docker_toolfactory: DockerToolFactory.py annotate

annotate DockerToolFactory.py @ 0:0fa46413d0d9 draft

planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty

author	mvdbeek
date	Sat, 03 Oct 2015 08:34:39 -0400
parents
children	fccbc118bb5b

rev	line source
0 0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	1 # DockerToolFactory.py
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	2 # see https://bitbucket.org/mvdbeek/DockerToolFactory
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	3
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	4 import sys
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	5 import shutil
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	6 import subprocess
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	7 import os
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	8 import time
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	9 import tempfile
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	10 import argparse
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	11 import tarfile
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	12 import re
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	13 import shutil
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	14 import math
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	15 import fileinput
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	16 from os.path import abspath
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	17
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	18 progname = os.path.split(sys.argv[0])[1]
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	19 myversion = 'V001.1 March 2014'
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	20 verbose = False
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	21 debug = False
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	22 toolFactoryURL = 'https://bitbucket.org/fubar/galaxytoolfactory'
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	23
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	24 # if we do html we need these dependencies specified in a tool_dependencies.xml file and referred to in the generated
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	25 # tool xml
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	26 toolhtmldepskel = """<?xml version="1.0"?>
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	27 <tool_dependency>
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	28 <package name="ghostscript" version="9.10">
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	29 <repository name="package_ghostscript_9_10" owner="devteam"/>
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	30 </package>
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	31 <package name="graphicsmagick" version="1.3.20">
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	32 <repository name="package_graphicsmagick_1_3_20" owner="iuc"/>
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	33 </package>
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	34 <package name="docker-py" version="0.4.0">
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	35 <install version="1.0">
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	36 <actions>
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	37 <action type="setup_virtualenv">docker-py==0.4.0
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	38 </action>
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	39 </actions>
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	40 </install>
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	41 </package>
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	42 <readme>
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	43 %s
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	44 </readme>
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	45 </tool_dependency>
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	46 """
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	47
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	48 protorequirements = """<requirements>
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	49 <requirement type="package" version="9.10">ghostscript</requirement>
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	50 <requirement type="package" version="1.3.20">graphicsmagick</requirement>
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	51 <container type="docker">toolfactory/custombuild:%s</container>
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	52 </requirements>"""
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	53
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	54
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	55 def timenow():
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	56 """return current time as a string
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	57 """
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	58 return time.strftime('%d/%m/%Y %H:%M:%S', time.localtime(time.time()))
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	59
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	60
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	61 html_escape_table = {
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	62 "&": "&",
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	63 ">": ">",
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	64 "<": "<",
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	65 "$": "\$"
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	66 }
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	67
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	68
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	69 def html_escape(text):
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	70 """Produce entities within text."""
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	71 return "".join(html_escape_table.get(c, c) for c in text)
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	72
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	73
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	74 def cmd_exists(cmd):
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	75 return subprocess.call("type " + cmd, shell=True,
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	76 stdout=subprocess.PIPE, stderr=subprocess.PIPE) == 0
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	77
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	78
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	79 def edit_dockerfile(dockerfile):
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	80 '''we have to change the userid of galaxy inside the container to the id with which the tool is run,
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	81 otherwise we have a mismatch in the file permissions inside the container'''
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	82 uid = os.getuid()
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	83 for line in fileinput.FileInput(dockerfile, inplace=1):
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	84 sys.stdout.write(re.sub("RUN adduser galaxy.*", "RUN adduser galaxy -u {0}\n".format(uid), line))
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	85
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	86
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	87 # TODO: try to download image it it exists.
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	88 def build_docker(dockerfile, docker_client, image_tag='base'):
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	89 '''Given the path to a dockerfile, and a docker_client, try to build the image, if it does not
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	90 exist yet.'''
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	91 image_id = 'toolfactory/custombuild:' + image_tag
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	92 existing_images = ", ".join(["".join(d['RepoTags']) for d in docker_client.images()])
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	93 if image_id in existing_images:
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	94 print 'docker container exists, skipping build'
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	95 return image_id
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	96 print "Building Docker image, using Dockerfile:{0}".format(dockerfile)
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	97 build_process = docker_client.build(fileobj=open(dockerfile, 'r'), tag=image_id)
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	98 print "succesfully dispatched docker build process, building now"
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	99 build_log = [line for line in build_process] # will block until image is built.
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	100 return image_id
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	101
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	102
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	103 def construct_bind(host_path, container_path=False, binds=None, ro=True):
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	104 # TODO remove container_path if it's alwyas going to be the same as host_path
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	105 '''build or extend binds dictionary with container path. binds is used
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	106 to mount all files using the docker-py client.'''
