skunkworks: rgToolFactory.py annotate

annotate rgToolFactory.py @ 34:c6fdf2c6d0f4 draft

Citations added (thanks John!) and a few more output formats for Alistair Chilcott

author	fubar
date	Thu, 28 Aug 2014 02:33:05 -0400
parents	fb3fa6a2874d
children

rev	line source
29 bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	1 # rgToolFactory.py
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	2 # see https://bitbucket.org/fubar/galaxytoolfactory/wiki/Home
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	3 #
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	4 # copyright ross lazarus (ross stop lazarus at gmail stop com) May 2012
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	5 #
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	6 # all rights reserved
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	7 # Licensed under the LGPL
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	8 # suggestions for improvement and bug fixes welcome at https://bitbucket.org/fubar/galaxytoolfactory/wiki/Home
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	9 #
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	10 # march 2014
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	11 # had to remove dependencies because cross toolshed dependencies are not possible - can't pre-specify a toolshed url for graphicsmagick and ghostscript
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	12 # grrrrr - night before a demo
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	13 # added dependencies to a tool_dependencies.xml if html page generated so generated tool is properly portable
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	14 #
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	15 # added ghostscript and graphicsmagick as dependencies
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	16 # fixed a wierd problem where gs was trying to use the new_files_path from universe (database/tmp) as ./database/tmp
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	17 # errors ensued
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	18 #
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	19 # august 2013
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	20 # found a problem with GS if $TMP or $TEMP missing - now inject /tmp and warn
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	21 #
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	22 # july 2013
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	23 # added ability to combine images and individual log files into html output
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	24 # just make sure there's a log file foo.log and it will be output
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	25 # together with all images named like "foo_*.pdf
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	26 # otherwise old format for html
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	27 #
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	28 # January 2013
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	29 # problem pointed out by Carlos Borroto
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	30 # added escaping for <>$ - thought I did that ages ago...
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	31 #
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	32 # August 11 2012
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	33 # changed to use shell=False and cl as a sequence
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	34
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	35 # This is a Galaxy tool factory for simple scripts in python, R or whatever ails ye.
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	36 # It also serves as the wrapper for the new tool.
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	37 #
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	38 # you paste and run your script
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	39 # Only works for simple scripts that read one input from the history.
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	40 # Optionally can write one new history dataset,
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	41 # and optionally collect any number of outputs into links on an autogenerated HTML page.
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	42
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	43 # DO NOT install on a public or important site - please.
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	44
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	45 # installed generated tools are fine if the script is safe.
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	46 # They just run normally and their user cannot do anything unusually insecure
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	47 # but please, practice safe toolshed.
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	48 # Read the fucking code before you install any tool
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	49 # especially this one
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	50
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	51 # After you get the script working on some test data, you can
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	52 # optionally generate a toolshed compatible gzip file
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	53 # containing your script safely wrapped as an ordinary Galaxy script in your local toolshed for
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	54 # safe and largely automated installation in a production Galaxy.
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	55
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	56 # If you opt for an HTML output, you get all the script outputs arranged
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	57 # as a single Html history item - all output files are linked, thumbnails for all the pdfs.
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	58 # Ugly but really inexpensive.
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	59 #
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	60 # Patches appreciated please.
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	61 #
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	62 #
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	63 # long route to June 2012 product
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	64 # Behold the awesome power of Galaxy and the toolshed with the tool factory to bind them
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	65 # derived from an integrated script model
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	66 # called rgBaseScriptWrapper.py
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	67 # Note to the unwary:
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	68 # This tool allows arbitrary scripting on your Galaxy as the Galaxy user
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	69 # There is nothing stopping a malicious user doing whatever they choose
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	70 # Extremely dangerous!!
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	71 # Totally insecure. So, trusted users only
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	72 #
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	73 # preferred model is a developer using their throw away workstation instance - ie a private site.
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	74 # no real risk. The universe_wsgi.ini admin_users string is checked - only admin users are permitted to run this tool.
