docker_scriptrunner: scriptrunner.py annotate

annotate scriptrunner.py @ 0:21d312776891 draft

planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty

author	mvdbeek
date	Sat, 09 Jul 2016 16:57:13 -0400
parents
children	495946ffc2d6

rev	line source
0 21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	1 # DockerToolFactory.py
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	2 # see https://github.com/mvdbeek/scriptrunner
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	3
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	4 import sys
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	5 import shutil
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	6 import subprocess
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	7 import os
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	8 import time
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	9 import tempfile
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	10 import argparse
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	11 import getpass
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	12 import tarfile
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	13 import re
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	14 import shutil
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	15 import math
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	16 import fileinput
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	17 from os.path import abspath
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	18
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	19
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	20 progname = os.path.split(sys.argv[0])[1]
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	21 verbose = False
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	22 debug = False
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	23
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	24 def timenow():
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	25 """return current time as a string
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	26 """
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	27 return time.strftime('%d/%m/%Y %H:%M:%S', time.localtime(time.time()))
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	28
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	29 html_escape_table = {
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	30 "&": "&",
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	31 ">": ">",
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	32 "<": "<",
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	33 "$": "\$"
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	34 }
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	35
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	36 def html_escape(text):
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	37 """Produce entities within text."""
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	38 return "".join(html_escape_table.get(c,c) for c in text)
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	39
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	40 def cmd_exists(cmd):
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	41 return subprocess.call("type " + cmd, shell=True,
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	42 stdout=subprocess.PIPE, stderr=subprocess.PIPE) == 0
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	43
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	44 def construct_bind(host_path, container_path=False, binds=None, ro=True):
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	45 #TODO remove container_path if it's alwyas going to be the same as host_path
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	46 '''build or extend binds dictionary with container path. binds is used
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	47 to mount all files using the docker-py client.'''
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	48 if not binds:
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	49 binds={}
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	50 if isinstance(host_path, list):
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	51 for k,v in enumerate(host_path):
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	52 if not container_path:
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	53 container_path=host_path[k]
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	54 binds[host_path[k]]={'bind':container_path, 'ro':ro}
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	55 container_path=False #could be more elegant
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	56 return binds
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	57 else:
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	58 if not container_path:
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	59 container_path=host_path
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	60 binds[host_path]={'bind':container_path, 'ro':ro}
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	61 return binds
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	62
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	63 def switch_to_docker(opts):
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	64 import docker #need local import, as container does not have docker-py
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	65 user_id = os.getuid()
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	66 group_id = os.getgid()
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	67 docker_client=docker.Client()
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	68 toolfactory_path=abspath(sys.argv[0])
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	69 binds=construct_bind(host_path=opts.script_path, ro=False)
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	70 binds=construct_bind(binds=binds, host_path=abspath(opts.output_dir), ro=False)
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	71 if len(opts.input_tab)>0:
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	72 binds=construct_bind(binds=binds, host_path=opts.input_tab, ro=True)
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	73 if not opts.output_tab == 'None':
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	74 binds=construct_bind(binds=binds, host_path=opts.output_tab, ro=False)
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	75 if opts.make_HTML:
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	76 binds=construct_bind(binds=binds, host_path=opts.output_html, ro=False)
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	77 binds=construct_bind(binds=binds, host_path=toolfactory_path)
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	78 volumes=binds.keys()
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	79 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
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	80 cmd=['python', '-u']+sys.argv+['--dockerized', '1', "--user_id", str(user_id), "--group_id", str(group_id)]
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	81 image_exists = [ True for image in docker_client.images() if opts.docker_image in image['RepoTags'] ]
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	82 if not image_exists:
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	83 docker_client.pull(opts.docker_image)
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	84 container=docker_client.create_container(
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	85 image=opts.docker_image,