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	107 if not binds:
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	108 binds = {}
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	109 if isinstance(host_path, list):
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	110 for k, v in enumerate(host_path):
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	111 if not container_path:
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	112 container_path = host_path[k]
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	113 binds[host_path[k]] = {'bind': container_path, 'ro': ro}
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	114 container_path = False # could be more elegant
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	115 return binds
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	116 else:
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	117 if not container_path:
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	118 container_path = host_path
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	119 binds[host_path] = {'bind': container_path, 'ro': ro}
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	120 return binds
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	121
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	122
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	123 def exists_boot2docker():
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	124 '''
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	125 Try to see if boot2docker command is available.
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	126 If it is, run boot2docker shellinit
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	127 '''
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	128 return cmd_exists('boot2docker')
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	129
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	130
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	131 def boot2docker_shellinit():
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	132 '''
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	133 '''
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	134 cmd = "eval \"\$(boot2docker shellinit)\""
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	135 subprocess.call(cmd, shell=True)
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	136
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	137
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	138 def switch_to_docker(opts):
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	139 import docker # need local import, as container does not have docker-py
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	140 if exists_boot2docker():
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	141 boot2docker_shellinit()
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	142 from docker.utils import kwargs_from_env
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	143 kwargs = kwargs_from_env()
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	144 kwargs['tls'].assert_hostname = False
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	145 docker_client = docker.Client(**kwargs)
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	146 else:
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	147 docker_client = docker.Client()
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	148 toolfactory_path = abspath(sys.argv[0])
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	149 dockerfile = os.path.dirname(toolfactory_path) + '/Dockerfile'
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	150 edit_dockerfile(dockerfile)
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	151 image_id = build_docker(dockerfile, docker_client)
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	152 binds = construct_bind(host_path=opts.script_path, ro=False)
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	153 binds = construct_bind(binds=binds, host_path=abspath(opts.output_dir), ro=False)
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	154 if len(opts.input_tab) > 0:
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	155 binds = construct_bind(binds=binds, host_path=opts.input_tab, ro=True)
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	156 if not opts.output_tab == 'None':
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	157 binds = construct_bind(binds=binds, host_path=opts.output_tab, ro=False)
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	158 if opts.make_HTML:
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	159 binds = construct_bind(binds=binds, host_path=opts.output_html, ro=False)
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	160 if opts.make_Tool:
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	161 binds = construct_bind(binds=binds, host_path=opts.new_tool, ro=False)
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	162 binds = construct_bind(binds=binds, host_path=opts.help_text, ro=True)
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	163 binds = construct_bind(binds=binds, host_path=toolfactory_path)
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	164 volumes = binds.keys()
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	165 sys.argv = [abspath(opts.output_dir) if sys.argv[i - 1] == '--output_dir' else arg for i, arg in
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	166 enumerate(sys.argv)] ##inject absolute path of working_dir
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	167 cmd = ['python', '-u'] + sys.argv + ['--dockerized', '1']
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	168 container = docker_client.create_container(
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	169 image=image_id,
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	170 user=os.getuid(),
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	171 volumes=volumes,
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	172 command=cmd
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	173 )
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	174 docker_client.start(container=container[u'Id'], binds=binds)
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	175 docker_client.wait(container=container[u'Id'])
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	176 logs = docker_client.logs(container=container[u'Id'])
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	177 print "".join([log for log in logs])
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	178
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	179
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	180 class ScriptRunner:
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	181 """class is a wrapper for an arbitrary script
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	182 """
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	183
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	184 def __init__(self, opts=None, treatbashSpecial=True, image_tag='base'):
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	185 """
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	186 cleanup inputs, setup some outputs
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	187
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	188 """
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	189 self.opts = opts
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	190 self.useGM = cmd_exists('gm')
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	191 self.useIM = cmd_exists('convert')
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	192 self.useGS = cmd_exists('gs')
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	193 self.temp_warned = False # we want only one warning if $TMP not set
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	194 self.treatbashSpecial = treatbashSpecial
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	195 self.image_tag = image_tag
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	196 os.chdir(abspath(opts.output_dir))
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	197 self.thumbformat = 'png'
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	198 self.toolname_sanitized = re.sub('[^a-zA-Z0-9_]+', '_', opts.tool_name) # a sanitizer now does this but..
