# -----------------------------------------------------------------------------
# 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 json import loads
from os.path import basename
from tornado.web import HTTPError
import pandas as pd
import qiita_db as qdb
from .oauth2 import OauthBaseHandler, authenticate_oauth
def _get_prep_template(pid):
"""Returns the prep template with the given `pid` if it exists
Parameters
----------
pid : str
The prep template id
Returns
-------
qiita_db.metadata_template.prep_template.PrepTemplate
The requested prep template
Raises
------
HTTPError
If the prep template does not exist, with error code 404
If there is a problem instantiating the template, with error code 500
"""
try:
pid = int(pid)
pt = qdb.metadata_template.prep_template.PrepTemplate(pid)
except qdb.exceptions.QiitaDBUnknownIDError:
raise HTTPError(404)
except Exception as e:
raise HTTPError(500, reason='Error instantiating prep template %s: %s'
% (pid, str(e)))
return pt
class PrepTemplateDBHandler(OauthBaseHandler):
@authenticate_oauth
def get(self, prep_id):
"""Retrieves the prep template information
Parameters
----------
prep_id: str
The id of the prep template whose information is being retrieved
Returns
-------
dict
The prep information:
'data_type': prep info data type
'artifact': artifact attached to the given prep
'investigation_type': prep info investigation type
'study': study that the prep info belongs to
'status': prep info status
'sample-file': the path to the sample information file
'prep-file': the path to the prep info file
"""
with qdb.sql_connection.TRN:
pt = _get_prep_template(prep_id)
prep_files = [fp for _, fp in pt.get_filepaths()
if 'qiime' not in basename(fp)]
artifact = pt.artifact.id if pt.artifact is not None else None
sid = pt.study_id
response = {
'data_type': pt.data_type(),
'artifact': artifact,
'investigation_type': pt.investigation_type,
'study': sid,
'status': pt.status,
# get_filepaths returns an ordered list of [filepath_id,
# filepath] and we want the last pair
'sample-file': qdb.study.Study(
sid).sample_template.get_filepaths()[0][1],
# The first element in the prep_files is the newest
# prep information file - hence the correct one
'prep-file': prep_files[0]
}
self.write(response)
class PrepTemplateDataHandler(OauthBaseHandler):
@authenticate_oauth
def get(self, prep_id):
"""Retrieves the prep contents
Parameters
----------
prep_id : str
The id of the prep template whose information is being retrieved
Returns
-------
dict
The contents of the prep information keyed by sample id
"""
sample_info = self.get_argument('sample_information', False)
with qdb.sql_connection.TRN:
pt = _get_prep_template(prep_id)
if not sample_info:
response = {'data': pt.to_dataframe().to_dict(orient='index')}
else:
ST = qdb.metadata_template.sample_template.SampleTemplate
response = {'data': ST(pt.study_id).to_dataframe(
samples=list(pt)).to_dict(orient='index')}
self.write(response)
class PrepTemplateAPIHandler(OauthBaseHandler):
@authenticate_oauth
def post(self):
prep_info_dict = loads(self.get_argument('prep_info'))
study = self.get_argument('study')
data_type = self.get_argument('data_type')
name = self.get_argument('name', None)
jid = self.get_argument('job-id', None)
metadata = pd.DataFrame.from_dict(prep_info_dict, orient='index')
pt = qdb.metadata_template.prep_template.PrepTemplate.create(
metadata, qdb.study.Study(study), data_type, name=name,
creation_job_id=jid)
self.write({'prep': pt.id})
class PrepTemplateAPItestHandler(PrepTemplateAPIHandler):
pass
Datasets
Models
