#!/usr/bin/env python3
import logging
import os
import codecs
from .container import Container
from .utils import *
from tooldog import TMP_DIR
LOGGER = logging.getLogger(__name__)
[docs]class LanguageAnalyzer(object):
"""
This should be the abstract class for all analyzer.
"""
[docs] def __init__(self, biotool):
"""
:param biotool: Biotool object
:type biotool: :class:`tooldog.biotool_model.Biotool`
"""
self.biotool = biotool
[docs] def analyse(self):
"""
Run source code analysis.
"""
pass
[docs]class PythonAnalyzer(LanguageAnalyzer):
"""
Object to specifically analyze Python source code.
"""
[docs] def __init__(self, gen_format, source_code):
"""
:param gen_format: tool description language (Galaxy XML or CWL)
:type gen_format: STRING
:param source_code: path to source code.
:type source_code: STRING
"""
self.gen_format = gen_format # To be used as an option when running Docker
self.source_code = source_code
[docs] def analyse(self):
"""
Run source code analysis.
"""
try:
LOGGER.info("Trying to analyse the code as python2")
return self._analyse(2)
except DockerException:
try:
LOGGER.warn("Unable to analyse the code as python2")
LOGGER.info("Trying to analyse the code as python3")
return self._analyse(3)
except DockerException:
LOGGER.warn("Unable to analyse the code as python3")
LOGGER.info("Skipping analysis...")
return None
except Exception: # TODO: Add more fine-grained error handlers.
LOGGER.warn("Unknown Docker client error: Docker is not installed/started or unable to use network due to the network restrictions.")
LOGGER.info("Skipping analysis...")
return None
def _analyse(self, version):
python_path = "/usr/local/lib/python3.6/dist-packages/" if version == 3 else \
"/usr/local/lib/python2.7/dist-packages/"
c = Container("tooldog/analyser",
"tail -f /dev/null", # run until we will stop the container
environment={'PYTHONPATH': python_path})
c.put(self.source_code, "/")
output = ''
workdir = ''
toolname = ''
with c:
workdir = get_workdir(execute(c, "unzip /tool.zip"))
toolname = execute(c, cd(workdir, "python setup.py --name"))
execute(c,
cd(workdir, pip(version, "install .")))
#execute(c,
# cd(workdir, pip(version, "install git+https://github.com/erasche/argparse2tool")))
output = execute(c, cd(workdir, gen_cmd(toolname, self.gen_format)))
# Deals with the bytes output of export from etree (used in galaxyxml)
if output.startswith("b'"):
output = codecs.decode(output, 'unicode_escape')[2:-1]
if if_installed(toolname, output) and not output.lstrip().startswith('Traceback'):
output_path = os.path.join(TMP_DIR, tool_filename(toolname, self.gen_format))
write_to_file(output_path, output, 'w')
return output_path
else:
raise DockerException("Tool was not installed properly")
