# Copyright (C) 2013-2016 DNAnexus, Inc. # # This file is part of dx-toolkit (DNAnexus platform client libraries). # # Licensed under the Apache License, Version 2.0 (the "License"); you may not # use this file except in compliance with the License. You may obtain a copy # of the License at # # http://www.apache.org/licenses/LICENSE-2.0 # # Unless required by applicable law or agreed to in writing, software # distributed under the License is distributed on an "AS IS" BASIS, WITHOUT # WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the # License for the specific language governing permissions and limitations # under the License. ''' bash templating code ''' from __future__ import print_function, unicode_literals, division, absolute_import from ..utils.printing import fill def get_interpreter(): return 'bash' def get_path(): return 'bash' def get_array_output_str(output_param_name, output_param_class): return ' for i in "${!' + output_param_name + '[@]}"; do\n dx-jobutil-add-output ' + output_param_name + ' "${' + output_param_name + '[$i]}" --class=' + output_param_class + '\n done' def get_strings(app_json, required_file_input_names, optional_file_input_names, required_file_array_input_names, optional_file_array_input_names, file_output_names, dummy_output_hash): init_inputs_str = '' dl_files_str = '' ul_files_str = '' outputs_str = '' if 'inputSpec' in app_json and app_json['inputSpec']: init_inputs_str = "\n" + "\n".join([" echo \"Value of {name}: '${var}'\"".format(name=input_param['name'], var=(("{" + input_param['name'] + "[@]}") if input_param['class'].startswith('array:') else input_param['name'])) for input_param in app_json['inputSpec']]) + "\n" if required_file_input_names or optional_file_input_names or \ required_file_array_input_names or optional_file_array_input_names: dl_files_str = "\n" + fill('''The following line(s) use the dx command-line tool to download your file inputs to the local file system using variable names for the filenames. To recover the original filenames, you can use the output of "dx describe "$variable" --name".''', initial_indent=' # ', subsequent_indent=' # ', width=80) + '\n\n' if required_file_input_names: dl_files_str += "\n".join([''' dx download "${name}" -o {name} '''.format(name=name) for name in required_file_input_names]) if optional_file_input_names: dl_files_str += "\n".join([''' if [ -n "${name}" ] then dx download "${name}" -o {name} fi'''.format(name=name) for name in optional_file_input_names]) + '\n' if required_file_array_input_names or optional_file_array_input_names: dl_files_str += "\n".join([''' for i in ${{!{name}[@]}} do dx download "${{{name}[$i]}}" -o {name}-$i done '''.format(name=name) for name in required_file_array_input_names + optional_file_array_input_names]) if file_output_names: ul_files_str = "\n" if init_inputs_str != '' else "" ul_files_str += fill('''The following line(s) use the dx command-line tool to upload your file outputs after you have created them on the local file system. It assumes that you have used the output field name for the filename for each output, but you can change that behavior to suit your needs. Run "dx upload -h" to see more options to set metadata.''', initial_indent=' # ', subsequent_indent=' # ', width=80) + '\n\n' ul_files_str += "\n".join([' {name}=$(dx upload {name} --brief)'.format(name=name) for name in file_output_names]) + "\n" if 'outputSpec' in app_json and app_json['outputSpec']: outputs_str = "\n" + fill('''The following line(s) use the utility dx-jobutil-add-output to format and add output variables to your job's output as appropriate for the output class. Run \"dx-jobutil-add-output -h\" for more information on what it does.''', initial_indent=' # ', subsequent_indent=' # ', width=80) + '\n\n' outputs_str += "\n".join([" dx-jobutil-add-output " + output_param['name'] + ' "$' + output_param['name'] + '" --class=' + output_param['class'] if 'array' not in output_param['class'] else get_array_output_str(output_param['name'], output_param['class']) for output_param in app_json['outputSpec']]) elif 'outputSpec' not in app_json: outputs_str = "\n" + fill('''No output spec is specified, but if you would like to add output fields, you can add invocations of the dx-jobutil-add-output utility to format and add values to the job_output.json file. For example, "dx-jobutil-add-output keyname 32" will add an output field called "keyname" with value equal to the number 32. Run \"dx-jobutil-add-output -h\" for more details on what it does.''', initial_indent=' # ', subsequent_indent=' # ', width=80) return '', init_inputs_str, dl_files_str, ul_files_str, outputs_str