def execute( self, tool, trans, incoming={}, set_output_hid=True, history=None, **kwargs ):
dataset_upload_inputs = []
for input_name, input in tool.inputs.iteritems():
if input.type == "upload_dataset":
dataset_upload_inputs.append( input )
assert dataset_upload_inputs, Exception( "No dataset upload groups were found." )
persisting_uploads_timer = ExecutionTimer()
precreated_datasets = upload_common.get_precreated_datasets( trans, incoming, trans.app.model.HistoryDatasetAssociation )
incoming = upload_common.persist_uploads( incoming )
log.debug("Persisted uploads %s" % persisting_uploads_timer)
# We can pass an empty string as the cntrller here since it is used to check whether we
# are in an admin view, and this tool is currently not used there.
check_and_cleanup_timer = ExecutionTimer()
uploaded_datasets = upload_common.get_uploaded_datasets( trans, '', incoming, precreated_datasets, dataset_upload_inputs, history=history )
upload_common.cleanup_unused_precreated_datasets( precreated_datasets )
if not uploaded_datasets:
return None, 'No data was entered in the upload form, please go back and choose data to upload.'
log.debug("Checked and cleaned uploads %s" % check_and_cleanup_timer)
create_job_timer = ExecutionTimer()
json_file_path = upload_common.create_paramfile( trans, uploaded_datasets )
data_list = [ ud.data for ud in uploaded_datasets ]
rval = upload_common.create_job( trans, incoming, tool, json_file_path, data_list, history=history )
log.debug("Created upload job %s" % create_job_timer)
return rval
def execute(self, tool, trans, incoming={}, set_output_hid=True, history=None, **kwargs):
dataset_upload_inputs = []
for input_name, input in tool.inputs.items():
if input.type == "upload_dataset":
dataset_upload_inputs.append(input)
assert dataset_upload_inputs, Exception("No dataset upload groups were found.")
persisting_uploads_timer = ExecutionTimer()
precreated_datasets = upload_common.get_precreated_datasets(trans, incoming, trans.app.model.HistoryDatasetAssociation)
incoming = upload_common.persist_uploads(incoming, trans)
log.debug("Persisted uploads %s" % persisting_uploads_timer)
# We can pass an empty string as the cntrller here since it is used to check whether we
# are in an admin view, and this tool is currently not used there.
check_and_cleanup_timer = ExecutionTimer()
uploaded_datasets = upload_common.get_uploaded_datasets(trans, '', incoming, precreated_datasets, dataset_upload_inputs, history=history)
upload_common.cleanup_unused_precreated_datasets(precreated_datasets)
if not uploaded_datasets:
return None, 'No data was entered in the upload form, please go back and choose data to upload.'
log.debug("Checked and cleaned uploads %s" % check_and_cleanup_timer)
create_job_timer = ExecutionTimer()
json_file_path = upload_common.create_paramfile(trans, uploaded_datasets)
data_list = [ud.data for ud in uploaded_datasets]
rval = upload_common.create_job(trans, incoming, tool, json_file_path, data_list, history=history)
log.debug("Created upload job %s" % create_job_timer)
return rval
def _upload_dataset(self, trans, library_id, folder_id, replace_dataset=None, **kwd):
# Set up the traditional tool state/params
cntrller = 'api'
tool_id = 'upload1'
message = None
tool = trans.app.toolbox.get_tool(tool_id)
state = tool.new_state(trans)
populate_state(trans, tool.inputs, kwd, state.inputs)
tool_params = state.inputs
dataset_upload_inputs = []
for input_name, input in tool.inputs.items():
if input.type == "upload_dataset":
dataset_upload_inputs.append(input)
# Library-specific params
server_dir = kwd.get('server_dir', '')
upload_option = kwd.get('upload_option', 'upload_file')
response_code = 200
if upload_option == 'upload_directory':
full_dir, import_dir_desc = validate_server_directory_upload(trans, server_dir)
message = 'Select a directory'
elif upload_option == 'upload_paths':
# Library API already checked this - following check isn't actually needed.
validate_path_upload(trans)
# Some error handling should be added to this method.
try:
# FIXME: instead of passing params here ( which have been processed by util.Params(), the original kwd
# should be passed so that complex objects that may have been included in the initial request remain.
library_bunch = upload_common.handle_library_params(trans, kwd, folder_id, replace_dataset)
except Exception:
response_code = 500
message = "Unable to parse upload parameters, please report this error."