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	75 #
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	76
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	77 import sys
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	78 import shutil
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	79 import subprocess
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	80 import os
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	81 import time
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	82 import tempfile
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	83 import optparse
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	84 import tarfile
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	85 import re
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	86 import shutil
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	87 import math
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	88
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	89 progname = os.path.split(sys.argv[0])[1]
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	90 myversion = 'V001.1 March 2014'
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	91 verbose = False
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	92 debug = False
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	93 toolFactoryURL = 'https://bitbucket.org/fubar/galaxytoolfactory'
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	94
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	95 # if we do html we need these dependencies specified in a tool_dependencies.xml file and referred to in the generated
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	96 # tool xml
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	97 toolhtmldepskel = """<?xml version="1.0"?>
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	98 <tool_dependency>
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	99 <package name="ghostscript" version="9.10">
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	100 <repository name="package_ghostscript_9_10" owner="devteam" prior_installation_required="True" />
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	101 </package>
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	102 <package name="graphicsmagick" version="1.3.18">
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	103 <repository name="package_graphicsmagick_1_3" owner="iuc" prior_installation_required="True" />
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	104 </package>
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	105 <readme>
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	106 %s
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	107 </readme>
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	108 </tool_dependency>
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	109 """
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	110
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	111 protorequirements = """<requirements>
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	112 <requirement type="package" version="9.10">ghostscript</requirement>
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	113 <requirement type="package" version="1.3.18">graphicsmagick</requirement>
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	114 </requirements>"""
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	115
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	116 def timenow():
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	117 """return current time as a string
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	118 """
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	119 return time.strftime('%d/%m/%Y %H:%M:%S', time.localtime(time.time()))
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	120
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	121 html_escape_table = {
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	122 "&": "&",
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	123 ">": ">",
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	124 "<": "<",
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	125 "$": "\$"
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	126 }
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	127
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	128 def html_escape(text):
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	129 """Produce entities within text."""
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	130 return "".join(html_escape_table.get(c,c) for c in text)
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	131
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	132 def cmd_exists(cmd):
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	133 return subprocess.call("type " + cmd, shell=True,
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	134 stdout=subprocess.PIPE, stderr=subprocess.PIPE) == 0
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	135
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	136
30 fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: 29 diff changeset	137 def parse_citations(citations_text):
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: 29 diff changeset	138 """
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: 29 diff changeset	139 """
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: 29 diff changeset	140 citations = [c for c in citations_text.split("ENTRY") if c.strip()]
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: 29 diff changeset	141 citation_tuples = []
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: 29 diff changeset	142 for citation in citations:
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: 29 diff changeset	143 if citation.startswith("doi"):
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: 29 diff changeset	144 citation_tuples.append( ("doi", citation[len("doi"):].strip() ) )
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: 29 diff changeset	145 else:
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: 29 diff changeset	146 citation_tuples.append( ("bibtex", citation[len("bibtex"):].strip() ) )
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: 29 diff changeset	147 return citation_tuples
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: 29 diff changeset	148
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: 29 diff changeset	149
29 bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	150 class ScriptRunner:
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	151 """class is a wrapper for an arbitrary script
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	152 """
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	153
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	154 def __init__(self,opts=None,treatbashSpecial=True):
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	155 """
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	156 cleanup inputs, setup some outputs
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	157
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	158 """
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	159 self.useGM = cmd_exists('gm')
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	160 self.useIM = cmd_exists('convert')
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	161 self.useGS = cmd_exists('gs')
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	162 self.temp_warned = False # we want only one warning if $TMP not set
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	163 self.treatbashSpecial = treatbashSpecial
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	164 if opts.output_dir: # simplify for the tool tarball
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	165 os.chdir(opts.output_dir)
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	166 self.thumbformat = 'png'
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	167 self.opts = opts
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	168 self.toolname = re.sub('[^a-zA-Z0-9_]+', '', opts.tool_name) # a sanitizer now does this but..
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	169 self.toolid = self.toolname
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	170 self.myname = sys.argv[0] # get our name because we write ourselves out as a tool later
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	171 self.pyfile = self.myname # crude but efficient - the cruft won't hurt much
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	172 self.xmlfile = '%s.xml' % self.toolname
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	173 s = open(self.opts.script_path,'r').readlines()
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	174 s = [x.rstrip() for x in s] # remove pesky dos line endings if needed
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	175 self.script = '\n'.join(s)
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	176 fhandle,self.sfile = tempfile.mkstemp(prefix=self.toolname,suffix=".%s" % (opts.interpreter))
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	177 tscript = open(self.sfile,'w') # use self.sfile as script source for Popen
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	178 tscript.write(self.script)
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	179 tscript.close()
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	180 self.indentedScript = '\n'.join([' %s' % html_escape(x) for x in s]) # for restructured text in help
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	181 self.escapedScript = '\n'.join([html_escape(x) for x in s])
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	182 self.elog = os.path.join(self.opts.output_dir,"%s_error.log" % self.toolname)
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	183 if opts.output_dir: # may not want these complexities
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	184 self.tlog = os.path.join(self.opts.output_dir,"%s_runner.log" % self.toolname)
