def test_display(self):
"""Test if displaying jobs works as expected"""
rv = self.client.get('/display/invalid')
self.assert404(rv)
j = Job()
redis_store = self._ctx.g._database
redis_store.hmset(u"job:%s" % j.uid, j.get_dict())
rv = self.client.get('/display/%s' % j.uid)
assert "Status of job" in rv.data
def status(task_id):
redis_store = get_db()
res = redis_store.hgetall(u'job:%s' % task_id)
if res == {}:
abort(404)
job = Job(**res)
if job.status == 'done':
result_url = "%s/%s" % (app.config['RESULTS_URL'], job.uid)
if job.jobtype == 'antismash':
result_url += "/display.xhtml"
else:
result_url += "/index.html"
res['result_url'] = result_url
res['short_status'] = job.get_short_status()
return jsonify(res)
def test_job_get_status(self):
"""Test that Job.get_status() is sane"""
job = Job()
assert job.get_status() == 'pending'
assert job.status == job.get_status()
job = Job(status='funky')
assert job.get_status() == 'funky'
def display(task_id):
redis_store = get_db()
results_path = app.config['RESULTS_URL']
res = redis_store.hgetall(u'job:%s' % task_id)
if res == {}:
abort(404)
else:
job = Job(**res)
return render_template('display.html', job=job, results_path=results_path)
def _get_oldest_job(queue):
"""Get the oldest job in a queue"""
redis_store = get_db()
try:
res = redis_store.hgetall("job:%s" %
redis_store.lrange(queue, -1, -1)[0])
except IndexError:
return None
return Job(**res)
def test_submit_job_download(self):
"""Test if submitting a job with a downloaded sequence works"""
data = dict(ncbi='TESTING', cluster_1=u'on')
rv = self.client.post('/', data=data, follow_redirects=True)
assert "Status of job" in rv.data
redis_store = self._ctx.g._database
job_id = redis_store.keys('job:*')[0]
res = redis_store.hgetall(job_id)
assert res != {}
j = Job(**res)
assert j is not None
self.assertEquals(j.download, 'TESTING')
def new():
redis_store = get_db()
error = None
results_path = app.config['RESULTS_URL']
old_email = ''
try:
if request.method == 'POST':
kwargs = {}
kwargs['ncbi'] = request.form.get('ncbi', '').strip()
kwargs['email'] = request.form.get('email', '').strip()
old_email = kwargs['email']
# This webapi is for plantiSMASH, so create plantiSMASH jobs
kwargs['jobtype'] = 'plantismash'
clusterblast = request.form.get('clusterblast', u'off')
knownclusterblast = request.form.get('knownclusterblast', u'off')
subclusterblast = request.form.get('subclusterblast', u'off')
fullhmmer = request.form.get('fullhmmer', u'off')
coexpress_mad = request.form.get('coexpress_mad', u'')
kwargs['cdh_cutoff'] = request.form.get('cdh_cutoff',
0.5,
type=float)
kwargs['min_domain_number'] = request.form.get('min_domain_number',
2,
type=int)
# Use boolean values instead of "on/off" strings
kwargs['clusterblast'] = (clusterblast == u'on')
kwargs['knownclusterblast'] = (knownclusterblast == u'on')
try:
kwargs['min_mad'] = int(coexpress_mad)
except ValueError:
pass
job = Job(**kwargs)
dirname = path.join(app.config['RESULTS_PATH'], job.uid)
os.mkdir(dirname)
upload = None
if kwargs['ncbi'] != '':
job.download = kwargs['ncbi']
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 Exception("Could not save file!")
job.filename = filename
else:
raise Exception("Uploading input file failed!")
if 'gff' in request.files:
gff = request.files['gff']
if gff is not None and gff.filename != '':
filename = secure_filename(gff.filename)
gff.save(path.join(dirname, filename))
if not path.exists(path.join(dirname, filename)):
raise Exception("Could not save file!")
job.gff3 = filename
if 'coexpress_file' in request.files:
coexpress_file = request.files['coexpress_file']
if coexpress_file is not None and coexpress_file.filename != '':
filename = secure_filename(coexpress_file.filename)
coexpress_file.save(path.join(dirname, filename))
if not path.exists(path.join(dirname, filename)):
raise Exception("Could not save file!")
job.coexpress = True
_, ext = path.splitext(filename)
if ext.lower() == '.soft':
job.soft_file = filename
elif ext.lower() == '.csv':
job.csv_file = filename
else:
job.coexpress = False
_submit_job(redis_store, job)
return redirect(url_for('.display', task_id=job.uid))
except Exception as e:
error = unicode(e)
return render_template('new.html',
error=error,
old_email=old_email,
results_path=results_path)
def test_job_instantiate(self):
"""Test if job can be instantiated"""
job = Job()
assert job is not None
def test_job_jobtype_default(self):
"""Test that Job.jobtype is 'antismash' if not specified"""
job = Job()
assert job.jobtype == "antismash"
def test_job_email(self):
"""Test that Job.email returns the correct value"""
job = Job(email="*****@*****.**")
assert job.email == "*****@*****.**"
def test_job_get_short_status(self):
"""Test that Job.get_short_status() is sane"""
job = Job(status='pending: Waiting for Godot')
assert job.get_short_status() == 'pending'
def test_job_repr(self):
"""Test that the repr matches the job data"""
job = Job()
assert job.uid in str(job)
assert job.status in str(job)
def test_job_unique_uid(self):
"""Test if two different job objects get different uids"""
first = Job()
second = Job()
assert first.uid != second.uid