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):
user = self.current_user
# make sure user is admin and can therefore actually submit to EBI
if user.level != 'admin':
raise HTTPError(403, "User %s cannot submit to EBI!" %
user.id)
submission_type = self.get_argument('submission_type')
if submission_type not in ['ADD', 'MODIFY']:
raise HTTPError(403, "User: %s, %s is not a recognized submission "
"type" % (user.id, submission_type))
msg = ''
msg_level = 'success'
preprocessed_data = PreprocessedData(preprocessed_data_id)
state = preprocessed_data.submitted_to_insdc_status()
if state == 'submitting':
msg = "Cannot resubmit! Current state is: %s" % state
msg_level = 'danger'
elif state == 'success' and submission_type == "ADD":
msg = "Cannot resubmit! Current state is: %s, use MODIFY" % state
msg_level = 'danger'
else:
channel = user.id
job_id = submit(channel, submit_to_ebi, int(preprocessed_data_id),
submission_type)
self.render('compute_wait.html',
job_id=job_id, title='EBI Submission',
completion_redirect='/compute_complete/%s' % job_id)
return
self.display_template(preprocessed_data_id, msg, msg_level)
def post(self, preprocessed_data_id):
user = self.current_user
# make sure user is admin and can therefore actually submit to VAMPS
if user.level != 'admin':
raise HTTPError(403, "User %s cannot submit to VAMPS!" % user.id)
msg = ''
msg_level = 'success'
study = Artifact(preprocessed_data_id).study
study_id = study.id
state = study.ebi_submission_status
if state == 'submitting':
msg = "Cannot resubmit! Current state is: %s" % state
msg_level = 'danger'
else:
channel = 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=('/study/description/%s?top_tab='
'preprocessed_data_tab&sub_tab=%s' %
(study_id, preprocessed_data_id)))
return
self.display_template(preprocessed_data_id, msg, msg_level)
def post(self):
study_id = int(self.get_argument('study_id'))
prep_template_id = int(self.get_argument('prep_template_id'))
raw_data_id = PrepTemplate(prep_template_id).raw_data
# Get the preprocessing parameters
form_data = PreprocessParametersForm()
form_data.process(data=self.request.arguments)
rcomp_mapping_barcodes = form_data.data['rev_comp_mapping_barcodes']
# currently only allow the user to change a single parameter of split
# libraries: --rev_comp_mapping_barcodes. The parameter ids 1 and 2
# contain the same set of values except for that flag. If param_id = 1,
# the flag is not activated, while in param_id = 2; it is.
if rcomp_mapping_barcodes:
# Choose the parameter set with the --rev_comp_mapping_barcodes
# flag activated
param_id = 2
else:
# Choose the parameter set with the --rev_comp_mapping_barcodes
# flag not activated
param_id = 1
param_constructor = PreprocessedIlluminaParams
job_id = submit(self.current_user, preprocessor, study_id,
prep_template_id, param_id, param_constructor)
self.render('compute_wait.html', user=self.current_user,
job_id=job_id, title='Preprocessing',
completion_redirect='/study/description/%d?top_tab='
'raw_data_tab&sub_tab=%s&prep_tab=%s'
% (study_id, raw_data_id,
prep_template_id))
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):
user = self.current_user
# make sure user is admin and can therefore actually submit to VAMPS
if user.level != 'admin':
raise HTTPError(403, "User %s cannot submit to VAMPS!" %
user.id)
msg = ''
msg_level = 'success'
study = Artifact(preprocessed_data_id).study
study_id = study.id
state = study.ebi_submission_status
if state == 'submitting':
msg = "Cannot resubmit! Current state is: %s" % state
msg_level = 'danger'
else:
channel = 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=('/study/description/%s?top_tab='
'preprocessed_data_tab&sub_tab=%s'
% (study_id,
preprocessed_data_id)))
return
self.display_template(preprocessed_data_id, msg, msg_level)
def post(self, preprocessed_data_id):
user = self.current_user
