def test_make_xml(self): output_fp = path.join(self.output_dir, 'example_script.xml') self._paths_to_clean_up = [output_fp, './example_script.py'] copyfile(self.script_fp, './example_script.py') make_xml(self.script_fp, self.output_dir, None) self.assertTrue(path.exists(output_fp), 'The xml file was not created in the appropiate location')
def integrate(scripts_dir, galaxy_dist_dir, config_file, update_tool_conf,
log_fp):
"""Integrates the tools in the scripts folder into the given Galaxy instance
Inputs:
scripts_dir: path to the directory containing all the scripts to be
integrated on Galaxy
galaxy_dist_dir: path to the Galaxy's installation folder
config_file: path to the Galaxy-QIIME configuration file
update_tool_conf: boolean showing if the current tool_conf file should
be updated or a new tool_conf file should be created
log_fp: path to where the log file should be written
Walks through all the scripts present in the 'scripts_dir' folder and
integrates them in the Galaxy instance 'galaxy_dist_dir'. The integration is
done according to the 'config_file', which specifies: the different sections
in which the scripts will be grouped, which scripts of the script folder
will be integrated and which option of these script will NOT be included
in the Galaxy interface.
If update_tool_conf is True, it will update the current tool_conf.xml file
present in the Galaxy instance. Otherwise, it will override it with a new
tool_conf.xml configuration file.
If a log_fp is given, the script will write the log file into this path.
Otherwise, it will create a log file in the scripts_dir folder
"""
script_dict, sections = parse_config_file(open(config_file, 'U'))
galaxy_dist_dir = path.abspath(galaxy_dist_dir)
create_dirs(galaxy_dist_dir, sections)
tool_conf = get_galaxy_tool_conf_file(galaxy_dist_dir, update_tool_conf)
section_dict = {}
for section in sections:
section_dict[section] = []
if not log_fp:
log_fp = path.join(scripts_dir, 'integration.log')
log_file = open(log_fp, 'w')
addsitedir(scripts_dir)
for root, dirs, files in walk(scripts_dir):
for name in files:
if name.endswith('.py'):
log_file.write("Generating XML file for %s script... " % name)
if name in script_dict.keys():
section, remove_opts = script_dict[name]
output_dir = path.join(galaxy_dist_dir, 'tools',
section.replace(" ", "").lower())
try:
make_xml(name, output_dir, remove_opts)
section_dict[section].append(name)
log_file.write("Ok\n")
except Exception as exc:
log_file.write(str(type(exc)) + " : " + str(exc) + "\n")
else:
log_file.write("skipped - not in configuration file\n")
log_file.write("Generating tool_conf... ")
update_tool_conf_xml(tool_conf, section_dict)
log_file.write("Ok\n")
log_file.write("Writing tool_conf... ")
# Write tool_conf.xml file
tool_conf_fp = path.join(galaxy_dist_dir, 'tool_conf.xml')
f = open(tool_conf_fp, 'w')
f.write(tool_conf.toprettyxml(indent='\t'))
f.close()
log_file.write("Ok\n")
log_file.write("Generating activate.sh file... ")
create_activate_file(galaxy_dist_dir)
log_file.write("Ok\n")
# Close log file
log_file.close()
__email__ = "*****@*****.**"
__status__ = "Development"
from cogent.util.option_parsing import parse_command_line_parameters, make_option
from xml_generator import make_xml
script_info = {}
script_info['brief_description'] = "Generates a Galaxy XML file from a given QIIME script"
script_info['script_description'] = "Reads the input script, looks for his 'script_info' and extract all the information necessary to generate the XML file. The script generated takes the same name as the original script, but changing his extension to XML. Once the XML is generated, the script must be put into the Galaxy's tools folder and edit tool_conf.xml "
script_info['script_usage'] = [("Example:", "Generate the Galaxy XML file from the script 'my_script.py' without including the '--opt_a' and the '--opt_b' options.", "%prog -i my_script.py -r opt_a,opt_b")]
script_info['output_description'] = "An XML file that Galaxy can reads and make the tool available via web browser"
script_info['required_options'] = [
make_option('-i', '--script_fp', type="existing_filepath",
help='the QIIME python script filepath to generate'),
make_option('-o', '--output_dir', type="existing_dirpath",
help='output directory where to save the XML file')
]
script_info['optional_options'] = [
make_option('-r', '--remove_opts', type="string",
help='List of option names (e.g. "option1,option2") that will not appear in the xml'),
]
script_info['version'] = __version__
if __name__ == '__main__':
option_parser, opts, args = parse_command_line_parameters(**script_info)
script_fp = opts.script_fp
output_dir = opts.output_dir
remove_opts = opts.remove_opts
make_xml(script_fp, output_dir, remove_opts)
def integrate(scripts_dir, galaxy_dist_dir, config_file, update_tool_conf, log_fp):
"""
scripts_dir: full path to the directory which contains the scripts to integrate
galaxy_dist_dir: full path to the Galaxy home directory
config_file: path to the configuration file which contains the section structure of the scripts
"""
script_dict, sections = parse_config_file(open(config_file, 'U'))
create_dirs(galaxy_dist_dir, sections)
tool_conf = get_galaxy_tool_conf_file(galaxy_dist_dir, update_tool_conf)
section_dict = {}
for section in sections:
section_dict[section] = []
if not log_fp:
log_fp = path.join(scripts_dir, 'integration.log')
log_file = open(log_fp, 'w')
addsitedir(scripts_dir)
for root, dirs, files in walk(scripts_dir):
for name in files:
if name.endswith('.py'):
log_file.write("Generating XML file for %s script... " % name)
if name in script_dict.keys():
section, remove_opts = script_dict[name]
output_dir = path.join(galaxy_dist_dir, 'tools', section.replace(" ", "").lower())
try:
make_xml(name, output_dir, remove_opts)
section_dict[section].append(name)
log_file.write("Ok\n")
except Exception as exc:
log_file.write(str(type(exc)) + " : " + str(exc) + "\n")
else:
log_file.write("skipped - not in configuration file\n")
log_file.write("Generating tool_conf... ")
update_tool_conf_xml(tool_conf, section_dict)
log_file.write("Ok\n")
log_file.write("Writing tool_conf... ")
# Write tool_conf.xml file
tool_conf_fp = path.join(galaxy_dist_dir, 'tool_conf.xml')
f = open(tool_conf_fp, 'w')
f.write(tool_conf.toprettyxml(indent='\t'))
f.close()
log_file.write("Ok\n")
log_file.write("Updating environment... ")
command_string = 'echo "\nexport GALAXY_HOME=%s" >> ~/.bashrc' % path.abspath(galaxy_dist_dir)
(append_status, append_out) = commands.getstatusoutput(command_string)
if append_status != 0:
raise ValueError, "Error updating environment"
else:
log_file.write("Ok\n")
# Close log file
log_file.close()
