATOR_URI)
config = read_config(config_file)
resolvers = config.get(
ID_RESOLVER_TAG,
DEFAULT_ID_RESOLVERS) if config else DEFAULT_ID_RESOLVERS
fetched = bag.fetch_entries()
local = bag.payload_files()
for url, length, filename in fetched:
if url.startswith("minid:") or url.startswith("ark:"):
url = "".join(["http://", resolvers[0], "/", url])
bdbro.add_file_metadata(ro_metadata,
source_url=url,
bundled_as=bdbro.make_bundled_as(
folder=os.path.dirname(filename),
filename=os.path.basename(filename)),
update_existing=True)
for path in local:
bdbro.add_file_metadata(ro_metadata,
local_path=path.replace("\\", "/"),
bundled_as=bdbro.make_bundled_as(),
update_existing=True)
bdbro.write_bag_ro_metadata(ro_metadata, bag_path)
profile = bag.info.get(BAG_PROFILE_TAG)
if profile == BDBAG_PROFILE_ID:
bag.info.update({BAG_PROFILE_TAG: BDBAG_RO_PROFILE_ID})
bag.save()
def test_generate_ro_manifest_update(self):
logger.info(
self.getTestHeader(
'create bag with auto-generation of RO manifest in update mode'
))
try:
bdb.make_bag(self.test_data_dir,
algs=['md5', 'sha1', 'sha256', 'sha512'],
remote_file_manifest=ospj(self.test_config_dir,
'test-fetch-manifest.json'))
bdb.generate_ro_manifest(self.test_data_dir, overwrite=True)
ro = bdbro.read_bag_ro_metadata(self.test_data_dir)
old_agg_dict = dict()
for entry in ro.get("aggregates", []):
old_agg_dict[entry["uri"]] = entry
bdbro.add_file_metadata(ro,
local_path="../data/FAKE.txt",
bundled_as=bdbro.make_bundled_as())
bdbro.write_bag_ro_metadata(ro, self.test_data_dir)
bdb.generate_ro_manifest(self.test_data_dir, overwrite=False)
ro = bdbro.read_bag_ro_metadata(self.test_data_dir)
for entry in ro.get("aggregates", []):
if entry["uri"] in old_agg_dict:
self.assertTrue(entry["bundledAs"]["uri"] == old_agg_dict[
entry["uri"]]["bundledAs"]["uri"])
except Exception as e:
self.fail(get_typed_exception(e))
def downloadFiles(self, input_manifest):
logging.info("Retrieving file(s)...")
try:
with open(input_manifest, "r") as in_file:
file_list = list()
for line in in_file:
entry = json.loads(line)
url = entry.get('url')
if not url:
raise RuntimeError(
"Missing required attribute \"url\" in download manifest entry %s" % json.dumps(entry))
store = self.getHatracStore(url)
filename = entry.get('filename')
envvars = self.envars.copy()
envvars.update(entry)
subdir = self.sub_path.format(**envvars)
if not filename:
if store:
head = store.head(url, headers=self.HEADERS)
content_disposition = head.headers.get("Content-Disposition") if head.ok else None
filename = os.path.basename(filename).split(":")[0] if not content_disposition else \
parse_content_disposition(content_disposition)
else:
filename = os.path.basename(url)
file_path = os.path.abspath(os.path.join(
self.base_path, 'data' if self.is_bag else '', subdir, filename))
output_dir = os.path.dirname(file_path)
self.makeDirs(output_dir)
if store:
resp = store.get_obj(url, self.HEADERS, file_path)
length = int(resp.headers.get('Content-Length'))
content_type = resp.headers.get("Content-Type")
url = self.getExternalUrl(url)
else:
url = self.getExternalUrl(url)
file_path, resp = self.getExternalFile(url, file_path, self.HEADERS)
length = int(resp.headers.get('Content-Length'))
content_type = resp.headers.get("Content-Type")
file_bytes = os.path.getsize(file_path)
if length != file_bytes:
raise RuntimeError(
"File size of %s does not match expected size of %s for file %s" %
(length, file_bytes, file_path))
output_path = ''.join([subdir, "/", filename]) if subdir else filename
if self.ro_manifest:
ro.add_file_metadata(self.ro_manifest,
source_url=url,
local_path=output_path,
media_type=content_type,
retrieved_on=ro.make_retrieved_on(),
retrieved_by=ro.make_retrieved_by(
self.ro_author_name, orcid=self.ro_author_orcid),
bundled_as=ro.make_bundled_as())
file_list.append(output_path)
return file_list
finally:
os.remove(input_manifest)
def add_remote_file_manifest_to_ro(ro_manifest, entries):
for (minid, _, _, uri, _, _) in entries:
ro.add_aggregate(ro_manifest, NAME2THING+minid,
mediatype=None,
conforms_to=ro.BAG_CONFORMS_TO,
bundled_as=ro.make_bundled_as(None, '', uri))
ro.add_annotation(ro_manifest,
'../',
'../data/README',
motivatedBy={"@id": "oa:describing"})
def process(self):
headers = self.HEADERS