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	86 volumes=volumes,
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	87 command=cmd
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	88 )
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	89 docker_client.start(container=container[u'Id'], binds=binds)
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	90 docker_client.wait(container=container[u'Id'])
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	91 logs=docker_client.logs(container=container[u'Id'])
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	92 print "".join([log for log in logs])
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	93 docker_client.remove_container(container[u'Id'])
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	94
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	95 class ScriptRunner:
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	96 """class is a wrapper for an arbitrary script
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	97 """
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	98
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	99 def __init__(self,opts=None,treatbashSpecial=True, image_tag='base'):
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	100 """
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	101 cleanup inputs, setup some outputs
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	102
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	103 """
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	104 self.opts = opts
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	105 self.scriptname = 'script'
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	106 self.useIM = cmd_exists('convert')
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	107 self.useGS = cmd_exists('gs')
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	108 self.temp_warned = False # we want only one warning if $TMP not set
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	109 self.treatbashSpecial = treatbashSpecial
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	110 self.image_tag = image_tag
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	111 os.chdir(abspath(opts.output_dir))
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	112 self.thumbformat = 'png'
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	113 s = open(self.opts.script_path,'r').readlines()
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	114 s = [x.rstrip() for x in s] # remove pesky dos line endings if needed
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	115 self.script = '\n'.join(s)
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	116 fhandle,self.sfile = tempfile.mkstemp(prefix='script',suffix=".%s" % (opts.interpreter))
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	117 tscript = open(self.sfile,'w') # use self.sfile as script source for Popen
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	118 tscript.write(self.script)
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	119 tscript.close()
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	120 self.indentedScript = '\n'.join([' %s' % html_escape(x) for x in s]) # for restructured text in help
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	121 self.escapedScript = '\n'.join([html_escape(x) for x in s])
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	122 self.elog = os.path.join(self.opts.output_dir,"%s_error.log" % self.scriptname)
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	123 if opts.output_dir: # may not want these complexities
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	124 self.tlog = os.path.join(self.opts.output_dir,"%s_runner.log" % self.scriptname)
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	125 art = '%s.%s' % (self.scriptname,opts.interpreter)
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	126 artpath = os.path.join(self.opts.output_dir,art) # need full path
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	127 artifact = open(artpath,'w') # use self.sfile as script source for Popen
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	128 artifact.write(self.script)
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	129 artifact.close()
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	130 self.cl = []
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	131 self.html = []
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	132 a = self.cl.append
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	133 a(opts.interpreter)
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	134 if self.treatbashSpecial and opts.interpreter in ['bash','sh']:
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	135 a(self.sfile)
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	136 else:
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	137 a('-') # stdin
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	138 for input in opts.input_tab:
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	139 a(input)
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	140 if opts.output_tab == 'None': #If tool generates only HTML, set output name to toolname
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	141 a(str(self.scriptname)+'.out')
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	142 a(opts.output_tab)
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	143 for param in opts.additional_parameters:
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	144 param, value=param.split(',')
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	145 a('--'+param)
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	146 a(value)
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	147 self.outFormats = opts.output_format
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	148 self.inputFormats = [formats for formats in opts.input_formats]
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	149 self.test1Input = '%s_test1_input.xls' % self.scriptname
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	150 self.test1Output = '%s_test1_output.xls' % self.scriptname
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	151 self.test1HTML = '%s_test1_output.html' % self.scriptname
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	152
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	153
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	154 def compressPDF(self,inpdf=None,thumbformat='png'):
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	155 """need absolute path to pdf
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	156 note that GS gets confoozled if no $TMP or $TEMP
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	157 so we set it
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	158 """
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	159 assert os.path.isfile(inpdf), "## Input %s supplied to %s compressPDF not found" % (inpdf,self.myName)
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	160 hlog = os.path.join(self.opts.output_dir,"compress_%s.txt" % os.path.basename(inpdf))
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	161 sto = open(hlog,'a')
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	162 our_env = os.environ.copy()
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	163 our_tmp = our_env.get('TMP',None)
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	164 if not our_tmp:
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	165 our_tmp = our_env.get('TEMP',None)
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	166 if not (our_tmp and os.path.exists(our_tmp)):