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	185 art = '%s.%s' % (self.toolname,opts.interpreter)
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	186 artpath = os.path.join(self.opts.output_dir,art) # need full path
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	187 artifact = open(artpath,'w') # use self.sfile as script source for Popen
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	188 artifact.write(self.script)
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	189 artifact.close()
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	190 self.cl = []
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	191 self.html = []
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	192 a = self.cl.append
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	193 a(opts.interpreter)
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	194 if self.treatbashSpecial and opts.interpreter in ['bash','sh']:
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	195 a(self.sfile)
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	196 else:
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	197 a('-') # stdin
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	198 a(opts.input_tab)
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	199 a(opts.output_tab)
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	200 self.outFormats = 'tabular' # TODO make this an option at tool generation time
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	201 self.inputFormats = 'tabular,txt' # TODO make this an option at tool generation time
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	202 self.test1Input = '%s_test1_input.xls' % self.toolname
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	203 self.test1Output = '%s_test1_output.xls' % self.toolname
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	204 self.test1HTML = '%s_test1_output.html' % self.toolname
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	205
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	206 def makeXML(self):
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	207 """
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	208 Create a Galaxy xml tool wrapper for the new script as a string to write out
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	209 fixme - use templating or something less fugly than this example of what we produce
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	210
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	211 <tool id="reverse" name="reverse" version="0.01">
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	212 <description>a tabular file</description>
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	213 <command interpreter="python">
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	214 reverse.py --script_path "$runMe" --interpreter "python"
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	215 --tool_name "reverse" --input_tab "$input1" --output_tab "$tab_file"
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	216 </command>
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	217 <inputs>
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	218 <param name="input1" type="data" format="tabular" label="Select a suitable input file from your history"/><param name="job_name" type="text" label="Supply a name for the outputs to remind you what they contain" value="reverse"/>
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	219
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	220 </inputs>
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	221 <outputs>
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	222 <data format="tabular" name="tab_file" label="${job_name}"/>
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	223
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	224 </outputs>
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	225 <help>
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	226
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	227 What it Does
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	228
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	229 Reverse the columns in a tabular file
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	230
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	231 </help>
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	232 <configfiles>
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	233 <configfile name="runMe">
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	234
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	235 # reverse order of columns in a tabular file
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	236 import sys
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	237 inp = sys.argv[1]
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	238 outp = sys.argv[2]
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	239 i = open(inp,'r')
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	240 o = open(outp,'w')
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	241 for row in i:
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	242 rs = row.rstrip().split('\t')
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	243 rs.reverse()
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	244 o.write('\t'.join(rs))
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	245 o.write('\n')
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	246 i.close()
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	247 o.close()
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	248
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	249
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	250 </configfile>
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	251 </configfiles>
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	252 </tool>
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	253
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	254 """
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	255 newXML="""<tool id="%(toolid)s" name="%(toolname)s" version="%(tool_version)s">
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	256 %(tooldesc)s
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	257 %(requirements)s
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	258 <command interpreter="python">
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	259 %(command)s
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	260 </command>
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	261 <inputs>
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	262 %(inputs)s
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	263 </inputs>
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	264 <outputs>
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	265 %(outputs)s
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	266 </outputs>
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	267 <configfiles>
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	268 <configfile name="runMe">
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	269 %(script)s
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	270 </configfile>
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	271 </configfiles>
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	272
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	273 %(tooltests)s
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	274
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	275 <help>
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	276
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	277 %(help)s
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	278
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	279 </help>
30 fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: 29 diff changeset	280 <citations>
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: 29 diff changeset	281 %(citations)s
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: 29 diff changeset	282 <citation type="doi">10.1093/bioinformatics/bts573</citation>
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: 29 diff changeset	283 </citations>
29 bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	284 </tool>""" # needs a dict with toolname, toolid, interpreter, scriptname, command, inputs as a multi line string ready to write, outputs ditto, help ditto
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	285
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	286 newCommand="""
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	287 %(toolname)s.py --script_path "$runMe" --interpreter "%(interpreter)s"
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	288 --tool_name "%(toolname)s" %(command_inputs)s %(command_outputs)s """
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	289 # may NOT be an input or htmlout - appended later
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	290 tooltestsTabOnly = """
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	291 <tests>
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	292 <test>
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	293 <param name="input1" value="%(test1Input)s" ftype="tabular"/>
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	294 <param name="job_name" value="test1"/>
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	295 <param name="runMe" value="$runMe"/>
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	296 <output name="tab_file" file="%(test1Output)s" ftype="tabular"/>
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	297 </test>
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	298 </tests>
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	299 """
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	300 tooltestsHTMLOnly = """
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	301 <tests>
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	302 <test>
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	303 <param name="input1" value="%(test1Input)s" ftype="tabular"/>
