# -----------------------------------------------------------------------------
# Copyright (c) 2014--, The Qiita Development Team.
#
# Distributed under the terms of the BSD 3-clause License.
#
# The full license is in the file LICENSE, distributed with this software.
# -----------------------------------------------------------------------------
from tornado.web import authenticated, HTTPError
from tornado.escape import url_escape
from json import dumps
from qiita_files.demux import stats as demux_stats
from qiita_core.qiita_settings import r_client, qiita_config
from qiita_core.util import execute_as_transaction
from qiita_db.metadata_template.constants import (SAMPLE_TEMPLATE_COLUMNS,
PREP_TEMPLATE_COLUMNS)
from qiita_db.exceptions import QiitaDBUnknownIDError
from qiita_db.artifact import Artifact
from qiita_db.processing_job import ProcessingJob
from qiita_db.software import Software, Parameters
from qiita_pet.handlers.base_handlers import BaseHandler
VALID_SUBMISSION_TYPES = ['Demultiplexed', 'per_sample_FASTQ']
class EBISubmitHandler(BaseHandler):
@execute_as_transaction
def display_template(self, artifact_id, msg, msg_level):
"""Simple function to avoid duplication of code"""
artifact_id = int(artifact_id)
try:
artifact = Artifact(artifact_id)
except QiitaDBUnknownIDError:
raise HTTPError(404, reason="Artifact %d does not exist!" %
artifact_id)
else:
user = self.current_user
if user.level != 'admin':
raise HTTPError(403, reason="No permissions of admin, "
"get/EBISubmitHandler: %s!" % user.id)
prep_templates = artifact.prep_templates
allow_submission = len(prep_templates) == 1
msg_list = ["Submission to EBI disabled:"]
if not allow_submission:
msg_list.append(
"Only artifacts with a single prep template can be submitted")
# If allow_submission is already false, we technically don't need to
# do the following work. However, there is no clean way to fix this
# using the current structure, so we perform the work as we
# did so it doesn't fail.
# We currently support only one prep template for submission, so
# grabbing the first one
prep_template = prep_templates[0]
study = artifact.study
sample_template = study.sample_template
stats = {
'Number of samples': len(prep_template),
'Number of metadata headers': len(sample_template.categories),
'Number of sequences': 'N/A',
'Total forward': 'N/A',
'Total reverse': 'N/A'
}
artifact_type = artifact.artifact_type
if artifact_type not in VALID_SUBMISSION_TYPES:
msg = "You can only submit: '%s' and this artifact is '%s'" % (
', '.join(VALID_SUBMISSION_TYPES), artifact_type)
msg_level = 'danger'
elif artifact_type == 'Demultiplexed':
demux = [x['fp'] for x in artifact.filepaths
if x['fp_type'] == 'preprocessed_demux']
demux_length = len(demux)
if demux_length > 1:
msg = "Study appears to have multiple demultiplexed files!"
msg_level = 'danger'
else:
demux_file = demux[0]
demux_file_stats = demux_stats(demux_file)
stats['Number of sequences'] = demux_file_stats.n
msg_level = 'success'
elif artifact_type == 'per_sample_FASTQ':
raw_forward_seqs = []
raw_reverse_seqs = []
for x in artifact.filepaths:
if x['fp_type'] == 'raw_forward_seqs':
raw_forward_seqs.append(x['fp'])
elif x['fp_type'] == 'raw_reverse_seqs':
raw_reverse_seqs.append(x['fp'])
stats['Total forward'] = len(raw_forward_seqs)
stats['Total reverse'] = len(raw_reverse_seqs)
msg_level = 'success'
# Check if the templates have all the required columns for EBI
pt_missing_cols = prep_template.check_restrictions(
[PREP_TEMPLATE_COLUMNS['EBI']])
st_missing_cols = sample_template.check_restrictions(
[SAMPLE_TEMPLATE_COLUMNS['EBI']])
allow_submission = (len(pt_missing_cols) == 0 and
len(st_missing_cols) == 0 and allow_submission)
if not allow_submission:
if len(pt_missing_cols) > 0:
msg_list.append("Columns missing in prep template: %s"
% ', '.join(pt_missing_cols))
if len(st_missing_cols) > 0:
msg_list.append("Columns missing in sample template: %s"
% ', '.join(st_missing_cols))
ebi_disabled_msg = "<br/>".join(msg_list)
else:
ebi_disabled_msg = None
self.render('ebi_submission.html',
study_title=study.title, stats=stats.items(), message=msg,
study_id=study.id, level=msg_level,
preprocessed_data_id=artifact_id,
investigation_type=prep_template.investigation_type,
allow_submission=allow_submission,
ebi_disabled_msg=ebi_disabled_msg)
@authenticated
def get(self, preprocessed_data_id):
self.display_template(preprocessed_data_id, "", "")
@authenticated
@execute_as_transaction
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, reason="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, reason="User: %s, %s is not a recognized "
"submission type" % (user.id, submission_type))
study = Artifact(preprocessed_data_id).study
state = study.ebi_submission_status
if state == 'submitting':
message = "Cannot resubmit! Current state is: %s" % state
self.display_template(preprocessed_data_id, message, 'danger')
else:
qiita_plugin = Software.from_name_and_version('Qiita', 'alpha')
cmd = qiita_plugin.get_command('submit_to_EBI')
params = Parameters.load(
cmd, values_dict={'artifact': preprocessed_data_id,
'submission_type': submission_type})
job = ProcessingJob.create(user, params, True)
r_client.set('ebi_submission_%s' % preprocessed_data_id,
dumps({'job_id': job.id, 'is_qiita_job': True}))
job.submit()
level = 'success'
message = 'EBI submission started. Job id: %s' % job.id
self.redirect("%s/study/description/%d?level=%s&message=%s" % (
qiita_config.portal_dir, study.id, level, url_escape(message)))
Datasets
Models