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	199 self.toolname = opts.tool_name
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	200 self.toolid = self.toolname
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	201 self.myname = sys.argv[0] # get our name because we write ourselves out as a tool later
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	202 self.pyfile = self.myname # crude but efficient - the cruft won't hurt much
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	203 self.xmlfile = '%s.xml' % self.toolname_sanitized
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	204 s = open(self.opts.script_path, 'r').readlines()
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	205 s = [x.rstrip() for x in s] # remove pesky dos line endings if needed
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	206 self.script = '\n'.join(s)
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	207 fhandle, self.sfile = tempfile.mkstemp(prefix=self.toolname_sanitized, suffix=".%s" % (opts.interpreter))
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	208 tscript = open(self.sfile, 'w') # use self.sfile as script source for Popen
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	209 tscript.write(self.script)
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	210 tscript.close()
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	211 self.indentedScript = '\n'.join([' %s' % html_escape(x) for x in s]) # for restructured text in help
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	212 self.escapedScript = '\n'.join([html_escape(x) for x in s])
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	213 self.elog = os.path.join(self.opts.output_dir, "%s_error.log" % self.toolname_sanitized)
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	214 if opts.output_dir: # may not want these complexities
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	215 self.tlog = os.path.join(self.opts.output_dir, "%s_runner.log" % self.toolname_sanitized)
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	216 art = '%s.%s' % (self.toolname_sanitized, opts.interpreter)
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	217 artpath = os.path.join(self.opts.output_dir, art) # need full path
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	218 artifact = open(artpath, 'w') # use self.sfile as script source for Popen
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	219 artifact.write(self.script)
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	220 artifact.close()
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	221 self.cl = []
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	222 self.html = []
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	223 a = self.cl.append
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	224 a(opts.interpreter)
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	225 if self.treatbashSpecial and opts.interpreter in ['bash', 'sh']:
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	226 a(self.sfile)
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	227 else:
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	228 a('-') # stdin
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	229 for input in opts.input_tab:
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	230 a(input)
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	231 if opts.output_tab == 'None': # If tool generates only HTML, set output name to toolname
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	232 a(str(self.toolname_sanitized) + '.out')
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	233 a(opts.output_tab)
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	234 for param in opts.additional_parameters:
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	235 param, value = param.split(',')
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	236 a('--' + param)
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	237 a(value)
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	238 # print self.cl
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	239 self.outFormats = opts.output_format
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	240 self.inputFormats = [formats for formats in opts.input_formats]
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	241 self.test1Input = '%s_test1_input.xls' % self.toolname_sanitized
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	242 self.test1Output = '%s_test1_output.xls' % self.toolname_sanitized
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	243 self.test1HTML = '%s_test1_output.html' % self.toolname_sanitized
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	244
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	245 def makeXML(self):
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	246 """
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	247 Create a Galaxy xml tool wrapper for the new script as a string to write out
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	248 fixme - use templating or something less fugly than this example of what we produce
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	249
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	250 <tool id="reverse" name="reverse" version="0.01">
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	251 <description>a tabular file</description>
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	252 <command interpreter="python">
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	253 reverse.py --script_path "$runMe" --interpreter "python"
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	254 --tool_name "reverse" --input_tab "$input1" --output_tab "$tab_file"
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	255 </command>
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	256 <inputs>
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	257 <param name="input1" type="data" format="tabular" label="Select a suitable input file from your history"/>
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	258
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	259 </inputs>
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	260 <outputs>
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	261 <data format=opts.output_format name="tab_file"/>
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	262
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	263 </outputs>
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	264 <help>
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	265
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	266 What it Does
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	267
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	268 Reverse the columns in a tabular file
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	269
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	270 </help>
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	271 <configfiles>
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	272 <configfile name="runMe">
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	273
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	274 # reverse order of columns in a tabular file
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	275 import sys
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	276 inp = sys.argv[1]
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	277 outp = sys.argv[2]
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	278 i = open(inp,'r')
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	279 o = open(outp,'w')
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	280 for row in i:
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	281 rs = row.rstrip().split('\t')
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	282 rs.reverse()
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	283 o.write('\t'.join(rs))
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	284 o.write('\n')
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	285 i.close()
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	286 o.close()
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	287
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	288
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	289 </configfile>
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	290 </configfiles>
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	291 </tool>
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	292
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	293 """
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	294 newXML = """<tool id="%(toolid)s" name="%(toolname)s" version="%(tool_version)s">
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	295 %(tooldesc)s
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	296 %(requirements)s
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	297 <command interpreter="python">
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	298 %(command)s
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	299 </command>
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	300 <inputs>
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	301 %(inputs)s
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	302 </inputs>
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	303 <outputs>
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	304 %(outputs)s
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	305 </outputs>
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	306 <configfiles>
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	307 <configfile name="runMe">
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	308 %(script)s
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	309 </configfile>
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	310 </configfiles>
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	311
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	312 %(tooltests)s
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	313
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	314 <help>
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	315
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	316 %(help)s
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	317
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	318 </help>
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	319 </tool>""" # needs a dict with toolname, toolname_sanitized, toolid, interpreter, scriptname, command, inputs as a multi line string ready to write, outputs ditto, help ditto
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	320
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	321 newCommand = """
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	322 %(toolname_sanitized)s.py --script_path "$runMe" --interpreter "%(interpreter)s"
