# -----------------------------------------------------------------------------
# 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 os.path import join, relpath
from tornado.web import authenticated
from tornado.escape import url_escape
import pandas as pd
from qiita_core.qiita_settings import qiita_config
from qiita_pet.handlers.util import to_int
from qiita_pet.handlers.base_handlers import BaseHandler
from qiita_db.util import (get_files_from_uploads_folders, get_mountpoint,
supported_filepath_types)
from qiita_db.metadata_template.prep_template import PrepTemplate
from qiita_pet.handlers.api_proxy import (
prep_template_ajax_get_req, new_prep_template_get_req,
prep_template_summary_get_req)
class NewPrepTemplateAjax(BaseHandler):
@authenticated
def get(self):
study_id = to_int(self.get_argument('study_id'))
result = new_prep_template_get_req(study_id)
self.render('study_ajax/add_prep_template.html',
prep_files=result['prep_files'],
data_types=result['data_types'],
ontology=result['ontology'],
study_id=study_id)
class AddDefaultWorkflowHandler(BaseHandler):
@authenticated
def post(self):
prep_id = self.get_argument('prep_id')
msg_error = None
data = None
try:
workflow = PrepTemplate(prep_id).add_default_workflow(
self.current_user)
data = workflow.id
except Exception as error:
msg_error = str(error)
self.write({'data': data, 'msg_error': msg_error})
class PrepTemplateSummaryAJAX(BaseHandler):
@authenticated
def get(self):
prep_id = to_int(self.get_argument('prep_id'))
res = prep_template_summary_get_req(prep_id, self.current_user.id)
self.render('study_ajax/prep_summary_table.html', pid=prep_id,
stats=res['summary'], editable=res['editable'],
num_samples=res['num_samples'])
class PrepTemplateAJAX(BaseHandler):
@authenticated
def get(self):
"""Send formatted summary page of prep template"""
prep_id = to_int(self.get_argument('prep_id'))
row_id = self.get_argument('row_id', '0')
current_user = self.current_user
res = prep_template_ajax_get_req(current_user.id, prep_id)
res['prep_id'] = prep_id
res['row_id'] = row_id
# Escape the message just in case javascript breaking characters in it
res['alert_message'] = url_escape(res['alert_message'])
res['user_level'] = current_user.level
if res['creation_job'] is not None:
fp = res['creation_job'].parameters.values['sample_sheet']
res['creation_job_filename'] = fp['filename']
res['creation_job_filename_body'] = fp['body']
summary = None
if res['creation_job'].status == 'success':
if res['creation_job'].outputs:
# [0] is the id, [1] is the filepath
_file = res['creation_job'].outputs[
'output'].html_summary_fp[1]
summary = relpath(_file, qiita_config.base_data_dir)
res['creation_job_artifact_summary'] = summary
# res['']
res['human_reads_filter_method'] = None
a = PrepTemplate(prep_id).artifact
if a is not None:
hrfm = a.human_reads_filter_method
if hrfm is not None:
res['human_reads_filter_method'] = hrfm
self.render('study_ajax/prep_summary.html', **res)
class PrepFilesHandler(BaseHandler):
@authenticated
def get(self):
study_id = self.get_argument('study_id')
prep_file = self.get_argument('prep_file')
prep_type = self.get_argument('type')
# TODO: Get file types for the artifact type
# FILE TYPE IN POSTION 0 MUST BE DEFAULT FOR SELECTED
file_types = supported_filepath_types(prep_type)
selected = []
not_selected = []
_, base = get_mountpoint("uploads")[0]
uploaded = get_files_from_uploads_folders(study_id)
prep = pd.read_table(join(base, study_id, prep_file), sep='\t')
if 'run_prefix' in prep.columns:
# Use run_prefix column of prep template to auto-select
# per-prefix uploaded files if available.
per_prefix = True
prep_prefixes = set(prep['run_prefix'])
for _, filename in uploaded:
for prefix in prep_prefixes:
if filename.startswith(prefix):
selected.append(filename)
else:
not_selected.append(filename)
else:
per_prefix = False
not_selected = [f for _, f, _ in uploaded]
# Write out if this prep template supports per-prefix files, and the
# as well as pre-selected and remaining files
self.write({
'per_prefix': per_prefix,
'file_types': file_types,
'selected': selected,
'remaining': not_selected})
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