skunkworks: rgToolFactory.py annotate

annotate rgToolFactory.py @ 16:e052aadae3e9 draft

Uploaded

author	fubar
date	Thu, 20 Mar 2014 06:18:54 -0400
parents	824d21b5c773
children	903e3748f735

rev	line source
7 1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	1 # rgToolFactory.py
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	2 # see https://bitbucket.org/fubar/galaxytoolfactory/wiki/Home
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	3 #
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	4 # copyright ross lazarus (ross stop lazarus at gmail stop com) May 2012
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	5 #
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	6 # all rights reserved
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	7 # Licensed under the LGPL
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	8 # suggestions for improvement and bug fixes welcome at https://bitbucket.org/fubar/galaxytoolfactory/wiki/Home
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	9 #
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	10 # march 2014
11 704ccaade924 Uploaded fubar parents: 7 diff changeset	11 # added dependencies to a tool_dependencies.xml if html page generated so generated tool is properly portable
704ccaade924 Uploaded fubar parents: 7 diff changeset	12 #
7 1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	13 # added ghostscript and graphicsmagick as dependencies
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	14 # fixed a wierd problem where gs was trying to use the new_files_path from universe (database/tmp) as ./database/tmp
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	15 # errors ensued
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	16 #
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	17 # august 2013
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	18 # found a problem with GS if $TMP or $TEMP missing - now inject /tmp and warn
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	19 #
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	20 # july 2013
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	21 # added ability to combine images and individual log files into html output
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	22 # just make sure there's a log file foo.log and it will be output
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	23 # together with all images named like "foo_*.pdf
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	24 # otherwise old format for html
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	25 #
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	26 # January 2013
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	27 # problem pointed out by Carlos Borroto
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	28 # added escaping for <>$ - thought I did that ages ago...
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	29 #
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	30 # August 11 2012
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	31 # changed to use shell=False and cl as a sequence
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	32
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	33 # This is a Galaxy tool factory for simple scripts in python, R or whatever ails ye.
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	34 # It also serves as the wrapper for the new tool.
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	35 #
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	36 # you paste and run your script
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	37 # Only works for simple scripts that read one input from the history.
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	38 # Optionally can write one new history dataset,
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	39 # and optionally collect any number of outputs into links on an autogenerated HTML page.
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	40
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	41 # DO NOT install on a public or important site - please.
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	42
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	43 # installed generated tools are fine if the script is safe.
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	44 # They just run normally and their user cannot do anything unusually insecure
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	45 # but please, practice safe toolshed.
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	46 # Read the fucking code before you install any tool
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	47 # especially this one
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	48
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	49 # After you get the script working on some test data, you can
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	50 # optionally generate a toolshed compatible gzip file
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	51 # containing your script safely wrapped as an ordinary Galaxy script in your local toolshed for
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	52 # safe and largely automated installation in a production Galaxy.
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	53
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	54 # If you opt for an HTML output, you get all the script outputs arranged
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	55 # as a single Html history item - all output files are linked, thumbnails for all the pdfs.
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	56 # Ugly but really inexpensive.
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	57 #
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	58 # Patches appreciated please.
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	59 #
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	60 #
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	61 # long route to June 2012 product
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	62 # Behold the awesome power of Galaxy and the toolshed with the tool factory to bind them
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	63 # derived from an integrated script model
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	64 # called rgBaseScriptWrapper.py
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	65 # Note to the unwary:
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	66 # This tool allows arbitrary scripting on your Galaxy as the Galaxy user
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	67 # There is nothing stopping a malicious user doing whatever they choose
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	68 # Extremely dangerous!!
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	69 # Totally insecure. So, trusted users only
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	70 #
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	71 # preferred model is a developer using their throw away workstation instance - ie a private site.
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	72 # no real risk. The universe_wsgi.ini admin_users string is checked - only admin users are permitted to run this tool.
