def delete(archive_no):
"""Delete a archive record from the system table."""
import subprocess
try:
# Read cookie
session_id = request.cookies.get('session_id')
# Credential check
try:
admin_user = aux.admin_check(session_id)
except Exception as e:
logger.info(e)
return aux.responder('Client error - Invalid credentials(1)', 400)
if not admin_user:
return aux.responder('Client error - Invalid credentials(2)', 400)
try:
# Remove DB record
aux.delete_archive(archive_no)
# Remove actual data file and data service response header
realpath = '/'.join([datapath, str(archive_no)])
headerpath = f'{realpath}.header'
archivepath = f'{realpath}.bz2'
syscall = subprocess.run(['rm', headerpath, archivepath])
logger.info(f'Files deleted: {headerpath}, {archivepath}')
return aux.responder('Success', 200, archive_no)
except Exception as e:
logger.info('Deletion error: {0:s}'.format(e))
return aux.responder('Deletion error', 500, archive_no)
except Exception as e:
logger.error(e)
logger.error(traceback.format_exc())
return aux.responder('Error', 509)
def retrieve(archive_no):
"""Retrieve an existing archive given an archive number."""
from flask import send_from_directory
try:
filename = ''.join([str(archive_no), '.bz2'])
file_type = aux.get_file_type(archive_no)
attachment_filename = ''.join(
['pbdb_archive_',
str(archive_no), file_type, '.bz2'])
if archive_no:
try:
return send_from_directory(
datapath,
filename,
as_attachment=True,
attachment_filename=attachment_filename,
mimetype='application/x-compressed')
logger.info('Retrieved archive {0:d}'.format(archive_no))
except Exception as e:
logger.info('Retrieval error archive {0:d}'.format(archive_no))
logger.info(e)
return aux.responder('Retrieval error', 500, archive_no)
else:
logger.info('Unspecified archive number')
return aux.responder('Unspecified archive number', 400, archive_no)
except Exception as e:
logger.error(e)
logger.error(traceback.format_exc())
return aux.responder('Error', 509)
def update(archive_no):
"""Update the archive metadata."""
try:
# Read cookie
if request.json.get('session_id'):
session_id = request.json['session_id']
else:
session_id = request.cookies.get('session_id')
# Credential check
try:
admin_user = aux.admin_check(session_id)
except Exception as e:
logger.info(e)
return aux.responder('Client error - Invalid credentials(1)', 400)
if not admin_user:
return aux.responder('Client error - Invalid credentials(2)', 400)
title = request.json.get('title')
desc = request.json.get('description')
authors = request.json.get('authors')
doi = request.json.get('doi')
if title or desc or authors or doi:
try:
aux.update_record(archive_no, title, desc, authors, doi)
except Exception as e:
logger.info(e)
return aux.responder('Server error - record update', 500,
archive_no)
logger.info('Updated {0:d}'.format(archive_no))
return aux.responder('Success', 200, archive_no)
else:
logger.info('ERROR: Unsupported parameters for update')
return aux.responder('Parameter error', 400, archive_no)
except Exception as e:
logger.error(e)
logger.error(traceback.format_exc())
return aux.responder('Error', 509)
def test():
"""Dev path."""
logger.info(request.json)
return aux.responder('test endpoint', 200)
def index():
"""Base path, server listening check."""
logger.info('Base path access')
return aux.responder('PBDB data archive API running', 200)
def not_found(error):
"""Return an error if route does not exist."""
logger.info('404 Not found')
return aux.responder('Not found', 404)
def create():
"""Create an archive file on disk."""
import subprocess
import os
from datetime import datetime as dt
import time
try:
# Attempt to find session_id in the payload (testing only)
if request.json.get('session_id'):
session_id = request.json['session_id']
# Otherwise pull it out of the browser cookie (normal functionalty)
else:
session_id = request.cookies.get('session_id')
# Determine authorizer and enter numbers from the session_id
try:
auth, ent = aux.user_info(session_id)
except Exception as e:
logger.info(e)
return aux.responder('Client error - Invalid session ID', 400)
# Determine if the user has an ORCID
has_orcid = aux.check_for_orcid(ent)
logger.info(f'Enter ID {ent} has ORCID {has_orcid}')
if not has_orcid:
return aux.responder('Missing ORCID', 403)
# Extract user entered metadata from payload
authors = request.json.get('authors', 'Enter No. ' + str(ent))
title = request.json.get('title')
desc = request.json.get('description', 'No description')
# Extract components of data service call from payload
path = request.json.get('uri_path')
args = request.json.get('uri_args')
# Parameter checks
if not title:
return aux.responder('Missing title', 400)
if not args:
return aux.responder('Missing uri_args', 400)
if path:
if path[0] != '/':
return aux.responder('uri_path not preceeded by "/"', 400)
else:
return aux.responder('Missing uri_path', 400)
# Build data service URI
base = aux.get_config('dataservice')
uri = ''.join([base, path, '?', args])
uri = uri.replace(' ', '%20')
# Initiate new record in database
try:
aux.create_record(auth, ent, authors, title, desc, path, args)
logger.info('Record created. Enterer No: {0:d}'.format(ent))
except Exception as e:
logger.info(e)
return aux.responder('Server error - Record creation', 500)
time.sleep(2)
# Read archive_no back from the table and create filename
try:
archive_no = aux.get_archive_no(ent)
logger.info('Record created. Archive No: {0:d}'.format(archive_no))
except Exception as e:
logger.info(e)
aux.archive_status(archive_no, success=False)
return aux.responder('Server error - Archive number not found',
500, archive_no)
# Append the data path and remove extra "/" if one was added in config
realpath = '/'.join([datapath, str(archive_no)])
realpath = realpath.replace('//', '/')
# Use cURL to retrive the dataset
token = '='.join(['session_id', session_id])
headerpath = realpath + '.header'
syscall = subprocess.run([
'curl', '-s', '--cookie', token, '-o', realpath, '-D', headerpath,
uri
])
# Check to see that there were no errors in the data service return
if syscall.returncode != 0 or not os.path.exists(headerpath):
logger.info('Archive download error')
aux.archive_status(archive_no, success=False)
return aux.responder('Server error - File retrieval', 500,
archive_no)
with open(headerpath, 'r') as f:
content = f.readlines()
if '200' not in content[0]:
logger.info('Data service error')
aux.archive_status(archive_no, success=False)
return aux.responder('Server error - Data service', 500,
archive_no)
# Compress and replace the retrieved dataset on disk
syscall = subprocess.run(['bzip2', '-f', realpath])
if syscall.returncode != 0:
logger.info('Archive compression error')
aux.archive_status(archive_no=archive_no, success=False)
return aux.responder('Server error - File compression', 500,
archive_no)
# Archive was successfully created on disk
logger.info('Created archive number: {0:d}'.format(archive_no))
aux.archive_status(archive_no=archive_no, success=True)
# Determine the current year
yr = dt.now().year
# Dispatch email requesting DOI
result = aux.request_doi(archive_no, title, yr, authors, ent)
if result == 0:
logger.info('DOI email sent')
else:
logger.info(f'Server error - Email: {result}')
# Return 200 OK
return aux.responder('success', 200, archive_no)
except Exception as e:
logger.error(e)
logger.error(traceback.format_exc())
return aux.responder('Error', 509)