def test_04_process_oag(self):
job = models.SpreadsheetJob()
job.save()
oag_register = [{
"id": "PMC1234",
"type": "pmcid"
}, {
"id": "10.1234",
"type": "doi"
}, {
"id": "10.5678",
"type": "doi"
}, {
"id": "abcd",
"type": "pmid"
}]
workflow.process_oag(oag_register, job)
time.sleep(2)
link = models.OAGRLink.by_spreadsheet_id(job.id)
assert link is not None
assert link.spreadsheet_id == job.id
assert link.oagrjob_id is not None
oj = oagr.dao.JobsDAO.pull(link.oagrjob_id)
assert oj is not None
state = oj.state()
assert len(state.pending) == 4
def test_04_process_oag(self):
job = models.SpreadsheetJob()
job.save()
oag_register = [
{"id" : "PMC1234", "type" : "pmcid"},
{"id" : "10.1234", "type" : "doi"},
{"id" : "10.5678", "type" : "doi"},
{"id" : "abcd", "type" : "pmid"}
]
workflow.process_oag(oag_register, job)
time.sleep(2)
link = models.OAGRLink.by_spreadsheet_id(job.id)
assert link is not None
assert link.spreadsheet_id == job.id
assert link.oagrjob_id is not None
oj = oagr.dao.JobsDAO.pull(link.oagrjob_id)
assert oj is not None
state = oj.state()
assert len(state.pending) == 4
record.upload_pos = 1
if args.type.lower() == "pmcid":
record.pmcid = args.identifier
elif args.type.lower() == "pmid":
record.pmid = args.identifier
elif args.type.lower() == "doi":
record.doi = args.identifier
record.save()
time.sleep(2)
oag_register = []
msg = workflow.WorkflowMessage(job, record, oag_register)
workflow.process_record(msg)
workflow.process_oag(oag_register, job)
time.sleep(2)
i = 0
while True:
i += 1
pcc = job.pc_complete
print i, job.pc_complete, "%",
sys.stdout.flush()
if int(pcc) == 100:
break
time.sleep(2)
out = workflow.output_csv(job)
print out
record.upload_pos = 1
if args.type.lower() == "pmcid":
record.pmcid = args.identifier
elif args.type.lower() == "pmid":
record.pmid = args.identifier
elif args.type.lower() == "doi":
record.doi = args.identifier
record.save()
time.sleep(2)
oag_register = []
msg = workflow.WorkflowMessage(job, record, oag_register)
workflow.process_record(msg)
workflow.process_oag(oag_register, job)
time.sleep(2)
i = 0
while True:
i += 1
pcc = job.pc_complete
print i, job.pc_complete, "%",
sys.stdout.flush()
if int(pcc) == 100:
break
time.sleep(2)
out = workflow.output_csv(job)
print out