def post(self, preprocessed_data_id):
# make sure user is admin and can therefore actually submit to VAMPS
if self.current_user.level != 'admin':
raise HTTPError(
403, "User %s cannot submit to VAMPS!" % self.current_user.id)
msg = ''
msg_level = 'success'
preprocessed_data = Artifact(preprocessed_data_id)
state = preprocessed_data.submitted_to_vamps_status()
demux = [
path for _, path, ftype in preprocessed_data.get_filepaths()
if ftype == 'preprocessed_demux'
]
demux_length = len(demux)
if state in ('submitting', 'success'):
msg = "Cannot resubmit! Current state is: %s" % state
msg_level = 'danger'
elif demux_length != 1:
msg = "The study doesn't have demux files or have too many" % state
msg_level = 'danger'
else:
channel = self.current_user.id
job_id = submit(channel, submit_to_VAMPS,
int(preprocessed_data_id))
self.render('compute_wait.html',
job_id=job_id,
title='VAMPS Submission',
completion_redirect='/compute_complete/%s' % job_id)
return
self.display_template(preprocessed_data_id, msg, msg_level)
def post(self, preprocessed_data_id):
# make sure user is admin and can therefore actually submit to VAMPS
if self.current_user.level != "admin":
raise HTTPError(403, "User %s cannot submit to VAMPS!" % self.current_user.id)
msg = ""
msg_level = "success"
preprocessed_data = Artifact(preprocessed_data_id)
state = preprocessed_data.submitted_to_vamps_status()
demux = [path for _, path, ftype in preprocessed_data.get_filepaths() if ftype == "preprocessed_demux"]
demux_length = len(demux)
if state in ("submitting", "success"):
msg = "Cannot resubmit! Current state is: %s" % state
msg_level = "danger"
elif demux_length != 1:
msg = "The study doesn't have demux files or have too many" % state
msg_level = "danger"
else:
channel = self.current_user.id
job_id = submit(channel, submit_to_VAMPS, int(preprocessed_data_id))
self.render(
"compute_wait.html",
job_id=job_id,
title="VAMPS Submission",
completion_redirect="/compute_complete/%s" % job_id,
)
return
self.display_template(preprocessed_data_id, msg, msg_level)
def display_template(self, preprocessed_data_id, msg, msg_level):
"""Simple function to avoid duplication of code"""
preprocessed_data_id = int(preprocessed_data_id)
try:
preprocessed_data = Artifact(preprocessed_data_id)
except QiitaDBUnknownIDError:
raise HTTPError(
404, "Artifact %d does not exist!" % preprocessed_data_id)
else:
user = self.current_user
if user.level != 'admin':
raise HTTPError(
403, "No permissions of admin, "
"get/VAMPSSubmitHandler: %s!" % user.id)
prep_template = PrepTemplate(preprocessed_data.prep_template)
sample_template = SampleTemplate(preprocessed_data.study)
study = Study(preprocessed_data.study)
stats = [('Number of samples', len(prep_template)),
('Number of metadata headers',
len(sample_template.categories()))]
demux = [
path for _, path, ftype in preprocessed_data.get_filepaths()
if ftype == 'preprocessed_demux'
]
demux_length = len(demux)
if not demux_length:
msg = ("Study does not appear to have demultiplexed "
"sequences associated")
msg_level = 'danger'
elif demux_length > 1:
msg = ("Study appears to have multiple demultiplexed files!")
msg_level = 'danger'
elif demux_length == 1:
demux_file = demux[0]
demux_file_stats = demux_stats(demux_file)
stats.append(('Number of sequences', demux_file_stats.n))
msg_level = 'success'
self.render('vamps_submission.html',
study_title=study.title,
stats=stats,
message=msg,
study_id=study.id,
level=msg_level,
preprocessed_data_id=preprocessed_data_id)
def display_template(self, preprocessed_data_id, msg, msg_level):
"""Simple function to avoid duplication of code"""
preprocessed_data_id = int(preprocessed_data_id)
try:
preprocessed_data = Artifact(preprocessed_data_id)
except QiitaDBUnknownIDError:
raise HTTPError(404, "Artifact %d does not exist!" % preprocessed_data_id)
else:
user = self.current_user
if user.level != "admin":
raise HTTPError(403, "No permissions of admin, " "get/VAMPSSubmitHandler: %s!" % user.id)
prep_template = PrepTemplate(preprocessed_data.prep_template)
sample_template = SampleTemplate(preprocessed_data.study)
study = Study(preprocessed_data.study)
stats = [
("Number of samples", len(prep_template)),
("Number of metadata headers", len(sample_template.categories())),
]
demux = [path for _, path, ftype in preprocessed_data.get_filepaths() if ftype == "preprocessed_demux"]
demux_length = len(demux)
if not demux_length:
msg = "Study does not appear to have demultiplexed " "sequences associated"
msg_level = "danger"
elif demux_length > 1:
msg = "Study appears to have multiple demultiplexed files!"
msg_level = "danger"
elif demux_length == 1:
demux_file = demux[0]
demux_file_stats = demux_stats(demux_file)
stats.append(("Number of sequences", demux_file_stats.n))
msg_level = "success"
self.render(
"vamps_submission.html",
study_title=study.title,
stats=stats,
message=msg,
study_id=study.id,
level=msg_level,
preprocessed_data_id=preprocessed_data_id,
)
self.display_template(preprocessed_data_id, "", "")
@authenticated
@execute_as_transaction
def post(self, preprocessed_data_id):
# make sure user is admin and can therefore actually submit to VAMPS
<<<<<<< HEAD
if self.current_user.level != 'admin':
raise HTTPError(403, "User %s cannot submit to VAMPS!" %
self.current_user.id)
msg = ''
msg_level = 'success'
preprocessed_data = Artifact(preprocessed_data_id)
state = preprocessed_data.submitted_to_vamps_status()
demux = [path for _, path, ftype in preprocessed_data.get_filepaths()
if ftype == 'preprocessed_demux']
demux_length = len(demux)
if state in ('submitting', 'success'):
msg = "Cannot resubmit! Current state is: %s" % state
msg_level = 'danger'
elif demux_length != 1:
msg = "The study doesn't have demux files or have too many" % state
msg_level = 'danger'
else:
channel = self.current_user.id
job_id = submit(channel, submit_to_VAMPS,
int(preprocessed_data_id))
self.render('compute_wait.html',