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	73 #
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	74
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	75 import sys
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	76 import shutil
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	77 import subprocess
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	78 import os
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	79 import time
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	80 import tempfile
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	81 import optparse
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	82 import tarfile
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	83 import re
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	84 import shutil
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	85 import math
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	86
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	87 progname = os.path.split(sys.argv[0])[1]
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	88 myversion = 'V001.1 March 2014'
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	89 verbose = False
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	90 debug = False
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	91 toolFactoryURL = 'https://bitbucket.org/fubar/galaxytoolfactory'
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	92
15 824d21b5c773 Uploaded fubar parents: 14 diff changeset	93 # if we do html we need these dependencies specified in a tool_dependencies.xml file and referred to in the generated
824d21b5c773 Uploaded fubar parents: 14 diff changeset	94 # tool xml
14 43ab59672f78 Uploaded fubar parents: 13 diff changeset	95 toolhtmldepskel = """<?xml version="1.0"?>
11 704ccaade924 Uploaded fubar parents: 7 diff changeset	96 <tool_dependency>
704ccaade924 Uploaded fubar parents: 7 diff changeset	97 <package name="ghostscript" version="9.10">
704ccaade924 Uploaded fubar parents: 7 diff changeset	98 <repository name="package_ghostscript_9_10" owner="devteam" prior_installation_required="True" toolshed="http://toolshed.g2.bx.psu.edu/" />
704ccaade924 Uploaded fubar parents: 7 diff changeset	99 </package>
704ccaade924 Uploaded fubar parents: 7 diff changeset	100 <package name="graphicsmagick" version="1.3.18">
704ccaade924 Uploaded fubar parents: 7 diff changeset	101 <repository name="package_graphicsmagick_1_3" owner="iuc" prior_installation_required="True" toolshed="http://toolshed.g2.bx.psu.edu/" />
704ccaade924 Uploaded fubar parents: 7 diff changeset	102 </package>
704ccaade924 Uploaded fubar parents: 7 diff changeset	103 <readme>
704ccaade924 Uploaded fubar parents: 7 diff changeset	104 %s
704ccaade924 Uploaded fubar parents: 7 diff changeset	105 </readme>
704ccaade924 Uploaded fubar parents: 7 diff changeset	106 </tool_dependency>
704ccaade924 Uploaded fubar parents: 7 diff changeset	107 """
704ccaade924 Uploaded fubar parents: 7 diff changeset	108
15 824d21b5c773 Uploaded fubar parents: 14 diff changeset	109 protorequirements = """<requirements>
824d21b5c773 Uploaded fubar parents: 14 diff changeset	110 <requirement type="package" version="9.10">ghostscript</requirement>
824d21b5c773 Uploaded fubar parents: 14 diff changeset	111 <requirement type="package" version="1.3.18">graphicsmagick</requirement>
824d21b5c773 Uploaded fubar parents: 14 diff changeset	112 </requirements>"""
824d21b5c773 Uploaded fubar parents: 14 diff changeset	113
7 1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	114 def timenow():
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	115 """return current time as a string
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	116 """
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	117 return time.strftime('%d/%m/%Y %H:%M:%S', time.localtime(time.time()))
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	118
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	119 html_escape_table = {
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	120 "&": "&",
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	121 ">": ">",
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	122 "<": "<",
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	123 "$": "\$"
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	124 }
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	125
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	126 def html_escape(text):
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	127 """Produce entities within text."""
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	128 return "".join(html_escape_table.get(c,c) for c in text)
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	129
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	130 def cmd_exists(cmd):
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	131 return subprocess.call("type " + cmd, shell=True,
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	132 stdout=subprocess.PIPE, stderr=subprocess.PIPE) == 0
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	133
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	134
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	135 class ScriptRunner:
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	136 """class is a wrapper for an arbitrary script
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	137 """
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	138
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	139 def __init__(self,opts=None,treatbashSpecial=True):
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	140 """
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	141 cleanup inputs, setup some outputs
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	142
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	143 """
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	144 self.useGM = cmd_exists('gm')
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	145 self.useIM = cmd_exists('convert')
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	146 self.useGS = cmd_exists('gs')
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	147 self.temp_warned = False # we want only one warning if $TMP not set
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	148 self.treatbashSpecial = treatbashSpecial
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	149 if opts.output_dir: # simplify for the tool tarball
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	150 os.chdir(opts.output_dir)
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	151 self.thumbformat = 'png'
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	152 self.opts = opts
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	153 self.toolname = re.sub('[^a-zA-Z0-9_]+', '', opts.tool_name) # a sanitizer now does this but..
