#!/usr/bin/env python

import arvados
import re
import os
import subprocess
import sys
import shutil
import subst

os.umask(0077)

t = arvados.current_task().tmpdir

os.chdir(arvados.current_task().tmpdir)
os.mkdir("tmpdir")
os.mkdir("output")

os.chdir("output")

if len(arvados.current_task()['parameters']) > 0:
    p = arvados.current_task()['parameters']
else:
    p = arvados.current_job()['script_parameters']

links = []

def sub_link(v):
    r = os.path.basename(v)
    os.symlink(os.path.join(os.environ['TASK_KEEPMOUNT'], v) , r)
    links.append(r)
    return r

def sub_tmpdir(v):
    return os.path.join(arvados.current_task().tmpdir, 'tmpdir')

subst.default_subs["link "] = sub_link
subst.default_subs["tmpdir"] = sub_tmpdir

rcode = 1

try:
    cmd = []
    for c in p["command"]:
        cmd.append(subst.do_substitution(p, c))

    stdoutname = None
    stdoutfile = None
    if "stdout" in p:
        stdoutname = subst.do_substitution(p, p["stdout"])
        stdoutfile = open(stdoutname, "wb")

    print("run-command running: {}{}".format(' '.join(cmd), (" > " + stdoutname) if stdoutname != None else ""))

    rcode = subprocess.call(cmd, stdout=stdoutfile)

    print("run-command completed with exit code %i" % rcode)

except Exception as e:
    print("run-command exception: {}".format(e))

finally:
    for l in links:
        os.unlink(l)

    out = arvados.CollectionWriter()
    out.write_directory_tree(".", max_manifest_depth=0)
    outuuid = out.finish()
    arvados.api('v1').job_tasks().update(uuid=arvados.current_task()['uuid'],
                                         body={
                                             'output':outuuid,
                                             'success': (rcode == 0),
                                             'progress':1.0
                                         }).execute()

if rcode == 0:
    os.chdir("..")
    shutil.rmtree("tmpdir")
    shutil.rmtree("output")

sys.exit(rcode)