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score_email.cwl
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score_email.cwl
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#!/usr/bin/env cwl-runner
#
# Sends score emails to participants
#
$namespaces:
s: https://schema.org/
s:author:
- class: s:Person
s:identifier: https://orcid.org/0000-0002-5841-0198
s:email: thomas.yu@sagebionetworks.org
s:name: Thomas Yu
s:contributor:
- class: s:Person
s:identifier: https://orcid.org/0000-0002-5622-7998
s:email: verena.chung@sagebase.org
s:name: Verena Chung
cwlVersion: v1.0
class: CommandLineTool
baseCommand: python3
hints:
DockerRequirement:
dockerPull: sagebionetworks/synapsepythonclient:v2.3.1
inputs:
- id: submissionid
type: int
- id: synapse_config
type: File
- id: results
type: File
- id: dataset_id
type: string
- id: private_annotations
type: string[]?
arguments:
- valueFrom: score_email.py
- valueFrom: $(inputs.submissionid)
prefix: -s
- valueFrom: $(inputs.synapse_config.path)
prefix: -c
- valueFrom: $(inputs.results)
prefix: -r
- valueFrom: $(inputs.private_annotations)
prefix: -p
- valueFrom: $(inputs.dataset_id)
prefix: -d
requirements:
- class: InlineJavascriptRequirement
- class: InitialWorkDirRequirement
listing:
- entryname: score_email.py
entry: |
#!/usr/bin/env python
import synapseclient
import argparse
import json
import os
parser = argparse.ArgumentParser()
parser.add_argument("-s", "--submissionid", required=True, help="Submission ID")
parser.add_argument("-c", "--synapse_config", required=True, help="credentials file")
parser.add_argument("-r", "--results", required=True, help="Resulting scores")
parser.add_argument("-p", "--private_annotations", nargs="+", default=[], help="annotations to not be sent via e-mail")
parser.add_argument("-d", "--dataset_id", required=True, help="Dataset Version")
args = parser.parse_args()
syn = synapseclient.Synapse(configPath=args.synapse_config)
syn.login()
sub = syn.getSubmission(args.submissionid)
participantid = sub.get("teamId")
if participantid is not None:
name = syn.getTeam(participantid)['name']
else:
participantid = sub.userId
name = syn.getUserProfile(participantid)['userName']
evaluation = syn.getEvaluation(sub.evaluationId)
with open(args.results) as json_data:
annots = json.load(json_data)
if annots.get('submission_status') is None:
raise Exception("score.cwl must return submission_status as a json key")
status = annots['submission_status']
if status == "SCORED":
del annots['submission_status']
subject = "Submission to '%s' scored!" % evaluation.name
for annot in args.private_annotations:
del annots[annot]
if len(annots) == 0:
message = "Your submission has been scored. Results will be announced at a later time."
else:
message = ["Hello %s,\n\n" % name,
"Your submission (id: %s) is scored, below are your results for %s:\n\n" % (sub.id, args.dataset_id),
"\n".join([i + " : " + str(annots[i]) for i in annots]),
"\n\nSincerely,\nChallenge Administrator"]
syn.sendMessage(
userIds=[participantid],
messageSubject=subject,
messageBody="".join(message))
outputs: []