docker_scriptrunner: scriptrunner.py annotate

annotate scriptrunner.py @ 0:b6211faea403 draft

planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty

author	mvdbeek
date	Fri, 08 Jul 2016 15:09:10 -0400
parents
children	813b55d27809

rev	line source
0 b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	1 # DockerToolFactory.py
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	2 # see https://github.com/mvdbeek/scriptrunner
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	3
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	4 import sys
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	5 import shutil
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	6 import subprocess
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	7 import os
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	8 import time
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	9 import tempfile
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	10 import argparse
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	11 import getpass
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	12 import tarfile
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	13 import re
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	14 import shutil
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	15 import math
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	16 import fileinput
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	17 from os.path import abspath
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	18
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	19
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	20 progname = os.path.split(sys.argv[0])[1]
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	21 verbose = False
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	22 debug = False
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	23
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	24 def timenow():
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	25 """return current time as a string
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	26 """
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	27 return time.strftime('%d/%m/%Y %H:%M:%S', time.localtime(time.time()))
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	28
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	29 html_escape_table = {
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	30 "&": "&",
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	31 ">": ">",
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	32 "<": "<",
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	33 "$": "\$"
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	34 }
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	35
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	36 def html_escape(text):
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	37 """Produce entities within text."""
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	38 return "".join(html_escape_table.get(c,c) for c in text)
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	39
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	40 def cmd_exists(cmd):
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	41 return subprocess.call("type " + cmd, shell=True,
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	42 stdout=subprocess.PIPE, stderr=subprocess.PIPE) == 0
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	43
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	44 def construct_bind(host_path, container_path=False, binds=None, ro=True):
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	45 #TODO remove container_path if it's alwyas going to be the same as host_path
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	46 '''build or extend binds dictionary with container path. binds is used
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	47 to mount all files using the docker-py client.'''
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	48 if not binds:
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	49 binds={}
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	50 if isinstance(host_path, list):
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	51 for k,v in enumerate(host_path):
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	52 if not container_path:
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	53 container_path=host_path[k]
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	54 binds[host_path[k]]={'bind':container_path, 'ro':ro}
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	55 container_path=False #could be more elegant
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	56 return binds
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	57 else:
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	58 if not container_path:
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	59 container_path=host_path
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	60 binds[host_path]={'bind':container_path, 'ro':ro}
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	61 return binds
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	62
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	63 def switch_to_docker(opts):
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	64 import docker #need local import, as container does not have docker-py
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	65 current_user = getpass.getuser()
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	66 docker_client=docker.Client()
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	67 toolfactory_path=abspath(sys.argv[0])
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	68 binds=construct_bind(host_path=opts.script_path, ro=False)
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	69 binds=construct_bind(binds=binds, host_path=abspath(opts.output_dir), ro=False)
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	70 if len(opts.input_tab)>0:
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	71 binds=construct_bind(binds=binds, host_path=opts.input_tab, ro=True)
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	72 if not opts.output_tab == 'None':
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	73 binds=construct_bind(binds=binds, host_path=opts.output_tab, ro=False)
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	74 if opts.make_HTML:
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	75 binds=construct_bind(binds=binds, host_path=opts.output_html, ro=False)
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	76 binds=construct_bind(binds=binds, host_path=toolfactory_path)
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	77 volumes=binds.keys()
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	78 sys.argv=[abspath(opts.output_dir) if sys.argv[i-1]=='--output_dir' else arg for i,arg in enumerate(sys.argv)] ##inject absolute path of working_dir
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	79 cmd=['python', '-u']+sys.argv+['--dockerized', '1']
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	80 container=docker_client.create_container(
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	81 image=opts.docker_image, # Make this configureable through job_conf
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	82 user=current_user, # TODO: make this configurable on the current user
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	83 volumes=volumes,
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	84 command=cmd
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	85 )
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	86 docker_client.start(container=container[u'Id'], binds=binds)
