示例#1
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def main_non_archive(args):
    # validation
    if not args.galaxy_root:
        raise ValueError(
                'in non-archive mode the galaxy root must be specified')
    if not args.tools_subdir:
        raise ValueError(
                'in non-archive mode the tools subdirectory must be specified')
    # get the module names
    module_names = meta.get_module_names(
            args.manifest, args.create_all, args.create_tagged)
    # create the python subtree
    tools_subdir_path = os.path.join(
            args.galaxy_root, 'tools', args.tools_subdir)
    meta.add_python_files(module_names, tools_subdir_path)
    shutil.copyfile('galaxy_format_tweak.py',
            os.path.join(tools_subdir_path, 'galaxy_format_tweak.py'))
    # create the galaxy xml interface files
    xml_filenames, import_errors = add_xml_files(args.galaxy_root,
            module_names, args.short_length, args.tools_subdir)
    for e in import_errors:
        print e
    # create the toolbox xml pointing to the installed xmls
    toolbox_pathname = os.path.join(args.galaxy_root, args.tool_conf)
    section_name = args.tools_subdir
    section_id = args.tools_subdir
    toolbox_xml = get_toolbox_xml(section_name, section_id,
            args.tools_subdir, xml_filenames)
    with open(toolbox_pathname, 'wt') as fout:
        fout.write(toolbox_xml)
示例#2
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def main_non_archive(args):
    # validation
    if not args.galaxy_root:
        raise ValueError(
            'in non-archive mode the galaxy root must be specified')
    if not args.tools_subdir:
        raise ValueError(
            'in non-archive mode the tools subdirectory must be specified')
    # get the module names
    module_names = meta.get_module_names(args.manifest, args.create_all,
                                         args.create_tagged)
    # create the python subtree
    tools_subdir_path = os.path.join(args.galaxy_root, 'tools',
                                     args.tools_subdir)
    meta.add_python_files(module_names, tools_subdir_path)
    shutil.copyfile('galaxy_format_tweak.py',
                    os.path.join(tools_subdir_path, 'galaxy_format_tweak.py'))
    # create the galaxy xml interface files
    xml_filenames, import_errors = add_xml_files(args.galaxy_root,
                                                 module_names,
                                                 args.short_length,
                                                 args.tools_subdir)
    for e in import_errors:
        print e
    # create the toolbox xml pointing to the installed xmls
    toolbox_pathname = os.path.join(args.galaxy_root, args.tool_conf)
    section_name = args.tools_subdir
    section_id = args.tools_subdir
    toolbox_xml = get_toolbox_xml(section_name, section_id, args.tools_subdir,
                                  xml_filenames)
    with open(toolbox_pathname, 'wt') as fout:
        fout.write(toolbox_xml)
示例#3
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def create_installer(args, cat_info, env_info, module_names):
    """
    Overwrite a staging subtree of the current directory.
    The idea it to tgz this directory and send it to the target server.
    On the target server it should be unzipped and extracted,
    and the installer script should put everything in the correct
    prespecified directories.
    """
    # define the local staging directory
    stage = args.make_installer
    # remove the old staging directory if it exists
    if os.path.isdir(stage):
        shutil.rmtree(stage)
    # create some directories
    os.makedirs(os.path.join(stage, 'python-files'))
    os.makedirs(os.path.join(stage, 'xml-files'))
    # add the appropriate python files and the const data
    meta.add_python_files(module_names, os.path.join(stage, 'python-files'))
    # create the xml files
    identifiers, import_errors = mobyle.add_xml_files(
            cat_info, env_info,
            module_names, args.short_length,
            os.path.join(stage, 'xml-files'),
            args.runbsub)
    for e in import_errors:
        print e
    # copy the installer script
    shutil.copy('install-mob-tools.py',
            os.path.join(stage, 'install-mob-tools.py'))
    # copy the installer script dependency
    shutil.copy('mobenv.py',
            os.path.join(stage, 'mobenv.py'))
    # create the installer configuration
    with open(os.path.join(stage, 'install-mob-tools.conf'), 'w') as fout:
        print >> fout, '#', ' '.join(sys.argv)
        print >> fout, '\t'.join(['auto_path', env_info.auto_path])
        print >> fout, '\t'.join(['python_path', env_info.python_path])
        print >> fout, '\t'.join(['mob_core', env_info.mob_core])
        print >> fout, '\t'.join(['mob_version', args.mobyle_version])
    # create a file with a fragment that could be added to the config
    with open(os.path.join(stage, 'sys.config.fragment'), 'w') as fout:
        print >> fout, '# begin autogenerated code'
        print >> fout, 'my_pca_names = ['
        for ident in sorted(identifiers):
            print >> fout, "\t\t'%s'," % ident
        print >> fout, "\t\t]"
        dstring = "dict((x, 'Sys') for x in my_pca_names)"
        print >> fout, 'PARTICULAR_BATCH.update(%s)' % dstring
        print >> fout, '# end autogenerated code'
    # use subprocess instead of tarfile to create the tgz
    cmd = ['tar', 'czvf', stage + '.tgz', stage]
    subprocess.call(cmd)
示例#4
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def create_installer(args, cat_info, env_info, module_names):
    """
    Overwrite a staging subtree of the current directory.
