skunkworks: rgToolFactoryMultIn.py annotate

author	fubar
date	Thu, 28 Aug 2014 02:22:39 -0400
parents
children

rev	line source
30 fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	1 # rgToolFactoryMultIn.py
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	2 # see https://bitbucket.org/fubar/galaxytoolfactory/wiki/Home
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	3 #
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	4 # copyright ross lazarus (ross stop lazarus at gmail stop com) May 2012
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	5 #
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	6 # all rights reserved
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	7 # Licensed under the LGPL
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	8 # suggestions for improvement and bug fixes welcome at https://bitbucket.org/fubar/galaxytoolfactory/wiki/Home
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	9 #
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	10 # august 2014
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	11 # Allows arbitrary number of input files
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	12 # NOTE positional parameters are now passed to script
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	13 # and output (may be "None") is before arbitrary number of inputs
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	14 #
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	15 # march 2014
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	16 # had to remove dependencies because cross toolshed dependencies are not possible - can't pre-specify a toolshed url for graphicsmagick and ghostscript
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	17 # grrrrr - night before a demo
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	18 # added dependencies to a tool_dependencies.xml if html page generated so generated tool is properly portable
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	19 #
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	20 # added ghostscript and graphicsmagick as dependencies
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	21 # fixed a wierd problem where gs was trying to use the new_files_path from universe (database/tmp) as ./database/tmp
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	22 # errors ensued
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	23 #
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	24 # august 2013
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	25 # found a problem with GS if $TMP or $TEMP missing - now inject /tmp and warn
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	26 #
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	27 # july 2013
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	28 # added ability to combine images and individual log files into html output
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	29 # just make sure there's a log file foo.log and it will be output
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	30 # together with all images named like "foo_*.pdf
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	31 # otherwise old format for html
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	32 #
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	33 # January 2013
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	34 # problem pointed out by Carlos Borroto
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	35 # added escaping for <>$ - thought I did that ages ago...
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	36 #
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	37 # August 11 2012
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	38 # changed to use shell=False and cl as a sequence
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	39
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	40 # This is a Galaxy tool factory for simple scripts in python, R or whatever ails ye.
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	41 # It also serves as the wrapper for the new tool.
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	42 #
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	43 # you paste and run your script
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	44 # Only works for simple scripts that read one input from the history.
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	45 # Optionally can write one new history dataset,
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	46 # and optionally collect any number of outputs into links on an autogenerated HTML page.
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	47
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	48 # DO NOT install on a public or important site - please.
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	49
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	50 # installed generated tools are fine if the script is safe.
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	51 # They just run normally and their user cannot do anything unusually insecure
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	52 # but please, practice safe toolshed.
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	53 # Read the fucking code before you install any tool
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	54 # especially this one
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	55
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	56 # After you get the script working on some test data, you can
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	57 # optionally generate a toolshed compatible gzip file
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	58 # containing your script safely wrapped as an ordinary Galaxy script in your local toolshed for
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	59 # safe and largely automated installation in a production Galaxy.
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	60
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	61 # If you opt for an HTML output, you get all the script outputs arranged
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	62 # as a single Html history item - all output files are linked, thumbnails for all the pdfs.
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	63 # Ugly but really inexpensive.
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	64 #
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	65 # Patches appreciated please.
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	66 #
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	67 #
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	68 # long route to June 2012 product
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	69 # Behold the awesome power of Galaxy and the toolshed with the tool factory to bind them
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	70 # derived from an integrated script model
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	71 # called rgBaseScriptWrapper.py
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	72 # Note to the unwary:
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	73 # This tool allows arbitrary scripting on your Galaxy as the Galaxy user
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	74 # There is nothing stopping a malicious user doing whatever they choose
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	75 # Extremely dangerous!!
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	76 # Totally insecure. So, trusted users only
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	77 #
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	78 # preferred model is a developer using their throw away workstation instance - ie a private site.
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	79 # no real risk. The universe_wsgi.ini admin_users string is checked - only admin users are permitted to run this tool.
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	80 #
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	81
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	82 import sys
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	83 import shutil
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	84 import subprocess
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	85 import os
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	86 import time
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	87 import tempfile
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	88 import optparse
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	89 import tarfile
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	90 import re
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	91 import shutil
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	92 import math
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	93
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	94 progname = os.path.split(sys.argv[0])[1]
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	95 myversion = 'V001.1 March 2014'
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	96 verbose = False
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	97 debug = False
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	98 toolFactoryURL = 'https://bitbucket.org/fubar/galaxytoolfactory'
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	99
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	100 # if we do html we need these dependencies specified in a tool_dependencies.xml file and referred to in the generated
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	101 # tool xml
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	102 toolhtmldepskel = """<?xml version="1.0"?>
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	103 <tool_dependency>
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	104 <package name="ghostscript" version="9.10">
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	105 <repository name="package_ghostscript_9_10" owner="devteam" prior_installation_required="True" />
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	106 </package>
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	107 <package name="graphicsmagick" version="1.3.18">
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	108 <repository name="package_graphicsmagick_1_3" owner="iuc" prior_installation_required="True" />
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	109 </package>
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	110 <readme>
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	111 %s
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	112 </readme>
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	113 </tool_dependency>
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	114 """
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	115
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	116 protorequirements = """<requirements>
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	117 <requirement type="package" version="9.10">ghostscript</requirement>
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	118 <requirement type="package" version="1.3.18">graphicsmagick</requirement>
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	119 </requirements>"""
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	120
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	121 def timenow():
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	122 """return current time as a string
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	123 """
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	124 return time.strftime('%d/%m/%Y %H:%M:%S', time.localtime(time.time()))
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	125
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	126 html_escape_table = {
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	127 "&": "&",
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	128 ">": ">",
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	129 "<": "<",
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	130 "$": "\$"
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	131 }
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	132
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	133 def html_escape(text):
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	134 """Produce entities within text."""
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	135 return "".join(html_escape_table.get(c,c) for c in text)
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	136
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	137 def cmd_exists(cmd):
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	138 return subprocess.call("type " + cmd, shell=True,
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	139 stdout=subprocess.PIPE, stderr=subprocess.PIPE) == 0
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	140
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	141
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	142 class ScriptRunner:
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	143 """class is a wrapper for an arbitrary script
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	144 """
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	145
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	146 def __init__(self,opts=None,treatbashSpecial=True):
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	147 """
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	148 cleanup inputs, setup some outputs
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	149
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	150 """
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	151 self.useGM = cmd_exists('gm')
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	152 self.useIM = cmd_exists('convert')
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	153 self.useGS = cmd_exists('gs')
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	154 self.temp_warned = False # we want only one warning if $TMP not set
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	155 self.treatbashSpecial = treatbashSpecial
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	156 if opts.output_dir: # simplify for the tool tarball
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	157 os.chdir(opts.output_dir)
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	158 self.thumbformat = 'png'
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	159 self.opts = opts
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	160 self.toolname = re.sub('[^a-zA-Z0-9_]+', '', opts.tool_name) # a sanitizer now does this but..
