X-Git-Url: https://git.arvados.org/arvados.git/blobdiff_plain/aed823dfc63b6d6876c2736ac3b7e11b312378d5..d56b21609ddd2e2e096f5c30e991d24aa213f7f4:/crunch_scripts/pgp-survey-import diff --git a/crunch_scripts/pgp-survey-import b/crunch_scripts/pgp-survey-import index df5758bc57..f12e84b2da 100755 --- a/crunch_scripts/pgp-survey-import +++ b/crunch_scripts/pgp-survey-import @@ -1,4 +1,7 @@ #!/usr/bin/env python +# Copyright (C) The Arvados Authors. All rights reserved. +# +# SPDX-License-Identifier: Apache-2.0 import arvados import string @@ -31,7 +34,7 @@ for input_file in arvados.CollectionReader(this_job_input).all_files(): if line_number == 0: headings = words for t in arvados.api('v1').traits().list( - where=json.dumps({'name':words}), + where={'name':words}, limit=1000 ).execute()['items']: traits[t['name']] = t @@ -39,19 +42,19 @@ for input_file in arvados.CollectionReader(this_job_input).all_files(): # find or create trait if trait_name not in traits: traits_match = arvados.api('v1').traits().list( - where=json.dumps({'name':trait_name}) + where={'name':trait_name} ).execute()['items'] if len(traits_match) > 0: traits[trait_name] = traits_match[0] else: traits[trait_name] = arvados.api('v1').traits().create( - trait=json.dumps({'name':trait_name})).execute() + trait={'name':trait_name}).execute() out.write(separator) out.write(json.dumps(traits[trait_name])) separator = ",\n" else: huID_links_match = arvados.api('v1').links().list( - where=json.dumps({'link_class':'identifier','name':words[0]}) + where={'link_class':'identifier','name':words[0]} ).execute()['items'] if len(huID_links_match) > 0: human_uuid = huID_links_match[0]['head_uuid'] @@ -71,13 +74,13 @@ for input_file in arvados.CollectionReader(this_job_input).all_files(): human_trait = {} for t in arvados.api('v1').links().list( limit=10000, - where=json.dumps({ + where={ 'tail_uuid':human_uuid, 'tail_kind':'arvados#human', 'head_kind':'arvados#trait', 'link_class':'human_trait', 'name':'pgp-survey-response' - }) + } ).execute()['items']: human_trait[t['head_uuid']] = t for i, trait_value in enumerate(words[3:], start=3):