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	167 newtmp = os.path.join(self.opts.output_dir,'tmp')
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	168 try:
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	169 os.mkdir(newtmp)
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	170 except:
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	171 sto.write('## WARNING - cannot make %s - it may exist or permissions need fixing\n' % newtmp)
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	172 our_env['TEMP'] = newtmp
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	173 if not self.temp_warned:
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	174 sto.write('## WARNING - no $TMP or $TEMP!!! Please fix - using %s temporarily\n' % newtmp)
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	175 self.temp_warned = True
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	176 outpdf = '%s_compressed' % inpdf
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	177 cl = ["gs", "-sDEVICE=pdfwrite", "-dNOPAUSE", "-dUseCIEColor", "-dBATCH","-dPDFSETTINGS=/printer", "-sOutputFile=%s" % outpdf,inpdf]
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	178 x = subprocess.Popen(cl,stdout=sto,stderr=sto,cwd=self.opts.output_dir,env=our_env)
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	179 retval1 = x.wait()
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	180 sto.close()
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	181 if retval1 == 0:
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	182 os.unlink(inpdf)
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	183 shutil.move(outpdf,inpdf)
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	184 os.unlink(hlog)
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	185 hlog = os.path.join(self.opts.output_dir,"thumbnail_%s.txt" % os.path.basename(inpdf))
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	186 sto = open(hlog,'w')
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	187 outpng = '%s.%s' % (os.path.splitext(inpdf)[0],thumbformat)
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	188 cl2 = ['convert', inpdf, outpng]
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	189 x = subprocess.Popen(cl2,stdout=sto,stderr=sto,cwd=self.opts.output_dir,env=our_env)
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	190 retval2 = x.wait()
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	191 sto.close()
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	192 if retval2 == 0:
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	193 os.unlink(hlog)
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	194 retval = retval1 or retval2
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	195 return retval
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	196
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	197
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	198 def getfSize(self,fpath,outpath):
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	199 """
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	200 format a nice file size string
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	201 """
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	202 size = ''
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	203 fp = os.path.join(outpath,fpath)
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	204 if os.path.isfile(fp):
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	205 size = '0 B'
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	206 n = float(os.path.getsize(fp))
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	207 if n > 2**20:
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	208 size = '%1.1f MB' % (n/2**20)
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	209 elif n > 2**10:
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	210 size = '%1.1f KB' % (n/2**10)
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	211 elif n > 0:
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	212 size = '%d B' % (int(n))
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	213 return size
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	214
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	215 def makeHtml(self):
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	216 """ Create an HTML file content to list all the artifacts found in the output_dir
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	217 """
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	218
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	219 galhtmlprefix = """<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	220 <html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	221 <head> <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	222 <meta name="generator" content="Galaxy %s tool output - see http://g2.trac.bx.psu.edu/" />
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	223 <title></title>
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	224 <link rel="stylesheet" href="/static/style/base.css" type="text/css" />
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	225 </head>
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	226 <body>
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	227 <div class="toolFormBody">
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	228 """
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	229 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/>"""
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	230 galhtmlpostfix = """</div></body></html>\n"""
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	231
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	232 flist = os.listdir(self.opts.output_dir)
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	233 flist = [x for x in flist if x <> 'Rplots.pdf']
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	234 flist.sort()
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	235 html = []
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	236 html.append(galhtmlprefix % progname)
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	237 html.append('<div class="infomessage">Galaxy Tool "%s" run at %s</div><br/>' % (self.scriptname,timenow()))
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	238 fhtml = []
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	239 if len(flist) > 0:
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	240 logfiles = [x for x in flist if x.lower().endswith('.log')] # log file names determine sections
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	241 logfiles.sort()
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	242 logfiles = [x for x in logfiles if abspath(x) <> abspath(self.tlog)]
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	243 logfiles.append(abspath(self.tlog)) # make it the last one
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	244 pdflist = []
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	245 npdf = len([x for x in flist if os.path.splitext(x)[-1].lower() == '.pdf'])
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	246 for rownum,fname in enumerate(flist):
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	247 dname,e = os.path.splitext(fname)
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	248 sfsize = self.getfSize(fname,self.opts.output_dir)
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	249 if e.lower() == '.pdf' : # compress and make a thumbnail
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	250 thumb = '%s.%s' % (dname,self.thumbformat)