    The idea it to tgz this directory and send it to the target server.
    On the target server it should be unzipped and extracted,
    and the installer script should put everything in the correct
    prespecified directories.
    """
    # define the local staging directory
    stage = args.make_installer
    # remove the old staging directory if it exists
    if os.path.isdir(stage):
        shutil.rmtree(stage)
    # create some directories
    os.makedirs(os.path.join(stage, 'python-files'))
    os.makedirs(os.path.join(stage, 'xml-files'))
    # add the appropriate python files and the const data
    meta.add_python_files(module_names, os.path.join(stage, 'python-files'))
    # create the xml files
    identifiers, import_errors = mobyle.add_xml_files(
        cat_info, env_info, module_names, args.short_length,
        os.path.join(stage, 'xml-files'), args.runbsub)
    for e in import_errors:
        print e
    # copy the installer script
    shutil.copy('install-mob-tools.py',
                os.path.join(stage, 'install-mob-tools.py'))
    # copy the installer script dependency
    shutil.copy('mobenv.py', os.path.join(stage, 'mobenv.py'))
    # create the installer configuration
    with open(os.path.join(stage, 'install-mob-tools.conf'), 'w') as fout:
        print >> fout, '#', ' '.join(sys.argv)
        print >> fout, '\t'.join(['auto_path', env_info.auto_path])
        print >> fout, '\t'.join(['python_path', env_info.python_path])
        print >> fout, '\t'.join(['mob_core', env_info.mob_core])
        print >> fout, '\t'.join(['mob_version', args.mobyle_version])
    # create a file with a fragment that could be added to the config
    with open(os.path.join(stage, 'sys.config.fragment'), 'w') as fout:
        print >> fout, '# begin autogenerated code'
        print >> fout, 'my_pca_names = ['
        for ident in sorted(identifiers):
            print >> fout, "\t\t'%s'," % ident
        print >> fout, "\t\t]"
        dstring = "dict((x, 'Sys') for x in my_pca_names)"
        print >> fout, 'PARTICULAR_BATCH.update(%s)' % dstring
        print >> fout, '# end autogenerated code'
    # use subprocess instead of tarfile to create the tgz
    cmd = ['tar', 'czvf', stage + '.tgz', stage]
    subprocess.call(cmd)
示例#5
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def main_archive(args):
    # validation
    if args.galaxy_root:
        raise ValueError(
            'in archive mode the galaxy root must not be specified')
    if args.tools_subdir:
        raise ValueError(
            'in archive mode the tools subdirectory must not be specified')
    # define the archive extension and the compression command
    archive_extension = '.tar.bz2'
    archive_prefix = os.path.basename(args.suite_archive.rstrip('/'))
    archive_name = archive_prefix + archive_extension
    archive_cmd = ['tar', 'cjvf', archive_name, args.suite_archive]
    # delete the suite directory and archive if they exist
    try:
        shutil.rmtree(args.suite_archive)
        os.remove(archive_name)
    except OSError as e:
        pass
    # get the module names
    module_names = meta.get_module_names(args.manifest, args.create_all,
                                         args.create_tagged)
    # create the empty suite directory
    os.makedirs(args.suite_archive)
    # add the python files
    meta.add_python_files(module_names, args.suite_archive)
    shutil.copyfile('galaxy_format_tweak.py',
                    os.path.join(args.suite_archive, 'galaxy_format_tweak.py'))
    # create the galaxy xml interface files
    mod_infos, import_errors = add_xml_archive_files(module_names,
                                                     args.short_length,
                                                     args.suite_archive)
    for e in import_errors:
        print e
    # create the toolbox xml pointing to the installed xmls
    config_pathname = os.path.join(args.suite_archive, 'suite_config.xml')
    config_xml = get_suite_config_xml(mod_infos, archive_prefix)
    with open(config_pathname, 'wt') as fout:
        fout.write(config_xml)
    # use subprocess instead of tarfile to create the tgz
    subprocess.call(archive_cmd)
示例#6
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def main_archive(args):
    # validation
    if args.galaxy_root:
        raise ValueError(
                'in archive mode the galaxy root must not be specified')
    if args.tools_subdir:
        raise ValueError(
                'in archive mode the tools subdirectory must not be specified')
    # define the archive extension and the compression command
    archive_extension = '.tar.bz2'
    archive_prefix = os.path.basename(args.suite_archive.rstrip('/'))
