def test__submit_job_minimal(app):
"""Test fast mode job submission works as expected"""
fake_db = get_db()
queue = app.config['FAST_QUEUE']
assert app.config['FAKE_DB']
old_len = fake_db.llen(queue)
job = Job(fake_db, 'taxon-fake')
job.minimal = True
job.commit()
utils._submit_job(fake_db, job, app.config)
assert old_len + 1 == fake_db.llen(queue)
fake_db.ltrim(app.config['DOWNLOAD_QUEUE'], 2, 1) # clear queue
job = Job(fake_db, 'taxon-fake')
job.minimal = True
job.needs_download = True
job.commit()
utils._submit_job(fake_db, job, app.config)
assert 1 == fake_db.llen(app.config['DOWNLOAD_QUEUE'])
job.fetch()
assert job.target_queues == [queue]
def dispatch_job():
"""Internal helper to dispatch a new job"""
redis_store = get_db()
taxon = app.config['TAXON']
job_id = _generate_jobid(taxon)
job = Job(redis_store, job_id)
if 'X-Forwarded-For' in request.headers:
job.ip_addr = request.headers.getlist("X-Forwarded-For")[0].rpartition(
' ')[-1]
else:
job.ip_addr = request.remote_addr or 'untrackable'
ncbi = request.form.get('ncbi', '').strip()
val = request.form.get('email', '').strip()
if val:
job.email = val
job.minimal = _get_checkbox(request, 'minimal')
job.all_orfs = _get_checkbox(request, 'all_orfs')
job.smcogs = _get_checkbox(request, 'smcogs')
job.clusterblast = _get_checkbox(request, 'clusterblast')
job.knownclusterblast = _get_checkbox(request, 'knownclusterblast')
job.subclusterblast = _get_checkbox(request, 'subclusterblast')
job.cc_mibig = _get_checkbox(request, 'cc_mibig')
job.jobtype = request.form.get('jobtype', app.config['DEFAULT_JOBTYPE'])
if job.jobtype not in (app.config['LEGACY_JOBTYPE'],
app.config['DEFAULT_JOBTYPE']):
raise BadRequest(f"Invalid jobtype {job.jobtype}")
genefinder = request.form.get('genefinder', '')
if genefinder:
job.genefinder = genefinder
hmmdetection_strictness = request.form.get('hmmdetection_strictness', '')
if hmmdetection_strictness:
job.hmmdetection_strictness = hmmdetection_strictness
val = request.form.get('from', 0, type=int)
if val:
job.from_pos = val
val = request.form.get('to', 0, type=int)
if val:
job.to_pos = val
job.asf = _get_checkbox(request, 'asf')
job.tta = _get_checkbox(request, 'tta')
job.cassis = _get_checkbox(request, 'cassis')
job.clusterhmmer = _get_checkbox(request, 'clusterhmmer')
job.pfam2go = _get_checkbox(request, 'pfam2go')
job.rre = _get_checkbox(request, 'rre')
job.tigrfam = _get_checkbox(request, 'tigrfam')
dirname = path.join(app.config['RESULTS_PATH'], job.job_id, 'input')
os.makedirs(dirname)
if ncbi != '':
if ' ' in ncbi:
raise BadRequest("Spaces are not allowed in an NCBI ID.")
job.download = ncbi
job.needs_download = True
else:
upload = request.files['seq']
if upload is not None:
filename = secure_filename(upload.filename)
upload.save(path.join(dirname, filename))
if not path.exists(path.join(dirname, filename)):
raise BadRequest("Could not save file!")
job.filename = filename
job.needs_download = False
else:
raise BadRequest("Uploading input file failed!")
if 'gff3' in request.files:
gff_upload = request.files['gff3']
if gff_upload is not None:
gff_filename = secure_filename(gff_upload.filename)
gff_upload.save(path.join(dirname, gff_filename))
if not path.exists(path.join(dirname, gff_filename)):
raise BadRequest("Could not save GFF file!")
job.gff3 = gff_filename
if 'sideload' in request.files:
sideload = request.files['sideload']
if sideload is not None:
sideload_filename = secure_filename(sideload.filename)
sideload.save(path.join(dirname, sideload_filename))
if not path.exists(path.join(dirname, sideload_filename)):
raise BadRequest("Could not save sideload info file!")
job.sideload = sideload_filename
job.trace.append("{}-api".format(platform.node()))
_submit_job(redis_store, job, app.config)
_dark_launch_job(redis_store, job, app.config)
return job