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	251 pdff = os.path.join(self.opts.output_dir,fname)
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	252 retval = self.compressPDF(inpdf=pdff,thumbformat=self.thumbformat)
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	253 if retval == 0:
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	254 pdflist.append((fname,thumb))
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	255 else:
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	256 pdflist.append((fname,fname))
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	257 if (rownum+1) % 2 == 0:
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	258 fhtml.append('<tr class="odd_row"><td><a href="%s">%s</a></td><td>%s</td></tr>' % (fname,fname,sfsize))
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	259 else:
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	260 fhtml.append('<tr><td><a href="%s">%s</a></td><td>%s</td></tr>' % (fname,fname,sfsize))
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	261 for logfname in logfiles: # expect at least tlog - if more
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	262 if abspath(logfname) == abspath(self.tlog): # handled later
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	263 sectionname = 'All tool run'
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	264 if (len(logfiles) > 1):
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	265 sectionname = 'Other'
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	266 ourpdfs = pdflist
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	267 else:
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	268 realname = os.path.basename(logfname)
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	269 sectionname = os.path.splitext(realname)[0].split('_')[0] # break in case _ added to log
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	270 ourpdfs = [x for x in pdflist if os.path.basename(x[0]).split('_')[0] == sectionname]
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	271 pdflist = [x for x in pdflist if os.path.basename(x[0]).split('_')[0] <> sectionname] # remove
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	272 nacross = 1
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	273 npdf = len(ourpdfs)
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	274
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	275 if npdf > 0:
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	276 nacross = math.sqrt(npdf) ## int(round(math.log(npdf,2)))
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	277 if int(nacross)**2 != npdf:
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	278 nacross += 1
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	279 nacross = int(nacross)
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	280 width = min(400,int(1200/nacross))
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	281 html.append('<div class="toolFormTitle">%s images and outputs</div>' % sectionname)
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	282 html.append('(Click on a thumbnail image to download the corresponding original PDF image)<br/>')
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	283 ntogo = nacross # counter for table row padding with empty cells
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	284 html.append('<div><table class="simple" cellpadding="2" cellspacing="2">\n<tr>')
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	285 for i,paths in enumerate(ourpdfs):
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	286 fname,thumb = paths
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	287 s= """<td><a href="%s"><img src="%s" title="Click to download a PDF of %s" hspace="5" width="%d"
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	288 alt="Image called %s"/></a></td>\n""" % (fname,thumb,fname,width,fname)
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	289 if ((i+1) % nacross == 0):
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	290 s += '</tr>\n'
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	291 ntogo = 0
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	292 if i < (npdf - 1): # more to come
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	293 s += '<tr>'
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	294 ntogo = nacross
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	295 else:
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	296 ntogo -= 1
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	297 html.append(s)
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	298 if html[-1].strip().endswith('</tr>'):
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	299 html.append('</table></div>\n')
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	300 else:
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	301 if ntogo > 0: # pad
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	302 html.append('<td> </td>'*ntogo)
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	303 html.append('</tr></table></div>\n')
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	304 logt = open(logfname,'r').readlines()
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	305 logtext = [x for x in logt if x.strip() > '']
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	306 html.append('<div class="toolFormTitle">%s log output</div>' % sectionname)
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	307 if len(logtext) > 1:
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	308 html.append('\n<pre>\n')
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	309 html += logtext
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	310 html.append('\n</pre>\n')
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	311 else:
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	312 html.append('%s is empty<br/>' % logfname)
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	313 if len(fhtml) > 0:
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	314 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')
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	315 fhtml.append('</table></div><br/>')
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	316 html.append('<div class="toolFormTitle">All output files available for downloading</div>\n')
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	317 html += fhtml # add all non-pdf files to the end of the display
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	318 else:
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	319 html.append('<div class="warningmessagelarge">### Error - %s returned no files - please confirm that parameters are sane</div>' % self.opts.interpreter)
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	320 html.append(galhtmlpostfix)
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	321 htmlf = file(self.opts.output_html,'w')
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	322 htmlf.write('\n'.join(html))
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	323 htmlf.write('\n')
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	324 htmlf.close()
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	325 self.html = html
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	326
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	327
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	328 def run(self):
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	329 """
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	330 scripts must be small enough not to fill the pipe!
