def generate_base_submission():
file_name = "base_submission.json"
path = os.path.join(TEST_SUBMISSIONS_DIR, file_name)
mdfcc = MDFConnectClient() # service_instance is irrelevant
mdfcc.create_dc_block(title="Base Deploy Testing Dataset",
authors="jgaff",
affiliations="UChicago")
mdfcc.add_data_source(DATA_SOURCES)
mdfcc.set_test(True)
mdfcc.update = UPDATE_FLAG
submission = mdfcc.get_submission()
with open(path, 'w') as f:
json.dump(submission, f)
return {"success": True}
def generate_base_failure():
file_name = "base_failure.json"
path = os.path.join(TEST_SUBMISSIONS_DIR, file_name)
mdfcc = MDFConnectClient() # service_instance is irrelevant
mdfcc.create_dc_block(title="Base Deploy Fail Dataset",
authors="jgaff",
affiliations="UChicago")
mdfcc.add_data_source(DATA_SOURCES)
# Failure point: Submission not in nanomfg organization,
# but attempting to write to nanomfg project block
mdfcc.set_project_block("nanomfg", {"catalyst": "bad data testing"})
mdfcc.set_test(True)
mdfcc.update = UPDATE_FLAG
submission = mdfcc.get_submission()
with open(path, 'w') as f:
json.dump(submission, f)
return {"success": True}
def mdf_submit(local_json_path,
globus_uri,
test=True,
with_doi=True,
update=False):
"""Submit dataset to MDF Connect.
Arguments:
local_json_path (str): The path to the local JSON metadata file.
globus_uri (str): The URI to the Globus Endpoint and path, in the form:
"globus://[endpoint id]/[path to data directory]"
test (bool): Is this a test submission (test submissions generate test DOIs
and populate the Search index "mdf-test" instead of "mdf")?
Default True.
with_doi (bool): Should a DOI be minted? (Includes test DOI.)
Default True.
update (bool): Has this submission been made before? If so, an update will be made
to the previous submission. Test submissions and non-test submissions
are separate.
"""
import json
import os
from mdf_connect_client import MDFConnectClient
mapping = {
"custom.dynamic_mean_window_size": "xpcs.dynamic_mean_window_size",
"custom.lld": "xpcs.lld",
"custom.sigma": "xpcs.sigma",
"custom.snophi": "xpcs.snophi",
"custom.snoq": "xpcs.snoq"
}
mdfcc = MDFConnectClient()
with open(local_json_path) as f:
md = json.load(f)
# DC block (title, authors, publisher, pub year, subjects)
mdfcc.create_dc_block(
title=os.path.basename(local_json_path).replace(".json", ""),
authors=[creator["creatorName"] for creator in md["creators"]],
publisher=md.get("publisher"),
publication_year=md.get("publication_year"),
subjects=[subject["subject"] for subject in md.get("subjects", [])])
# Add data
mdfcc.add_data_source(globus_uri)
# Add JSON mapping
mdfcc.add_index("json", mapping)
# Set test flag
mdfcc.set_test(test)
# Add XPCS as organization
mdfcc.add_organization("XPCS 8-ID")
# Set group-by-dir flag
mdfcc.set_conversion_config({"group_by_dir": True})
# Add MDF Publish service
if with_doi:
mdfcc.add_service("mdf_publish")
# Submit dataset
sub_res = mdfcc.submit_dataset(update=update)
if not sub_res["success"]:
raise RuntimeError(sub_res["error"])
else:
print("Submission '{}' started".format(sub_res["source_id"]))
return "Submission '{}' started".format(sub_res["source_id"])