def setUp(self):
# Call father's method
super().setUp()
log.info("\n### Creating a test token (for ANONYMOUS IRODS user) ###")
credentials = json.dumps({'username': self._anonymous_user})
endpoint = self._auth_uri + self._auth_endpoint
log.debug('*** Testing anonymous authentication on %s' % endpoint)
r = self.app.post(endpoint, data=credentials)
self.assertEqual(r.status_code, self._hcodes.HTTP_OK_BASIC)
content = self.get_content(r)
self.save_token(content.get('token'), suffix=self._anonymous_user)
self.irods_vars = detector.services_classes.get('irods').variables
self._filename = 'some_file.txt'
home_dirname = 'home'
self._ipath = str(
path.join(path.root(), self.irods_vars.get('zone'), home_dirname,
self.irods_vars.get('guest_user'), self._filename))
self._no_permission_path = str(
path.join(path.root(), self.irods_vars.get('zone'), home_dirname,
'nonexisting'))
log.debug('*** Upload a test file: %s' % self._ipath)
# Upload entity in test folder
endpoint = self._api_uri + self._register_endpoint + self._ipath
r = self.app.put(endpoint,
data=dict(file=(io.BytesIO(b"just a test"),
self._filename)),
headers=self.__class__.auth_header)
self.assertEqual(r.status_code, self._hcodes.HTTP_OK_BASIC)
def publish_helper(self, icom, ipath, check_only=True, unpublish=False):
from utilities import path
current_zone = icom.get_current_zone()
ipath_steps = path.parts(ipath)
current = ''
for ipath_step in ipath_steps:
current = path.join(current, ipath_step, return_str=True)
# print("PUB STEP:", ipath_step, current, len(current))
# to skip: root dir, zone and home
if len(ipath_step) == 1 \
or ipath_step == current_zone or ipath_step == 'home':
continue
# find out if already published
check = self.single_path_check(icom, current_zone, str(current))
# if only checking
if check_only and not check:
return False
# otherwise you want to publish/unpublish this path
else:
if unpublish:
self.single_permission(icom, current, permission=None)
else:
self.single_permission(icom, current, permission='read')
return True
def get_download(self,
imain,
order_id,
order_path,
files,
restricted=False,
index=None):
zip_file_name = get_order_zip_file_name(order_id, restricted, index)
if zip_file_name not in files:
return None
zip_ipath = path.join(order_path, zip_file_name, return_str=True)
log.debug("Zip irods path: %s", zip_ipath)
code = self.no_slash_ticket(imain, zip_ipath)
ftype = ""
if restricted:
ftype += "1"
else:
ftype += "0"
if index is None:
ftype += "0"
else:
ftype += str(index)
route = '%s%s/%s/%s/download/%s/c/%s' % (CURRENT_HTTPAPI_SERVER,
API_URL, ORDERS_ENDPOINT,
order_id, ftype, code)
# If metadata already exists, remove them:
# FIXME: verify if iticket_code is set and then invalidate it
imain.remove_metadata(zip_ipath, 'iticket_code')
imain.remove_metadata(zip_ipath, 'download')
##################
# Set the url as Metadata in the irods file
imain.set_metadata(zip_ipath, download=route)
# TOFIX: we should add a database or cache to save this,
# not irods metadata (known for low performances)
imain.set_metadata(zip_ipath, iticket_code=code)
info = files[zip_file_name]
return {
'name': zip_file_name,
'url': route,
'size': info.get('content_length', 0)
}
def delete(self):
json_input = self.get_input()
# imain = self.get_service_instance(service_name='irods')
imain = self.get_main_irods_connection()
order_path = self.get_irods_order_path(imain)
local_order_path = str(path.join(MOUNTPOINT, ORDERS_DIR))
log.debug("Order collection: %s", order_path)
log.debug("Order path: %s", local_order_path)
task = CeleryExt.delete_orders.apply_async(
args=[order_path, local_order_path, json_input])