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	323 --tool_name "%(toolname)s" %(command_inputs)s %(command_outputs)s """
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	324 # may NOT be an input or htmlout - appended later
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	325 tooltestsTabOnly = """
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	326 <tests>
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	327 <test>
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	328 <param name="input1" value="%(test1Input)s" ftype="tabular"/>
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	329 <param name="runMe" value="$runMe"/>
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	330 <output name="tab_file" file="%(test1Output)s" ftype="tabular"/>
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	331 </test>
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	332 </tests>
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	333 """
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	334 tooltestsHTMLOnly = """
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	335 <tests>
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	336 <test>
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	337 <param name="input1" value="%(test1Input)s" ftype="tabular"/>
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	338 <param name="runMe" value="$runMe"/>
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	339 <output name="html_file" file="%(test1HTML)s" ftype="html" lines_diff="5"/>
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	340 </test>
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	341 </tests>
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	342 """
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	343 tooltestsBoth = """<tests>
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	344 <test>
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	345 <param name="input1" value="%(test1Input)s" ftype="tabular"/>
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	346 <param name="runMe" value="$runMe"/>
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	347 <output name="tab_file" file="%(test1Output)s" ftype="tabular" />
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	348 <output name="html_file" file="%(test1HTML)s" ftype="html" lines_diff="10"/>
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	349 </test>
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	350 </tests>
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	351 """
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	352 xdict = {}
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	353 # xdict['requirements'] = ''
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	354 # if self.opts.make_HTML:
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	355 xdict['requirements'] = protorequirements % self.image_tag
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	356 xdict['tool_version'] = self.opts.tool_version
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	357 xdict['test1Input'] = self.test1Input
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	358 xdict['test1HTML'] = self.test1HTML
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	359 xdict['test1Output'] = self.test1Output
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	360 if self.opts.make_HTML and self.opts.output_tab <> 'None':
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	361 xdict['tooltests'] = tooltestsBoth % xdict
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	362 elif self.opts.make_HTML:
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	363 xdict['tooltests'] = tooltestsHTMLOnly % xdict
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	364 else:
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	365 xdict['tooltests'] = tooltestsTabOnly % xdict
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	366 xdict['script'] = self.escapedScript
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	367 # configfile is least painful way to embed script to avoid external dependencies
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	368 # but requires escaping of <, > and $ to avoid Mako parsing
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	369 if self.opts.help_text:
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	370 helptext = open(self.opts.help_text, 'r').readlines()
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	371 helptext = [html_escape(x) for x in helptext] # must html escape here too - thanks to Marius van den Beek
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	372 xdict['help'] = ''.join([x for x in helptext])
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	373 else:
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	374 xdict['help'] = 'Please ask the tool author (%s) for help as none was supplied at tool generation\n' % (
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	375 self.opts.user_email)
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	376 coda = ['Script',
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	377 'Pressing execute will run the following code over your input file and generate some outputs in your history::']
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	378 coda.append('\n')
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	379 coda.append(self.indentedScript)
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	380 coda.append('\nAttribution\nThis Galaxy tool was created by %s at %s\nusing the Galaxy Tool Factory.\n' % (
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	381 self.opts.user_email, timenow()))
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	382 coda.append('See %s for details of that project' % (toolFactoryURL))
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	383 coda.append(
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	384 'Please cite: Creating re-usable tools from scripts: The Galaxy Tool Factory. Ross Lazarus; Antony Kaspi; Mark Ziemann; The Galaxy Team. ')
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	385 coda.append('Bioinformatics 2012; doi: 10.1093/bioinformatics/bts573\n')
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	386 xdict['help'] = '%s\n%s' % (xdict['help'], '\n'.join(coda))
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	387 if self.opts.tool_desc:
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	388 xdict['tooldesc'] = '<description>%s</description>' % self.opts.tool_desc
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	389 else:
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	390 xdict['tooldesc'] = ''
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	391 xdict['command_outputs'] = ''
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	392 xdict['outputs'] = ''
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	393 if self.opts.input_tab <> 'None':
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	394 xdict['command_inputs'] = '--input_tab'
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	395 xdict['inputs'] = ''
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	396 for i, input in enumerate(self.inputFormats):
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	397 xdict[
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	398 'inputs'] += '<param name="input{0}" type="data" format="{1}" label="Select a suitable input file from your history"/> \n'.format(
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	399 i + 1, input)
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	400 xdict['command_inputs'] += ' $input{0}'.format(i + 1)
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	401 else:
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	402 xdict['command_inputs'] = '' # assume no input - eg a random data generator
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	403 xdict['inputs'] = ''
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	404 # I find setting the job name not very logical. can be changed in workflows anyway. xdict['inputs'] += '<param name="job_name" type="text" label="Supply a name for the outputs to remind you what they contain" value="%s"/> \n' % self.toolname
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	405 xdict['toolname'] = self.toolname
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	406 xdict['toolname_sanitized'] = self.toolname_sanitized
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	407 xdict['toolid'] = self.toolid
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	408 xdict['interpreter'] = self.opts.interpreter
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	409 xdict['scriptname'] = self.sfile
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	410 if self.opts.make_HTML:
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	411 xdict[
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	412 'command_outputs'] += ' --output_dir "$html_file.files_path" --output_html "$html_file" --make_HTML "yes"'
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	413 xdict['outputs'] += ' <data format="html" name="html_file"/>\n'
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	414 else:
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	415 xdict['command_outputs'] += ' --output_dir "./"'
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	416 # print self.opts.output_tab
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	417 if self.opts.output_tab != "None":
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	418 xdict['command_outputs'] += ' --output_tab "$tab_file"'
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	419 xdict['outputs'] += ' <data format="%s" name="tab_file"/>\n' % self.outFormats
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	420 xdict['command'] = newCommand % xdict
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	421 # print xdict['outputs']
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	422 xmls = newXML % xdict
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	423 xf = open(self.xmlfile, 'w')
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	424 xf.write(xmls)
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	425 xf.write('\n')
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	426 xf.close()
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	427 # ready for the tarball
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	428
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	429 def makeTooltar(self):
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	430 """
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	431 a tool is a gz tarball with eg
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	432 /toolname_sanitized/tool.xml /toolname_sanitized/tool.py /toolname_sanitized/test-data/test1_in.foo ...
