import subprocess
import os
import tempfile
import glob
import json
import yaml
import logging
import sys
import requests
import docker
from process import get_feature, empty_subtree
from errors import WorkflowException
import shutil
import stat
import re
import shellescape
from docker_uid import docker_vm_uid

_logger = logging.getLogger("cwltool")

needs_shell_quoting_re = re.compile(r"""(^$|[\s|&;()<>\'"$@])""")

def deref_links(outputs):
    if isinstance(outputs, dict):
        if outputs.get("class") == "File":
            st = os.lstat(outputs["path"])
            if stat.S_ISLNK(st.st_mode):
                outputs["path"] = os.readlink(outputs["path"])
        else:
            for v in outputs.values():
                deref_links(v)
    if isinstance(outputs, list):
        for v in outputs:
            deref_links(v)

class CommandLineJob(object):
    def run(self, dry_run=False, pull_image=True, rm_container=True, rm_tmpdir=True, move_outputs=True, **kwargs):
        if not os.path.exists(self.outdir):
            os.makedirs(self.outdir)

        #with open(os.path.join(outdir, "cwl.input.json"), "w") as fp:
        #    json.dump(self.joborder, fp)

        runtime = []
        env = {"TMPDIR": self.tmpdir}

        (docker_req, docker_is_req) = get_feature(self, "DockerRequirement")

        for f in self.pathmapper.files():
            if not os.path.exists(self.pathmapper.mapper(f)[0]):
                raise WorkflowException("Required input file %s not found" % self.pathmapper.mapper(f)[0])

        img_id = None
        if docker_req and kwargs.get("use_container") is not False:
            env = os.environ
            img_id = docker.get_from_requirements(docker_req, docker_is_req, pull_image)

        if docker_is_req and img_id is None:
            raise WorkflowException("Docker is required for running this tool.")

        if img_id:
            runtime = ["docker", "run", "-i"]
            for src in self.pathmapper.files():
                vol = self.pathmapper.mapper(src)
                runtime.append("--volume=%s:%s:ro" % vol)
            runtime.append("--volume=%s:%s:rw" % (os.path.abspath(self.outdir), "/var/spool/cwl"))
            runtime.append("--volume=%s:%s:rw" % (os.path.abspath(self.tmpdir), "/tmp"))
            runtime.append("--workdir=%s" % ("/var/spool/cwl"))
            runtime.append("--read-only=true")
            euid = docker_vm_uid() or os.geteuid()
            runtime.append("--user=%s" % (euid))

            if rm_container:
                runtime.append("--rm")

            runtime.append("--env=TMPDIR=/tmp")

            for t,v in self.environment.items():
                runtime.append("--env=%s=%s" % (t, v))

            runtime.append(img_id)
        else:
            env = self.environment
            if not os.path.exists(self.tmpdir):
                os.makedirs(self.tmpdir)
            env["TMPDIR"] = self.tmpdir
            vars_to_preserve = kwargs.get("preserve_environment")
            if vars_to_preserve is not None:
                for key, value in os.environ.items():
                    if key in vars_to_preserve and key not in env:
                        env[key] = value

        stdin = None
        stdout = None

        scr, _  = get_feature(self, "ShellCommandRequirement")

        if scr:
            shouldquote = lambda x: False
        else:
            shouldquote = needs_shell_quoting_re.search

        _logger.info("[job %s] %s$ %s%s%s",
                     self.name,
                     self.outdir,
                     " ".join([shellescape.quote(str(arg)) if shouldquote(str(arg)) else str(arg) for arg in (runtime + self.command_line)]),
                     ' < %s' % (self.stdin) if self.stdin else '',
                     ' > %s' % os.path.join(self.outdir, self.stdout) if self.stdout else '')

        if dry_run:
            return (self.outdir, {})

        outputs = {}

        try:
            for t in self.generatefiles:
                if isinstance(self.generatefiles[t], dict):
                    src = self.generatefiles[t]["path"]
                    dst = os.path.join(self.outdir, t)
                    if os.path.dirname(self.pathmapper.reversemap(src)[1]) != self.outdir:
                        _logger.debug("symlinking %s to %s", dst, src)
                        os.symlink(src, dst)
                else:
                    with open(os.path.join(self.outdir, t), "w") as f:
                        f.write(self.generatefiles[t])

            if self.stdin:
                stdin = open(self.pathmapper.mapper(self.stdin)[0], "rb")
            else:
                stdin = subprocess.PIPE

            if self.stdout:
                absout = os.path.join(self.outdir, self.stdout)
                dn = os.path.dirname(absout)
                if dn and not os.path.exists(dn):
                    os.makedirs(dn)
                stdout = open(absout, "wb")
            else:
                stdout = sys.stderr

            sp = subprocess.Popen([str(x) for x in runtime + self.command_line],
                                  shell=False,
                                  close_fds=True,
                                  stdin=stdin,
                                  stdout=stdout,
                                  env=env,
                                  cwd=self.outdir)

            if stdin == subprocess.PIPE:
                sp.stdin.close()

            rcode = sp.wait()

            if stdin != subprocess.PIPE:
                stdin.close()

            if stdout is not sys.stderr:
                stdout.close()

            if self.successCodes and rcode in self.successCodes:
                processStatus = "success"
            elif self.temporaryFailCodes and rcode in self.temporaryFailCodes:
                processStatus = "temporaryFail"
            elif self.permanentFailCodes and rcode in self.permanentFailCodes:
                processStatus = "permanentFail"
            elif rcode == 0:
                processStatus = "success"
            else:
                processStatus = "permanentFail"

            for t in self.generatefiles:
                if isinstance(self.generatefiles[t], dict):
                    src = self.generatefiles[t]["path"]
                    dst = os.path.join(self.outdir, t)
                    if os.path.dirname(self.pathmapper.reversemap(src)[1]) != self.outdir:
                        os.remove(dst)
                        os.symlink(self.pathmapper.reversemap(src)[1], dst)

            outputs = self.collect_outputs(self.outdir)

        except OSError as e:
            if e.errno == 2:
                if runtime:
                    _logger.error("'%s' not found", runtime[0])
                else:
                    _logger.error("'%s' not found", self.command_line[0])
            else:
                _logger.exception("Exception while running job")
            processStatus = "permanentFail"
        except WorkflowException as e:
            _logger.error("Error while running job: %s" % e)
            processStatus = "permanentFail"
        except Exception as e:
            _logger.exception("Exception while running job")
            processStatus = "permanentFail"

        if processStatus != "success":
            _logger.warn("[job %s] completed %s", self.name, processStatus)
        else:
            _logger.debug("[job %s] completed %s", self.name, processStatus)
        _logger.debug("[job %s] %s", self.name, json.dumps(outputs, indent=4))

        self.output_callback(outputs, processStatus)

        if rm_tmpdir:
            _logger.debug("[job %s] Removing temporary directory %s", self.name, self.tmpdir)
            shutil.rmtree(self.tmpdir, True)

        if move_outputs and empty_subtree(self.outdir):
            _logger.debug("[job %s] Removing empty output directory %s", self.name, self.outdir)
            shutil.rmtree(self.outdir, True)

@@ -2385,16 +2385,57 @@
 =true%22)%0A
+            runtime.append(%22--net=none%22)%0A
         

Add --net=none to disable networking for Docker containers by default.