# -----------------------------------------------------------------------------
# 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 os.path import join, exists
from os import remove, chmod
from json import loads, dumps
from collections import defaultdict
from shutil import rmtree, move
from .util import check_access
from .base_handlers import BaseHandler
from qiita_core.qiita_settings import qiita_config, r_client
from qiita_core.util import execute_as_transaction
from qiita_db.util import (get_files_from_uploads_folders,
get_mountpoint, move_upload_files_to_trash)
from qiita_db.study import Study
from qiita_db.processing_job import ProcessingJob
from qiita_db.software import Software, Parameters
from qiita_db.exceptions import QiitaDBUnknownIDError
from qiita_db.util import create_nested_path
UPLOAD_STUDY_FORMAT = 'upload_study_%s'
class StudyUploadFileHandler(BaseHandler):
@authenticated
@execute_as_transaction
def display_template(self, study_id, msg):
"""Simple function to avoid duplication of code"""
study_id = int(study_id)
study = Study(study_id)
user = self.current_user
level = 'info'
message = ''
remote_url = ''
remote_files = []
check_access(user, study, no_public=True, raise_error=True)
job_info = r_client.get(UPLOAD_STUDY_FORMAT % study_id)
if job_info:
job_info = defaultdict(lambda: '', loads(job_info))
job_id = job_info['job_id']
job = ProcessingJob(job_id)
job_status = job.status
processing = job_status not in ('success', 'error')
url = job.parameters.values['url']
if processing:
if job.command.name == 'list_remote_files':
message = 'Retrieving remote files: listing %s' % url
else:
message = 'Retrieving remote files: download %s' % url
elif job_status == 'error':
level = 'danger'
message = job.log.msg.replace('\n', '</br>')
# making errors nicer for users
if 'No such file' in message:
message = 'URL not valid: <i>%s</i>, please review.' % url
else:
remote_url = job_info['url']
remote_files = job_info['files']
level = job_info['alert_type']
message = job_info['alert_msg'].replace('\n', '</br>')
# getting the ontologies
self.render('upload.html',
study_title=study.title, study_info=study.info,
study_id=study_id, is_admin=user.level == 'admin',
extensions=','.join(qiita_config.valid_upload_extension),
max_upload_size=qiita_config.max_upload_size, level=level,
message=message, remote_url=remote_url,
remote_files=remote_files,
files=get_files_from_uploads_folders(str(study_id)))
@authenticated
@execute_as_transaction
def get(self, study_id):
try:
study = Study(int(study_id))
except QiitaDBUnknownIDError:
raise HTTPError(404, reason="Study %s does not exist" % study_id)
check_access(self.current_user, study, no_public=True,
raise_error=True)
self.display_template(study_id, "")
@authenticated
@execute_as_transaction
def post(self, study_id):
try:
study = Study(int(study_id))
except QiitaDBUnknownIDError:
raise HTTPError(404, reason="Study %s does not exist" % study_id)
check_access(self.current_user, study, no_public=True,
raise_error=True)
files_to_move = []
for v in self.get_arguments('files_to_erase', strip=True):
v = v.split('-', 1)
# if the file was just uploaded JS will not know which id the
# current upload folder has so we need to retrieve it
if v[0] == 'undefined':
v[0], _ = get_mountpoint("uploads")[0]
files_to_move.append((int(v[0]), v[1]))
move_upload_files_to_trash(study.id, files_to_move)
self.display_template(study_id, "")
class StudyUploadViaRemote(BaseHandler):
@authenticated
@execute_as_transaction
def post(self, study_id):
method = self.get_argument('remote-request-type')
url = self.get_argument('inputURL')
ssh_key = self.request.files['ssh-key'][0]['body']
status = 'success'
message = ''
try:
study = Study(int(study_id))
except QiitaDBUnknownIDError:
raise HTTPError(404, reason="Study %s does not exist" % study_id)
check_access(
self.current_user, study, no_public=True, raise_error=True)
_, upload_folder = get_mountpoint("uploads")[0]
upload_folder = join(upload_folder, study_id)
ssh_key_fp = join(upload_folder, '.key.txt')
create_nested_path(upload_folder)
with open(ssh_key_fp, 'wb') as f:
f.write(ssh_key)
chmod(ssh_key_fp, 0o600)
qiita_plugin = Software.from_name_and_version('Qiita', 'alpha')
if method == 'list':
cmd = qiita_plugin.get_command('list_remote_files')
params = Parameters.load(cmd, values_dict={
'url': url, 'private_key': ssh_key_fp, 'study_id': study_id})
elif method == 'transfer':
cmd = qiita_plugin.get_command('download_remote_files')
params = Parameters.load(cmd, values_dict={
'url': url, 'private_key': ssh_key_fp,
'destination': upload_folder})
else:
status = 'error'
message = 'Not a valid method'
if status == 'success':
job = ProcessingJob.create(self.current_user, params, True)
job.submit()
r_client.set(
UPLOAD_STUDY_FORMAT % study_id, dumps({'job_id': job.id}))
self.write({'status': status, 'message': message})
class UploadFileHandler(BaseHandler):
# """ main upload class
# based on
# https://github.com/23/resumable.js/blob/master/samples/Backend%20on%20PHP.md
# """
def validate_file_extension(self, filename):
"""simple method to avoid duplication of code
This validation is server side in case they can go around the client
side validation
"""
if not filename.endswith(tuple(qiita_config.valid_upload_extension)):
self.set_status(415)
raise HTTPError(415, reason="User %s is trying to upload %s" %
(self.current_user, str(filename)))
@authenticated
@execute_as_transaction
def post(self):
resumable_identifier = self.get_argument('resumableIdentifier')
resumable_filename = self.get_argument('resumableFilename')
resumable_chunk_number = int(self.get_argument('resumableChunkNumber'))
resumable_total_chunks = int(self.get_argument('resumableTotalChunks'))
study_id = self.get_argument('study_id')
data = self.request.files['file'][0]['body']
check_access(self.current_user, Study(int(study_id)),
no_public=True, raise_error=True)
self.validate_file_extension(resumable_filename)
_, base_fp = get_mountpoint("uploads")[0]
# creating temporal folder for upload of the file
temp_dir = join(base_fp, study_id, resumable_identifier)
create_nested_path(temp_dir)
# location of the file as it is transmitted
temporary_location = join(temp_dir, resumable_filename)
# this is the result of a failed upload
if resumable_chunk_number == 1 and exists(temporary_location):
remove(temporary_location)
# append every transmitted chunk
with open(temporary_location, 'ab') as tmp_file:
tmp_file.write(bytes(data))
if resumable_chunk_number == resumable_total_chunks:
final_location = join(base_fp, study_id, resumable_filename)
if exists(final_location):
remove(final_location)
move(temporary_location, final_location)
rmtree(temp_dir)
self.set_status(200)
@authenticated
@execute_as_transaction
def get(self):
""" this is the first point of entry into the upload service
this should either set the status as 400 (error) so the file/chunk is
sent via post or 200 (valid) to not send the file
"""
study_id = self.get_argument('study_id')
resumable_filename = self.get_argument('resumableFilename')
check_access(self.current_user, Study(int(study_id)),
no_public=True, raise_error=True)
self.validate_file_extension(resumable_filename)
# in the original version we used to check if a chunk was already
# uploaded and if it was we would send self.set_status(200). Now, as
# we are not chunking by file we can simply pass the no exists
# response
self.set_status(400)