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	154 self.toolid = self.toolname
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	155 self.myname = sys.argv[0] # get our name because we write ourselves out as a tool later
11 704ccaade924 Uploaded fubar parents: 7 diff changeset	156 self.pyfile = self.myname # crude but efficient - the cruft won't hurt muchself.tooldepfile)
7 1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	157 self.xmlfile = '%s.xml' % self.toolname
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	158 s = open(self.opts.script_path,'r').readlines()
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	159 s = [x.rstrip() for x in s] # remove pesky dos line endings if needed
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	160 self.script = '\n'.join(s)
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	161 fhandle,self.sfile = tempfile.mkstemp(prefix=self.toolname,suffix=".%s" % (opts.interpreter))
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	162 tscript = open(self.sfile,'w') # use self.sfile as script source for Popen
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	163 tscript.write(self.script)
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	164 tscript.close()
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	165 self.indentedScript = '\n'.join([' %s' % x for x in s]) # for restructured text in help
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	166 self.escapedScript = '\n'.join([html_escape(x) for x in s])
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	167 self.elog = os.path.join(self.opts.output_dir,"%s_error.log" % self.toolname)
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	168 if opts.output_dir: # may not want these complexities
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	169 self.tlog = os.path.join(self.opts.output_dir,"%s_runner.log" % self.toolname)
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	170 art = '%s.%s' % (self.toolname,opts.interpreter)
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	171 artpath = os.path.join(self.opts.output_dir,art) # need full path
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	172 artifact = open(artpath,'w') # use self.sfile as script source for Popen
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	173 artifact.write(self.script)
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	174 artifact.close()
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	175 self.cl = []
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	176 self.html = []
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	177 a = self.cl.append
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	178 a(opts.interpreter)
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	179 if self.treatbashSpecial and opts.interpreter in ['bash','sh']:
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	180 a(self.sfile)
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	181 else:
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	182 a('-') # stdin
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	183 a(opts.input_tab)
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	184 a(opts.output_tab)
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	185 self.outFormats = 'tabular' # TODO make this an option at tool generation time
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	186 self.inputFormats = 'tabular' # TODO make this an option at tool generation time
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	187 self.test1Input = '%s_test1_input.xls' % self.toolname
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	188 self.test1Output = '%s_test1_output.xls' % self.toolname
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	189 self.test1HTML = '%s_test1_output.html' % self.toolname
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	190
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	191 def makeXML(self):
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	192 """
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	193 Create a Galaxy xml tool wrapper for the new script as a string to write out
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	194 fixme - use templating or something less fugly than this example of what we produce
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	195
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	196 <tool id="reverse" name="reverse" version="0.01">
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	197 <description>a tabular file</description>
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	198 <command interpreter="python">
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	199 reverse.py --script_path "$runMe" --interpreter "python"
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	200 --tool_name "reverse" --input_tab "$input1" --output_tab "$tab_file"
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	201 </command>
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	202 <inputs>
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	203 <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"/>
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	204
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	205 </inputs>
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	206 <outputs>
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	207 <data format="tabular" name="tab_file" label="${job_name}"/>
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	208
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	209 </outputs>
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	210 <help>
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	211
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	212 What it Does
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	213
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	214 Reverse the columns in a tabular file
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	215
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	216 </help>
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	217 <configfiles>
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	218 <configfile name="runMe">
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	219
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	220 # reverse order of columns in a tabular file
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	221 import sys
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	222 inp = sys.argv[1]
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	223 outp = sys.argv[2]
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	224 i = open(inp,'r')
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	225 o = open(outp,'w')
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	226 for row in i:
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	227 rs = row.rstrip().split('\t')
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	228 rs.reverse()
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	229 o.write('\t'.join(rs))
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	230 o.write('\n')
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	231 i.close()
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	232 o.close()
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	233
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	234
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	235 </configfile>
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	236 </configfiles>
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	237 </tool>
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	238
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	239 """
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	240 newXML="""<tool id="%(toolid)s" name="%(toolname)s" version="%(tool_version)s">
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	241 %(tooldesc)s
15 824d21b5c773 Uploaded fubar parents: 14 diff changeset	242 %(requirements)s
7 1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	243 %(command)s
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	244 <inputs>
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	245 %(inputs)s
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	246 </inputs>
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	247 <outputs>
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	248 %(outputs)s
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	249 </outputs>
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	250 <configfiles>
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	251 <configfile name="runMe">
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	252 %(script)s
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	253 </configfile>
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	254 </configfiles>
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	255 %(tooltests)s
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	256 <help>
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	257 %(help)s
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	258 </help>
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	259 </tool>""" # needs a dict with toolname, toolid, interpreter, scriptname, command, inputs as a multi line string ready to write, outputs ditto, help ditto