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	304 <param name="job_name" value="test1"/>
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	305 <param name="runMe" value="$runMe"/>
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	306 <output name="html_file" file="%(test1HTML)s" ftype="html" lines_diff="5"/>
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	307 </test>
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	308 </tests>
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	309 """
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	310 tooltestsBoth = """<tests>
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	311 <test>
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	312 <param name="input1" value="%(test1Input)s" ftype="tabular"/>
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	313 <param name="job_name" value="test1"/>
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	314 <param name="runMe" value="$runMe"/>
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	315 <output name="tab_file" file="%(test1Output)s" ftype="tabular" />
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	316 <output name="html_file" file="%(test1HTML)s" ftype="html" lines_diff="10"/>
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	317 </test>
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	318 </tests>
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	319 """
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	320 xdict = {}
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	321 xdict['requirements'] = ''
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	322 if self.opts.make_HTML:
30 fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: 29 diff changeset	323 if self.opts.include_dependencies == "yes":
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: 29 diff changeset	324 xdict['requirements'] = protorequirements
29 bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	325 xdict['tool_version'] = self.opts.tool_version
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	326 xdict['test1Input'] = self.test1Input
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	327 xdict['test1HTML'] = self.test1HTML
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	328 xdict['test1Output'] = self.test1Output
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	329 if self.opts.make_HTML and self.opts.output_tab <> 'None':
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	330 xdict['tooltests'] = tooltestsBoth % xdict
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	331 elif self.opts.make_HTML:
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	332 xdict['tooltests'] = tooltestsHTMLOnly % xdict
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	333 else:
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	334 xdict['tooltests'] = tooltestsTabOnly % xdict
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	335 xdict['script'] = self.escapedScript
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	336 # configfile is least painful way to embed script to avoid external dependencies
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	337 # but requires escaping of <, > and $ to avoid Mako parsing
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	338 if self.opts.help_text:
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	339 helptext = open(self.opts.help_text,'r').readlines()
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	340 helptext = [html_escape(x) for x in helptext] # must html escape here too - thanks to Marius van den Beek
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	341 xdict['help'] = ''.join([x for x in helptext])
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	342 else:
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	343 xdict['help'] = 'Please ask the tool author (%s) for help as none was supplied at tool generation\n' % (self.opts.user_email)
30 fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: 29 diff changeset	344 if self.opts.citations:
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: 29 diff changeset	345 citationstext = open(self.opts.citations,'r').read()
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: 29 diff changeset	346 citation_tuples = parse_citations(citationstext)
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: 29 diff changeset	347 citations_xml = ""
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: 29 diff changeset	348 for citation_type, citation_content in citation_tuples:
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: 29 diff changeset	349 citation_xml = """<citation type="%s">%s</citation>""" % (citation_type, html_escape(citation_content))
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: 29 diff changeset	350 citations_xml += citation_xml
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: 29 diff changeset	351 xdict['citations'] = citations_xml
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: 29 diff changeset	352 else:
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: 29 diff changeset	353 xdict['citations'] = ""
29 bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	354 coda = ['Script','Pressing execute will run the following code over your input file and generate some outputs in your history::']
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	355 coda.append('\n')
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	356 coda.append(self.indentedScript)
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	357 coda.append('\nAttribution\nThis Galaxy tool was created by %s at %s\nusing the Galaxy Tool Factory.\n' % (self.opts.user_email,timenow()))
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	358 coda.append('See %s for details of that project' % (toolFactoryURL))
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	359 coda.append('Please cite: Creating re-usable tools from scripts: The Galaxy Tool Factory. Ross Lazarus; Antony Kaspi; Mark Ziemann; The Galaxy Team. ')
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	360 coda.append('Bioinformatics 2012; doi: 10.1093/bioinformatics/bts573\n')
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	361 xdict['help'] = '%s\n%s' % (xdict['help'],'\n'.join(coda))
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	362 if self.opts.tool_desc:
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	363 xdict['tooldesc'] = '<description>%s</description>' % self.opts.tool_desc
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	364 else:
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	365 xdict['tooldesc'] = ''
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	366 xdict['command_outputs'] = ''
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	367 xdict['outputs'] = ''
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	368 if self.opts.input_tab <> 'None':
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	369 xdict['command_inputs'] = '--input_tab "$input1" ' # the space may matter a lot if we append something
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	370 xdict['inputs'] = '<param name="input1" type="data" format="%s" label="Select a suitable input file from your history"/> \n' % self.inputFormats
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	371 else:
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	372 xdict['command_inputs'] = '' # assume no input - eg a random data generator
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	373 xdict['inputs'] = ''
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	374 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
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	375 xdict['toolname'] = self.toolname
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	376 xdict['toolid'] = self.toolid
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	377 xdict['interpreter'] = self.opts.interpreter
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	378 xdict['scriptname'] = self.sfile
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	379 if self.opts.make_HTML:
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	380 xdict['command_outputs'] += ' --output_dir "$html_file.files_path" --output_html "$html_file" --make_HTML "yes"'
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	381 xdict['outputs'] += ' <data format="html" name="html_file" label="${job_name}.html"/>\n'
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	382 else:
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	383 xdict['command_outputs'] += ' --output_dir "./"'
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	384 if self.opts.output_tab <> 'None':
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	385 xdict['command_outputs'] += ' --output_tab "$tab_file"'
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	386 xdict['outputs'] += ' <data format="%s" name="tab_file" label="${job_name}"/>\n' % self.outFormats
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	387 xdict['command'] = newCommand % xdict
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	388 xmls = newXML % xdict
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	389 xf = open(self.xmlfile,'w')
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	390 xf.write(xmls)
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	391 xf.write('\n')
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	392 xf.close()
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	393 # ready for the tarball
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	394
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	395
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	396 def makeTooltar(self):
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	397 """
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	398 a tool is a gz tarball with eg
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	399 /toolname/tool.xml /toolname/tool.py /toolname/test-data/test1_in.foo ...