# make sure user is admin and can therefore actually submit to EBI
if user.level != 'admin':
raise HTTPError(403, "User %s cannot submit to EBI!" %
user.id)
submission_type = self.get_argument('submission_type')
if submission_type not in ['ADD', 'MODIFY']:
raise HTTPError(403, "User: %s, %s is not a recognized submission "
"type" % (user.id, submission_type))
msg = ''
msg_level = 'success'
study = Artifact(preprocessed_data_id).study
study_id = study.id
state = study.ebi_submission_status
if state == 'submitting':
msg = "Cannot resubmit! Current state is: %s" % state
msg_level = 'danger'
else:
channel = user.id
job_id = submit(channel, submit_to_ebi, int(preprocessed_data_id),
submission_type)
self.render('compute_wait.html',
job_id=job_id, title='EBI Submission',
completion_redirect=('/study/description/%s?top_tab='
'preprocessed_data_tab&sub_tab=%s'
% (study_id,
preprocessed_data_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 = PreprocessedData(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 create_from_scratch(self, prep_template, study_id):
raw_data_filetype = self.get_argument('filetype')
barcodes_str = self.get_argument('barcodes')
forward_reads_str = self.get_argument('forward')
sff_str = self.get_argument('sff')
fasta_str = self.get_argument('fasta')
qual_str = self.get_argument('qual')
reverse_reads_str = self.get_argument('reverse')
def _split(x):
return x.split(',') if x else []
filepaths, fps = [], []
fps.append((_split(barcodes_str), 'raw_barcodes'))
fps.append((_split(fasta_str), 'raw_fasta'))
fps.append((_split(qual_str), 'raw_qual'))
fps.append((_split(forward_reads_str), 'raw_forward_seqs'))
fps.append((_split(reverse_reads_str), 'raw_reverse_seqs'))
fps.append((_split(sff_str), 'raw_sff'))
# We need to retrieve the full path for all the files, as the
# arguments only contain the file name. Since we don't know in which
# mountpoint the data lives, we retrieve all of them and we loop
# through all the files checking if they exist or not.
for _, f in get_mountpoint("uploads", retrieve_all=True):
f = join(f, str(study_id))
for fp_set, filetype in fps:
for t in fp_set:
ft = join(f, t)
if exists(ft):
filepaths.append((ft, filetype))
return submit(self.current_user.id, create_raw_data, raw_data_filetype,
prep_template, filepaths)
def create_from_scratch(self, prep_template, study_id):
raw_data_filetype = self.get_argument("filetype")
barcodes_str = self.get_argument("barcodes")
forward_reads_str = self.get_argument("forward")
sff_str = self.get_argument("sff")
fasta_str = self.get_argument("fasta")
qual_str = self.get_argument("qual")
reverse_reads_str = self.get_argument("reverse")
def _split(x):
return x.split(",") if x else []
filepaths, fps = [], []
fps.append((_split(barcodes_str), "raw_barcodes"))
fps.append((_split(fasta_str), "raw_fasta"))
fps.append((_split(qual_str), "raw_qual"))
fps.append((_split(forward_reads_str), "raw_forward_seqs"))
fps.append((_split(reverse_reads_str), "raw_reverse_seqs"))
fps.append((_split(sff_str), "raw_sff"))
# We need to retrieve the full path for all the files, as the
# arguments only contain the file name. Since we don't know in which
# mountpoint the data lives, we retrieve all of them and we loop
# through all the files checking if they exist or not.
for _, f in get_mountpoint("uploads", retrieve_all=True):
f = join(f, str(study_id))
for fp_set, filetype in fps:
for t in fp_set:
ft = join(f, t)
if exists(ft):
filepaths.append((ft, filetype))
return submit(self.current_user.id, create_raw_data, raw_data_filetype, prep_template, filepaths)
def post(self, preprocessed_data_id):
# make sure user is admin and can therefore actually submit to EBI
if User(self.current_user).level != 'admin':
raise HTTPError(403, "User %s cannot submit to EBI!" %
self.current_user)
submission_type = self.get_argument('submission_type')
if submission_type not in ['ADD', 'MODIFY']:
raise HTTPError(403, "User: %s, %s is not a recognized submission "
"type" % (self.current_user, submission_type))
msg = ''
msg_level = 'success'
preprocessed_data = PreprocessedData(preprocessed_data_id)
state = preprocessed_data.submitted_to_insdc_status()
if state == 'submitting':
msg = "Cannot resubmit! Current state is: %s" % state
msg_level = 'danger'
elif state == 'success' and submission_type == "ADD":
msg = "Cannot resubmit! Current state is: %s, use MODIFY" % state
msg_level = 'danger'
else:
channel = self.current_user
job_id = submit(channel, submit_to_ebi, int(preprocessed_data_id),
submission_type)
self.render('compute_wait.html', user=self.current_user,
job_id=job_id, title='EBI Submission',
completion_redirect='/compute_complete/%s' % job_id)
return
self.display_template(preprocessed_data_id, msg, msg_level)
def post(self):
# vars to add files to raw data
study_id = self.get_argument('study_id')
raw_data_id = self.get_argument('raw_data_id')
barcodes_str = self.get_argument('barcodes')
forward_reads_str = self.get_argument('forward')
reverse_reads_str = self.get_argument('reverse', None)
study_id = int(study_id)
try:
study = Study(study_id)
except QiitaDBUnknownIDError:
# Study not in database so fail nicely
raise HTTPError(404, "Study %d does not exist" % study_id)
else:
check_access(User(self.current_user), study, raise_error=True)
barcodes, forward_reads, reverse_reads = [], [], []
for _, f in get_mountpoint("uploads", retrive_all=True):
f = join(f, str(study_id))
for t in barcodes_str.split(','):
ft = join(f, t)
if exists(ft):
barcodes.append([ft, "raw_barcodes"])
for t in forward_reads_str.split(','):
ft = join(f, t)
if exists(ft):
forward_reads.append([ft, "raw_forward_seqs"])
if reverse_reads_str:
for t in reverse_reads_str.split(','):
ft = join(f, t)
if exists(ft):
reverse_reads.append([ft, "raw_reverse_seqs"])
# this should never happen if following the GUI pipeline
# but rather be save than sorry
if (len(barcodes) != len(forward_reads)
or (barcodes and len(barcodes) != len(forward_reads))):
raise HTTPError(404, "user %s tried to submit a wrong pair of "
"barcodes/forward/reverse reads" %
self.current_user)
# join all files to send on single var
filepaths = barcodes
filepaths.extend(forward_reads)
if reverse_reads:
filepaths.extend(reverse_reads)
job_id = submit(self.current_user, add_files_to_raw_data, raw_data_id,
filepaths)
self.render('compute_wait.html', user=self.current_user,
job_id=job_id, title='Adding files to your raw data',
completion_redirect=(
'/study/description/%s?top_tab=raw_data_tab&sub_tab=%s'
% (study_id, raw_data_id)))
def post(self):
# vars to add files to raw data
study_id = self.get_argument('study_id')
raw_data_id = self.get_argument('raw_data_id')
barcodes_str = self.get_argument('barcodes')
forward_reads_str = self.get_argument('forward')
sff_str = self.get_argument('sff')
fasta_str = self.get_argument('fasta')
qual_str = self.get_argument('qual')
reverse_reads_str = self.get_argument('reverse')
study_id = int(study_id)
try:
study = Study(study_id)
except QiitaDBUnknownIDError:
# Study not in database so fail nicely
raise HTTPError(404, "Study %d does not exist" % study_id)
else:
check_access(self.current_user, study, raise_error=True)
def _split(x):
return x.split(',') if x else []
filepaths, fps = [], []
fps.append((_split(barcodes_str), 'raw_barcodes'))
fps.append((_split(fasta_str), 'raw_fasta'))
fps.append((_split(qual_str), 'raw_qual'))
fps.append((_split(forward_reads_str), 'raw_forward_seqs'))
fps.append((_split(reverse_reads_str), 'raw_reverse_seqs'))
fps.append((_split(sff_str), 'raw_sff'))
for _, f in get_mountpoint("uploads", retrieve_all=True):
f = join(f, str(study_id))
for fp_set, filetype in fps:
for t in fp_set:
ft = join(f, t)
if exists(ft):
filepaths.append((ft, filetype))
job_id = submit(self.current_user.id, add_files_to_raw_data,