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	161 self.toolid = self.toolname
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	162 self.myname = sys.argv[0] # get our name because we write ourselves out as a tool later
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	163 self.pyfile = self.myname # crude but efficient - the cruft won't hurt much
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	164 self.xmlfile = '%s.xml' % self.toolname
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	165 s = open(self.opts.script_path,'r').readlines()
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	166 s = [x.rstrip() for x in s] # remove pesky dos line endings if needed
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	167 self.script = '\n'.join(s)
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	168 fhandle,self.sfile = tempfile.mkstemp(prefix=self.toolname,suffix=".%s" % (opts.interpreter))
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	169 tscript = open(self.sfile,'w') # use self.sfile as script source for Popen
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	170 tscript.write(self.script)
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	171 tscript.close()
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	172 self.indentedScript = '\n'.join([' %s' % html_escape(x) for x in s]) # for restructured text in help
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	173 self.escapedScript = '\n'.join([html_escape(x) for x in s])
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	174 self.elog = os.path.join(self.opts.output_dir,"%s_error.log" % self.toolname)
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	175 if opts.output_dir: # may not want these complexities
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	176 self.tlog = os.path.join(self.opts.output_dir,"%s_runner.log" % self.toolname)
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	177 art = '%s.%s' % (self.toolname,opts.interpreter)
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	178 artpath = os.path.join(self.opts.output_dir,art) # need full path
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	179 artifact = open(artpath,'w') # use self.sfile as script source for Popen
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	180 artifact.write(self.script)
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	181 artifact.close()
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	182 self.cl = []
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	183 self.html = []
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	184 self.test1Inputs = [] # now a list
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	185 a = self.cl.append
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	186 a(opts.interpreter)
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	187 if self.treatbashSpecial and opts.interpreter in ['bash','sh']:
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	188 a(self.sfile)
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	189 else:
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	190 a('-') # stdin
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	191 # if multiple inputs - positional or need to distinguish them with cl params
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	192 if opts.output_tab:
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	193 a('%s' % opts.output_tab)
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	194 if opts.input_tab:
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	195 tests = []
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	196 for i,intab in enumerate(opts.input_tab): # if multiple, make tests
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	197 if intab.find(',') <> -1:
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	198 (gpath,uname) = intab.split(',')
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	199 else:
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	200 gpath = uname = intab
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	201 a('"%s"' % (intab))
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	202 tests.append(os.path.basename(gpath))
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	203 self.test1Inputs = '<param name="input_tab" value="%s" />' % (','.join(tests))
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	204 else:
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	205 self.test1Inputs = ''
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	206 self.outFormats = opts.output_format
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	207 self.inputFormats = opts.input_formats
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	208 self.test1Output = '%s_test1_output.xls' % self.toolname
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	209 self.test1HTML = '%s_test1_output.html' % self.toolname
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	210
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	211 def makeXML(self):
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	212 """
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	213 Create a Galaxy xml tool wrapper for the new script as a string to write out
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	214 fixme - use templating or something less fugly than this example of what we produce
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	215
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	216 <tool id="reverse" name="reverse" version="0.01">
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	217 <description>a tabular file</description>
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	218 <command interpreter="python">
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	219 reverse.py --script_path "$runMe" --interpreter "python"
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	220 --tool_name "reverse" --input_tab "$input1" --output_tab "$tab_file"
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	221 </command>
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	222 <inputs>
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	223 <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"/>
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	224
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	225 </inputs>
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	226 <outputs>
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	227 <data format="tabular" name="tab_file" label="${job_name}"/>
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	228
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	229 </outputs>
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	230 <help>
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	231
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	232 What it Does
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	233
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	234 Reverse the columns in a tabular file
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	235
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	236 </help>
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	237 <configfiles>
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	238 <configfile name="runMe">
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	239
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	240 # reverse order of columns in a tabular file
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	241 import sys
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	242 inp = sys.argv[1]
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	243 outp = sys.argv[2]
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	244 i = open(inp,'r')
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	245 o = open(outp,'w')
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	246 for row in i:
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	247 rs = row.rstrip().split('\t')
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	248 rs.reverse()
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	249 o.write('\t'.join(rs))
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	250 o.write('\n')
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	251 i.close()
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	252 o.close()
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	253
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	254
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	255 </configfile>
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	256 </configfiles>
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	257 </tool>
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	258
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	259 """
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	260 newXML="""<tool id="%(toolid)s" name="%(toolname)s" version="%(tool_version)s">
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	261 %(tooldesc)s
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	262 %(requirements)s
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	263 <command interpreter="python">
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	264 %(command)s
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	265 </command>
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	266 <inputs>
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	267 %(inputs)s
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	268 </inputs>
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	269 <outputs>
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	270 %(outputs)s
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	271 </outputs>
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	272 <configfiles>
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	273 <configfile name="runMe">
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	274 %(script)s
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	275 </configfile>
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	276 </configfiles>
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	277 <tests>
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	278 %(tooltests)s
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	279 </tests>
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	280 <help>
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	281
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	282 %(help)s
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	283
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	284 </help>
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	285 </tool>""" # needs a dict with toolname, toolid, interpreter, scriptname, command, inputs as a multi line string ready to write, outputs ditto, help ditto
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	286
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	287 newCommand="""
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	288 %(toolname)s.py --script_path "$runMe" --interpreter "%(interpreter)s"
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	289 --tool_name "%(toolname)s"
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	290 %(command_inputs)s
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	291 %(command_outputs)s
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	292 """
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	293 # may NOT be an input or htmlout - appended later
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	294 tooltestsTabOnly = """
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	295 <test>
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	296 %(test1Inputs)s
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	297 <param name="job_name" value="test1"/>
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	298 <param name="runMe" value="$runMe"/>
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	299 <output name="tab_file" file="%(test1Output)s" ftype="tabular"/>
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	300 </test>
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	301 </tests>
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	302 """
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	303 tooltestsHTMLOnly = """
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	304 <test>
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	305 %(test1Inputs)s
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	306 <param name="job_name" value="test1"/>
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	307 <param name="runMe" value="$runMe"/>
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	308 <output name="html_file" file="%(test1HTML)s" ftype="html" lines_diff="5"/>
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	309 </test>
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	310 </tests>
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	311 """
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	312 tooltestsBoth = """
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	313 <test>
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	314 %(test1Inputs)s
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	315 <param name="job_name" value="test1"/>
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	316 <param name="runMe" value="$runMe"/>
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	317 <output name="tab_file" file="%(test1Output)s" ftype="tabular" />
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	318 <output name="html_file" file="%(test1HTML)s" ftype="html" lines_diff="10"/>
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	319 </test>
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	320 </tests>
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	321 """
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	322 xdict = {}
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	323 xdict['requirements'] = ''
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	324 if self.opts.make_HTML:
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	325 if self.opts.include_dependencies == "yes":
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	326 xdict['requirements'] = protorequirements
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	327 xdict['tool_version'] = self.opts.tool_version
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	328 xdict['test1HTML'] = self.test1HTML
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	329 xdict['test1Output'] = self.test1Output
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	330 xdict['test1Inputs'] = self.test1Inputs
