Source code for galaxy.tools.actions.upload

from __init__ import ToolAction
from galaxy.tools.actions import upload_common

import logging
log = logging.getLogger( __name__ )


class UploadToolAction( ToolAction ):

    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." )

        precreated_datasets = upload_common.get_precreated_datasets( trans, incoming, trans.app.model.HistoryDatasetAssociation )
        incoming = upload_common.persist_uploads( incoming )
        # 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.
        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.'

        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, history=history )