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	433 """
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	434 retval = self.run()
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	435 if retval:
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	436 print >> sys.stderr, '## Run failed. Cannot build yet. Please fix and retry'
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	437 sys.exit(1)
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	438 tdir = self.toolname_sanitized
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	439 os.mkdir(tdir)
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	440 self.makeXML()
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	441 if self.opts.make_HTML:
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	442 if self.opts.help_text:
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	443 hlp = open(self.opts.help_text, 'r').read()
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	444 else:
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	445 hlp = 'Please ask the tool author for help as none was supplied at tool generation\n'
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	446 if self.opts.include_dependencies:
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	447 tooldepcontent = toolhtmldepskel % hlp
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	448 depf = open(os.path.join(tdir, 'tool_dependencies.xml'), 'w')
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	449 depf.write(tooldepcontent)
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	450 depf.write('\n')
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	451 depf.close()
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	452 if self.opts.input_tab <> 'None': # no reproducible test otherwise? TODO: maybe..
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	453 testdir = os.path.join(tdir, 'test-data')
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	454 os.mkdir(testdir) # make tests directory
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	455 for i in self.opts.input_tab:
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	456 # print i
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	457 shutil.copyfile(i, os.path.join(testdir, self.test1Input))
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	458 if not self.opts.output_tab:
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	459 shutil.copyfile(self.opts.output_tab, os.path.join(testdir, self.test1Output))
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	460 if self.opts.make_HTML:
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	461 shutil.copyfile(self.opts.output_html, os.path.join(testdir, self.test1HTML))
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	462 if self.opts.output_dir:
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	463 shutil.copyfile(self.tlog, os.path.join(testdir, 'test1_out.log'))
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	464 outpif = '%s.py' % self.toolname_sanitized # new name
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	465 outpiname = os.path.join(tdir, outpif) # path for the tool tarball
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	466 pyin = os.path.basename(self.pyfile) # our name - we rewrite ourselves (TM)
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	467 notes = ['# %s - a self annotated version of %s generated by running %s\n' % (outpiname, pyin, pyin), ]
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	468 notes.append('# to make a new Galaxy tool called %s\n' % self.toolname)
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	469 notes.append('# User %s at %s\n' % (self.opts.user_email, timenow()))
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	470 pi = [line.replace('if opts.dockerized==0:', 'if False:') for line in
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	471 open(self.pyfile)] # do not run docker in the generated tool
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	472 notes += pi
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	473 outpi = open(outpiname, 'w')
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	474 outpi.write(''.join(notes))
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	475 outpi.write('\n')
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	476 outpi.close()
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	477 stname = os.path.join(tdir, self.sfile)
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	478 if not os.path.exists(stname):
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	479 shutil.copyfile(self.sfile, stname)
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	480 xtname = os.path.join(tdir, self.xmlfile)
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	481 if not os.path.exists(xtname):
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	482 shutil.copyfile(self.xmlfile, xtname)
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	483 tarpath = "%s.gz" % self.toolname_sanitized
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	484 tar = tarfile.open(tarpath, "w:gz")
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	485 tar.add(tdir, arcname=self.toolname_sanitized)
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	486 tar.close()
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	487 shutil.copyfile(tarpath, self.opts.new_tool)
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	488 shutil.rmtree(tdir)
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	489 ## TODO: replace with optional direct upload to local toolshed?