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	331 if self.opts.make_HTML and self.opts.output_tab <> 'None':
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	332 xdict['tooltests'] = tooltestsBoth % xdict
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	333 elif self.opts.make_HTML:
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	334 xdict['tooltests'] = tooltestsHTMLOnly % xdict
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	335 else:
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	336 xdict['tooltests'] = tooltestsTabOnly % xdict
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	337 xdict['script'] = self.escapedScript
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	338 # configfile is least painful way to embed script to avoid external dependencies
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	339 # but requires escaping of <, > and $ to avoid Mako parsing
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	340 if self.opts.help_text:
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	341 helptext = open(self.opts.help_text,'r').readlines()
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	342 helptext = [html_escape(x) for x in helptext] # must html escape here too - thanks to Marius van den Beek
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	343 xdict['help'] = ''.join([x for x in helptext])
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	344 else:
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	345 xdict['help'] = 'Please ask the tool author (%s) for help as none was supplied at tool generation\n' % (self.opts.user_email)
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	346 coda = ['Script','Pressing execute will run the following code over your input file and generate some outputs in your history::']
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	347 coda.append('\n')
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	348 coda.append(self.indentedScript)
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	349 coda.append('\nAttribution\nThis Galaxy tool was created by %s at %s\nusing the Galaxy Tool Factory.\n' % (self.opts.user_email,timenow()))
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	350 coda.append('See %s for details of that project' % (toolFactoryURL))
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	351 coda.append('Please cite: Creating re-usable tools from scripts: The Galaxy Tool Factory. Ross Lazarus; Antony Kaspi; Mark Ziemann; The Galaxy Team. ')
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	352 coda.append('Bioinformatics 2012; doi: 10.1093/bioinformatics/bts573\n')
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	353 xdict['help'] = '%s\n%s' % (xdict['help'],'\n'.join(coda))
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	354 if self.opts.tool_desc:
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	355 xdict['tooldesc'] = '<description>%s</description>' % self.opts.tool_desc
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	356 else:
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	357 xdict['tooldesc'] = ''
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	358 xdict['command_outputs'] = ''
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	359 xdict['outputs'] = ''
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	360 if self.opts.input_tab <> 'None':
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	361 cins = ['\n',]
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	362 cins.append('#for intab in $input1:')
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	363 cins.append('--input_tab "$intab"')
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	364 cins.append('#end for\n')
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	365 xdict['command_inputs'] = '\n'.join(cins)
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	366 xdict['inputs'] = '''<param name="input1" multiple="true" type="data" format="%s" label="Select a suitable input file from your history"
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	367 help="Multiple inputs may be selected if the script can deal with them..."/> \n''' % self.inputFormats
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	368 else:
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	369 xdict['command_inputs'] = '' # assume no input - eg a random data generator
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	370 xdict['inputs'] = ''
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	371 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
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	372 xdict['toolname'] = self.toolname
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	373 xdict['toolid'] = self.toolid
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	374 xdict['interpreter'] = self.opts.interpreter
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	375 xdict['scriptname'] = self.sfile
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	376 if self.opts.make_HTML:
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	377 xdict['command_outputs'] += ' --output_dir "$html_file.files_path" --output_html "$html_file" --make_HTML "yes"'
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	378 xdict['outputs'] += ' <data format="html" name="html_file" label="${job_name}.html"/>\n'
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	379 else:
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	380 xdict['command_outputs'] += ' --output_dir "./"'
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	381 if self.opts.output_tab <> 'None':
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	382 xdict['command_outputs'] += ' --output_tab "$tab_file"'
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	383 xdict['outputs'] += ' <data format="%s" name="tab_file" label="${job_name}"/>\n' % self.outFormats
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	384 xdict['command'] = newCommand % xdict
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	385 xmls = newXML % xdict
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	386 xf = open(self.xmlfile,'w')
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	387 xf.write(xmls)
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	388 xf.write('\n')
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	389 xf.close()
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	390 # ready for the tarball
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	391
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	392
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	393 def makeTooltar(self):
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	394 """
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	395 a tool is a gz tarball with eg
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	396 /toolname/tool.xml /toolname/tool.py /toolname/test-data/test1_in.foo ...
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	397 """
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	398 retval = self.run()
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	399 if retval:
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	400 print >> sys.stderr,'## Run failed. Cannot build yet. Please fix and retry'
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	401 sys.exit(1)
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	402 tdir = self.toolname
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	403 os.mkdir(tdir)
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	404 self.makeXML()
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	405 if self.opts.make_HTML:
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	406 if self.opts.help_text:
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	407 hlp = open(self.opts.help_text,'r').read()
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	408 else:
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	409 hlp = 'Please ask the tool author for help as none was supplied at tool generation\n'
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	410 if self.opts.include_dependencies == "yes":
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	411 tooldepcontent = toolhtmldepskel % hlp
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	412 depf = open(os.path.join(tdir,'tool_dependencies.xml'),'w')
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	413 depf.write(tooldepcontent)
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	414 depf.write('\n')
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	415 depf.close()
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	416 if self.opts.input_tab <> 'None': # no reproducible test otherwise? TODO: maybe..
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	417 testdir = os.path.join(tdir,'test-data')
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	418 os.mkdir(testdir) # make tests directory
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	419 for i,intab in enumerate(self.opts.input_tab):
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	420 si = self.opts.input_tab[i]
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	421 if si.find(',') <> -1:
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	422 s = si.split(',')[0]
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	423 si = s
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	424 dest = os.path.join(testdir,os.path.basename(si))
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	425 if si <> dest:
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	426 shutil.copyfile(si,dest)
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	427 if self.opts.output_tab <> 'None':
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	428 shutil.copyfile(self.opts.output_tab,os.path.join(testdir,self.test1Output))
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	429 if self.opts.make_HTML:
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	430 shutil.copyfile(self.opts.output_html,os.path.join(testdir,self.test1HTML))
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	431 if self.opts.output_dir:
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	432 shutil.copyfile(self.tlog,os.path.join(testdir,'test1_out.log'))
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	433 outpif = '%s.py' % self.toolname # new name
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	434 outpiname = os.path.join(tdir,outpif) # path for the tool tarball
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	435 pyin = os.path.basename(self.pyfile) # our name - we rewrite ourselves (TM)
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	436 notes = ['# %s - a self annotated version of %s generated by running %s\n' % (outpiname,pyin,pyin),]
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	437 notes.append('# to make a new Galaxy tool called %s\n' % self.toolname)
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	438 notes.append('# User %s at %s\n' % (self.opts.user_email,timenow()))
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	439 pi = open(self.pyfile,'r').readlines() # our code becomes new tool wrapper (!) - first Galaxy worm
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	440 notes += pi
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	441 outpi = open(outpiname,'w')
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	442 outpi.write(''.join(notes))
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	443 outpi.write('\n')
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	444 outpi.close()
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	445 stname = os.path.join(tdir,self.sfile)
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	446 if not os.path.exists(stname):
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	447 shutil.copyfile(self.sfile, stname)
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	448 xtname = os.path.join(tdir,self.xmlfile)
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	449 if not os.path.exists(xtname):
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	450 shutil.copyfile(self.xmlfile,xtname)
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	451 tarpath = "%s.gz" % self.toolname
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	452 tar = tarfile.open(tarpath, "w:gz")
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	453 tar.add(tdir,arcname=self.toolname)
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	454 tar.close()
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	455 shutil.copyfile(tarpath,self.opts.new_tool)
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	456 shutil.rmtree(tdir)
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	457 ## TODO: replace with optional direct upload to local toolshed?
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	458 return retval
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	459
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	460
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	461 def compressPDF(self,inpdf=None,thumbformat='png'):
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	462 """need absolute path to pdf
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	463 note that GS gets confoozled if no $TMP or $TEMP
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	464 so we set it
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	465 """
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	466 assert os.path.isfile(inpdf), "## Input %s supplied to %s compressPDF not found" % (inpdf,self.myName)
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	467 hlog = os.path.join(self.opts.output_dir,"compress_%s.txt" % os.path.basename(inpdf))
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	468 sto = open(hlog,'a')
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	469 our_env = os.environ.copy()
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	470 our_tmp = our_env.get('TMP',None)
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	471 if not our_tmp:
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	472 our_tmp = our_env.get('TEMP',None)
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	473 if not (our_tmp and os.path.exists(our_tmp)):
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	474 newtmp = os.path.join(self.opts.output_dir,'tmp')
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	475 try:
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	476 os.mkdir(newtmp)
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	477 except:
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	478 sto.write('## WARNING - cannot make %s - it may exist or permissions need fixing\n' % newtmp)
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30