raw_data_id, filepaths)
self.render(
'compute_wait.html',
job_id=job_id,
title='Adding files to your raw data',
completion_redirect=(
'/study/description/%s?top_tab=raw_data_tab&sub_tab=%s' %
(study_id, raw_data_id)))
def post(self):
# vars to add files to raw data
study_id = self.get_argument('study_id')
raw_data_id = self.get_argument('raw_data_id')
prep_template_id = self.get_argument('prep_template_id')
barcodes_str = self.get_argument('barcodes')
forward_reads_str = self.get_argument('forward')
sff_str = self.get_argument('sff')
fasta_str = self.get_argument('fasta')
qual_str = self.get_argument('qual')
reverse_reads_str = self.get_argument('reverse')
study_id = int(study_id)
try:
study = Study(study_id)
except QiitaDBUnknownIDError:
# Study not in database so fail nicely
raise HTTPError(404, "Study %d does not exist" % study_id)
else:
check_access(self.current_user, study, raise_error=True)
def _split(x):
return x.split(',') if x else []
filepaths, fps = [], []
fps.append((_split(barcodes_str), 'raw_barcodes'))
fps.append((_split(fasta_str), 'raw_fasta'))
fps.append((_split(qual_str), 'raw_qual'))
fps.append((_split(forward_reads_str), 'raw_forward_seqs'))
fps.append((_split(reverse_reads_str), 'raw_reverse_seqs'))
fps.append((_split(sff_str), 'raw_sff'))
for _, f in get_mountpoint("uploads", retrieve_all=True):
f = join(f, str(study_id))
for fp_set, filetype in fps:
for t in fp_set:
ft = join(f, t)
if exists(ft):
filepaths.append((ft, filetype))
job_id = submit(self.current_user.id, add_files_to_raw_data,
raw_data_id, filepaths)
self.render('compute_wait.html',
job_id=job_id, title='Adding files to your raw data',
completion_redirect=(
'/study/description/%s?top_tab=prep_template_tab'
'&sub_tab=%s' % (study_id, prep_template_id)))
def post(self):
study_id = int(self.get_argument('study_id'))
preprocessed_data_id = int(self.get_argument('preprocessed_data_id'))
param_id = self.get_argument('parameter-set-%s' % preprocessed_data_id)
# The only parameter type supported is the ProcessedSortmernaParams
# so we can hardcode the constructor here
param_constructor = ProcessedSortmernaParams
job_id = submit(self.current_user.id, processor, preprocessed_data_id,
param_id, param_constructor)
self.render('compute_wait.html',
job_id=job_id,
title='Processing',
completion_redirect='/study/description/%d?top_tab='
'preprocessed_data_tab&sub_tab=%s' %
(study_id, preprocessed_data_id))
def post(self):
study_id = int(self.get_argument("study_id"))
preprocessed_data_id = int(self.get_argument("preprocessed_data_id"))
param_id = self.get_argument("parameter-set-%s" % preprocessed_data_id)
# The only parameter type supported is the ProcessedSortmernaParams
# so we can hardcode the constructor here
param_constructor = ProcessedSortmernaParams
job_id = submit(self.current_user.id, processor, preprocessed_data_id, param_id, param_constructor)
self.render(
"compute_wait.html",
job_id=job_id,
title="Processing",
completion_redirect="/study/description/%d?top_tab="
"preprocessed_data_tab&sub_tab=%s" % (study_id, preprocessed_data_id),
)
def post(self):
pt_id = self.get_argument('prep_template_id')
raw_data_filetype = self.get_argument('filetype')
barcodes_str = self.get_argument('barcodes')
forward_reads_str = self.get_argument('forward')
sff_str = self.get_argument('sff')
fasta_str = self.get_argument('fasta')
qual_str = self.get_argument('qual')
reverse_reads_str = self.get_argument('reverse')
pt = PrepTemplate(pt_id)
study_id = pt.study_id
def _split(x):
return x.split(',') if x else []
filepaths, fps = [], []
fps.append((_split(barcodes_str), 'raw_barcodes'))
fps.append((_split(fasta_str), 'raw_fasta'))
fps.append((_split(qual_str), 'raw_qual'))
fps.append((_split(forward_reads_str), 'raw_forward_seqs'))
fps.append((_split(reverse_reads_str), 'raw_reverse_seqs'))
fps.append((_split(sff_str), 'raw_sff'))