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	490 return retval
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	491
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	492 def compressPDF(self, inpdf=None, thumbformat='png'):
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	493 """need absolute path to pdf
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	494 note that GS gets confoozled if no $TMP or $TEMP
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	495 so we set it
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	496 """
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	497 assert os.path.isfile(inpdf), "## Input %s supplied to %s compressPDF not found" % (inpdf, self.myName)
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	498 hlog = os.path.join(self.opts.output_dir, "compress_%s.txt" % os.path.basename(inpdf))
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	499 sto = open(hlog, 'a')
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	500 our_env = os.environ.copy()
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	501 our_tmp = our_env.get('TMP', None)
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	502 if not our_tmp:
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	503 our_tmp = our_env.get('TEMP', None)
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	504 if not (our_tmp and os.path.exists(our_tmp)):
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	505 newtmp = os.path.join(self.opts.output_dir, 'tmp')
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	506 try:
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	507 os.mkdir(newtmp)
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	508 except:
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	509 sto.write('## WARNING - cannot make %s - it may exist or permissions need fixing\n' % newtmp)
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	510 our_env['TEMP'] = newtmp
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	511 if not self.temp_warned:
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	512 sto.write('## WARNING - no $TMP or $TEMP!!! Please fix - using %s temporarily\n' % newtmp)
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	513 self.temp_warned = True
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	514 outpdf = '%s_compressed' % inpdf
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	515 cl = ["gs", "-sDEVICE=pdfwrite", "-dNOPAUSE", "-dUseCIEColor", "-dBATCH", "-dPDFSETTINGS=/printer",
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	516 "-sOutputFile=%s" % outpdf, inpdf]
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	517 x = subprocess.Popen(cl, stdout=sto, stderr=sto, cwd=self.opts.output_dir, env=our_env)
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	518 retval1 = x.wait()
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	519 sto.close()
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	520 if retval1 == 0:
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	521 os.unlink(inpdf)
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	522 shutil.move(outpdf, inpdf)
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	523 os.unlink(hlog)
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	524 hlog = os.path.join(self.opts.output_dir, "thumbnail_%s.txt" % os.path.basename(inpdf))
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	525 sto = open(hlog, 'w')
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	526 outpng = '%s.%s' % (os.path.splitext(inpdf)[0], thumbformat)
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	527 if self.useGM:
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	528 cl2 = ['gm', 'convert', inpdf, outpng]
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	529 else: # assume imagemagick
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	530 cl2 = ['convert', inpdf, outpng]
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	531 x = subprocess.Popen(cl2, stdout=sto, stderr=sto, cwd=self.opts.output_dir, env=our_env)
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	532 retval2 = x.wait()
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	533 sto.close()
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	534 if retval2 == 0:
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	535 os.unlink(hlog)
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	536 retval = retval1 or retval2
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	537 return retval
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	538
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	539 def getfSize(self, fpath, outpath):
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	540 """
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	541 format a nice file size string
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	542 """
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	543 size = ''
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	544 fp = os.path.join(outpath, fpath)
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	545 if os.path.isfile(fp):
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	546 size = '0 B'
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	547 n = float(os.path.getsize(fp))
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	548 if n > 2 ** 20:
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	549 size = '%1.1f MB' % (n / 2 ** 20)
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	550 elif n > 2 ** 10:
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	551 size = '%1.1f KB' % (n / 2 ** 10)
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	552 elif n > 0:
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	553 size = '%d B' % (int(n))
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	554 return size
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	555
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	556 def makeHtml(self):
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	557 """ Create an HTML file content to list all the artifacts found in the output_dir
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	558 """
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	559
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	560 galhtmlprefix = """<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	561 <html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	562 <head> <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	563 <meta name="generator" content="Galaxy %s tool output - see http://g2.trac.bx.psu.edu/" />
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	564 <title></title>
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	565 <link rel="stylesheet" href="/static/style/base.css" type="text/css" />
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	566 </head>
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	567 <body>
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	568 <div class="toolFormBody">
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	569 """
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	570 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/>"""
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	571 galhtmlpostfix = """</div></body></html>\n"""
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	572
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	573 flist = os.listdir(self.opts.output_dir)
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	574 flist = [x for x in flist if x <> 'Rplots.pdf']
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	575 flist.sort()
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	576 html = []
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	577 html.append(galhtmlprefix % progname)
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	578 html.append('<div class="infomessage">Galaxy Tool "%s" run at %s</div><br/>' % (self.toolname, timenow()))
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	579 fhtml = []
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	580 if len(flist) > 0:
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	581 logfiles = [x for x in flist if x.lower().endswith('.log')] # log file names determine sections
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	582 logfiles.sort()
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	583 logfiles = [x for x in logfiles if abspath(x) <> abspath(self.tlog)]
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	584 logfiles.append(abspath(self.tlog)) # make it the last one