11 704ccaade924 Uploaded fubar parents: 7 diff changeset	260
7 1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	261 newCommand="""<command interpreter="python">
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	262 %(toolname)s.py --script_path "$runMe" --interpreter "%(interpreter)s"
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	263 --tool_name "%(toolname)s" %(command_inputs)s %(command_outputs)s
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	264 </command>""" # may NOT be an input or htmlout
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	265 tooltestsTabOnly = """<tests><test>
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	266 <param name="input1" value="%(test1Input)s" ftype="tabular"/>
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	267 <param name="job_name" value="test1"/>
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	268 <param name="runMe" value="$runMe"/>
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	269 <output name="tab_file" file="%(test1Output)s" ftype="tabular"/>
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	270 </test></tests>"""
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	271 tooltestsHTMLOnly = """<tests><test>
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	272 <param name="input1" value="%(test1Input)s" ftype="tabular"/>
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	273 <param name="job_name" value="test1"/>
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	274 <param name="runMe" value="$runMe"/>
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	275 <output name="html_file" file="%(test1HTML)s" ftype="html" lines_diff="5"/>
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	276 </test></tests>"""
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	277 tooltestsBoth = """<tests><test>
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	278 <param name="input1" value="%(test1Input)s" ftype="tabular"/>
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	279 <param name="job_name" value="test1"/>
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	280 <param name="runMe" value="$runMe"/>
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	281 <output name="tab_file" file="%(test1Output)s" ftype="tabular" />
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	282 <output name="html_file" file="%(test1HTML)s" ftype="html" lines_diff="10"/>
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	283 </test></tests>"""
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	284 xdict = {}
15 824d21b5c773 Uploaded fubar parents: 14 diff changeset	285 xdict['requirements'] = ''
824d21b5c773 Uploaded fubar parents: 14 diff changeset	286 if self.opts.make_HTML:
824d21b5c773 Uploaded fubar parents: 14 diff changeset	287 xdict['requirements'] = protorequirements
7 1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	288 xdict['tool_version'] = self.opts.tool_version
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	289 xdict['test1Input'] = self.test1Input
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	290 xdict['test1HTML'] = self.test1HTML
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	291 xdict['test1Output'] = self.test1Output
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	292 if self.opts.make_HTML and self.opts.output_tab <> 'None':
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	293 xdict['tooltests'] = tooltestsBoth % xdict
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	294 elif self.opts.make_HTML:
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	295 xdict['tooltests'] = tooltestsHTMLOnly % xdict
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	296 else:
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	297 xdict['tooltests'] = tooltestsTabOnly % xdict
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	298 xdict['script'] = self.escapedScript
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	299 # configfile is least painful way to embed script to avoid external dependencies
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	300 # but requires escaping of <, > and $ to avoid Mako parsing
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	301 if self.opts.help_text:
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	302 xdict['help'] = open(self.opts.help_text,'r').read()
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	303 else:
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	304 xdict['help'] = 'Please ask the tool author for help as none was supplied at tool generation'
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	305 coda = ['Script','Pressing execute will run the following code over your input file and generate some outputs in your history::']
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	306 coda.append(self.indentedScript)
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	307 coda.append('Attribution This Galaxy tool was created by %s at %s\nusing the Galaxy Tool Factory.' % (self.opts.user_email,timenow()))
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	308 coda.append('See %s for details of that project' % (toolFactoryURL))
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	309 coda.append('Please cite: Creating re-usable tools from scripts: The Galaxy Tool Factory. Ross Lazarus; Antony Kaspi; Mark Ziemann; The Galaxy Team. ')
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	310 coda.append('Bioinformatics 2012; doi: 10.1093/bioinformatics/bts573')
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	311 xdict['help'] = '%s\n%s' % (xdict['help'],'\n'.join(coda))
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	312 if self.opts.tool_desc:
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	313 xdict['tooldesc'] = '<description>%s</description>' % self.opts.tool_desc
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	314 else:
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	315 xdict['tooldesc'] = ''
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	316 xdict['command_outputs'] = ''
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	317 xdict['outputs'] = ''
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	318 if self.opts.input_tab <> 'None':
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	319 xdict['command_inputs'] = '--input_tab "$input1" ' # the space may matter a lot if we append something
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	320 xdict['inputs'] = '<param name="input1" type="data" format="%s" label="Select a suitable input file from your history"/> \n' % self.inputFormats
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	321 else:
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	322 xdict['command_inputs'] = '' # assume no input - eg a random data generator
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	323 xdict['inputs'] = ''
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	324 xdict['inputs'] += '<param name="job_name" type="text" label="Supply a name for the outputs to remind you what they contain" value="%s"/> \n' % self.toolname
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	325 xdict['toolname'] = self.toolname
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	326 xdict['toolid'] = self.toolid
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	327 xdict['interpreter'] = self.opts.interpreter
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	328 xdict['scriptname'] = self.sfile
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	329 if self.opts.make_HTML:
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	330 xdict['command_outputs'] += ' --output_dir "$html_file.files_path" --output_html "$html_file" --make_HTML "yes" '
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	331 xdict['outputs'] += ' <data format="html" name="html_file" label="${job_name}.html"/>\n'
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	332 if self.opts.output_tab <> 'None':
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	333 xdict['command_outputs'] += ' --output_tab "$tab_file"'
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	334 xdict['outputs'] += ' <data format="%s" name="tab_file" label="${job_name}"/>\n' % self.outFormats
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	335 xdict['command'] = newCommand % xdict
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	336 xmls = newXML % xdict
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	337 xf = open(self.xmlfile,'w')
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	338 xf.write(xmls)
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	339 xf.write('\n')
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	340 xf.close()
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	341 # ready for the tarball
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	342
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	343
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	344 def makeTooltar(self):
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	345 """
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	346 a tool is a gz tarball with eg
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	347 /toolname/tool.xml /toolname/tool.py /toolname/test-data/test1_in.foo ...
