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[WIP] Improve SQL study listing #3162

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[WIP] Improve SQL study listing #3162

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8ed412b
Study._ebi_submission_jobs
antgonza Nov 12, 2021
16ae916
fix error
antgonza Nov 12, 2021
259f27c
cache
antgonza Nov 12, 2021
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31 changes: 18 additions & 13 deletions qiita_db/study.py
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Original file line number Diff line number Diff line change
Expand Up @@ -1001,24 +1001,23 @@ def _ebi_submission_jobs(self):
'Qiita', 'alpha')
cmd = plugin.get_command('submit_to_EBI')

sql = """SELECT processing_job_id,
sql = f"""SELECT processing_job_id,
pj.command_parameters->>'artifact' as aid,
processing_job_status, can_be_submitted_to_ebi,
array_agg(ebi_run_accession)
processing_job_status
FROM qiita.processing_job pj
LEFT JOIN qiita.processing_job_status
USING (processing_job_status_id)
LEFT JOIN qiita.artifact ON (
artifact_id = (
pj.command_parameters->>'artifact')::INT)
LEFT JOIN qiita.ebi_run_accession era USING (artifact_id)
LEFT JOIN qiita.artifact_type USING (artifact_type_id)
LEFT JOIN qiita.ebi_run_accession USING (artifact_id)

WHERE pj.command_parameters->>'artifact' IN (
SELECT artifact_id::text
FROM qiita.study_artifact WHERE study_id = {0})
AND pj.command_id = {1}
GROUP BY processing_job_id, aid, processing_job_status,
can_be_submitted_to_ebi""".format(self._id, cmd.id)
FROM qiita.study_artifact
WHERE study_id = {self._id})
AND pj.command_id = {cmd.id}"""
qdb.sql_connection.TRN.add(sql)

return qdb.sql_connection.TRN.execute_fetchindex()
Expand Down Expand Up @@ -1047,11 +1046,10 @@ def ebi_submission_status(self):
status = 'submitted'

jobs = defaultdict(dict)
for info in self._ebi_submission_jobs():
jid, aid, js, cbste, era = info
if not cbste or era != [None]:
continue
artifacts = defaultdict()
for jid, aid, js in self._ebi_submission_jobs():
jobs[js][aid] = jid
artifacts[aid] = None

if 'queued' in jobs or 'running' in jobs:
status = 'submitting'
Expand All @@ -1060,7 +1058,14 @@ def ebi_submission_status(self):
aids_other = []
for s, aids in jobs.items():
for aid in aids.keys():
if s == 'error':
if artifacts[aid] is None:
a = qdb.artifact.Artifact(aid)
cbste = a.can_be_submitted_to_ebi
era = False
if cbste:
era = bool(a.ebi_run_accessions)
artifacts[aid] = [cbste, era]
if s == 'error' and artifacts[aid] == [True, False]:
aids_error.append(aid)
else:
aids_other.append(aid)
Expand Down
2 changes: 1 addition & 1 deletion qiita_ware/private_plugin.py
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Original file line number Diff line number Diff line change
Expand Up @@ -108,7 +108,7 @@ def submit_to_EBI(job):
artifact = qdb.artifact.Artifact(artifact_id)

for info in artifact.study._ebi_submission_jobs():
jid, aid, js, cbste, era = info
jid, aid, js = info
if js in ('running', 'queued') and jid != job.id:
error_msg = ("Cannot perform parallel EBI submission for "
"the same study. Current job running: %s" % js)
Expand Down