log.info("Async job: %s", task.id)
return self.return_async_id(task.id)
def get(self, batch_id):
log.info("Batch request: %s", batch_id)
# json = {'batch_id': batch_id}
# msg = prepare_message(
# self, json=json, user=ingestion_user, log_string='start')
# log_into_queue(self, msg)
########################
# get irods session
# imain = self.get_service_instance(service_name='irods')
imain = self.get_main_irods_connection()
batch_path = self.get_irods_batch_path(imain, batch_id)
local_path = path.join(MOUNTPOINT, INGESTION_DIR, batch_id)
log.info("Batch irods path: %s", batch_path)
log.info("Batch local path: %s", local_path)
batch_status, batch_files = self.get_batch_status(
imain, batch_path, local_path)
########################
# if not imain.is_collection(batch_path):
if batch_status == MISSING_BATCH:
return self.send_errors(
"Batch '%s' not enabled or you have no permissions" % batch_id,
code=hcodes.HTTP_BAD_NOTFOUND)
if batch_status == BATCH_MISCONFIGURATION:
log.error('Misconfiguration: %s files in %s (expected 1)',
len(batch_files), batch_path)
return self.send_errors("Misconfiguration for batch_id %s" %
batch_id,
code=hcodes.HTTP_BAD_RESOURCE)
data = {}
data['batch'] = batch_id
if batch_status == NOT_FILLED_BATCH:
data['status'] = 'not_filled'
elif batch_status == ENABLED_BATCH:
data['status'] = 'enabled'
elif batch_status == PARTIALLY_ENABLED_BATCH:
data['status'] = 'partially_enabled'
data['files'] = batch_files
return data
def delete(self):
json_input = self.get_input()
# imain = self.get_service_instance(service_name='irods')
imain = self.get_main_irods_connection()
batch_path = self.get_irods_batch_path(imain)
local_batch_path = str(path.join(MOUNTPOINT, INGESTION_DIR))
log.debug("Batch collection: %s", batch_path)
log.debug("Batch path: %s", local_batch_path)
task = CeleryExt.delete_batches.apply_async(
args=[batch_path, local_batch_path, json_input],
queue='ingestion',
routing_key='ingestion')
log.info("Async job: %s", task.id)
return self.return_async_id(task.id)
def put(self, batch_id, qc_name):
""" Launch a quality check inside a container """
###########################
# get name from batch
# imain = self.get_service_instance(service_name='irods')
imain = self.get_main_irods_connection()
batch_path = self.get_irods_batch_path(imain, batch_id)
local_path = path.join(MOUNTPOINT, INGESTION_DIR, batch_id)
log.info("Batch irods path: %s", batch_path)
log.info("Batch local path: %s", local_path)
batch_status, batch_files = self.get_batch_status(
imain, batch_path, local_path)
if batch_status == MISSING_BATCH:
return self.send_errors(
"Batch '%s' not found (or no permissions)" % batch_id,
code=hcodes.HTTP_BAD_NOTFOUND)
if batch_status == NOT_FILLED_BATCH:
return self.send_errors("Batch '%s' not yet filled" % batch_id,
code=hcodes.HTTP_BAD_RESOURCE)
if batch_status == BATCH_MISCONFIGURATION:
log.error('Misconfiguration: %s files in %s (expected 1)',
len(batch_files), batch_path)
return self.send_errors("Misconfiguration for batch_id %s" %
batch_id,
code=hcodes.HTTP_BAD_RESOURCE)
###################
# Parameters (and checks)
envs = {}
input_json = self.get_input()
# TODO: backdoor check - remove me
bd = input_json.pop('eudat_backdoor', False)
if bd:
im_prefix = 'eudat'
else:
im_prefix = 'maris'
log.debug("Image prefix: %s", im_prefix)
# input parameters to be passed to container
pkey = "parameters"
param_keys = [
"request_id", "edmo_code", "datetime", "api_function", "version",
"test_mode", pkey
]
for key in param_keys:
if key == pkey:
continue
value = input_json.get(key, None)
if value is None:
return self.send_errors('Missing JSON key: %s' % key,
code=hcodes.HTTP_BAD_REQUEST)
response = {
'batch_id': batch_id,
'qc_name': qc_name,
'status': 'executed',
'input': input_json,
}
###################
try:
rancher = self.get_or_create_handle()
except BaseException as e:
log.critical(str(e))
return self.send_errors(
'Cannot establish a connection with Rancher',
code=hcodes.HTTP_SERVER_ERROR)
container_name = self.get_container_name(batch_id, qc_name,
rancher._qclabel)
# Duplicated quality checks on the same batch are not allowed
container_obj = rancher.get_container_object(container_name)
if container_obj is not None:
log.error("Docker container %s already exists!", container_name)
response['status'] = 'existing'
code = hcodes.HTTP_BAD_CONFLICT
return self.force_response(response,
errors=[response['status']],
code=code)
docker_image_name = self.get_container_image(qc_name, prefix=im_prefix)
###########################
# ## ENVS
host_ingestion_path = self.get_ingestion_path_on_host(batch_id)
container_ingestion_path = self.get_ingestion_path_in_container()
envs['BATCH_DIR_PATH'] = container_ingestion_path
from seadata.apis.commons.queue import QUEUE_VARS
from seadata.apis.commons.cluster import CONTAINERS_VARS
for key, value in QUEUE_VARS.items():
if key in ['enable']:
continue
elif key == 'user':
value = CONTAINERS_VARS.get('rabbituser')
elif key == 'password':
value = CONTAINERS_VARS.get('rabbitpass')
envs['LOGS_' + key.upper()] = value
# envs['DB_USERNAME'] = CONTAINERS_VARS.get('dbuser')
# envs['DB_PASSWORD'] = CONTAINERS_VARS.get('dbpass')
# envs['DB_USERNAME_EDIT'] = CONTAINERS_VARS.get('dbextrauser')
# envs['DB_PASSWORD_EDIT'] = CONTAINERS_VARS.get('dbextrapass')
# FOLDER inside /batches to store temporary json inputs
# TODO: to be put into the configuration
JSON_DIR = 'json_inputs'
# Mount point of the json dir into the QC container
QC_MOUNTPOINT = '/json'
json_path_backend = os.path.join(MOUNTPOINT, INGESTION_DIR, JSON_DIR)
if not os.path.exists(json_path_backend):
log.info("Creating folder %s", json_path_backend)
os.mkdir(json_path_backend)
json_path_backend = os.path.join(json_path_backend, batch_id)
if not os.path.exists(json_path_backend):
log.info("Creating folder %s", json_path_backend)
os.mkdir(json_path_backend)
json_input_file = "input.%s.json" % int(time.time())
json_input_path = os.path.join(json_path_backend, json_input_file)
with open(json_input_path, "w+") as f:
f.write(json.dumps(input_json))
json_path_qc = self.get_ingestion_path_on_host(JSON_DIR)
json_path_qc = os.path.join(json_path_qc, batch_id)
envs['JSON_FILE'] = os.path.join(QC_MOUNTPOINT, json_input_file)
extra_params = {
'dataVolumes': [
"%s:%s" % (host_ingestion_path, container_ingestion_path),
"%s:%s" % (json_path_qc, QC_MOUNTPOINT)
],
'environment':
envs
}
if bd:
extra_params['command'] = ['/bin/sleep', '999999']
# log.info(extra_params)
###########################
errors = rancher.run(container_name=container_name,
image_name=docker_image_name,
private=True,
extras=extra_params)
if errors is not None:
if isinstance(errors, dict):
edict = errors.get('error', {})
# This case should never happens, since already verified before
if edict.get('code') == 'NotUnique':
response['status'] = 'existing'
code = hcodes.HTTP_BAD_CONFLICT
else:
response['status'] = 'could NOT be started'
response['description'] = edict
code = hcodes.HTTP_SERVER_ERROR
else:
response['status'] = 'failure'
code = hcodes.HTTP_SERVER_ERROR
return self.force_response(response,
errors=[response['status']],
code=code)
return response
def get(self, order_id, ftype, code):
""" downloading (not authenticated) """