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	348 """
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	349 retval = self.run()
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	350 if retval:
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	351 print >> sys.stderr,'## Run failed. Cannot build yet. Please fix and retry'
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	352 sys.exit(1)
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	353 tdir = self.toolname
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	354 os.mkdir(tdir)
11 704ccaade924 Uploaded fubar parents: 7 diff changeset	355 self.makeXML()
704ccaade924 Uploaded fubar parents: 7 diff changeset	356 if self.opts.make_HTML:
704ccaade924 Uploaded fubar parents: 7 diff changeset	357 if self.opts.help_text:
704ccaade924 Uploaded fubar parents: 7 diff changeset	358 hlp = open(self.opts.help_text,'r').read()
704ccaade924 Uploaded fubar parents: 7 diff changeset	359 else:
704ccaade924 Uploaded fubar parents: 7 diff changeset	360 hlp = 'Please ask the tool author for help as none was supplied at tool generation\n'
14 43ab59672f78 Uploaded fubar parents: 13 diff changeset	361 tooldepcontent = toolhtmldepskel % hlp
12 a898ba82496e Uploaded fubar parents: 11 diff changeset	362 depf = open(os.path.join(tdir,'tool_dependencies.xml'),'w')
14 43ab59672f78 Uploaded fubar parents: 13 diff changeset	363 depf.write(tooldepcontent)
11 704ccaade924 Uploaded fubar parents: 7 diff changeset	364 depf.write('\n')
704ccaade924 Uploaded fubar parents: 7 diff changeset	365 depf.close()
7 1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	366 if self.opts.input_tab <> 'None': # no reproducible test otherwise? TODO: maybe..
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	367 testdir = os.path.join(tdir,'test-data')
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	368 os.mkdir(testdir) # make tests directory
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	369 shutil.copyfile(self.opts.input_tab,os.path.join(testdir,self.test1Input))
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	370 if self.opts.output_tab <> 'None':
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	371 shutil.copyfile(self.opts.output_tab,os.path.join(testdir,self.test1Output))
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	372 if self.opts.make_HTML:
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	373 shutil.copyfile(self.opts.output_html,os.path.join(testdir,self.test1HTML))
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	374 if self.opts.output_dir:
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	375 shutil.copyfile(self.tlog,os.path.join(testdir,'test1_out.log'))
12 a898ba82496e Uploaded fubar parents: 11 diff changeset	376 outpif = '%s.py' % self.toolname # new name
a898ba82496e Uploaded fubar parents: 11 diff changeset	377 outpiname = os.path.join(tdir,outpif) # path for the tool tarball
7 1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	378 pyin = os.path.basename(self.pyfile) # our name - we rewrite ourselves (TM)
13 d5a5f9c2c108 Uploaded fubar parents: 12 diff changeset	379 notes = ['# %s - a self annotated version of %s generated by running %s\n' % (outpiname,pyin,pyin),]
7 1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	380 notes.append('# to make a new Galaxy tool called %s\n' % self.toolname)
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	381 notes.append('# User %s at %s\n' % (self.opts.user_email,timenow()))
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	382 pi = open(self.pyfile,'r').readlines() # our code becomes new tool wrapper (!) - first Galaxy worm
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	383 notes += pi
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	384 outpi = open(outpiname,'w')
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	385 outpi.write(''.join(notes))
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	386 outpi.write('\n')
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	387 outpi.close()
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	388 stname = os.path.join(tdir,self.sfile)
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	389 if not os.path.exists(stname):
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	390 shutil.copyfile(self.sfile, stname)
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	391 xtname = os.path.join(tdir,self.xmlfile)
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	392 if not os.path.exists(xtname):
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	393 shutil.copyfile(self.xmlfile,xtname)
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	394 tarpath = "%s.gz" % self.toolname
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	395 tar = tarfile.open(tarpath, "w:gz")
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	396 tar.add(tdir,arcname=self.toolname)
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	397 tar.close()
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	398 shutil.copyfile(tarpath,self.opts.new_tool)
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	399 shutil.rmtree(tdir)
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	400 ## TODO: replace with optional direct upload to local toolshed?