headers.update({'accept': self.content_type})
resp = self.catalogQuery(headers)
if self.ro_manifest and self.ro_file_provenance:
ro.add_file_metadata(self.ro_manifest,
source_url=self.url,
local_path=self.output_relpath,
media_type=self.content_type,
retrieved_on=ro.make_retrieved_on(),
retrieved_by=ro.make_retrieved_by(self.ro_author_name, orcid=self.ro_author_orcid),
bundled_as=ro.make_bundled_as())
self.outputs.update({self.output_relpath: {LOCAL_PATH_KEY: self.output_abspath, SOURCE_URL_KEY: self.url}})
return self.outputs
def createRemoteFileManifest(self):
logging.info("Creating remote file manifest")
input_manifest = self.output_abspath
remote_file_manifest = self.args.get("remote_file_manifest")
with open(input_manifest, "r") as in_file, open(remote_file_manifest, "a") as remote_file:
for line in in_file:
# get the required bdbag remote file manifest vars from each line of the json-stream input file
entry = json.loads(line)
entry = self.createManifestEntry(entry)
remote_file.write(json.dumps(entry) + "\n")
if self.ro_manifest:
ro.add_file_metadata(self.ro_manifest,
source_url=entry["url"],
media_type=entry.get("content_type"),
bundled_as=ro.make_bundled_as(
folder=os.path.dirname(entry["filename"]),
filename=os.path.basename(entry["filename"])))
os.remove(input_manifest)
return os.path.relpath(remote_file_manifest, self.base_path)
def process(self):
if self.ro_manifest and self.ro_file_provenance:
ro.add_file_metadata(
self.ro_manifest,
source_url=self.url,
local_path=self.output_relpath,
media_type=guess_content_type(self.output_abspath),
retrieved_on=ro.make_retrieved_on(),
retrieved_by=ro.make_retrieved_by(self.ro_author_name,
orcid=self.ro_author_orcid),
bundled_as=ro.make_bundled_as())
if self.delete_input:
self._delete_input()
self.outputs.update({
self.output_relpath: {
LOCAL_PATH_KEY: self.output_abspath,
SOURCE_URL_KEY: self.url
}
})
return self.outputs
def downloadFiles(self, input_manifest):
logging.info(
"Attempting to download file(s) based on the results of query: %s"
% self.query)
try:
with open(input_manifest, "r") as in_file:
file_list = dict()
for line in in_file:
entry = json.loads(line)
url = entry.get('url')
if not url:
logging.warning(
"Skipping download due to missing required attribute \"url\" in download manifest entry %s"
% json.dumps(entry))
continue
store = self.getHatracStore(url)
filename = entry.get('filename')
envvars = self.envars.copy()
envvars.update(entry)
subdir = self.sub_path.format(**envvars)
if not filename:
if store:
try:
head = store.head(url, headers=self.HEADERS)
except requests.HTTPError as e:
raise DerivaDownloadError(
"HEAD request for [%s] failed: %s" %
(url, e))
content_disposition = head.headers.get(
"Content-Disposition") if head.ok else None
filename = os.path.basename(filename).split(":")[0] if not content_disposition else \
parse_content_disposition(content_disposition)
else:
filename = os.path.basename(url)
file_path = os.path.abspath(
os.path.join(self.base_path,
'data' if self.is_bag else '', subdir,
filename))
output_dir = os.path.dirname(file_path)
make_dirs(output_dir)
if store:
try:
resp = store.get_obj(url, self.HEADERS, file_path)
except requests.HTTPError as e:
raise DerivaDownloadError(
"File [%s] transfer failed: %s" %
(file_path, e))
length = int(resp.headers.get('Content-Length'))
content_type = resp.headers.get("Content-Type")
url = self.getExternalUrl(url)
else:
url = self.getExternalUrl(url)
file_path, resp = self.getExternalFile(
url, file_path, self.HEADERS)
length = int(resp.headers.get('Content-Length'))
content_type = resp.headers.get("Content-Type")
file_bytes = os.path.getsize(file_path)
if length != file_bytes:
raise DerivaDownloadError(
"File size of %s does not match expected size of %s for file %s"
% (length, file_bytes, file_path))
output_path = ''.join([subdir, "/", filename
]) if subdir else filename
if self.ro_manifest:
ro.add_file_metadata(
self.ro_manifest,
source_url=url,
local_path=output_path,
media_type=content_type,
retrieved_on=ro.make_retrieved_on(),
retrieved_by=ro.make_retrieved_by(
self.ro_author_name,
orcid=self.ro_author_orcid),
bundled_as=ro.make_bundled_as())
file_list.update(
{output_path: {
LOCAL_PATH_KEY: file_path
}})
return file_list
finally:
os.remove(input_manifest)