def fetch_files(user, plug, **kw):
# fetch files if any
inputs_directory = ''
try:
inputs_directory = fetchurls(user, plug, kw)
except Exception as e:
return {'error': 'error while fetching files : ' + str(e)}
debug('Failed to fetch inputs')
return {'inputs_dir' : inputs_directory}
def fetch_files(user, plug, **kw):
# fetch files if any
inputs_directory = ''
try:
inputs_directory = fetchurls(user, plug, kw)
except Exception as e:
return {'error': 'error while fetching files : ' + str(e)}
debug('Failed to fetch inputs')
return {'inputs_dir': inputs_directory}
def plugin_job(user, plug, inputs_directory, outputs_directory, dwdfiles, plugin_info,
user_parameters, service_callback, bioscript_callback, **form_parameters):
debug('FETCHING FILES ... %s' % form_parameters)
raised = False
task_id = plugin_job.request.id
try:
# FETCHING FILES
current_task.update_state(state='FETCHING FILES')
inputs_directory = fetchurls(user, plug, dwdfiles, inputs_directory, form_parameters)
debug('PLUGIN PROCESS STARTED ...')
# PLUGIN PROCESS
current_task.update_state(state='STARTED')
try:
debug('user params : %s' % user_parameters)
user_parameters = json.loads(user_parameters)
except TypeError as e:
debug(e)
if service_callback is not None:
callback_service(service_callback, plugin_info['generated_id'], task_id, 'RUNNING', additional=user_parameters)
debug('task launched user.name: %s, indir: %s, oudir: %s' % (user.name, inputs_directory, outputs_directory))
# get plugin class
plugin = operations.get_plugin_byId(plugin_info['generated_id'])
if plugin is None:
raise Exception('Plugin not found by the worker.')
plugin.is_debug = DEBUG_PLUGINS
debug('plugin operation start %s' % form_parameters)
plugin._start_timer()
results = []
# call plugin with form parameters
try:
os.chdir(TMP_DIR)
ret = plugin(**form_parameters)
results = [{'is_file': False,
'value': ret}]
except Exception as e:
debug("ERROR %s" % e)
util.print_traceback()
if service_callback is not None:
user_parameters.update({'error': str(e)})
callback_service(service_callback, plugin_info['generated_id'], task_id, 'FAILED', additional=user_parameters)
# deleting plugin temporary files
for todel in plugin.tmp_files:
debug('deleting %s' % todel)
shutil.rmtree(todel, onerror=shutilerror)
#debug('deleting %s' % outputs_directory)
#shutil.rmtree(outputs_directory, onerror=shutilerror)
if file_is_in_bs(TMP_DIR, inputs_directory):
debug('deleting %s' % inputs_directory)
shutil.rmtree(inputs_directory, onerror=shutilerror)
if len(plugin.debug_stack) > 0:
debug("Adding debug stack to error")
debug_error = '\n [x] DEBUG STACK : %s' % '\n'.join([d for d in plugin.debug_stack])
if not e.args:
e.args = ('',)
e.args = (e.args[0] + debug_error,) + e.args[1:]
raised = True
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)
debug('moving files')
# moving files to the output directory
for output_file, output_type in plugin.output_files:
debug('f: %s to : %s' % (output_file, out))
out_path = os.path.join(out, os.path.split(output_file)[1])
io.mv(output_file, out)
results.append({'is_file': True, 'path': out_path, 'type': output_type})
# deleting plugin temporary files
for todel in plugin.tmp_files:
debug('deleting %s' % todel)
shutil.rmtree(todel, onerror=shutilerror)
if file_is_in_bs(TMP_DIR, inputs_directory):
debug('deleting %s' % inputs_directory)
shutil.rmtree(inputs_directory, onerror=shutilerror)
# updating bioscript with the results
debug('CALLBACK to %s for task %s' % (bioscript_callback, task_id))
debug(cbbioscript(bioscript_callback, task_id, json.dumps(results)))
debug("END")
# callback
if service_callback is not None:
callback_service(service_callback, plugin_info['generated_id'], task_id, 'SUCCESS',
results=json.dumps(results), additional=user_parameters)
def plugin_job(user, plug, inputs_directory, outputs_directory, dwdfiles,
plugin_info, user_parameters, service_callback,
bioscript_callback, **form_parameters):
debug('FETCHING FILES ... %s' % form_parameters)
raised = False
task_id = plugin_job.request.id
try:
# FETCHING FILES
current_task.update_state(state='FETCHING FILES')
inputs_directory = fetchurls(user, plug, dwdfiles, inputs_directory,
form_parameters)
debug('PLUGIN PROCESS STARTED ...')
# PLUGIN PROCESS
current_task.update_state(state='STARTED')
try:
debug('user params : %s' % user_parameters)
user_parameters = json.loads(user_parameters)
except TypeError as e:
debug(e)
if service_callback is not None:
callback_service(service_callback,
plugin_info['generated_id'],
task_id,
'RUNNING',
additional=user_parameters)
debug('task launched user.name: %s, indir: %s, oudir: %s' %
(user.name, inputs_directory, outputs_directory))
# get plugin class
plugin = operations.get_plugin_byId(plugin_info['generated_id'])
if plugin is None:
raise Exception('Plugin not found by the worker.')
plugin.is_debug = DEBUG_PLUGINS
debug('plugin operation start %s' % form_parameters)
plugin._start_timer()
results = []
# call plugin with form parameters
try:
os.chdir(TMP_DIR)
ret = plugin(**form_parameters)
results = [{'is_file': False, 'value': ret}]
except Exception as e:
debug("ERROR %s" % e)
util.print_traceback()
if service_callback is not None:
user_parameters.update({'error': str(e)})
callback_service(service_callback,
plugin_info['generated_id'],
task_id,
'FAILED',
additional=user_parameters)
# deleting plugin temporary files
for todel in plugin.tmp_files:
debug('deleting %s' % todel)
shutil.rmtree(todel, onerror=shutilerror)
#debug('deleting %s' % outputs_directory)
#shutil.rmtree(outputs_directory, onerror=shutilerror)
if file_is_in_bs(TMP_DIR, inputs_directory):
debug('deleting %s' % inputs_directory)
shutil.rmtree(inputs_directory, onerror=shutilerror)
if len(plugin.debug_stack) > 0:
debug("Adding debug stack to error")
debug_error = '\n [x] DEBUG STACK : %s' % '\n'.join(
[d for d in plugin.debug_stack])
if not e.args:
e.args = ('', )
e.args = (e.args[0] + debug_error, ) + e.args[1:]
raised = True
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)
debug('moving files')
# moving files to the output directory
for output_file, output_type in plugin.output_files:
debug('f: %s to : %s' % (output_file, out))
out_path = os.path.join(out, os.path.split(output_file)[1])
io.mv(output_file, out)
results.append({
'is_file': True,
'path': out_path,
'type': output_type
})
# deleting plugin temporary files
for todel in plugin.tmp_files:
debug('deleting %s' % todel)
shutil.rmtree(todel, onerror=shutilerror)
if file_is_in_bs(TMP_DIR, inputs_directory):
debug('deleting %s' % inputs_directory)
shutil.rmtree(inputs_directory, onerror=shutilerror)
# updating bioscript with the results
debug('CALLBACK to %s for task %s' % (bioscript_callback, task_id))
debug(cbbioscript(bioscript_callback, task_id, json.dumps(results)))
debug("END")
# callback
if service_callback is not None:
callback_service(service_callback,
plugin_info['generated_id'],
task_id,
'SUCCESS',
results=json.dumps(results),
additional=user_parameters)