sys.exit(1)
else:
logger.error("Extracting metadata and provenance failed")
raise
shock_id = None
# Step 3: Package data files into a single compressed file and send to shock
try:
workspace_id = object_details["metadata"][0][4]
object_version = object_details["metadata"][0][2]
name = "KBase_{0}_{1}_{2}".format(workspace_name, object_name, object_version)
# gather a list of all files downloaded
files = [x for x in handler_utils.gen_recursive_filelist(transform_directory)]
# gather total size of all files
total = 0
for x in files:
total += os.path.getsize(x)
# TODO
# Workaround for Python 2.7.3 bug 9720, http://bugs.python.org/issue9720
# The awe workers and KBase V26 are at Python 2.7.3 and we should migrate
# to the same version of Python that Narrative uses, which is currently
# Python 2.7.6, after which this workaround can be removed
if total < 2**31:
archive_name = os.path.join(working_directory, name) + ".zip"
with zipfile.ZipFile(archive_name, 'w', zipfile.ZIP_DEFLATED) as archive:
for n in files:
# fill in any optional arguments provided by the user
if "optional_fields" in job_details["validate"]["handler_options"]:
for k in optional_arguments["validate"]:
if k in job_details["validate"]["handler_options"]["optional_fields"]:
validation_args[k] = optional_arguments["validate"][k]
# fill in any custom options needed to run the script
if "custom_options" in job_details["validate"]["handler_options"]:
for c in job_details["validate"]["handler_options"]["custom_options"]:
if c["type"] != "boolean":
validation_args[c["name"]] = c["value"]
else:
validation_args[c["name"]] = c["value"] # TODO: Fix later with example
# gather a list of all files downloaded
files = list(handler_utils.gen_recursive_filelist(download_directory))
# get the directories common to those files
directories = list()
for x in files:
path = os.path.dirname(x)
if path not in directories:
directories.append(path)
# TODO: 1) The following logic assumes all files are of the same type
# and will not work properly if there are multiple file types
# 2) input_directory assumes the script can handle files without
# using input_mapping
#
# validate everything in each directory
"validate"][k]
# fill in any custom options needed to run the script
if "custom_options" in job_details["validate"][
"handler_options"]:
for c in job_details["validate"]["handler_options"][
"custom_options"]:
if c["type"] != "boolean":
validation_args[c["name"]] = c["value"]
else:
validation_args[c["name"]] = c[
"value"] # TODO: Fix later with example
# gather a list of all files downloaded
files = list(
handler_utils.gen_recursive_filelist(download_directory))
# get the directories common to those files
directories = list()
for x in files:
path = os.path.dirname(x)
if path not in directories:
directories.append(path)
# TODO: 1) The following logic assumes all files are of the same type
# and will not work properly if there are multiple file types
# 2) input_directory assumes the script can handle files without
# using input_mapping
#
# validate everything in each directory
"Download from {0} failed.".format(workspace_name),
traceback.format_exc(),
None)
sys.exit(1)
else:
logger.error("Extracting metadata and provenance failed")
raise
shock_id = None
# Step 3: Package data files into a single compressed file and send to shock
try:
name = "KBase_{0}_{1}_to_{2}_{3}".format(object_name, kbase_type, external_type, datetime.datetime.utcnow().isoformat())
# gather a list of all files downloaded
files = list(handler_utils.gen_recursive_filelist(transform_directory))
archive_name = os.path.join(working_directory,name) + ".zip"
archive = zipfile.ZipFile(archive_name, 'w', zipfile.ZIP_DEFLATED, allowZip64=True)
for n in files:
archive.write(n)
archive.close()
shock_info = script_utils.upload_file_to_shock(logger = logger,
shock_service_url = shock_service_url,
filePath = archive_name,
token= kb_token)
shock_id = shock_info["id"]
except Exception, e:
logger.debug("Caught exception while creating archive and sending to SHOCK!")