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	331 """
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	332 if self.treatbashSpecial and self.opts.interpreter in ['bash','sh']:
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	333 retval = self.runBash()
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	334 else:
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	335 if self.opts.output_dir:
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	336 ste = open(self.elog,'w')
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	337 sto = open(self.tlog,'w')
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	338 sto.write('## Toolfactory generated command line = %s\n' % ' '.join(self.cl))
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	339 sto.flush()
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	340 p = subprocess.Popen(self.cl,shell=False,stdout=sto,stderr=ste,stdin=subprocess.PIPE,cwd=self.opts.output_dir)
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	341 else:
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	342 p = subprocess.Popen(self.cl,shell=False,stdin=subprocess.PIPE)
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	343 p.stdin.write(self.script)
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	344 p.stdin.close()
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	345 retval = p.wait()
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	346 if self.opts.output_dir:
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	347 sto.close()
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	348 ste.close()
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	349 err = open(self.elog,'r').readlines()
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	350 if retval <> 0 and err: # problem
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	351 print >> sys.stderr,err #same problem, need to capture docker stdin/stdout
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	352 if self.opts.make_HTML:
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	353 self.makeHtml()
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	354 return retval
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	355
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	356 def runBash(self):
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	357 """
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	358 cannot use - for bash so use self.sfile
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	359 """
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	360 if self.opts.output_dir:
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	361 s = '## Toolfactory generated command line = %s\n' % ' '.join(self.cl)
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	362 sto = open(self.tlog,'w')
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	363 sto.write(s)
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	364 sto.flush()
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	365 p = subprocess.Popen(self.cl,shell=False,stdout=sto,stderr=sto,cwd=self.opts.output_dir)
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	366 else:
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	367 p = subprocess.Popen(self.cl,shell=False)
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	368 retval = p.wait()
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	369 if self.opts.output_dir:
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	370 sto.close()
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	371 if self.opts.make_HTML:
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	372 self.makeHtml()
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	373 return retval
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	374
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	375
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	376 def change_user_id(new_uid, new_gid):
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	377 """
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	378 To avoid issues with wrong user ids, we change the user id of the 'galaxy' user in the container
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	379 to the user id with which the script has been called initially.
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	380 """
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	381 cmd1 = ["/usr/sbin/usermod", "-d", "/var/home/galaxy", "galaxy"]
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	382 cmd2 = ["/usr/sbin/usermod", "-u", new_uid, "galaxy"]
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	383 cmd3 = ["/usr/sbin/groupmod", "-g", new_gid, "galaxy"]
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	384 cmd4 = ["/usr/sbin/usermod", "-d", "/home/galaxy", "galaxy"]
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	385 [subprocess.call(cmd) for cmd in [cmd1, cmd2, cmd3, cmd4]]
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	386
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	387
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	388 def main():
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	389 u = """
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	390 This is a Galaxy wrapper. It expects to be called by a special purpose tool.xml as:
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	391 <command interpreter="python">rgBaseScriptWrapper.py --script_path "$scriptPath" --tool_name "foo" --interpreter "Rscript"
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	392 </command>
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	393 """
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	394 op = argparse.ArgumentParser()
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	395 a = op.add_argument
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	396 a('--docker_image',default=None)
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	397 a('--script_path',default=None)
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	398 a('--tool_name',default=None)
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	399 a('--interpreter',default=None)
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	400 a('--output_dir',default='./')
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	401 a('--output_html',default=None)
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	402 a('--input_tab',default='None', nargs='*')
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	403 a('--output_tab',default='None')
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	404 a('--user_email',default='Unknown')
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	405 a('--bad_user',default=None)
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	406 a('--make_HTML',default=None)
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	407 a('--new_tool',default=None)
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	408 a('--dockerized',default=0)
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	409 a('--group_id',default=None)
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	410 a('--user_id',default=None)
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	411 a('--output_format', default='tabular')
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	412 a('--input_format', dest='input_formats', action='append', default=[])
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	413 a('--additional_parameters', dest='additional_parameters', action='append', default=[])
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	414 opts = op.parse_args()
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	415 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)
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	416 assert os.path.isfile(opts.script_path),'## Tool Factory wrapper expects a script path - eg --script_path=foo.R'
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	417 if opts.output_dir:
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	418 try:
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	419 os.makedirs(opts.output_dir)
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	420 except:
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	421 pass
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	422 if opts.dockerized==0:
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	423 switch_to_docker(opts)
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	424 return
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	425 change_user_id(opts.user_id, opts.group_id)
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	426 os.setgid(int(opts.group_id))
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	427 os.setuid(int(opts.user_id))
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	428 r = ScriptRunner(opts)
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	429 retcode = r.run()
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	430 os.unlink(r.sfile)
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	431 if retcode:
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	432 sys.exit(retcode) # indicate failure to job runner
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	433
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	434
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	435 if __name__ == "__main__":
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty mvdbeek parents: diff changeset	436 main()

Mercurial > repos > mvdbeek > docker_scriptrunner

annotate scriptrunner.py @ 0:21d312776891 draft