# Proceed with (mostly) regular upload processing if we're still errorless
if response_code == 200:
precreated_datasets = upload_common.get_precreated_datasets(trans, tool_params, trans.app.model.LibraryDatasetDatasetAssociation, controller=cntrller)
if upload_option == 'upload_file':
tool_params = upload_common.persist_uploads(tool_params, trans)
uploaded_datasets = upload_common.get_uploaded_datasets(trans, cntrller, tool_params, precreated_datasets, dataset_upload_inputs, library_bunch=library_bunch)
elif upload_option == 'upload_directory':
uploaded_datasets, response_code, message = self._get_server_dir_uploaded_datasets(trans, kwd, full_dir, import_dir_desc, library_bunch, response_code, message)
elif upload_option == 'upload_paths':
uploaded_datasets, response_code, message = self._get_path_paste_uploaded_datasets(trans, kwd, library_bunch, response_code, message)
upload_common.cleanup_unused_precreated_datasets(precreated_datasets)
if upload_option == 'upload_file' and not uploaded_datasets:
response_code = 400
message = 'Select a file, enter a URL or enter text'
if response_code != 200:
return (response_code, message)
json_file_path = upload_common.create_paramfile(trans, uploaded_datasets)
data_list = [ud.data for ud in uploaded_datasets]
job_params = {}
job_params['link_data_only'] = json.dumps(kwd.get('link_data_only', 'copy_files'))
job_params['uuid'] = json.dumps(kwd.get('uuid', None))
job, output = upload_common.create_job(trans, tool_params, tool, json_file_path, data_list, folder=library_bunch.folder, job_params=job_params)
trans.sa_session.add(job)
trans.sa_session.flush()
return output
def execute(self, tool, trans, incoming={}, set_output_hid=True):
dataset_upload_inputs = []
for input_name, input in tool.inputs.iteritems():
if input.type == "upload_dataset":
dataset_upload_inputs.append(input)
assert dataset_upload_inputs, Exception(
"No dataset upload groups were found.")
precreated_datasets = upload_common.get_precreated_datasets(
trans, incoming, trans.app.model.HistoryDatasetAssociation)
incoming = upload_common.persist_uploads(incoming)
uploaded_datasets = upload_common.get_uploaded_datasets(
trans, incoming, precreated_datasets, dataset_upload_inputs)
upload_common.cleanup_unused_precreated_datasets(precreated_datasets)
if not uploaded_datasets:
return 'No data was entered in the upload form, please go back and choose data to upload.'
json_file_path = upload_common.create_paramfile(
trans, uploaded_datasets)
data_list = [ud.data for ud in uploaded_datasets]
return upload_common.create_job(trans, incoming, tool, json_file_path,
data_list)
def _upload_dataset(self,
trans,
library_id,
folder_id,
replace_dataset=None,
**kwd):
# Set up the traditional tool state/params
cntrller = 'api'
tool_id = 'upload1'
message = None
tool = trans.app.toolbox.get_tool(tool_id)
state = tool.new_state(trans)
populate_state(trans, tool.inputs, kwd, state.inputs)
tool_params = state.inputs
dataset_upload_inputs = []
for input_name, input in tool.inputs.items():
if input.type == "upload_dataset":
dataset_upload_inputs.append(input)
# Library-specific params
server_dir = kwd.get('server_dir', '')
upload_option = kwd.get('upload_option', 'upload_file')
response_code = 200
if upload_option == 'upload_directory':
full_dir, import_dir_desc = validate_server_directory_upload(
trans, server_dir)
message = 'Select a directory'
elif upload_option == 'upload_paths':
# Library API already checked this - following check isn't actually needed.
validate_path_upload(trans)
# Some error handling should be added to this method.
try:
# FIXME: instead of passing params here ( which have been processed by util.Params(), the original kwd
# should be passed so that complex objects that may have been included in the initial request remain.
library_bunch = upload_common.handle_library_params(
trans, kwd, folder_id, replace_dataset)
except Exception:
response_code = 500
message = "Unable to parse upload parameters, please report this error."