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	400 """
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	401 retval = self.run()
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	402 if retval:
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	403 print >> sys.stderr,'## Run failed. Cannot build yet. Please fix and retry'
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	404 sys.exit(1)
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	405 tdir = self.toolname
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	406 os.mkdir(tdir)
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	407 self.makeXML()
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	408 if self.opts.make_HTML:
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	409 if self.opts.help_text:
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	410 hlp = open(self.opts.help_text,'r').read()
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	411 else:
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	412 hlp = 'Please ask the tool author for help as none was supplied at tool generation\n'
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	413 if self.opts.include_dependencies:
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	414 tooldepcontent = toolhtmldepskel % hlp
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	415 depf = open(os.path.join(tdir,'tool_dependencies.xml'),'w')
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	416 depf.write(tooldepcontent)
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	417 depf.write('\n')
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	418 depf.close()
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	419 if self.opts.input_tab <> 'None': # no reproducible test otherwise? TODO: maybe..
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	420 testdir = os.path.join(tdir,'test-data')
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	421 os.mkdir(testdir) # make tests directory
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	422 shutil.copyfile(self.opts.input_tab,os.path.join(testdir,self.test1Input))
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	423 if self.opts.output_tab <> 'None':
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	424 shutil.copyfile(self.opts.output_tab,os.path.join(testdir,self.test1Output))
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	425 if self.opts.make_HTML:
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	426 shutil.copyfile(self.opts.output_html,os.path.join(testdir,self.test1HTML))
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	427 if self.opts.output_dir:
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	428 shutil.copyfile(self.tlog,os.path.join(testdir,'test1_out.log'))
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	429 outpif = '%s.py' % self.toolname # new name
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	430 outpiname = os.path.join(tdir,outpif) # path for the tool tarball
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	431 pyin = os.path.basename(self.pyfile) # our name - we rewrite ourselves (TM)
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	432 notes = ['# %s - a self annotated version of %s generated by running %s\n' % (outpiname,pyin,pyin),]
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	433 notes.append('# to make a new Galaxy tool called %s\n' % self.toolname)
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	434 notes.append('# User %s at %s\n' % (self.opts.user_email,timenow()))
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	435 pi = open(self.pyfile,'r').readlines() # our code becomes new tool wrapper (!) - first Galaxy worm
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	436 notes += pi
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	437 outpi = open(outpiname,'w')
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	438 outpi.write(''.join(notes))
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	439 outpi.write('\n')
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	440 outpi.close()
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	441 stname = os.path.join(tdir,self.sfile)
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	442 if not os.path.exists(stname):
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	443 shutil.copyfile(self.sfile, stname)
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	444 xtname = os.path.join(tdir,self.xmlfile)
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	445 if not os.path.exists(xtname):
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	446 shutil.copyfile(self.xmlfile,xtname)
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	447 tarpath = "%s.gz" % self.toolname
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	448 tar = tarfile.open(tarpath, "w:gz")
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	449 tar.add(tdir,arcname=self.toolname)
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	450 tar.close()
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	451 shutil.copyfile(tarpath,self.opts.new_tool)
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	452 shutil.rmtree(tdir)
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	453 ## TODO: replace with optional direct upload to local toolshed?