log.info("Order request: %s (code '%s')", order_id, code)
json = {'order_id': order_id, 'code': code}
msg = prepare_message(self,
json=json,
user='******',
log_string='start')
log_into_queue(self, msg)
log.info("DOWNLOAD DEBUG 1: %s (code '%s')", order_id, code)
##################
# imain = self.get_service_instance(service_name='irods')
imain = self.get_main_irods_connection()
log.info("DOWNLOAD DEBUG 2: %s (code '%s')", order_id, code)
order_path = self.get_irods_order_path(imain, order_id)
log.info("DOWNLOAD DEBUG 3: %s (code '%s') - %s", order_id, code,
order_path)
zip_file_name = self.get_filename_from_type(order_id, ftype)
if zip_file_name is None:
return self.send_errors("Invalid file type %s" % ftype)
zip_ipath = path.join(order_path, zip_file_name, return_str=True)
error = "Order '%s' not found (or no permissions)" % order_id
log.debug("Checking zip irods path: %s", zip_ipath)
log.info("DOWNLOAD DEBUG 4: %s (code '%s') - %s", order_id, code,
zip_ipath)
if not imain.is_dataobject(zip_ipath):
log.error("File not found %s", zip_ipath)
return self.send_errors({order_id: error},
code=hcodes.HTTP_BAD_NOTFOUND)
log.info("DOWNLOAD DEBUG 5: %s (code '%s')", order_id, code)
# TOFIX: we should use a database or cache to save this,
# not irods metadata (known for low performances)
metadata, _ = imain.get_metadata(zip_ipath)
log.info("DOWNLOAD DEBUG 6: %s (code '%s')", order_id, code)
iticket_code = metadata.get('iticket_code')
log.info("DOWNLOAD DEBUG 7: %s (code '%s')", order_id, code)
encoded_code = urllib.parse.quote_plus(code)
log.info("DOWNLOAD DEBUG 8: %s (code '%s')", order_id, code)
if iticket_code != encoded_code:
log.error("iticket code does not match %s", zip_ipath)
return self.send_errors({order_id: error},
code=hcodes.HTTP_BAD_NOTFOUND)
# NOTE: very important!
# use anonymous to get the session here
# because the ticket supply breaks the iuser session permissions
icom = self.get_service_instance(service_name='irods',
user='******',
password='******',
authscheme='credentials')
log.info("DOWNLOAD DEBUG 9: %s (code '%s')", order_id, code)
# obj = self.init_endpoint()
# icom = obj.icommands
icom.ticket_supply(code)
log.info("DOWNLOAD DEBUG 10: %s (code '%s')", order_id, code)
if not icom.test_ticket(zip_ipath):
log.error("Invalid iticket code %s", zip_ipath)
return self.send_errors({order_id: "Invalid code"},
code=hcodes.HTTP_BAD_NOTFOUND)
# # TODO: push pdonorio/prc
# tickets = imain.list_tickets()
# print(tickets)
# iticket mod "$TICKET" add user anonymous
# iticket mod "$TICKET" uses 1
# iticket mod "$TICKET" expire "2018-03-23.06:50:00"
# ##################
# response = {order_id: 'valid'}
# return self.force_response(response)
headers = {
'Content-Transfer-Encoding': 'binary',
'Content-Disposition': "attachment; filename=%s" % zip_file_name,
}
msg = prepare_message(self, json=json, log_string='end', status='sent')
log_into_queue(self, msg)
log.info("DOWNLOAD DEBUG 11: %s (code '%s')", order_id, code)
return icom.stream_ticket(zip_ipath, headers=headers)
def post(self):
##################
log.debug('POST request on orders')
json_input = self.get_input()
msg = prepare_message(self, json=json_input, log_string='start')
log_into_queue(self, msg)
##################
main_key = 'parameters'
params = json_input.get(main_key, {})
if len(params) < 1:
error = "'%s' missing" % main_key
return self.send_errors(error, code=hcodes.HTTP_BAD_REQUEST)
##################
key = 'order_number'
order_id = params.get(key)
if order_id is None:
error = "Order ID '%s': missing" % key
return self.send_errors(error, code=hcodes.HTTP_BAD_REQUEST)
else:
order_id = str(order_id)