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	401 return retval
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	402
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	403
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	404 def compressPDF(self,inpdf=None,thumbformat='png'):
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	405 """need absolute path to pdf
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	406 note that GS gets confoozled if no $TMP or $TEMP
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	407 so we set it
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	408 """
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	409 assert os.path.isfile(inpdf), "## Input %s supplied to %s compressPDF not found" % (inpdf,self.myName)
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	410 hlog = os.path.join(self.opts.output_dir,"compress_%s.txt" % os.path.basename(inpdf))
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	411 sto = open(hlog,'a')
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	412 our_env = os.environ.copy()
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	413 our_tmp = our_env.get('TMP',None)
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	414 if not our_tmp:
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	415 our_tmp = our_env.get('TEMP',None)
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	416 if not (our_tmp and os.path.exists(our_tmp)):
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	417 newtmp = os.path.join(self.opts.output_dir,'tmp')
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	418 try:
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	419 os.mkdir(newtmp)
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	420 except:
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	421 sto.write('## WARNING - cannot make %s - it may exist or permissions need fixing\n' % newtmp)
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	422 our_env['TEMP'] = newtmp
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	423 if not self.temp_warned:
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	424 sto.write('## WARNING - no $TMP or $TEMP!!! Please fix - using %s temporarily\n' % newtmp)
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	425 self.temp_warned = True
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	426 outpdf = '%s_compressed' % inpdf
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	427 cl = ["gs", "-sDEVICE=pdfwrite", "-dNOPAUSE", "-dUseCIEColor", "-dBATCH","-dPDFSETTINGS=/printer", "-sOutputFile=%s" % outpdf,inpdf]
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	428 x = subprocess.Popen(cl,stdout=sto,stderr=sto,cwd=self.opts.output_dir,env=our_env)
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	429 retval1 = x.wait()
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	430 sto.close()
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	431 if retval1 == 0:
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	432 os.unlink(inpdf)
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	433 shutil.move(outpdf,inpdf)
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	434 os.unlink(hlog)
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	435 hlog = os.path.join(self.opts.output_dir,"thumbnail_%s.txt" % os.path.basename(inpdf))
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	436 sto = open(hlog,'w')
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	437 outpng = '%s.%s' % (os.path.splitext(inpdf)[0],thumbformat)
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	438 if self.useGM:
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	439 cl2 = ['gm', 'convert', inpdf, outpng]
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	440 else: # assume imagemagick
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	441 cl2 = ['convert', inpdf, outpng]
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	442 x = subprocess.Popen(cl2,stdout=sto,stderr=sto,cwd=self.opts.output_dir,env=our_env)
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	443 retval2 = x.wait()
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	444 sto.close()
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	445 if retval2 == 0:
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	446 os.unlink(hlog)
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	447 retval = retval1 or retval2
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	448 return retval
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	449
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	450
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	451 def getfSize(self,fpath,outpath):
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	452 """
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	453 format a nice file size string
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	454 """
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	455 size = ''
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	456 fp = os.path.join(outpath,fpath)
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	457 if os.path.isfile(fp):
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	458 size = '0 B'
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	459 n = float(os.path.getsize(fp))
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	460 if n > 2**20:
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	461 size = '%1.1f MB' % (n/2**20)
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	462 elif n > 2**10:
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	463 size = '%1.1f KB' % (n/2**10)
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	464 elif n > 0:
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	465 size = '%d B' % (int(n))
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	466 return size
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	467
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	468 def makeHtml(self):
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	469 """ Create an HTML file content to list all the artifacts found in the output_dir
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	470 """
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	471
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	472 galhtmlprefix = """<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	473 <html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	474 <head> <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	475 <meta name="generator" content="Galaxy %s tool output - see http://g2.trac.bx.psu.edu/" />
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	476 <title></title>
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	477 <link rel="stylesheet" href="/static/style/base.css" type="text/css" />
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	478 </head>
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	479 <body>
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	480 <div class="toolFormBody">
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	481 """
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	482 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/>"""
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	483 galhtmlpostfix = """</div></body></html>\n"""
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	484
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	485 flist = os.listdir(self.opts.output_dir)
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	486 flist = [x for x in flist if x <> 'Rplots.pdf']
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	487 flist.sort()
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	488 html = []
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	489 html.append(galhtmlprefix % progname)
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	490 html.append('<div class="infomessage">Galaxy Tool "%s" run at %s</div><br/>' % (self.toolname,timenow()))
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	491 fhtml = []
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	492 if len(flist) > 0:
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	493 logfiles = [x for x in flist if x.lower().endswith('.log')] # log file names determine sections
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	494 logfiles.sort()
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	495 logfiles = [x for x in logfiles if os.path.abspath(x) <> os.path.abspath(self.tlog)]