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	454 return retval
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	455
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	456
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	457 def compressPDF(self,inpdf=None,thumbformat='png'):
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	458 """need absolute path to pdf
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	459 note that GS gets confoozled if no $TMP or $TEMP
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	460 so we set it
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	461 """
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	462 assert os.path.isfile(inpdf), "## Input %s supplied to %s compressPDF not found" % (inpdf,self.myName)
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	463 hlog = os.path.join(self.opts.output_dir,"compress_%s.txt" % os.path.basename(inpdf))
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	464 sto = open(hlog,'a')
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	465 our_env = os.environ.copy()
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	466 our_tmp = our_env.get('TMP',None)
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	467 if not our_tmp:
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	468 our_tmp = our_env.get('TEMP',None)
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	469 if not (our_tmp and os.path.exists(our_tmp)):
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	470 newtmp = os.path.join(self.opts.output_dir,'tmp')
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	471 try:
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	472 os.mkdir(newtmp)
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	473 except:
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	474 sto.write('## WARNING - cannot make %s - it may exist or permissions need fixing\n' % newtmp)
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	475 our_env['TEMP'] = newtmp
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	476 if not self.temp_warned:
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	477 sto.write('## WARNING - no $TMP or $TEMP!!! Please fix - using %s temporarily\n' % newtmp)
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	478 self.temp_warned = True
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	479 outpdf = '%s_compressed' % inpdf
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	480 cl = ["gs", "-sDEVICE=pdfwrite", "-dNOPAUSE", "-dUseCIEColor", "-dBATCH","-dPDFSETTINGS=/printer", "-sOutputFile=%s" % outpdf,inpdf]
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	481 x = subprocess.Popen(cl,stdout=sto,stderr=sto,cwd=self.opts.output_dir,env=our_env)
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	482 retval1 = x.wait()
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	483 sto.close()
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	484 if retval1 == 0:
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	485 os.unlink(inpdf)
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	486 shutil.move(outpdf,inpdf)
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	487 os.unlink(hlog)
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	488 hlog = os.path.join(self.opts.output_dir,"thumbnail_%s.txt" % os.path.basename(inpdf))
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	489 sto = open(hlog,'w')
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	490 outpng = '%s.%s' % (os.path.splitext(inpdf)[0],thumbformat)
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	491 if self.useGM:
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	492 cl2 = ['gm', 'convert', inpdf, outpng]
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	493 else: # assume imagemagick
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	494 cl2 = ['convert', inpdf, outpng]
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	495 x = subprocess.Popen(cl2,stdout=sto,stderr=sto,cwd=self.opts.output_dir,env=our_env)
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	496 retval2 = x.wait()
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	497 sto.close()
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	498 if retval2 == 0:
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	499 os.unlink(hlog)
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	500 retval = retval1 or retval2
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	501 return retval
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	502
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	503
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	504 def getfSize(self,fpath,outpath):
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	505 """
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	506 format a nice file size string
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	507 """
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	508 size = ''
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	509 fp = os.path.join(outpath,fpath)
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	510 if os.path.isfile(fp):
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	511 size = '0 B'
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	512 n = float(os.path.getsize(fp))
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	513 if n > 2**20:
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	514 size = '%1.1f MB' % (n/2**20)
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	515 elif n > 2**10:
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	516 size = '%1.1f KB' % (n/2**10)
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	517 elif n > 0:
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	518 size = '%d B' % (int(n))
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	519 return size
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	520
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	521 def makeHtml(self):
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	522 """ Create an HTML file content to list all the artifacts found in the output_dir
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	523 """
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	524
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	525 galhtmlprefix = """<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	526 <html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	527 <head> <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	528 <meta name="generator" content="Galaxy %s tool output - see http://g2.trac.bx.psu.edu/" />
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	529 <title></title>
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	530 <link rel="stylesheet" href="/static/style/base.css" type="text/css" />
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	531 </head>
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	532 <body>
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	533 <div class="toolFormBody">
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	534 """
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	535 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/>"""
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	536 galhtmlpostfix = """</div></body></html>\n"""
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	537
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	538 flist = os.listdir(self.opts.output_dir)
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	539 flist = [x for x in flist if x <> 'Rplots.pdf']
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	540 flist.sort()
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	541 html = []
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	542 html.append(galhtmlprefix % progname)
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	543 html.append('<div class="infomessage">Galaxy Tool "%s" run at %s</div><br/>' % (self.toolname,timenow()))
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	544 fhtml = []
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	545 if len(flist) > 0:
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	546 logfiles = [x for x in flist if x.lower().endswith('.log')] # log file names determine sections
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	547 logfiles.sort()
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	548 logfiles = [x for x in logfiles if os.path.abspath(x) <> os.path.abspath(self.tlog)]