# We need to retrieve the full path for all the files, as the
# arguments only contain the file name. Since we don't know in which
# mountpoint the data lives, we retrieve all of them and we loop
# through all the files checking if they exist or not.
for _, f in get_mountpoint("uploads", retrieve_all=True):
f = join(f, str(study_id))
for fp_set, filetype in fps:
for t in fp_set:
ft = join(f, t)
if exists(ft):
filepaths.append((ft, filetype))
job_id = submit(self.current_user.id, create_raw_data,
raw_data_filetype, pt, filepaths)
self.render('compute_wait.html',
job_id=job_id, title='Adding raw data',
completion_redirect=(
'/study/description/%s?top_tab=prep_template_tab'
'&sub_tab=%s' % (study_id, pt_id)))
def post(self):
study_id = int(self.get_argument('study_id'))
prep_template_id = int(self.get_argument('prep_template_id'))
rcomp_mapping_barcodes = self.get_argument('rev_comp_mapping_barcodes')
# currently forcing these values
# param_constructor = self.get_argument('param_constructor')
if rcomp_mapping_barcodes == 'false':
param_id = 1
else:
param_id = 2
param_constructor = PreprocessedIlluminaParams
job_id = submit(self.current_user, preprocessor, study_id,
prep_template_id, param_id, param_constructor)
self.render('compute_wait.html', user=self.current_user,
job_id=job_id, title='Preprocessing',
completion_redirect='/study/description/%d' % study_id)
def post(self):
# vars to remove all files from a raw data
study_id = self.get_argument('study_id', None)
raw_data_id = self.get_argument('raw_data_id', None)
study_id = int(study_id) if study_id else None
try:
study = Study(study_id)
except QiitaDBUnknownIDError:
# Study not in database so fail nicely
raise HTTPError(404, "Study %d does not exist" % study_id)
else:
check_access(User(self.current_user), study, raise_error=True)
job_id = submit(self.current_user, unlink_all_files, raw_data_id)
self.render('compute_wait.html', user=self.current_user,
job_id=job_id, title='Removing files from your raw data',
completion_redirect='/study/description/%d' % study_id)
def post(self):
study_id = int(self.get_argument('study_id'))
prep_template_id = int(self.get_argument('prep_template_id'))
raw_data = RawData(PrepTemplate(prep_template_id).raw_data)
param_id = int(self.get_argument('preprocessing_parameters_id'))
# Get the preprocessing parameters
if raw_data.filetype in ('FASTQ', 'per_sample_FASTQ'):
param_constructor = PreprocessedIlluminaParams
elif raw_data.filetype in ('FASTA', 'SFF'):
param_constructor = Preprocessed454Params
else:
raise ValueError('Unknown filetype')
job_id = submit(self.current_user.id, preprocessor, study_id,
prep_template_id, param_id, param_constructor)
self.render('compute_wait.html',
job_id=job_id, title='Preprocessing',
completion_redirect='/study/description/%d?top_tab='
'prep_template_tab&sub_tab=%s'
% (study_id, prep_template_id))
def post(self):
study_id = int(self.get_argument('study_id'))
prep_template_id = int(self.get_argument('prep_template_id'))
raw_data = RawData(PrepTemplate(prep_template_id).raw_data)
param_id = int(self.get_argument('preprocessing_parameters_id'))
# Get the preprocessing parameters
if raw_data.filetype == 'FASTQ':
param_constructor = PreprocessedIlluminaParams
elif raw_data.filetype in ('FASTA', 'SFF'):
param_constructor = Preprocessed454Params
else:
raise ValueError('Unknown filetype')
job_id = submit(self.current_user.id, preprocessor, study_id,
prep_template_id, param_id, param_constructor)
self.render('compute_wait.html',
job_id=job_id, title='Preprocessing',
completion_redirect='/study/description/%d?top_tab='
'raw_data_tab&sub_tab=%s&prep_tab=%s'
% (study_id, raw_data.id,
prep_template_id))
def post(self):
# vars to remove all files from a raw data
study_id = self.get_argument('study_id', None)
raw_data_id = self.get_argument('raw_data_id', None)
study_id = int(study_id) if study_id else None
try:
study = Study(study_id)
except QiitaDBUnknownIDError:
# Study not in database so fail nicely
raise HTTPError(404, "Study %d does not exist" % study_id)
else:
check_access(self.current_user, study, raise_error=True)
job_id = submit(self.current_user.id, unlink_all_files, raw_data_id)
self.render(
'compute_wait.html',
job_id=job_id,
title='Removing files from your raw data',
completion_redirect=(
'/study/description/%s?top_tab=raw_data_tab&sub_tab=%s' %
(study_id, raw_data_id)))
def create_from_artifact(self, prep_template, artifact_id):
return submit(self.current_user.id, copy_raw_data, prep_template, artifact_id)
def create_from_artifact(self, prep_template, artifact_id):
return submit(self.current_user.id, copy_raw_data, prep_template,
artifact_id)
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
=======
if user.level != 'admin':
raise HTTPError(403, reason="User %s cannot submit to VAMPS!" %
user.id)
msg = ''
msg_level = 'success'
plugin = Software.from_name_and_version('Qiita', 'alpha')
cmd = plugin.get_command('submit_to_VAMPS')
artifact = Artifact(preprocessed_data_id)