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	496 logfiles.append(os.path.abspath(self.tlog)) # make it the last one
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	497 pdflist = []
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	498 npdf = len([x for x in flist if os.path.splitext(x)[-1].lower() == '.pdf'])
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	499 for rownum,fname in enumerate(flist):
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	500 dname,e = os.path.splitext(fname)
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	501 sfsize = self.getfSize(fname,self.opts.output_dir)
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	502 if e.lower() == '.pdf' : # compress and make a thumbnail
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	503 thumb = '%s.%s' % (dname,self.thumbformat)
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	504 pdff = os.path.join(self.opts.output_dir,fname)
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	505 retval = self.compressPDF(inpdf=pdff,thumbformat=self.thumbformat)
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	506 if retval == 0:
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	507 pdflist.append((fname,thumb))
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	508 else:
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	509 pdflist.append((fname,fname))
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	510 if (rownum+1) % 2 == 0:
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	511 fhtml.append('<tr class="odd_row"><td><a href="%s">%s</a></td><td>%s</td></tr>' % (fname,fname,sfsize))
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	512 else:
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	513 fhtml.append('<tr><td><a href="%s">%s</a></td><td>%s</td></tr>' % (fname,fname,sfsize))
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	514 for logfname in logfiles: # expect at least tlog - if more
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	515 if os.path.abspath(logfname) == os.path.abspath(self.tlog): # handled later
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	516 sectionname = 'All tool run'
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	517 if (len(logfiles) > 1):
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	518 sectionname = 'Other'
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	519 ourpdfs = pdflist
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	520 else:
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	521 realname = os.path.basename(logfname)
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	522 sectionname = os.path.splitext(realname)[0].split('_')[0] # break in case _ added to log
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	523 ourpdfs = [x for x in pdflist if os.path.basename(x[0]).split('_')[0] == sectionname]
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	524 pdflist = [x for x in pdflist if os.path.basename(x[0]).split('_')[0] <> sectionname] # remove
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	525 nacross = 1
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	526 npdf = len(ourpdfs)
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	527
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	528 if npdf > 0:
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	529 nacross = math.sqrt(npdf) ## int(round(math.log(npdf,2)))
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	530 if int(nacross)**2 != npdf:
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	531 nacross += 1
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	532 nacross = int(nacross)
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	533 width = min(400,int(1200/nacross))
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	534 html.append('<div class="toolFormTitle">%s images and outputs</div>' % sectionname)
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	535 html.append('(Click on a thumbnail image to download the corresponding original PDF image)<br/>')
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	536 ntogo = nacross # counter for table row padding with empty cells
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	537 html.append('<div><table class="simple" cellpadding="2" cellspacing="2">\n<tr>')
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	538 for i,paths in enumerate(ourpdfs):
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	539 fname,thumb = paths
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	540 s= """<td><a href="%s"><img src="%s" title="Click to download a PDF of %s" hspace="5" width="%d"
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	541 alt="Image called %s"/></a></td>\n""" % (fname,thumb,fname,width,fname)
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	542 if ((i+1) % nacross == 0):
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	543 s += '</tr>\n'
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	544 ntogo = 0
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	545 if i < (npdf - 1): # more to come
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	546 s += '<tr>'
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	547 ntogo = nacross
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	548 else:
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	549 ntogo -= 1
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	550 html.append(s)
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	551 if html[-1].strip().endswith('</tr>'):
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	552 html.append('</table></div>\n')
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	553 else:
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	554 if ntogo > 0: # pad
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	555 html.append('<td> </td>'*ntogo)
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	556 html.append('</tr></table></div>\n')
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	557 logt = open(logfname,'r').readlines()
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	558 logtext = [x for x in logt if x.strip() > '']
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	559 html.append('<div class="toolFormTitle">%s log output</div>' % sectionname)
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	560 if len(logtext) > 1:
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	561 html.append('\n<pre>\n')
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	562 html += logtext
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	563 html.append('\n</pre>\n')
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	564 else:
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	565 html.append('%s is empty<br/>' % logfname)
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	566 if len(fhtml) > 0:
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	567 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')
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	568 fhtml.append('</table></div><br/>')
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	569 html.append('<div class="toolFormTitle">All output files available for downloading</div>\n')
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	570 html += fhtml # add all non-pdf files to the end of the display
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	571 else:
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	572 html.append('<div class="warningmessagelarge">### Error - %s returned no files - please confirm that parameters are sane</div>' % self.opts.interpreter)
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	573 html.append(galhtmlpostfix)
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	574 htmlf = file(self.opts.output_html,'w')
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	575 htmlf.write('\n'.join(html))
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	576 htmlf.write('\n')
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	577 htmlf.close()
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	578 self.html = html
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	579
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	580
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	581 def run(self):
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	582 """
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	583 scripts must be small enough not to fill the pipe!