    archive_name = archive_prefix + archive_extension
    archive_cmd = ['tar', 'cjvf', archive_name, args.suite_archive]
    # delete the suite directory and archive if they exist
    try:
        shutil.rmtree(args.suite_archive)
        os.remove(archive_name)
    except OSError as e:
        pass
    # get the module names
    module_names = meta.get_module_names(
            args.manifest, args.create_all, args.create_tagged)
    # create the empty suite directory
    os.makedirs(args.suite_archive)
    # add the python files
    meta.add_python_files(module_names, args.suite_archive)
    shutil.copyfile('galaxy_format_tweak.py',
            os.path.join(args.suite_archive, 'galaxy_format_tweak.py'))
    # create the galaxy xml interface files
    mod_infos, import_errors = add_xml_archive_files(
            module_names, args.short_length, args.suite_archive)
    for e in import_errors:
        print e
    # create the toolbox xml pointing to the installed xmls
    config_pathname = os.path.join(args.suite_archive, 'suite_config.xml')
    config_xml = get_suite_config_xml(mod_infos, archive_prefix)
    with open(config_pathname, 'wt') as fout:
        fout.write(config_xml)
    # use subprocess instead of tarfile to create the tgz
    subprocess.call(archive_cmd)
示例#7
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def main(args):
    # check for flag conflicts
    if args.deploy and args.make_installer:
        raise ValueError(
            'the "deploy" and "make_installer" flags are incompatible')
    # initialize the mobyle category information
    cat_info = mobyle.CategoryInfo(args.show_io_types, args.show_tags,
                                   args.universal_category)
    # get the module names
    module_names = meta.get_module_names(args.manifest, args.create_all,
                                         args.create_tagged)
    # define the environment on the target server
    auto_path = os.path.join(args.target, 'auto.py')
    env_info = mobenv.create_environment_info(auto_path, args.python_path,
                                              args.mobyle_core,
                                              args.mobyle_version)
    if args.make_installer:
        create_installer(args, cat_info, env_info, module_names)
    else:
        # create the python subtree
        meta.add_python_files(module_names, args.target)
        # create the mobyle xml interface files
        import_errors = mobyle.add_xml_files(cat_info, env_info, module_names,
                                             args.short_length,
                                             env_info.get_xml_dir(),
                                             args.runbsub)
        for e in import_errors:
            print e
    if args.clean:
        cmd = env_info.get_clean_command()
        subprocess.call(cmd)
    if args.index:
        cmd = env_info.get_index_command()
        subprocess.call(cmd)
    if args.deploy:
        cmd = env_info.get_deploy_command()
        subprocess.call(cmd)
示例#8
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def main(args):
    # check for flag conflicts
    if args.deploy and args.make_installer:
        raise ValueError(
                'the "deploy" and "make_installer" flags are incompatible')
    # initialize the mobyle category information
    cat_info = mobyle.CategoryInfo(
            args.show_io_types, args.show_tags, args.universal_category)
    # get the module names
    module_names = meta.get_module_names(
            args.manifest, args.create_all, args.create_tagged)
    # define the environment on the target server
    auto_path = os.path.join(args.target, 'auto.py')
    env_info = mobenv.create_environment_info(
            auto_path, args.python_path,
            args.mobyle_core, args.mobyle_version)
    if args.make_installer:
        create_installer(args, cat_info, env_info, module_names)
    else:
        # create the python subtree
        meta.add_python_files(module_names, args.target)
        # create the mobyle xml interface files
        import_errors = mobyle.add_xml_files(
                cat_info, env_info,
                module_names, args.short_length, env_info.get_xml_dir(),
                args.runbsub)
        for e in import_errors:
            print e
    if args.clean:
        cmd = env_info.get_clean_command()
        subprocess.call(cmd)
    if args.index:
        cmd = env_info.get_index_command()
        subprocess.call(cmd)
    if args.deploy:
        cmd = env_info.get_deploy_command()
        subprocess.call(cmd)
示例#9
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def main(args):
    with open(args.manifest) as fin:
        module_names = [x.strip() for x in fin]
    meta.add_python_files(module_names, args.target)