# ##################
# Get filename from json input. But it has to follow a
# specific pattern, so we ignore client input if it does not...
filename = "order_%s_unrestricted" % order_id
key = 'file_name'
if key in params and not params[key] == filename:
log.warn('Client provided wrong filename (%s), will use: %s',
params[key], filename)
params[key] = filename
##################
# PIDS: can be empty if restricted
key = 'pids'
pids = params.get(key, [])
##################
# Create the path
log.info("Order request: %s", order_id)
# imain = self.get_service_instance(service_name='irods')
imain = self.get_main_irods_connection()
order_path = self.get_irods_order_path(imain, order_id)
log.debug("Order path: %s", order_path)
if not imain.is_collection(order_path):
obj = self.init_endpoint()
# Create the path and set permissions
imain.create_collection_inheritable(order_path, obj.username)
##################
# Does the zip already exists?
# zip_file_name = path.append_compress_extension(order_id)
zip_file_name = path.append_compress_extension(filename)
zip_ipath = path.join(order_path, zip_file_name, return_str=True)
if imain.is_dataobject(zip_ipath):
# give error here
# return {order_id: 'already exists'}
# json_input['status'] = 'exists'
json_input['parameters'] = {'status': 'exists'}
return json_input
################
# ASYNC
if len(pids) > 0:
log.info("Submit async celery task")
task = CeleryExt.unrestricted_order.apply_async(
args=[order_id, order_path, zip_file_name, json_input])
log.info("Async job: %s", task.id)
return self.return_async_id(task.id)
# ################
# msg = prepare_message(self, log_string='end')
# # msg = prepare_message(self, log_string='end', status='created')
# msg['parameters'] = {
# "request_id": msg['request_id'],
# "zipfile_name": params['file_name'],
# "zipfile_count": 1,
# }
# log_into_queue(self, msg)
# ################
# # return {order_id: 'created'}
# # json_input['status'] = 'created'
# json_input['request_id'] = msg['request_id']
# json_input['parameters'] = msg['parameters']
# if len(errors) > 0:
# json_input['errors'] = errors
# # call Import manager to notify
# api = API()
# api.post(json_input)
return {'status': 'enabled'}
def post(self, batch_id):
json_input = self.get_input()
obj = self.init_endpoint()
imain = self.get_main_irods_connection()
batch_path = self.get_irods_batch_path(imain, batch_id)
log.info("Batch irods path: %s", batch_path)
local_path = path.join(MOUNTPOINT, INGESTION_DIR, batch_id)
log.info("Batch local path: %s", local_path)
"""
Create the batch folder if not exists
"""
# Log start (of enable) into RabbitMQ
log_msg = prepare_message(self,
json={'batch_id': batch_id},
user=ingestion_user,
log_string='start')
log_into_queue(self, log_msg)
##################
# Does it already exist?
# Create the collection and set permissions in irods
if not imain.is_collection(batch_path):
imain.create_collection_inheritable(batch_path, obj.username)
else:
log.warning("Irods batch collection already exists")
# Create the folder on filesystem
if not path.file_exists_and_nonzero(local_path):
# Create superdirectory and directory on file system:
try:
# TODO: REMOVE THIS WHEN path.create() has parents=True!
import os
superdir = os.path.join(MOUNTPOINT, INGESTION_DIR)
if not os.path.exists(superdir):
log.debug('Creating %s...', superdir)
os.mkdir(superdir)
log.info('Created %s...', superdir)
path.create(local_path, directory=True, force=True)
except (FileNotFoundError, PermissionError) as e:
err_msg = ('Could not create directory "%s" (%s)' %
(local_path, e))
log.critical(err_msg)
log.info('Removing collection from irods (%s)' % batch_path)
imain.remove(batch_path, recursive=True, force=True)
return self.send_errors(err_msg, code=hcodes.HTTP_SERVER_ERROR)
else:
log.debug("Batch path already exists on filesytem")
# Log end (of enable) into RabbitMQ
log_msg = prepare_message(self,
status='enabled',
user=ingestion_user,
log_string='end')
log_into_queue(self, log_msg)
"""
Download the file into the batch folder
"""
task = CeleryExt.download_batch.apply_async(
args=[batch_path, str(local_path), json_input],
queue='ingestion',
routing_key='ingestion')
log.info("Async job: %s", task.id)
return self.return_async_id(task.id)