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1 # rgToolFactoryMultIn.py

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2 # see https://bitbucket.org/fubar/galaxytoolfactory/wiki/Home

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3 #

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4 # copyright ross lazarus (ross stop lazarus at gmail stop com) May 2012

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5 #

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7 # Licensed under the LGPL

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8 # suggestions for improvement and bug fixes welcome at https://bitbucket.org/fubar/galaxytoolfactory/wiki/Home

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9 #

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10 # august 2014

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11 # Allows arbitrary number of input files

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12 # NOTE positional parameters are now passed to script

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13 # and output (may be "None") is *before* arbitrary number of inputs

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14 #

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15 # march 2014

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16 # had to remove dependencies because cross toolshed dependencies are not possible - can't pre-specify a toolshed url for graphicsmagick and ghostscript

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17 # grrrrr - night before a demo

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18 # added dependencies to a tool_dependencies.xml if html page generated so generated tool is properly portable

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19 #

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20 # added ghostscript and graphicsmagick as dependencies

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21 # fixed a wierd problem where gs was trying to use the new_files_path from universe (database/tmp) as ./database/tmp

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22 # errors ensued

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23 #

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24 # august 2013

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25 # found a problem with GS if $TMP or $TEMP missing - now inject /tmp and warn

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26 #

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27 # july 2013

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28 # added ability to combine images and individual log files into html output

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29 # just make sure there's a log file foo.log and it will be output

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30 # together with all images named like "foo_*.pdf

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31 # otherwise old format for html

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32 #

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33 # January 2013

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34 # problem pointed out by Carlos Borroto

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35 # added escaping for <>$ - thought I did that ages ago...

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36 #

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37 # August 11 2012

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38 # changed to use shell=False and cl as a sequence

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39

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40 # This is a Galaxy tool factory for simple scripts in python, R or whatever ails ye.

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41 # It also serves as the wrapper for the new tool.

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42 #

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43 # you paste and run your script

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44 # Only works for simple scripts that read one input from the history.

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45 # Optionally can write one new history dataset,

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46 # and optionally collect any number of outputs into links on an autogenerated HTML page.

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47

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48 # DO NOT install on a public or important site - please.

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49

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50 # installed generated tools are fine if the script is safe.

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51 # They just run normally and their user cannot do anything unusually insecure

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52 # but please, practice safe toolshed.

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53 # Read the fucking code before you install any tool

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54 # especially this one

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55

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56 # After you get the script working on some test data, you can

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57 # optionally generate a toolshed compatible gzip file

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58 # containing your script safely wrapped as an ordinary Galaxy script in your local toolshed for

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59 # safe and largely automated installation in a production Galaxy.

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60

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61 # If you opt for an HTML output, you get all the script outputs arranged

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62 # as a single Html history item - all output files are linked, thumbnails for all the pdfs.

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63 # Ugly but really inexpensive.

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64 #

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65 # Patches appreciated please.

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66 #

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67 #

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68 # long route to June 2012 product

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69 # Behold the awesome power of Galaxy and the toolshed with the tool factory to bind them

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70 # derived from an integrated script model

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71 # called rgBaseScriptWrapper.py

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72 # Note to the unwary:

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73 # This tool allows arbitrary scripting on your Galaxy as the Galaxy user

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74 # There is nothing stopping a malicious user doing whatever they choose

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75 # Extremely dangerous!!

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76 # Totally insecure. So, trusted users only

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77 #

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78 # preferred model is a developer using their throw away workstation instance - ie a private site.

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79 # no real risk. The universe_wsgi.ini admin_users string is checked - only admin users are permitted to run this tool.

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80 #

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81

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82 import sys

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83 import shutil

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84 import subprocess

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85 import os

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86 import time

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87 import tempfile

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88 import optparse

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89 import tarfile

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90 import re

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91 import shutil

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92 import math

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93

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94 progname = os.path.split(sys.argv[0])[1]

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95 myversion = 'V001.1 March 2014'

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96 verbose = False

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97 debug = False

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98 toolFactoryURL = 'https://bitbucket.org/fubar/galaxytoolfactory'

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99

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100 # if we do html we need these dependencies specified in a tool_dependencies.xml file and referred to in the generated

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101 # tool xml

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102 toolhtmldepskel = """<?xml version="1.0"?>

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103 <tool_dependency>

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104 <package name="ghostscript" version="9.10">

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105 <repository name="package_ghostscript_9_10" owner="devteam" prior_installation_required="True" />

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106 </package>

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107 <package name="graphicsmagick" version="1.3.18">

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108 <repository name="package_graphicsmagick_1_3" owner="iuc" prior_installation_required="True" />

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109 </package>

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110 <readme>

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111 %s

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112 </readme>

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113 </tool_dependency>

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114 """

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115

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116 protorequirements = """<requirements>

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117 <requirement type="package" version="9.10">ghostscript</requirement>

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118 <requirement type="package" version="1.3.18">graphicsmagick</requirement>

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119 </requirements>"""

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120

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121 def timenow():

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122 """return current time as a string

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123 """

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124 return time.strftime('%d/%m/%Y %H:%M:%S', time.localtime(time.time()))

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125

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126 html_escape_table = {

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127 "&": "&",

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128 ">": ">",

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129 "<": "<",

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130 "$": "\$"

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131 }

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132

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133 def html_escape(text):

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134 """Produce entities within text."""

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135 return "".join(html_escape_table.get(c,c) for c in text)

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136

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137 def cmd_exists(cmd):

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138 return subprocess.call("type " + cmd, shell=True,

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139 stdout=subprocess.PIPE, stderr=subprocess.PIPE) == 0

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140

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141

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142 class ScriptRunner:

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143 """class is a wrapper for an arbitrary script

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144 """

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145

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146 def __init__(self,opts=None,treatbashSpecial=True):

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147 """

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148 cleanup inputs, setup some outputs

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149

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150 """

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151 self.useGM = cmd_exists('gm')

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152 self.useIM = cmd_exists('convert')

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153 self.useGS = cmd_exists('gs')

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154 self.temp_warned = False # we want only one warning if $TMP not set

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155 self.treatbashSpecial = treatbashSpecial

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156 if opts.output_dir: # simplify for the tool tarball

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157 os.chdir(opts.output_dir)

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158 self.thumbformat = 'png'

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159 self.opts = opts

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160 self.toolname = re.sub('[^a-zA-Z0-9_]+', '', opts.tool_name) # a sanitizer now does this but..

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161 self.toolid = self.toolname

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162 self.myname = sys.argv[0] # get our name because we write ourselves out as a tool later

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163 self.pyfile = self.myname # crude but efficient - the cruft won't hurt much

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164 self.xmlfile = '%s.xml' % self.toolname

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165 s = open(self.opts.script_path,'r').readlines()

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166 s = [x.rstrip() for x in s] # remove pesky dos line endings if needed

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167 self.script = '\n'.join(s)

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168 fhandle,self.sfile = tempfile.mkstemp(prefix=self.toolname,suffix=".%s" % (opts.interpreter))

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169 tscript = open(self.sfile,'w') # use self.sfile as script source for Popen

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170 tscript.write(self.script)

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171 tscript.close()

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172 self.indentedScript = '\n'.join([' %s' % html_escape(x) for x in s]) # for restructured text in help

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173 self.escapedScript = '\n'.join([html_escape(x) for x in s])

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174 self.elog = os.path.join(self.opts.output_dir,"%s_error.log" % self.toolname)

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175 if opts.output_dir: # may not want these complexities

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176 self.tlog = os.path.join(self.opts.output_dir,"%s_runner.log" % self.toolname)

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177 art = '%s.%s' % (self.toolname,opts.interpreter)

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178 artpath = os.path.join(self.opts.output_dir,art) # need full path

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179 artifact = open(artpath,'w') # use self.sfile as script source for Popen

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180 artifact.write(self.script)

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181 artifact.close()

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182 self.cl = []

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183 self.html = []

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184 self.test1Inputs = [] # now a list

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185 a = self.cl.append

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186 a(opts.interpreter)

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187 if self.treatbashSpecial and opts.interpreter in ['bash','sh']:

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188 a(self.sfile)

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189 else:

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190 a('-') # stdin

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191 # if multiple inputs - positional or need to distinguish them with cl params

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192 if opts.output_tab:

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193 a('%s' % opts.output_tab)

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194 if opts.input_tab:

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195 tests = []

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196 for i,intab in enumerate(opts.input_tab): # if multiple, make tests

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197 if intab.find(',') <> -1:

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198 (gpath,uname) = intab.split(',')

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199 else:

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200 gpath = uname = intab

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201 a('"%s"' % (intab))

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202 tests.append(os.path.basename(gpath))

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203 self.test1Inputs = '<param name="input_tab" value="%s" />' % (','.join(tests))

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204 else:

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205 self.test1Inputs = ''

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206 self.outFormats = opts.output_format

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207 self.inputFormats = opts.input_formats

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208 self.test1Output = '%s_test1_output.xls' % self.toolname

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209 self.test1HTML = '%s_test1_output.html' % self.toolname

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210

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211 def makeXML(self):

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212 """

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213 Create a Galaxy xml tool wrapper for the new script as a string to write out

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214 fixme - use templating or something less fugly than this example of what we produce

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215

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216 <tool id="reverse" name="reverse" version="0.01">

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217 <description>a tabular file</description>

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218 <command interpreter="python">

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219 reverse.py --script_path "$runMe" --interpreter "python"

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220 --tool_name "reverse" --input_tab "$input1" --output_tab "$tab_file"

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221 </command>

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222 <inputs>

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223 <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"/>

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224

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225 </inputs>

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226 <outputs>

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227 <data format="tabular" name="tab_file" label="${job_name}"/>

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228

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229 </outputs>

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230 <help>

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231

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232 **What it Does**

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233

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234 Reverse the columns in a tabular file

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235

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236 </help>

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237 <configfiles>

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238 <configfile name="runMe">

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239

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240 # reverse order of columns in a tabular file

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241 import sys

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242 inp = sys.argv[1]

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243 outp = sys.argv[2]

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244 i = open(inp,'r')

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245 o = open(outp,'w')

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246 for row in i:

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247 rs = row.rstrip().split('\t')

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248 rs.reverse()

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249 o.write('\t'.join(rs))

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250 o.write('\n')

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251 i.close()

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252 o.close()

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253

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254

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255 </configfile>

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256 </configfiles>

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257 </tool>

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258

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259 """

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260 newXML="""<tool id="%(toolid)s" name="%(toolname)s" version="%(tool_version)s">

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261 %(tooldesc)s

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262 %(requirements)s

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263 <command interpreter="python">

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264 %(command)s

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265 </command>

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266 <inputs>

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267 %(inputs)s

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268 </inputs>

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269 <outputs>

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270 %(outputs)s

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271 </outputs>

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272 <configfiles>

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273 <configfile name="runMe">

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274 %(script)s

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275 </configfile>

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276 </configfiles>

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277 <tests>

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278 %(tooltests)s

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279 </tests>

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280 <help>

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281

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282 %(help)s

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283

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284 </help>

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285 </tool>""" # needs a dict with toolname, toolid, interpreter, scriptname, command, inputs as a multi line string ready to write, outputs ditto, help ditto

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286

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287 newCommand="""

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288 %(toolname)s.py --script_path "$runMe" --interpreter "%(interpreter)s"

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289 --tool_name "%(toolname)s"

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290 %(command_inputs)s

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291 %(command_outputs)s

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292 """

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293 # may NOT be an input or htmlout - appended later

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294 tooltestsTabOnly = """

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295 <test>

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296 %(test1Inputs)s

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297 <param name="job_name" value="test1"/>

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298 <param name="runMe" value="$runMe"/>

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299 <output name="tab_file" file="%(test1Output)s" ftype="tabular"/>

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300 </test>

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301 </tests>

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302 """

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303 tooltestsHTMLOnly = """

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304 <test>

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305 %(test1Inputs)s

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306 <param name="job_name" value="test1"/>

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307 <param name="runMe" value="$runMe"/>

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308 <output name="html_file" file="%(test1HTML)s" ftype="html" lines_diff="5"/>

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309 </test>

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310 </tests>

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311 """

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312 tooltestsBoth = """

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313 <test>

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314 %(test1Inputs)s

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315 <param name="job_name" value="test1"/>

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316 <param name="runMe" value="$runMe"/>

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317 <output name="tab_file" file="%(test1Output)s" ftype="tabular" />

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318 <output name="html_file" file="%(test1HTML)s" ftype="html" lines_diff="10"/>

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319 </test>

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320 </tests>

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321 """

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322 xdict = {}

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323 xdict['requirements'] = ''

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324 if self.opts.make_HTML:

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325 if self.opts.include_dependencies == "yes":

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326 xdict['requirements'] = protorequirements

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327 xdict['tool_version'] = self.opts.tool_version

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328 xdict['test1HTML'] = self.test1HTML

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329 xdict['test1Output'] = self.test1Output

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330 xdict['test1Inputs'] = self.test1Inputs

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331 if self.opts.make_HTML and self.opts.output_tab <> 'None':

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332 xdict['tooltests'] = tooltestsBoth % xdict

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333 elif self.opts.make_HTML:

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334 xdict['tooltests'] = tooltestsHTMLOnly % xdict

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335 else:

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336 xdict['tooltests'] = tooltestsTabOnly % xdict

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337 xdict['script'] = self.escapedScript

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338 # configfile is least painful way to embed script to avoid external dependencies

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339 # but requires escaping of <, > and $ to avoid Mako parsing

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340 if self.opts.help_text:

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341 helptext = open(self.opts.help_text,'r').readlines()

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342 helptext = [html_escape(x) for x in helptext] # must html escape here too - thanks to Marius van den Beek

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343 xdict['help'] = ''.join([x for x in helptext])

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344 else:

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345 xdict['help'] = 'Please ask the tool author (%s) for help as none was supplied at tool generation\n' % (self.opts.user_email)

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346 coda = ['**Script**','Pressing execute will run the following code over your input file and generate some outputs in your history::']

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347 coda.append('\n')

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348 coda.append(self.indentedScript)

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349 coda.append('\n**Attribution**\nThis Galaxy tool was created by %s at %s\nusing the Galaxy Tool Factory.\n' % (self.opts.user_email,timenow()))

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350 coda.append('See %s for details of that project' % (toolFactoryURL))

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351 coda.append('Please cite: Creating re-usable tools from scripts: The Galaxy Tool Factory. Ross Lazarus; Antony Kaspi; Mark Ziemann; The Galaxy Team. ')

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352 coda.append('Bioinformatics 2012; doi: 10.1093/bioinformatics/bts573\n')

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353 xdict['help'] = '%s\n%s' % (xdict['help'],'\n'.join(coda))

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354 if self.opts.tool_desc:

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355 xdict['tooldesc'] = '<description>%s</description>' % self.opts.tool_desc

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356 else:

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357 xdict['tooldesc'] = ''

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358 xdict['command_outputs'] = ''

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359 xdict['outputs'] = ''

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360 if self.opts.input_tab <> 'None':

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361 cins = ['\n',]

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362 cins.append('#for intab in $input1:')

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363 cins.append('--input_tab "$intab"')

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364 cins.append('#end for\n')

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365 xdict['command_inputs'] = '\n'.join(cins)

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366 xdict['inputs'] = '''<param name="input1" multiple="true" type="data" format="%s" label="Select a suitable input file from your history"

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367 help="Multiple inputs may be selected if the script can deal with them..."/> \n''' % self.inputFormats

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368 else:

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369 xdict['command_inputs'] = '' # assume no input - eg a random data generator

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370 xdict['inputs'] = ''

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371 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

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372 xdict['toolname'] = self.toolname

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373 xdict['toolid'] = self.toolid

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374 xdict['interpreter'] = self.opts.interpreter

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375 xdict['scriptname'] = self.sfile

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376 if self.opts.make_HTML:

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377 xdict['command_outputs'] += ' --output_dir "$html_file.files_path" --output_html "$html_file" --make_HTML "yes"'

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378 xdict['outputs'] += ' <data format="html" name="html_file" label="${job_name}.html"/>\n'

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379 else:

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380 xdict['command_outputs'] += ' --output_dir "./"'

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381 if self.opts.output_tab <> 'None':

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382 xdict['command_outputs'] += ' --output_tab "$tab_file"'

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383 xdict['outputs'] += ' <data format="%s" name="tab_file" label="${job_name}"/>\n' % self.outFormats

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384 xdict['command'] = newCommand % xdict

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385 xmls = newXML % xdict

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386 xf = open(self.xmlfile,'w')

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387 xf.write(xmls)

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388 xf.write('\n')

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389 xf.close()

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390 # ready for the tarball

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391

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392

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393 def makeTooltar(self):

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394 """

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395 a tool is a gz tarball with eg

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396 /toolname/tool.xml /toolname/tool.py /toolname/test-data/test1_in.foo ...