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	87 docker_client.wait(container=container[u'Id'])
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	88 logs=docker_client.logs(container=container[u'Id'])
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	89 print "".join([log for log in logs])
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	90 docker_client.remove_container(container[u'Id'])
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	91
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	92 class ScriptRunner:
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	93 """class is a wrapper for an arbitrary script
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	94 """
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	95
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	96 def __init__(self,opts=None,treatbashSpecial=True, image_tag='base'):
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	97 """
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	98 cleanup inputs, setup some outputs
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	99
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	100 """
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	101 self.opts = opts
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	102 self.scriptname = 'script'
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	103 self.useGM = cmd_exists('gm')
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	104 self.useIM = cmd_exists('convert')
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	105 self.useGS = cmd_exists('gs')
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	106 self.temp_warned = False # we want only one warning if $TMP not set
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	107 self.treatbashSpecial = treatbashSpecial
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	108 self.image_tag = image_tag
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	109 os.chdir(abspath(opts.output_dir))
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	110 self.thumbformat = 'png'
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	111 s = open(self.opts.script_path,'r').readlines()
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	112 s = [x.rstrip() for x in s] # remove pesky dos line endings if needed
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	113 self.script = '\n'.join(s)
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	114 fhandle,self.sfile = tempfile.mkstemp(prefix='script',suffix=".%s" % (opts.interpreter))
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	115 tscript = open(self.sfile,'w') # use self.sfile as script source for Popen
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	116 tscript.write(self.script)
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	117 tscript.close()
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	118 self.indentedScript = '\n'.join([' %s' % html_escape(x) for x in s]) # for restructured text in help
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	119 self.escapedScript = '\n'.join([html_escape(x) for x in s])
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	120 self.elog = os.path.join(self.opts.output_dir,"%s_error.log" % self.scriptname)
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	121 if opts.output_dir: # may not want these complexities
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	122 self.tlog = os.path.join(self.opts.output_dir,"%s_runner.log" % self.scriptname)
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	123 art = '%s.%s' % (self.scriptname,opts.interpreter)
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	124 artpath = os.path.join(self.opts.output_dir,art) # need full path
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	125 artifact = open(artpath,'w') # use self.sfile as script source for Popen
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	126 artifact.write(self.script)
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	127 artifact.close()
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	128 self.cl = []
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	129 self.html = []
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	130 a = self.cl.append
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	131 a(opts.interpreter)
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	132 if self.treatbashSpecial and opts.interpreter in ['bash','sh']:
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	133 a(self.sfile)
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	134 else:
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	135 a('-') # stdin
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	136 for input in opts.input_tab:
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	137 a(input)
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	138 if opts.output_tab == 'None': #If tool generates only HTML, set output name to toolname
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	139 a(str(self.scriptname)+'.out')
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	140 a(opts.output_tab)
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	141 for param in opts.additional_parameters:
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	142 param, value=param.split(',')
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	143 a('--'+param)
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	144 a(value)
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	145 self.outFormats = opts.output_format
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	146 self.inputFormats = [formats for formats in opts.input_formats]
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	147 self.test1Input = '%s_test1_input.xls' % self.scriptname
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	148 self.test1Output = '%s_test1_output.xls' % self.scriptname
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	149 self.test1HTML = '%s_test1_output.html' % self.scriptname
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	150
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	151
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	152 def compressPDF(self,inpdf=None,thumbformat='png'):
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	153 """need absolute path to pdf
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	154 note that GS gets confoozled if no $TMP or $TEMP
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	155 so we set it
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	156 """
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	157 assert os.path.isfile(inpdf), "## Input %s supplied to %s compressPDF not found" % (inpdf,self.myName)
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	158 hlog = os.path.join(self.opts.output_dir,"compress_%s.txt" % os.path.basename(inpdf))
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	159 sto = open(hlog,'a')
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	160 our_env = os.environ.copy()
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	161 our_tmp = our_env.get('TMP',None)
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	162 if not our_tmp:
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	163 our_tmp = our_env.get('TEMP',None)
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	164 if not (our_tmp and os.path.exists(our_tmp)):
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	165 newtmp = os.path.join(self.opts.output_dir,'tmp')
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	166 try:
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	167 os.mkdir(newtmp)