# Proceed with (mostly) regular upload processing if we're still errorless
if response_code == 200:
precreated_datasets = upload_common.get_precreated_datasets(
trans,
tool_params,
trans.app.model.LibraryDatasetDatasetAssociation,
controller=cntrller)
if upload_option == 'upload_file':
tool_params = upload_common.persist_uploads(tool_params, trans)
uploaded_datasets = upload_common.get_uploaded_datasets(
trans,
cntrller,
tool_params,
precreated_datasets,
dataset_upload_inputs,
library_bunch=library_bunch)
elif upload_option == 'upload_directory':
uploaded_datasets, response_code, message = self._get_server_dir_uploaded_datasets(
trans, kwd, full_dir, import_dir_desc, library_bunch,
response_code, message)
elif upload_option == 'upload_paths':
uploaded_datasets, response_code, message = self._get_path_paste_uploaded_datasets(
trans, kwd, library_bunch, response_code, message)
upload_common.cleanup_unused_precreated_datasets(
precreated_datasets)
if upload_option == 'upload_file' and not uploaded_datasets:
response_code = 400
message = 'Select a file, enter a URL or enter text'
if response_code != 200:
return (response_code, message)
json_file_path = upload_common.create_paramfile(
trans, uploaded_datasets)
data_list = [ud.data for ud in uploaded_datasets]
job_params = {}
job_params['link_data_only'] = json.dumps(
kwd.get('link_data_only', 'copy_files'))
job_params['uuid'] = json.dumps(kwd.get('uuid', None))
job, output = upload_common.create_job(trans,
tool_params,
tool,
json_file_path,
data_list,
folder=library_bunch.folder,
job_params=job_params)
trans.sa_session.add(job)
trans.sa_session.flush()
return output
def upload_dataset( self, trans, controller, library_id, folder_id, replace_dataset=None, **kwd ):
# Set up the traditional tool state/params
tool_id = 'upload1'
tool = trans.app.toolbox.tools_by_id[ tool_id ]
state = tool.new_state( trans )
errors = tool.update_state( trans, tool.inputs_by_page[0], state.inputs, kwd )
tool_params = state.inputs
dataset_upload_inputs = []
for input_name, input in tool.inputs.iteritems():
if input.type == "upload_dataset":
dataset_upload_inputs.append( input )
# Library-specific params
params = util.Params( kwd ) # is this filetoolparam safe?
library_bunch = upload_common.handle_library_params( trans, params, folder_id, replace_dataset )
msg = util.restore_text( params.get( 'msg', '' ) )
messagetype = params.get( 'messagetype', 'done' )
server_dir = util.restore_text( params.get( 'server_dir', '' ) )
if replace_dataset not in [ None, 'None' ]:
replace_id = replace_dataset.id
else:
replace_id = None
upload_option = params.get( 'upload_option', 'upload_file' )
err_redirect = False
if upload_option == 'upload_directory':
if server_dir in [ None, 'None', '' ]:
err_redirect = True
if controller == 'library_admin':
import_dir = trans.app.config.library_import_dir
import_dir_desc = 'library_import_dir'
full_dir = os.path.join( import_dir, server_dir )
else:
import_dir = trans.app.config.user_library_import_dir
import_dir_desc = 'user_library_import_dir'
if server_dir == trans.user.email:
full_dir = os.path.join( import_dir, server_dir )
else:
full_dir = os.path.join( import_dir, trans.user.email, server_dir )
if import_dir:
msg = 'Select a directory'
else:
msg = '"%s" is not defined in the Galaxy configuration file' % import_dir_desc
# Proceed with (mostly) regular upload processing
precreated_datasets = upload_common.get_precreated_datasets( trans, tool_params, trans.app.model.LibraryDatasetDatasetAssociation, controller=controller )
if upload_option == 'upload_file':
tool_params = upload_common.persist_uploads( tool_params )
uploaded_datasets = upload_common.get_uploaded_datasets( trans, tool_params, precreated_datasets, dataset_upload_inputs, library_bunch=library_bunch )
elif upload_option == 'upload_directory':
uploaded_datasets, err_redirect, msg = self.get_server_dir_uploaded_datasets( trans, params, full_dir, import_dir_desc, library_bunch, err_redirect, msg )
elif upload_option == 'upload_paths':