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	585 pdflist = []
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	586 npdf = len([x for x in flist if os.path.splitext(x)[-1].lower() == '.pdf'])
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	587 for rownum, fname in enumerate(flist):
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	588 dname, e = os.path.splitext(fname)
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	589 sfsize = self.getfSize(fname, self.opts.output_dir)
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	590 if e.lower() == '.pdf': # compress and make a thumbnail
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	591 thumb = '%s.%s' % (dname, self.thumbformat)
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	592 pdff = os.path.join(self.opts.output_dir, fname)
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	593 retval = self.compressPDF(inpdf=pdff, thumbformat=self.thumbformat)
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	594 if retval == 0:
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	595 pdflist.append((fname, thumb))
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	596 else:
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	597 pdflist.append((fname, fname))
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	598 if (rownum + 1) % 2 == 0:
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	599 fhtml.append(
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	600 '<tr class="odd_row"><td><a href="%s">%s</a></td><td>%s</td></tr>' % (fname, fname, sfsize))
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	601 else:
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	602 fhtml.append('<tr><td><a href="%s">%s</a></td><td>%s</td></tr>' % (fname, fname, sfsize))
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	603 for logfname in logfiles: # expect at least tlog - if more
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	604 if abspath(logfname) == abspath(self.tlog): # handled later
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	605 sectionname = 'All tool run'
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	606 if (len(logfiles) > 1):
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	607 sectionname = 'Other'
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	608 ourpdfs = pdflist
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	609 else:
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	610 realname = os.path.basename(logfname)
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	611 sectionname = os.path.splitext(realname)[0].split('_')[0] # break in case _ added to log
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	612 ourpdfs = [x for x in pdflist if os.path.basename(x[0]).split('_')[0] == sectionname]
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	613 pdflist = [x for x in pdflist if os.path.basename(x[0]).split('_')[0] <> sectionname] # remove
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	614 nacross = 1
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	615 npdf = len(ourpdfs)
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	616
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	617 if npdf > 0:
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	618 nacross = math.sqrt(npdf) ## int(round(math.log(npdf,2)))
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	619 if int(nacross) ** 2 != npdf:
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	620 nacross += 1
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	621 nacross = int(nacross)
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	622 width = min(400, int(1200 / nacross))
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	623 html.append('<div class="toolFormTitle">%s images and outputs</div>' % sectionname)
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	624 html.append('(Click on a thumbnail image to download the corresponding original PDF image)<br/>')
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	625 ntogo = nacross # counter for table row padding with empty cells
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	626 html.append('<div><table class="simple" cellpadding="2" cellspacing="2">\n<tr>')
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	627 for i, paths in enumerate(ourpdfs):
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	628 fname, thumb = paths
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	629 s = """<td><a href="%s"><img src="%s" title="Click to download a PDF of %s" hspace="5" width="%d"
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	630 alt="Image called %s"/></a></td>\n""" % (fname, thumb, fname, width, fname)
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	631 if ((i + 1) % nacross == 0):
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	632 s += '</tr>\n'
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	633 ntogo = 0
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	634 if i < (npdf - 1): # more to come
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	635 s += '<tr>'
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	636 ntogo = nacross
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	637 else:
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	638 ntogo -= 1
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	639 html.append(s)
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	640 if html[-1].strip().endswith('</tr>'):
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	641 html.append('</table></div>\n')
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	642 else:
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	643 if ntogo > 0: # pad
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	644 html.append('<td> </td>' * ntogo)
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	645 html.append('</tr></table></div>\n')
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	646 logt = open(logfname, 'r').readlines()
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	647 logtext = [x for x in logt if x.strip() > '']
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	648 html.append('<div class="toolFormTitle">%s log output</div>' % sectionname)
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	649 if len(logtext) > 1:
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	650 html.append('\n<pre>\n')
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	651 html += logtext
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	652 html.append('\n</pre>\n')
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	653 else:
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	654 html.append('%s is empty<br/>' % logfname)
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	655 if len(fhtml) > 0:
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	656 fhtml.insert(0,
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	657 '<div><table class="colored" cellpadding="3" cellspacing="3"><tr><th>Output File Name (click to view)</th><th>Size</th></tr>\n')
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	658 fhtml.append('</table></div><br/>')
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	659 html.append('<div class="toolFormTitle">All output files available for downloading</div>\n')
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	660 html += fhtml # add all non-pdf files to the end of the display
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	661 else:
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	662 html.append(
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	663 '<div class="warningmessagelarge">### Error - %s returned no files - please confirm that parameters are sane</div>' % self.opts.interpreter)
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	664 html.append(galhtmlpostfix)
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	665 htmlf = file(self.opts.output_html, 'w')
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	666 htmlf.write('\n'.join(html))
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	667 htmlf.write('\n')
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	668 htmlf.close()
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	669 self.html = html
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	670
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	671 def run(self):
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	672 """
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	673 scripts must be small enough not to fill the pipe!