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	549 logfiles.append(os.path.abspath(self.tlog)) # make it the last one
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	550 pdflist = []
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	551 npdf = len([x for x in flist if os.path.splitext(x)[-1].lower() == '.pdf'])
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	552 for rownum,fname in enumerate(flist):
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	553 dname,e = os.path.splitext(fname)
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	554 sfsize = self.getfSize(fname,self.opts.output_dir)
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	555 if e.lower() == '.pdf' : # compress and make a thumbnail
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	556 thumb = '%s.%s' % (dname,self.thumbformat)
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	557 pdff = os.path.join(self.opts.output_dir,fname)
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	558 retval = self.compressPDF(inpdf=pdff,thumbformat=self.thumbformat)
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	559 if retval == 0:
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	560 pdflist.append((fname,thumb))
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	561 else:
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	562 pdflist.append((fname,fname))
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	563 if (rownum+1) % 2 == 0:
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	564 fhtml.append('<tr class="odd_row"><td><a href="%s">%s</a></td><td>%s</td></tr>' % (fname,fname,sfsize))
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	565 else:
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	566 fhtml.append('<tr><td><a href="%s">%s</a></td><td>%s</td></tr>' % (fname,fname,sfsize))
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	567 for logfname in logfiles: # expect at least tlog - if more
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	568 if os.path.abspath(logfname) == os.path.abspath(self.tlog): # handled later
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	569 sectionname = 'All tool run'
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	570 if (len(logfiles) > 1):
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	571 sectionname = 'Other'
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	572 ourpdfs = pdflist
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	573 else:
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	574 realname = os.path.basename(logfname)
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	575 sectionname = os.path.splitext(realname)[0].split('_')[0] # break in case _ added to log
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	576 ourpdfs = [x for x in pdflist if os.path.basename(x[0]).split('_')[0] == sectionname]
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	577 pdflist = [x for x in pdflist if os.path.basename(x[0]).split('_')[0] <> sectionname] # remove
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	578 nacross = 1
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	579 npdf = len(ourpdfs)
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	580
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	581 if npdf > 0:
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	582 nacross = math.sqrt(npdf) ## int(round(math.log(npdf,2)))
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	583 if int(nacross)**2 != npdf:
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	584 nacross += 1
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	585 nacross = int(nacross)
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	586 width = min(400,int(1200/nacross))
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	587 html.append('<div class="toolFormTitle">%s images and outputs</div>' % sectionname)
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	588 html.append('(Click on a thumbnail image to download the corresponding original PDF image)<br/>')
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	589 ntogo = nacross # counter for table row padding with empty cells
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	590 html.append('<div><table class="simple" cellpadding="2" cellspacing="2">\n<tr>')
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	591 for i,paths in enumerate(ourpdfs):
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	592 fname,thumb = paths
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	593 s= """<td><a href="%s"><img src="%s" title="Click to download a PDF of %s" hspace="5" width="%d"
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	594 alt="Image called %s"/></a></td>\n""" % (fname,thumb,fname,width,fname)
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	595 if ((i+1) % nacross == 0):
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	596 s += '</tr>\n'
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	597 ntogo = 0
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	598 if i < (npdf - 1): # more to come
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	599 s += '<tr>'
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	600 ntogo = nacross
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	601 else:
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	602 ntogo -= 1
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	603 html.append(s)
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	604 if html[-1].strip().endswith('</tr>'):
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	605 html.append('</table></div>\n')
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	606 else:
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	607 if ntogo > 0: # pad
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	608 html.append('<td> </td>'*ntogo)
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	609 html.append('</tr></table></div>\n')
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	610 logt = open(logfname,'r').readlines()
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	611 logtext = [x for x in logt if x.strip() > '']
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	612 html.append('<div class="toolFormTitle">%s log output</div>' % sectionname)
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	613 if len(logtext) > 1:
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	614 html.append('\n<pre>\n')
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	615 html += logtext
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	616 html.append('\n</pre>\n')
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	617 else:
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	618 html.append('%s is empty<br/>' % logfname)
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	619 if len(fhtml) > 0:
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	620 fhtml.insert(0,'<div><table class="colored" cellpadding="3" cellspacing="3"><tr><th>Output File Name (click to view)</th><th>Size</th></tr>\n')
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	621 fhtml.append('</table></div><br/>')
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	622 html.append('<div class="toolFormTitle">All output files available for downloading</div>\n')
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	623 html += fhtml # add all non-pdf files to the end of the display
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	624 else:
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	625 html.append('<div class="warningmessagelarge">### Error - %s returned no files - please confirm that parameters are sane</div>' % self.opts.interpreter)
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	626 html.append(galhtmlpostfix)
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	627 htmlf = file(self.opts.output_html,'w')
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	628 htmlf.write('\n'.join(html))
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	629 htmlf.write('\n')
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	630 htmlf.close()
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	631 self.html = html
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	632
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	633
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	634 def run(self):
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	635 """
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	636 scripts must be small enough not to fill the pipe!
