def get(self, id, *args, **kw):
"""
Display the form by it's id
"""
# check plugin id
plug = None
try:
plug = putil.get_plugin_byId(id)
except:
tg.abort(400, "Bad plugin identifier")
debug('get plugin %s' % id)
# get the plugin
obj = plug
info = obj.info
form = info.get('output')()
desc = info.get('description')
debug('params = %s' % kw, 1)
# bioscript parameters
bs_private = {}
if 'bs_private' in kw:
bs_private = json.loads(kw['bs_private'])
debug("get bs private parameters %s" % bs_private, 2)
if 'prefill' in bs_private:
prefill_fields(info.get('in'), form, bs_private['prefill'], kw)
# {'bs_private': {'app': pp, 'cfg': handler.job.bioscript_config, 'prefill': prefill}})
# add some private parameters from BioScript
pp = {'id': id}
# if user is a serviec, add the key & the mail in the authentication
user = util.get_user(tg.request)
if user.is_service:
pp['mail'] = user.email
pp['key'] = user.key
bs_private['pp'] = pp
# prepare form output
main_proxy = tg.config.get('main.proxy')
widget = form(action=main_proxy + tg.url('/plugins/validate', {'id': id})).req()
widget.value = {'bs_private': json.dumps(bs_private), 'key': user.key}
debug('display plugin with bs_private : %s' % bs_private)
debug('vaaalue : %s' % widget.value)
debug(user)
return {'page': 'plugin', 'desc': desc, 'title': info.get('title'), 'widget': widget}
def plugin_job(username, inputs_directory, outputs_directory, plugin_info,
user_parameters, service_callback, bioscript_callback, **form_parameters):
task_id = plugin_job.request.id
if service_callback is not None:
callback_service(service_callback, plugin_info['generated_id'], task_id,
'RUNNING', additional=user_parameters)
debug('task launched')
# get plugin class
plugin = util.get_plugin_byId(plugin_info['generated_id'])
if plugin is None:
raise Exception('Plugin not found by the worker.')
debug('plugin operation start')
plugin._start_timer()
results = []
# call plugin with form parameters
try:
ret = plugin(**form_parameters)
results = [{'is_file': False,
'value': ret
}]
except Exception as e:
if service_callback is not None:
user_parameters.update({'error': e})
callback_service(service_callback, plugin_info['generated_id'], task_id, 'FAILED', additional=user_parameters)
raise
# mkdir output directory
out = os.path.join(outputs_directory, task_id)
debug('mkdir out path : %s' % out)
try:
os.mkdir(out)
except OSError, e:
if e.errno == errno.EEXIST:
io.rm(out)
os.mkdir(out)
def validate(self, **kw):
"""
plugin parameters validation
"""
user = util.get_user(tg.request)
debug('Got request validation from user %s' % user)
if not 'bs_private' in kw:
tg.abort(400, "Plugin identifier not found in the request.")
debug('params %s' % kw, 1)
bs_private = copy.deepcopy(json.loads(kw['bs_private']))
debug('private %s' % bs_private, 1)
plugin_id = bs_private['pp']['id']
if plugin_id is None:
tg.abort(400, "Plugin identifier not found in the request.")
# check plugin id
plug = putil.get_plugin_byId(plugin_id)
if plug is None:
tg.abort(400, "Bad plugin identifier")
# get plugin form output
obj = plug
info = obj.info
form = info.get('output')()
# callback for jsonP
callback = kw.get('callback', 'callback')
# get the plugin from the database
plugin_db = DBSession.query(Plugin).filter(Plugin.generated_id == obj.unique_id()).first()
plugin_request = _log_form_request(plugin_id=plugin_db.id, user=user, parameters=kw)
if 'prefill' in bs_private:
prefill_fields(info.get('in'), form, bs_private['prefill'], kw, replace_value=False)
debug('prefill in validation', 3)
del bs_private['prefill']
# validation
try:
form = form().req()
form.validate(kw)
except (tw2.core.ValidationError, Invalid) as e:
main_proxy = tg.config.get('main.proxy')
e.widget.action = main_proxy + tg.url('plugins/index', {'id': plugin_id})
debug('private after validation failed %s' % bs_private, 1)
#value = {'bs_private': json.dumps(bs_private)}
#debug('value %s' % value)
#e.widget.value = value
plugin_request.status = 'FAILED'
plugin_request.error = str(e)
DBSession.add(plugin_request)
return jsonp_response(**{'validation': 'failed', 'desc': info.get('description'),
'title': info.get('title'), 'widget': e.widget.display(), 'callback': callback})
debug('Validation pass')
#if the validation passes, remove private parameters from the request
del kw['bs_private']
if 'key' in kw:
del kw['key']
# fetch form files
try:
inputs_directory = filemanager.fetch(user, obj, kw)
except Exception as e:
plugin_request.status = 'FAILED'
plugin_request.error = str(e)
DBSession.add(plugin_request)
import sys
import traceback
etype, value, tb = sys.exc_info()
traceback.print_exception(etype, value, tb)
return jsonp_response(**{'validation': 'success', 'desc': info.get('description'),
'title': info.get('title'), 'error': 'error while fetching files : ' + str(e), 'callback': callback})
debug('Files fetched')
# get output directory to write results
outputs_directory = filemanager.temporary_directory(constants.paths['data'])
service_callback = None
debug(user)
if user.is_service:
debug('is service', 1)
# def out_path(service_name):
o = services.service_manager.get(user.name, constants.SERVICE_RESULT_ROOT_PARAMETER)
if o:
outputs_directory = o
service_callback = services.service_manager.get(user.name, constants.SERVICE_CALLBACK_URL_PARAMETER)
debug('Output dir = %s' % outputs_directory)
# get user parameters from the request
user_parameters = bs_private.get('app', "{}")
debug('get user parameters : %s' % user_parameters, 1)
# get response config from the request
resp_config = bs_private.get('cfg', None)
plugin_info = {'title': info['title'],
'plugin_id': plugin_db.id,
'generated_id': plugin_db.generated_id,
'description': info['description'],
'path': info['path'],
'in': info['in'],
'out': info['out'],
'meta': info['meta']}
# call plugin process
bioscript_callback = tg.config.get('main.proxy') + '/' + tg.url('plugins/callback_results')
async_res = tasks.plugin_job.delay(user.name, inputs_directory, outputs_directory, plugin_info,
user_parameters, service_callback, bioscript_callback, **kw)
task_id = async_res.task_id
_log_job_request(plugin_request.id, task_id)
if resp_config and resp_config.get('plugin_info', '') == 'min':
return jsonp_response(**{'validation': 'success', 'plugin_id': plugin_id, 'task_id': task_id, 'callback': callback, 'app': user_parameters})
return jsonp_response(**{
'validation': 'success',
'plugin_id': plugin_id,
'task_id': task_id,
'plugin_info': json.dumps(
{'title': info['title'],
'description': info['description'],
'path': info['path'],
'in': info['in'],
'out': info['out'],
'meta': info['meta']}),
'callback': callback, 'app': user_parameters})