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	168 except:
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	169 sto.write('## WARNING - cannot make %s - it may exist or permissions need fixing\n' % newtmp)
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	170 our_env['TEMP'] = newtmp
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	171 if not self.temp_warned:
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	172 sto.write('## WARNING - no $TMP or $TEMP!!! Please fix - using %s temporarily\n' % newtmp)
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	173 self.temp_warned = True
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	174 outpdf = '%s_compressed' % inpdf
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	175 cl = ["gs", "-sDEVICE=pdfwrite", "-dNOPAUSE", "-dUseCIEColor", "-dBATCH","-dPDFSETTINGS=/printer", "-sOutputFile=%s" % outpdf,inpdf]
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	176 x = subprocess.Popen(cl,stdout=sto,stderr=sto,cwd=self.opts.output_dir,env=our_env)
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	177 retval1 = x.wait()
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	178 sto.close()
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	179 if retval1 == 0:
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	180 os.unlink(inpdf)
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	181 shutil.move(outpdf,inpdf)
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	182 os.unlink(hlog)
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	183 hlog = os.path.join(self.opts.output_dir,"thumbnail_%s.txt" % os.path.basename(inpdf))
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	184 sto = open(hlog,'w')
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	185 outpng = '%s.%s' % (os.path.splitext(inpdf)[0],thumbformat)
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	186 # if self.useGM:
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	187 # cl2 = ['gm', 'convert', inpdf, outpng]
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	188 # else: # assume imagemagick
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	189 cl2 = ['convert', inpdf, outpng]
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	190 x = subprocess.Popen(cl2,stdout=sto,stderr=sto,cwd=self.opts.output_dir,env=our_env)
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	191 retval2 = x.wait()
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	192 sto.close()
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	193 if retval2 == 0:
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	194 os.unlink(hlog)
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	195 retval = retval1 or retval2
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	196 return retval
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	197
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	198
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	199 def getfSize(self,fpath,outpath):
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	200 """
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	201 format a nice file size string
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	202 """
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	203 size = ''
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	204 fp = os.path.join(outpath,fpath)
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	205 if os.path.isfile(fp):
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	206 size = '0 B'
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	207 n = float(os.path.getsize(fp))
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	208 if n > 2**20:
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	209 size = '%1.1f MB' % (n/2**20)
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	210 elif n > 2**10:
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	211 size = '%1.1f KB' % (n/2**10)
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	212 elif n > 0:
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	213 size = '%d B' % (int(n))
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	214 return size
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	215
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	216 def makeHtml(self):
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	217 """ Create an HTML file content to list all the artifacts found in the output_dir
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	218 """
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	219
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	220 galhtmlprefix = """<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	221 <html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	222 <head> <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	223 <meta name="generator" content="Galaxy %s tool output - see http://g2.trac.bx.psu.edu/" />
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	224 <title></title>
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	225 <link rel="stylesheet" href="/static/style/base.css" type="text/css" />
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	226 </head>
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	227 <body>
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	228 <div class="toolFormBody">
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	229 """
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	230 galhtmlattr = """<hr/><div class="infomessage">This tool (%s) was generated by the <a href="https://bitbucket.org/fubar/galaxytoolfactory/overview">Galaxy Tool Factory</a></div><br/>"""
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	231 galhtmlpostfix = """</div></body></html>\n"""
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	232
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	233 flist = os.listdir(self.opts.output_dir)
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	234 flist = [x for x in flist if x <> 'Rplots.pdf']
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	235 flist.sort()
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	236 html = []
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	237 html.append(galhtmlprefix % progname)
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	238 html.append('<div class="infomessage">Galaxy Tool "%s" run at %s</div><br/>' % (self.scriptname,timenow()))
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	239 fhtml = []
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	240 if len(flist) > 0:
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	241 logfiles = [x for x in flist if x.lower().endswith('.log')] # log file names determine sections
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	242 logfiles.sort()
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	243 logfiles = [x for x in logfiles if abspath(x) <> abspath(self.tlog)]
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	244 logfiles.append(abspath(self.tlog)) # make it the last one
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	245 pdflist = []
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	246 npdf = len([x for x in flist if os.path.splitext(x)[-1].lower() == '.pdf'])
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	247 for rownum,fname in enumerate(flist):
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	248 dname,e = os.path.splitext(fname)
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	249 sfsize = self.getfSize(fname,self.opts.output_dir)
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	250 if e.lower() == '.pdf' : # compress and make a thumbnail
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	251 thumb = '%s.%s' % (dname,self.thumbformat)