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	674 """
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	675 if self.treatbashSpecial and self.opts.interpreter in ['bash', 'sh']:
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	676 retval = self.runBash()
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	677 else:
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	678 if self.opts.output_dir:
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	679 ste = open(self.elog, 'w')
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	680 sto = open(self.tlog, 'w')
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	681 sto.write('## Toolfactory generated command line = %s\n' % ' '.join(self.cl))
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	682 sto.flush()
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	683 p = subprocess.Popen(self.cl, shell=False, stdout=sto, stderr=ste, stdin=subprocess.PIPE,
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	684 cwd=self.opts.output_dir)
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	685 else:
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	686 p = subprocess.Popen(self.cl, shell=False, stdin=subprocess.PIPE)
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	687 p.stdin.write(self.script)
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	688 p.stdin.close()
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	689 retval = p.wait()
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	690 if self.opts.output_dir:
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	691 sto.close()
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	692 ste.close()
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	693 err = open(self.elog, 'r').readlines()
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	694 if retval <> 0 and err: # problem
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	695 print >> sys.stderr, err # same problem, need to capture docker stdin/stdout
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	696 if self.opts.make_HTML:
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	697 self.makeHtml()
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	698 return retval
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	699
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	700 def runBash(self):
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	701 """
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	702 cannot use - for bash so use self.sfile
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	703 """
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	704 if self.opts.output_dir:
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	705 s = '## Toolfactory generated command line = %s\n' % ' '.join(self.cl)
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	706 sto = open(self.tlog, 'w')
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	707 sto.write(s)
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	708 sto.flush()
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	709 p = subprocess.Popen(self.cl, shell=False, stdout=sto, stderr=sto, cwd=self.opts.output_dir)
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	710 else:
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	711 p = subprocess.Popen(self.cl, shell=False)
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	712 retval = p.wait()
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	713 if self.opts.output_dir:
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	714 sto.close()
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	715 if self.opts.make_HTML:
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	716 self.makeHtml()
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	717 return retval
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	718
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	719
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	720 def main():
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	721 u = """
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	722 This is a Galaxy wrapper. It expects to be called by a special purpose tool.xml as:
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	723 <command interpreter="python">rgBaseScriptWrapper.py --script_path "$scriptPath" --tool_name "foo" --interpreter "Rscript"
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	724 </command>
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	725 """
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	726 op = argparse.ArgumentParser()
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	727 a = op.add_argument
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	728 a('--script_path', default=None)
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	729 a('--tool_name', default=None)
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	730 a('--interpreter', default=None)
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	731 a('--output_dir', default='./')
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	732 a('--output_html', default=None)
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	733 a('--input_tab', default='None', nargs='*')
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	734 a('--output_tab', default='None')
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	735 a('--user_email', default='Unknown')
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	736 a('--bad_user', default=None)
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	737 a('--make_Tool', default=None)
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	738 a('--make_HTML', default=None)
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	739 a('--help_text', default=None)
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	740 a('--tool_desc', default=None)
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	741 a('--new_tool', default=None)
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	742 a('--tool_version', default=None)
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	743 a('--include_dependencies', default=None)
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	744 a('--dockerized', default=0)
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	745 a('--output_format', default='tabular')
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	746 a('--input_format', dest='input_formats', action='append', default=[])
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	747 a('--additional_parameters', dest='additional_parameters', action='append', default=[])
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	748 opts = op.parse_args()
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	749 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' % (
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	750 opts.bad_user, opts.bad_user)
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	751 assert opts.tool_name, '## Tool Factory expects a tool name - eg --tool_name=DESeq'
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	752 assert opts.interpreter, '## Tool Factory wrapper expects an interpreter - eg --interpreter=Rscript'
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	753 assert os.path.isfile(opts.script_path), '## Tool Factory wrapper expects a script path - eg --script_path=foo.R'
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	754 if opts.output_dir:
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	755 try:
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	756 os.makedirs(opts.output_dir)
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	757 except:
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	758 pass
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	759 if opts.dockerized == 0:
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	760 switch_to_docker(opts)
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	761 return
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	762 r = ScriptRunner(opts)
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	763 if opts.make_Tool:
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	764 retcode = r.makeTooltar()
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	765 else:
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	766 retcode = r.run()
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	767 os.unlink(r.sfile)
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	768 if retcode:
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	769 sys.exit(retcode) # indicate failure to job runner
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	770
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	771
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	772 if __name__ == "__main__":
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty mvdbeek parents: diff changeset	773 main()

Mercurial > repos > mvdbeek > docker_toolfactory

annotate DockerToolFactory.py @ 0:0fa46413d0d9 draft