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	584 """
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	585 if self.treatbashSpecial and self.opts.interpreter in ['bash','sh']:
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	586 retval = self.runBash()
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	587 else:
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	588 if self.opts.output_dir:
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	589 ste = open(self.elog,'w')
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	590 sto = open(self.tlog,'w')
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	591 sto.write('## Toolfactory generated command line = %s\n' % ' '.join(self.cl))
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	592 sto.flush()
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	593 p = subprocess.Popen(self.cl,shell=False,stdout=sto,stderr=ste,stdin=subprocess.PIPE,cwd=self.opts.output_dir)
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	594 else:
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	595 p = subprocess.Popen(self.cl,shell=False,stdin=subprocess.PIPE)
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	596 p.stdin.write(self.script)
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	597 p.stdin.close()
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	598 retval = p.wait()
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	599 if self.opts.output_dir:
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	600 sto.close()
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	601 ste.close()
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	602 err = open(self.elog,'r').readlines()
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	603 if retval <> 0 and err: # problem
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	604 print >> sys.stderr,err
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	605 if self.opts.make_HTML:
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	606 self.makeHtml()
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	607 return retval
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	608
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	609 def runBash(self):
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	610 """
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	611 cannot use - for bash so use self.sfile
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	612 """
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	613 if self.opts.output_dir:
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	614 s = '## Toolfactory generated command line = %s\n' % ' '.join(self.cl)
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	615 sto = open(self.tlog,'w')
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	616 sto.write(s)
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	617 sto.flush()
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	618 p = subprocess.Popen(self.cl,shell=False,stdout=sto,stderr=sto,cwd=self.opts.output_dir)
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	619 else:
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	620 p = subprocess.Popen(self.cl,shell=False)
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	621 retval = p.wait()
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	622 if self.opts.output_dir:
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	623 sto.close()
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	624 if self.opts.make_HTML:
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	625 self.makeHtml()
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	626 return retval
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	627
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	628
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	629 def main():
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	630 u = """
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	631 This is a Galaxy wrapper. It expects to be called by a special purpose tool.xml as:
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	632 <command interpreter="python">rgBaseScriptWrapper.py --script_path "$scriptPath" --tool_name "foo" --interpreter "Rscript"
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	633 </command>
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	634 """
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	635 op = optparse.OptionParser()
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	636 a = op.add_option
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	637 a('--script_path',default=None)
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	638 a('--tool_name',default=None)
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	639 a('--interpreter',default=None)
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	640 a('--output_dir',default=None)
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	641 a('--output_html',default=None)
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	642 a('--input_tab',default="None")
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	643 a('--output_tab',default="None")
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	644 a('--user_email',default='Unknown')
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	645 a('--bad_user',default=None)
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	646 a('--make_Tool',default=None)
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	647 a('--make_HTML',default=None)
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	648 a('--help_text',default=None)
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	649 a('--tool_desc',default=None)
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	650 a('--new_tool',default=None)
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	651 a('--tool_version',default=None)
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	652 opts, args = op.parse_args()
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	653 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)
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	654 assert opts.tool_name,'## Tool Factory expects a tool name - eg --tool_name=DESeq'
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	655 assert opts.interpreter,'## Tool Factory wrapper expects an interpreter - eg --interpreter=Rscript'
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	656 assert os.path.isfile(opts.script_path),'## Tool Factory wrapper expects a script path - eg --script_path=foo.R'
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	657 if opts.output_dir:
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	658 try:
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	659 os.makedirs(opts.output_dir)
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	660 except:
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	661 pass
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	662 r = ScriptRunner(opts)
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	663 if opts.make_Tool:
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	664 retcode = r.makeTooltar()
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	665 else:
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	666 retcode = r.run()
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	667 os.unlink(r.sfile)
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	668 if retcode:
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	669 sys.exit(retcode) # indicate failure to job runner
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	670
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	671
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	672 if __name__ == "__main__":
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	673 main()
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	674
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	675

Mercurial > repos > fubar > toolfactory

annotate rgToolFactory.py @ 16:e052aadae3e9 draft