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	252 pdff = os.path.join(self.opts.output_dir,fname)
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	253 retval = self.compressPDF(inpdf=pdff,thumbformat=self.thumbformat)
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	254 if retval == 0:
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	255 pdflist.append((fname,thumb))
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	256 else:
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	257 pdflist.append((fname,fname))
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	258 if (rownum+1) % 2 == 0:
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	259 fhtml.append('<tr class="odd_row"><td><a href="%s">%s</a></td><td>%s</td></tr>' % (fname,fname,sfsize))
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	260 else:
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	261 fhtml.append('<tr><td><a href="%s">%s</a></td><td>%s</td></tr>' % (fname,fname,sfsize))
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	262 for logfname in logfiles: # expect at least tlog - if more
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	263 if abspath(logfname) == abspath(self.tlog): # handled later
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	264 sectionname = 'All tool run'
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	265 if (len(logfiles) > 1):
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	266 sectionname = 'Other'
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	267 ourpdfs = pdflist
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	268 else:
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	269 realname = os.path.basename(logfname)
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	270 sectionname = os.path.splitext(realname)[0].split('_')[0] # break in case _ added to log
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	271 ourpdfs = [x for x in pdflist if os.path.basename(x[0]).split('_')[0] == sectionname]
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	272 pdflist = [x for x in pdflist if os.path.basename(x[0]).split('_')[0] <> sectionname] # remove
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	273 nacross = 1
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	274 npdf = len(ourpdfs)
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	275
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	276 if npdf > 0:
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	277 nacross = math.sqrt(npdf) ## int(round(math.log(npdf,2)))
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	278 if int(nacross)**2 != npdf:
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	279 nacross += 1
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	280 nacross = int(nacross)
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	281 width = min(400,int(1200/nacross))
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	282 html.append('<div class="toolFormTitle">%s images and outputs</div>' % sectionname)
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	283 html.append('(Click on a thumbnail image to download the corresponding original PDF image)<br/>')
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	284 ntogo = nacross # counter for table row padding with empty cells
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	285 html.append('<div><table class="simple" cellpadding="2" cellspacing="2">\n<tr>')
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	286 for i,paths in enumerate(ourpdfs):
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	287 fname,thumb = paths
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	288 s= """<td><a href="%s"><img src="%s" title="Click to download a PDF of %s" hspace="5" width="%d"
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	289 alt="Image called %s"/></a></td>\n""" % (fname,thumb,fname,width,fname)
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	290 if ((i+1) % nacross == 0):
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	291 s += '</tr>\n'
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	292 ntogo = 0
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	293 if i < (npdf - 1): # more to come
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	294 s += '<tr>'
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	295 ntogo = nacross
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	296 else:
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	297 ntogo -= 1
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	298 html.append(s)
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	299 if html[-1].strip().endswith('</tr>'):
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	300 html.append('</table></div>\n')
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	301 else:
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	302 if ntogo > 0: # pad
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	303 html.append('<td> </td>'*ntogo)
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	304 html.append('</tr></table></div>\n')
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	305 logt = open(logfname,'r').readlines()
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	306 logtext = [x for x in logt if x.strip() > '']
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	307 html.append('<div class="toolFormTitle">%s log output</div>' % sectionname)
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	308 if len(logtext) > 1:
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	309 html.append('\n<pre>\n')
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	310 html += logtext
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	311 html.append('\n</pre>\n')
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	312 else:
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	313 html.append('%s is empty<br/>' % logfname)
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	314 if len(fhtml) > 0:
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	315 fhtml.insert(0,'<div><table class="colored" cellpadding="3" cellspacing="3"><tr><th>Output File Name (click to view)</th><th>Size</th></tr>\n')
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	316 fhtml.append('</table></div><br/>')
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	317 html.append('<div class="toolFormTitle">All output files available for downloading</div>\n')
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	318 html += fhtml # add all non-pdf files to the end of the display
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	319 else:
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	320 html.append('<div class="warningmessagelarge">### Error - %s returned no files - please confirm that parameters are sane</div>' % self.opts.interpreter)
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	321 html.append(galhtmlpostfix)
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	322 htmlf = file(self.opts.output_html,'w')
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	323 htmlf.write('\n'.join(html))
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	324 htmlf.write('\n')
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	325 htmlf.close()
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	326 self.html = html
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	327
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	328
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	329 def run(self):
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	330 """
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	331 scripts must be small enough not to fill the pipe!