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397 """

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398 retval = self.run()

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399 if retval:

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400 print >> sys.stderr,'## Run failed. Cannot build yet. Please fix and retry'

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401 sys.exit(1)

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402 tdir = self.toolname

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403 os.mkdir(tdir)

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404 self.makeXML()

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405 if self.opts.make_HTML:

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406 if self.opts.help_text:

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407 hlp = open(self.opts.help_text,'r').read()

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diff changeset

408 else:

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409 hlp = 'Please ask the tool author for help as none was supplied at tool generation\n'

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diff changeset

410 if self.opts.include_dependencies == "yes":

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411 tooldepcontent = toolhtmldepskel % hlp

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412 depf = open(os.path.join(tdir,'tool_dependencies.xml'),'w')

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413 depf.write(tooldepcontent)

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diff changeset

414 depf.write('\n')

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415 depf.close()

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416 if self.opts.input_tab <> 'None': # no reproducible test otherwise? TODO: maybe..

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417 testdir = os.path.join(tdir,'test-data')

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418 os.mkdir(testdir) # make tests directory

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419 for i,intab in enumerate(self.opts.input_tab):

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420 si = self.opts.input_tab[i]

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421 if si.find(',') <> -1:

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422 s = si.split(',')[0]

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423 si = s

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424 dest = os.path.join(testdir,os.path.basename(si))

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diff changeset

425 if si <> dest:

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diff changeset

426 shutil.copyfile(si,dest)

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427 if self.opts.output_tab <> 'None':

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428 shutil.copyfile(self.opts.output_tab,os.path.join(testdir,self.test1Output))

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429 if self.opts.make_HTML:

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430 shutil.copyfile(self.opts.output_html,os.path.join(testdir,self.test1HTML))

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431 if self.opts.output_dir:

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432 shutil.copyfile(self.tlog,os.path.join(testdir,'test1_out.log'))

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433 outpif = '%s.py' % self.toolname # new name

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434 outpiname = os.path.join(tdir,outpif) # path for the tool tarball

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435 pyin = os.path.basename(self.pyfile) # our name - we rewrite ourselves (TM)

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436 notes = ['# %s - a self annotated version of %s generated by running %s\n' % (outpiname,pyin,pyin),]

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437 notes.append('# to make a new Galaxy tool called %s\n' % self.toolname)

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438 notes.append('# User %s at %s\n' % (self.opts.user_email,timenow()))

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439 pi = open(self.pyfile,'r').readlines() # our code becomes new tool wrapper (!) - first Galaxy worm

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440 notes += pi

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441 outpi = open(outpiname,'w')

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442 outpi.write(''.join(notes))

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diff changeset

443 outpi.write('\n')

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diff changeset

444 outpi.close()

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445 stname = os.path.join(tdir,self.sfile)

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446 if not os.path.exists(stname):

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447 shutil.copyfile(self.sfile, stname)

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448 xtname = os.path.join(tdir,self.xmlfile)

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449 if not os.path.exists(xtname):

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diff changeset

450 shutil.copyfile(self.xmlfile,xtname)

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diff changeset

451 tarpath = "%s.gz" % self.toolname

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452 tar = tarfile.open(tarpath, "w:gz")

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diff changeset

453 tar.add(tdir,arcname=self.toolname)

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diff changeset

454 tar.close()

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diff changeset

455 shutil.copyfile(tarpath,self.opts.new_tool)

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diff changeset

456 shutil.rmtree(tdir)

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diff changeset

457 ## TODO: replace with optional direct upload to local toolshed?

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diff changeset

458 return retval

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diff changeset

459

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diff changeset

460

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diff changeset

461 def compressPDF(self,inpdf=None,thumbformat='png'):

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diff changeset

462 """need absolute path to pdf

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diff changeset

463 note that GS gets confoozled if no $TMP or $TEMP

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diff changeset

464 so we set it

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465 """

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466 assert os.path.isfile(inpdf), "## Input %s supplied to %s compressPDF not found" % (inpdf,self.myName)

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467 hlog = os.path.join(self.opts.output_dir,"compress_%s.txt" % os.path.basename(inpdf))

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468 sto = open(hlog,'a')

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469 our_env = os.environ.copy()

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470 our_tmp = our_env.get('TMP',None)

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diff changeset

471 if not our_tmp:

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472 our_tmp = our_env.get('TEMP',None)

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473 if not (our_tmp and os.path.exists(our_tmp)):

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474 newtmp = os.path.join(self.opts.output_dir,'tmp')

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diff changeset

475 try:

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diff changeset

476 os.mkdir(newtmp)

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diff changeset

477 except:

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478 sto.write('## WARNING - cannot make %s - it may exist or permissions need fixing\n' % newtmp)

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479 our_env['TEMP'] = newtmp

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diff changeset

480 if not self.temp_warned:

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481 sto.write('## WARNING - no $TMP or $TEMP!!! Please fix - using %s temporarily\n' % newtmp)

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diff changeset

482 self.temp_warned = True

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diff changeset

483 outpdf = '%s_compressed' % inpdf

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484 cl = ["gs", "-sDEVICE=pdfwrite", "-dNOPAUSE", "-dUseCIEColor", "-dBATCH","-dPDFSETTINGS=/printer", "-sOutputFile=%s" % outpdf,inpdf]

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485 x = subprocess.Popen(cl,stdout=sto,stderr=sto,cwd=self.opts.output_dir,env=our_env)

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diff changeset

486 retval1 = x.wait()

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diff changeset

487 sto.close()

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diff changeset

488 if retval1 == 0:

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diff changeset

489 os.unlink(inpdf)

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diff changeset

490 shutil.move(outpdf,inpdf)

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diff changeset

491 os.unlink(hlog)

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492 hlog = os.path.join(self.opts.output_dir,"thumbnail_%s.txt" % os.path.basename(inpdf))

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493 sto = open(hlog,'w')

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diff changeset

494 outpng = '%s.%s' % (os.path.splitext(inpdf)[0],thumbformat)

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diff changeset

495 if self.useGM:

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diff changeset

496 cl2 = ['gm', 'convert', inpdf, outpng]

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diff changeset

497 else: # assume imagemagick

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diff changeset

498 cl2 = ['convert', inpdf, outpng]

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diff changeset

499 x = subprocess.Popen(cl2,stdout=sto,stderr=sto,cwd=self.opts.output_dir,env=our_env)

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diff changeset

500 retval2 = x.wait()

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diff changeset

501 sto.close()

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diff changeset

502 if retval2 == 0:

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parents:

diff changeset

503 os.unlink(hlog)