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	637 """
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	638 if self.treatbashSpecial and self.opts.interpreter in ['bash','sh']:
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	639 retval = self.runBash()
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	640 else:
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	641 if self.opts.output_dir:
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	642 ste = open(self.elog,'w')
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	643 sto = open(self.tlog,'w')
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	644 sto.write('## Toolfactory generated command line = %s\n' % ' '.join(self.cl))
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	645 sto.flush()
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	646 p = subprocess.Popen(self.cl,shell=False,stdout=sto,stderr=ste,stdin=subprocess.PIPE,cwd=self.opts.output_dir)
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	647 else:
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	648 p = subprocess.Popen(self.cl,shell=False,stdin=subprocess.PIPE)
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	649 p.stdin.write(self.script)
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	650 p.stdin.close()
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	651 retval = p.wait()
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	652 if self.opts.output_dir:
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	653 sto.close()
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	654 ste.close()
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	655 err = open(self.elog,'r').readlines()
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	656 if retval <> 0 and err: # problem
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	657 print >> sys.stderr,err
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	658 if self.opts.make_HTML:
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	659 self.makeHtml()
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	660 return retval
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	661
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	662 def runBash(self):
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	663 """
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	664 cannot use - for bash so use self.sfile
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	665 """
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	666 if self.opts.output_dir:
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	667 s = '## Toolfactory generated command line = %s\n' % ' '.join(self.cl)
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	668 sto = open(self.tlog,'w')
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	669 sto.write(s)
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	670 sto.flush()
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	671 p = subprocess.Popen(self.cl,shell=False,stdout=sto,stderr=sto,cwd=self.opts.output_dir)
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	672 else:
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	673 p = subprocess.Popen(self.cl,shell=False)
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	674 retval = p.wait()
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	675 if self.opts.output_dir:
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	676 sto.close()
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	677 if self.opts.make_HTML:
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	678 self.makeHtml()
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	679 return retval
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	680
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	681
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	682 def main():
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	683 u = """
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	684 This is a Galaxy wrapper. It expects to be called by a special purpose tool.xml as:
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	685 <command interpreter="python">rgBaseScriptWrapper.py --script_path "$scriptPath" --tool_name "foo" --interpreter "Rscript"
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	686 </command>
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	687 """
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	688 op = optparse.OptionParser()
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	689 a = op.add_option
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	690 a('--script_path',default=None)
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	691 a('--tool_name',default=None)
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	692 a('--interpreter',default=None)
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	693 a('--output_dir',default='./')
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	694 a('--output_html',default=None)
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	695 a('--input_tab',default="None")
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	696 a('--output_tab',default="None")
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	697 a('--user_email',default='Unknown')
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	698 a('--bad_user',default=None)
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	699 a('--make_Tool',default=None)
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	700 a('--make_HTML',default=None)
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	701 a('--help_text',default=None)
30 fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: 29 diff changeset	702 a('--citations',default=None)
29 bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	703 a('--tool_desc',default=None)
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	704 a('--new_tool',default=None)
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	705 a('--tool_version',default=None)
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	706 a('--include_dependencies',default=None)
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	707 opts, args = op.parse_args()
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	708 assert not opts.bad_user,'UNAUTHORISED: %s is NOT authorized to use this tool until Galaxy admin adds %s to admin_users in universe_wsgi.ini' % (opts.bad_user,opts.bad_user)
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	709 assert opts.tool_name,'## Tool Factory expects a tool name - eg --tool_name=DESeq'
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	710 assert opts.interpreter,'## Tool Factory wrapper expects an interpreter - eg --interpreter=Rscript'
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	711 assert os.path.isfile(opts.script_path),'## Tool Factory wrapper expects a script path - eg --script_path=foo.R'
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	712 if opts.output_dir:
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	713 try:
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	714 os.makedirs(opts.output_dir)
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	715 except:
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	716 pass
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	717 r = ScriptRunner(opts)
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	718 if opts.make_Tool:
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	719 retcode = r.makeTooltar()
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	720 else:
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	721 retcode = r.run()
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	722 os.unlink(r.sfile)
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	723 if retcode:
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	724 sys.exit(retcode) # indicate failure to job runner
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	725
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	726
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	727 if __name__ == "__main__":
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	728 main()
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	729
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out fubar parents: diff changeset	730

Mercurial > repos > fubar > toolfactory

annotate rgToolFactory.py @ 34:c6fdf2c6d0f4 draft