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	332 """
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	333 if self.treatbashSpecial and self.opts.interpreter in ['bash','sh']:
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	334 retval = self.runBash()
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	335 else:
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	336 if self.opts.output_dir:
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	337 ste = open(self.elog,'w')
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	338 sto = open(self.tlog,'w')
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	339 sto.write('## Toolfactory generated command line = %s\n' % ' '.join(self.cl))
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	340 sto.flush()
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	341 print("commandline is %s" % (self.cl))
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	342 print("environment is %s" % (os.environ))
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	343 p = subprocess.Popen(self.cl,shell=False,stdout=sto,stderr=ste,stdin=subprocess.PIPE,cwd=self.opts.output_dir)
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	344 else:
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	345 p = subprocess.Popen(self.cl,shell=False,stdin=subprocess.PIPE)
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	346 p.stdin.write(self.script)
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	347 p.stdin.close()
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	348 retval = p.wait()
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	349 if self.opts.output_dir:
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	350 sto.close()
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	351 ste.close()
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	352 err = open(self.elog,'r').readlines()
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	353 if retval <> 0 and err: # problem
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	354 print >> sys.stderr,err #same problem, need to capture docker stdin/stdout
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	355 if self.opts.make_HTML:
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	356 self.makeHtml()
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	357 return retval
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	358
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	359 def runBash(self):
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	360 """
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	361 cannot use - for bash so use self.sfile
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	362 """
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	363 if self.opts.output_dir:
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	364 s = '## Toolfactory generated command line = %s\n' % ' '.join(self.cl)
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	365 sto = open(self.tlog,'w')
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	366 sto.write(s)
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	367 sto.flush()
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	368 p = subprocess.Popen(self.cl,shell=False,stdout=sto,stderr=sto,cwd=self.opts.output_dir)
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	369 else:
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	370 p = subprocess.Popen(self.cl,shell=False)
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	371 retval = p.wait()
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	372 if self.opts.output_dir:
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	373 sto.close()
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	374 if self.opts.make_HTML:
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	375 self.makeHtml()
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	376 return retval
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	377
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	378
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	379 def main():
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	380 u = """
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	381 This is a Galaxy wrapper. It expects to be called by a special purpose tool.xml as:
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	382 <command interpreter="python">rgBaseScriptWrapper.py --script_path "$scriptPath" --tool_name "foo" --interpreter "Rscript"
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	383 </command>
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	384 """
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	385 op = argparse.ArgumentParser()
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	386 a = op.add_argument
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	387 a('--docker_image',default=None)
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	388 a('--script_path',default=None)
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	389 a('--tool_name',default=None)
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	390 a('--interpreter',default=None)
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	391 a('--output_dir',default='./')
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	392 a('--output_html',default=None)
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	393 a('--input_tab',default='None', nargs='*')
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	394 a('--output_tab',default='None')
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	395 a('--user_email',default='Unknown')
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	396 a('--bad_user',default=None)
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	397 a('--make_HTML',default=None)
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	398 a('--new_tool',default=None)
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	399 a('--dockerized',default=0)
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	400 a('--output_format', default='tabular')
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	401 a('--input_format', dest='input_formats', action='append', default=[])
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	402 a('--additional_parameters', dest='additional_parameters', action='append', default=[])
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	403 opts = op.parse_args()
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	404 assert not opts.bad_user,'UNAUTHORISED: %s is NOT authorized to use this tool until Galaxy admin adds %s to admin_users in universe_wsgi.ini' % (opts.bad_user,opts.bad_user)
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	405 assert os.path.isfile(opts.script_path),'## Tool Factory wrapper expects a script path - eg --script_path=foo.R'
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	406 if opts.output_dir:
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	407 try:
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	408 os.makedirs(opts.output_dir)
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	409 except:
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	410 pass
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	411 if opts.dockerized==0:
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	412 switch_to_docker(opts)
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	413 return
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	414 r = ScriptRunner(opts)
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	415 retcode = r.run()
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	416 os.unlink(r.sfile)
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	417 if retcode:
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	418 sys.exit(retcode) # indicate failure to job runner
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	419
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	420
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	421 if __name__ == "__main__":
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty mvdbeek parents: diff changeset	422 main()

Mercurial > repos > mvdbeek > docker_scriptrunner

annotate scriptrunner.py @ 0:b6211faea403 draft