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diff changeset

504 retval = retval1 or retval2

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diff changeset

505 return retval

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diff changeset

506

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parents:

diff changeset

507

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parents:

diff changeset

508 def getfSize(self,fpath,outpath):

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diff changeset

509 """

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parents:

diff changeset

510 format a nice file size string

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parents:

diff changeset

511 """

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parents:

diff changeset

512 size = ''

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513 fp = os.path.join(outpath,fpath)

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parents:

diff changeset

514 if os.path.isfile(fp):

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parents:

diff changeset

515 size = '0 B'

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diff changeset

516 n = float(os.path.getsize(fp))

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diff changeset

517 if n > 2**20:

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parents:

diff changeset

518 size = '%1.1f MB' % (n/2**20)

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parents:

diff changeset

519 elif n > 2**10:

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parents:

diff changeset

520 size = '%1.1f KB' % (n/2**10)

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diff changeset

521 elif n > 0:

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diff changeset

522 size = '%d B' % (int(n))

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diff changeset

523 return size

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diff changeset

524

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parents:

diff changeset

525 def makeHtml(self):

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parents:

diff changeset

526 """ Create an HTML file content to list all the artifacts found in the output_dir

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parents:

diff changeset

527 """

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parents:

diff changeset

528

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diff changeset

529 galhtmlprefix = """<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">

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diff changeset

530 <html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">

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parents:

diff changeset

531 <head> <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />

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diff changeset

532 <meta name="generator" content="Galaxy %s tool output - see http://g2.trac.bx.psu.edu/" />

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parents:

diff changeset

533 <title></title>

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parents:

diff changeset

534 <link rel="stylesheet" href="/static/style/base.css" type="text/css" />

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diff changeset

535 </head>

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parents:

diff changeset

536 <body>

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parents:

diff changeset

537 <div class="toolFormBody">

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parents:

diff changeset

538 """

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parents:

diff changeset

539 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/>"""

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diff changeset

540 galhtmlpostfix = """</div></body></html>\n"""

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parents:

diff changeset

541

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parents:

diff changeset

542 flist = os.listdir(self.opts.output_dir)

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parents:

diff changeset

543 flist = [x for x in flist if x <> 'Rplots.pdf']

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parents:

diff changeset

544 flist.sort()

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parents:

diff changeset

545 html = []

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parents:

diff changeset

546 html.append(galhtmlprefix % progname)

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parents:

diff changeset

547 html.append('<div class="infomessage">Galaxy Tool "%s" run at %s</div><br/>' % (self.toolname,timenow()))

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parents:

diff changeset

548 fhtml = []

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parents:

diff changeset

549 if len(flist) > 0:

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parents:

diff changeset

550 logfiles = [x for x in flist if x.lower().endswith('.log')] # log file names determine sections

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parents:

diff changeset

551 logfiles.sort()

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parents:

diff changeset

552 logfiles = [x for x in logfiles if os.path.abspath(x) <> os.path.abspath(self.tlog)]

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parents:

diff changeset

553 logfiles.append(os.path.abspath(self.tlog)) # make it the last one

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parents:

diff changeset

554 pdflist = []

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parents:

diff changeset

555 npdf = len([x for x in flist if os.path.splitext(x)[-1].lower() == '.pdf'])

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parents:

diff changeset

556 for rownum,fname in enumerate(flist):

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parents:

diff changeset

557 dname,e = os.path.splitext(fname)

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parents:

diff changeset

558 sfsize = self.getfSize(fname,self.opts.output_dir)

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parents:

diff changeset

559 if e.lower() == '.pdf' : # compress and make a thumbnail

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parents:

diff changeset

560 thumb = '%s.%s' % (dname,self.thumbformat)

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parents:

diff changeset

561 pdff = os.path.join(self.opts.output_dir,fname)

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parents:

diff changeset

562 retval = self.compressPDF(inpdf=pdff,thumbformat=self.thumbformat)

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parents:

diff changeset

563 if retval == 0:

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parents:

diff changeset

564 pdflist.append((fname,thumb))

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parents:

diff changeset

565 else:

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parents:

diff changeset

566 pdflist.append((fname,fname))

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parents:

diff changeset

567 if (rownum+1) % 2 == 0:

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parents:

diff changeset

568 fhtml.append('<tr class="odd_row"><td><a href="%s">%s</a></td><td>%s</td></tr>' % (fname,fname,sfsize))

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parents:

diff changeset

569 else:

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parents:

diff changeset

570 fhtml.append('<tr><td><a href="%s">%s</a></td><td>%s</td></tr>' % (fname,fname,sfsize))

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parents:

diff changeset

571 for logfname in logfiles: # expect at least tlog - if more

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parents:

diff changeset

572 if os.path.abspath(logfname) == os.path.abspath(self.tlog): # handled later

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parents:

diff changeset

573 sectionname = 'All tool run'

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parents:

diff changeset

574 if (len(logfiles) > 1):

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parents:

diff changeset

575 sectionname = 'Other'

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parents:

diff changeset

576 ourpdfs = pdflist

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parents:

diff changeset

577 else:

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parents:

diff changeset

578 realname = os.path.basename(logfname)

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parents:

diff changeset

579 sectionname = os.path.splitext(realname)[0].split('_')[0] # break in case _ added to log

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parents:

diff changeset

580 ourpdfs = [x for x in pdflist if os.path.basename(x[0]).split('_')[0] == sectionname]

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parents:

diff changeset

581 pdflist = [x for x in pdflist if os.path.basename(x[0]).split('_')[0] <> sectionname] # remove

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parents:

diff changeset

582 nacross = 1

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parents:

diff changeset

583 npdf = len(ourpdfs)

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parents:

diff changeset

584

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parents:

diff changeset

585 if npdf > 0:

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parents:

diff changeset

586 nacross = math.sqrt(npdf) ## int(round(math.log(npdf,2)))

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parents:

diff changeset

587 if int(nacross)**2 != npdf:

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parents:

diff changeset

588 nacross += 1

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parents:

diff changeset

589 nacross = int(nacross)

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parents:

diff changeset

590 width = min(400,int(1200/nacross))

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parents:

diff changeset

591 html.append('<div class="toolFormTitle">%s images and outputs</div>' % sectionname)

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parents:

diff changeset

592 html.append('(Click on a thumbnail image to download the corresponding original PDF image)<br/>')

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parents:

diff changeset

593 ntogo = nacross # counter for table row padding with empty cells

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parents:

diff changeset

594 html.append('<div><table class="simple" cellpadding="2" cellspacing="2">\n<tr>')

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parents:

diff changeset

595 for i,paths in enumerate(ourpdfs):

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parents:

diff changeset

596 fname,thumb = paths

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parents:

diff changeset

597 s= """<td><a href="%s"><img src="%s" title="Click to download a PDF of %s" hspace="5" width="%d"

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parents:

diff changeset

598 alt="Image called %s"/></a></td>\n""" % (fname,thumb,fname,width,fname)

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parents:

diff changeset

599 if ((i+1) % nacross == 0):

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parents:

diff changeset

600 s += '</tr>\n'

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parents:

diff changeset

601 ntogo = 0

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parents:

diff changeset

602 if i < (npdf - 1): # more to come

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parents:

diff changeset

603 s += '<tr>'

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parents:

diff changeset

604 ntogo = nacross

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parents:

diff changeset

605 else:

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parents:

diff changeset

606 ntogo -= 1

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parents:

diff changeset

607 html.append(s)

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parents:

diff changeset

608 if html[-1].strip().endswith('</tr>'):

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parents:

diff changeset

609 html.append('</table></div>\n')

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parents:

diff changeset

610 else:

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parents:

diff changeset

611 if ntogo > 0: # pad

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parents:

diff changeset

612 html.append('<td> </td>'*ntogo)