uploaded_datasets, err_redirect, msg = self.get_path_paste_uploaded_datasets( trans, params, library_bunch, err_redirect, msg )
upload_common.cleanup_unused_precreated_datasets( precreated_datasets )
if upload_option == 'upload_file' and not uploaded_datasets:
msg = 'Select a file, enter a URL or enter text'
err_redirect = True
if err_redirect:
trans.response.send_redirect( web.url_for( controller=controller,
action='upload_library_dataset',
library_id=library_id,
folder_id=folder_id,
replace_id=replace_id,
upload_option=upload_option,
msg=util.sanitize_text( msg ),
messagetype='error' ) )
json_file_path = upload_common.create_paramfile( trans, uploaded_datasets )
data_list = [ ud.data for ud in uploaded_datasets ]
return upload_common.create_job( trans, tool_params, tool, json_file_path, data_list, folder=library_bunch.folder )
def upload_dataset(self,
trans,
controller,
library_id,
folder_id,
replace_dataset=None,
**kwd):
# Set up the traditional tool state/params
tool_id = 'upload1'
tool = trans.app.toolbox.tools_by_id[tool_id]
state = tool.new_state(trans)
errors = tool.update_state(trans, tool.inputs_by_page[0], state.inputs,
kwd)
tool_params = state.inputs
dataset_upload_inputs = []
for input_name, input in tool.inputs.iteritems():
if input.type == "upload_dataset":
dataset_upload_inputs.append(input)
# Library-specific params
params = util.Params(kwd) # is this filetoolparam safe?
library_bunch = upload_common.handle_library_params(
trans, params, folder_id, replace_dataset)
msg = util.restore_text(params.get('msg', ''))
messagetype = params.get('messagetype', 'done')
server_dir = util.restore_text(params.get('server_dir', ''))
if replace_dataset not in [None, 'None']:
replace_id = replace_dataset.id
else:
replace_id = None
upload_option = params.get('upload_option', 'upload_file')
err_redirect = False
if upload_option == 'upload_directory':
if server_dir in [None, 'None', '']:
err_redirect = True
if controller == 'library_admin':
import_dir = trans.app.config.library_import_dir
import_dir_desc = 'library_import_dir'
full_dir = os.path.join(import_dir, server_dir)
else:
import_dir = trans.app.config.user_library_import_dir
import_dir_desc = 'user_library_import_dir'
if server_dir == trans.user.email:
full_dir = os.path.join(import_dir, server_dir)
else:
full_dir = os.path.join(import_dir, trans.user.email,
server_dir)
if import_dir:
msg = 'Select a directory'
else:
msg = '"%s" is not defined in the Galaxy configuration file' % import_dir_desc
# Proceed with (mostly) regular upload processing
precreated_datasets = upload_common.get_precreated_datasets(
trans,
tool_params,
trans.app.model.LibraryDatasetDatasetAssociation,
controller=controller)
if upload_option == 'upload_file':
tool_params = upload_common.persist_uploads(tool_params)
uploaded_datasets = upload_common.get_uploaded_datasets(
trans,
tool_params,
precreated_datasets,
dataset_upload_inputs,
library_bunch=library_bunch)
elif upload_option == 'upload_directory':
uploaded_datasets, err_redirect, msg = self.get_server_dir_uploaded_datasets(
trans, params, full_dir, import_dir_desc, library_bunch,
err_redirect, msg)
elif upload_option == 'upload_paths':
uploaded_datasets, err_redirect, msg = self.get_path_paste_uploaded_datasets(
trans, params, library_bunch, err_redirect, msg)
upload_common.cleanup_unused_precreated_datasets(precreated_datasets)
if upload_option == 'upload_file' and not uploaded_datasets:
msg = 'Select a file, enter a URL or enter text'
err_redirect = True
if err_redirect:
trans.response.send_redirect(
web.url_for(controller=controller,
action='upload_library_dataset',
library_id=library_id,
folder_id=folder_id,
replace_id=replace_id,
upload_option=upload_option,
msg=util.sanitize_text(msg),
messagetype='error'))
json_file_path = upload_common.create_paramfile(
trans, uploaded_datasets)
data_list = [ud.data for ud in uploaded_datasets]
return upload_common.create_job(trans,
tool_params,
tool,
json_file_path,
data_list,
folder=library_bunch.folder)