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parents:

diff changeset

613 html.append('</tr></table></div>\n')

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parents:

diff changeset

614 logt = open(logfname,'r').readlines()

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parents:

diff changeset

615 logtext = [x for x in logt if x.strip() > '']

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parents:

diff changeset

616 html.append('<div class="toolFormTitle">%s log output</div>' % sectionname)

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parents:

diff changeset

617 if len(logtext) > 1:

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parents:

diff changeset

618 html.append('\n<pre>\n')

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parents:

diff changeset

619 html += logtext

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parents:

diff changeset

620 html.append('\n</pre>\n')

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parents:

diff changeset

621 else:

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parents:

diff changeset

622 html.append('%s is empty<br/>' % logfname)

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parents:

diff changeset

623 if len(fhtml) > 0:

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parents:

diff changeset

624 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')

fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott

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parents:

diff changeset

625 fhtml.append('</table></div><br/>')

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parents:

diff changeset

626 html.append('<div class="toolFormTitle">All output files available for downloading</div>\n')

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parents:

diff changeset

627 html += fhtml # add all non-pdf files to the end of the display

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parents:

diff changeset

628 else:

fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott

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parents:

diff changeset

629 html.append('<div class="warningmessagelarge">### Error - %s returned no files - please confirm that parameters are sane</div>' % self.opts.interpreter)

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parents:

diff changeset

630 html.append(galhtmlpostfix)

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parents:

diff changeset

631 htmlf = file(self.opts.output_html,'w')

fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott

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parents:

diff changeset

632 htmlf.write('\n'.join(html))

fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott

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parents:

diff changeset

633 htmlf.write('\n')

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fubar

parents:

diff changeset

634 htmlf.close()

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parents:

diff changeset

635 self.html = html

fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott

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parents:

diff changeset

636

fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott

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parents:

diff changeset

637

fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott

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parents:

diff changeset

638 def run(self):

fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott

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parents:

diff changeset

639 """

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parents:

diff changeset

640 scripts must be small enough not to fill the pipe!

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parents:

diff changeset

641 """

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parents:

diff changeset

642 if self.treatbashSpecial and self.opts.interpreter in ['bash','sh']:

fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott

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parents:

diff changeset

643 retval = self.runBash()

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parents:

diff changeset

644 else:

fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott

fubar

parents:

diff changeset

645 if self.opts.output_dir:

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parents:

diff changeset

646 ste = open(self.elog,'w')

fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott

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parents:

diff changeset

647 sto = open(self.tlog,'w')

fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott

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parents:

diff changeset

648 sto.write('## Toolfactory generated command line = %s\n' % ' '.join(self.cl))

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parents:

diff changeset

649 sto.flush()

fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott

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parents:

diff changeset

650 p = subprocess.Popen(self.cl,shell=False,stdout=sto,stderr=ste,stdin=subprocess.PIPE,cwd=self.opts.output_dir)

fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott

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parents:

diff changeset

651 else:

fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott

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parents:

diff changeset

652 p = subprocess.Popen(self.cl,shell=False,stdin=subprocess.PIPE)

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parents:

diff changeset

653 p.stdin.write(self.script)

fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott

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parents:

diff changeset

654 p.stdin.close()

fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott

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parents:

diff changeset

655 retval = p.wait()

fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott

fubar

parents:

diff changeset

656 if self.opts.output_dir:

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parents:

diff changeset

657 sto.close()

fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott

fubar

parents:

diff changeset

658 ste.close()

fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott

fubar

parents:

diff changeset

659 err = open(self.elog,'r').readlines()

fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott

fubar

parents:

diff changeset

660 if retval <> 0 and err: # problem

fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott

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parents:

diff changeset

661 print >> sys.stderr,err

fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott

fubar

parents:

diff changeset

662 if self.opts.make_HTML:

fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott

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parents:

diff changeset

663 self.makeHtml()

fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott

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parents:

diff changeset

664 return retval

fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott

fubar

parents:

diff changeset

665

fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott

fubar

parents:

diff changeset

666 def runBash(self):

fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott

fubar

parents:

diff changeset

667 """

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parents:

diff changeset

668 cannot use - for bash so use self.sfile

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parents:

diff changeset

669 """

fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott

fubar

parents:

diff changeset

670 if self.opts.output_dir:

fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott

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parents:

diff changeset

671 s = '## Toolfactory generated command line = %s\n' % ' '.join(self.cl)

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parents:

diff changeset

672 sto = open(self.tlog,'w')

fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott

fubar

parents:

diff changeset

673 sto.write(s)

fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott

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parents:

diff changeset

674 sto.flush()

fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott

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parents:

diff changeset

675 p = subprocess.Popen(self.cl,shell=False,stdout=sto,stderr=sto,cwd=self.opts.output_dir)

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fubar

parents:

diff changeset

676 else:

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677 p = subprocess.Popen(self.cl,shell=False)

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678 retval = p.wait()

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679 if self.opts.output_dir:

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680 sto.close()

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681 if self.opts.make_HTML:

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682 self.makeHtml()

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683 return retval

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684

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685

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686 def main():

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687 u = """

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688 This is a Galaxy wrapper. It expects to be called by a special purpose tool.xml as:

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689 <command interpreter="python">rgBaseScriptWrapper.py --script_path "$scriptPath" --tool_name "foo" --interpreter "Rscript"

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690 </command>

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691 """

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692 op = optparse.OptionParser()

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693 a = op.add_option

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694 a('--script_path',default=None)

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695 a('--tool_name',default=None)

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696 a('--interpreter',default=None)

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697 a('--output_dir',default='./')

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698 a('--output_html',default=None)

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699 a('--input_tab',default=[], action="append")

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700 a("--input_formats",default="tabular")

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701 a('--output_tab',default="None")

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702 a('--output_format',default='tabular')

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703 a('--user_email',default='Unknown')

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704 a('--bad_user',default=None)

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705 a('--make_Tool',default=None)

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706 a('--make_HTML',default=None)

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707 a('--help_text',default=None)

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fubar

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708 a('--tool_desc',default=None)

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709 a('--new_tool',default=None)

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parents:

diff changeset

710 a('--tool_version',default=None)

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fubar

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diff changeset

711 a('--include_dependencies',default=None)

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parents:

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712 opts, args = op.parse_args()

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parents:

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713 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)

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diff changeset

714 assert opts.tool_name,'## Tool Factory expects a tool name - eg --tool_name=DESeq'

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parents:

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715 assert opts.interpreter,'## Tool Factory wrapper expects an interpreter - eg --interpreter=Rscript'

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716 assert os.path.isfile(opts.script_path),'## Tool Factory wrapper expects a script path - eg --script_path=foo.R'

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717 if opts.output_dir:

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718 try:

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fubar

parents:

diff changeset

719 os.makedirs(opts.output_dir)

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parents:

diff changeset

720 except:

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parents:

diff changeset

721 pass

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parents:

diff changeset

722 opts.input_tab = [x.replace('"','').replace("'",'') for x in opts.input_tab]

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parents:

diff changeset

723 r = ScriptRunner(opts)

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diff changeset

724 if opts.make_Tool:

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parents:

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725 retcode = r.makeTooltar()

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726 else:

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727 retcode = r.run()

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728 os.unlink(r.sfile)

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diff changeset

729 if retcode:

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fubar

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730 sys.exit(retcode) # indicate failure to job runner

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731

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parents:

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732

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fubar

parents:

diff changeset

733 if __name__ == "__main__":

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fubar

parents:

diff changeset

734 main()

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parents:

diff changeset

735

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736

Mercurial > repos > fubar > toolfactory

annotate rgToolFactoryMultIn.py @ 30:fb3fa6a2874d draft