skunkworks: rgToolFactory.py annotate

author	fubar
date	Wed, 19 Mar 2014 21:06:28 -0400
parents
children	704ccaade924

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
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	11 # added ghostscript and graphicsmagick as dependencies
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	12 # 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	13 # errors ensued
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	14 #
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	15 # august 2013
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	16 # found a problem with GS if $TMP or $TEMP missing - now inject /tmp and warn
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	17 #
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	18 # july 2013
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	19 # added ability to combine images and individual log files into html output
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	20 # just make sure there's a log file foo.log and it will be output
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	21 # together with all images named like "foo_*.pdf
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	22 # otherwise old format for html
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	23 #
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	24 # January 2013
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	25 # problem pointed out by Carlos Borroto
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	26 # added escaping for <>$ - thought I did that ages ago...
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	27 #
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	28 # August 11 2012
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	29 # changed to use shell=False and cl as a sequence
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	30
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	31 # 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	32 # It also serves as the wrapper for the new tool.
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	33 #
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	34 # you paste and run your script
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	35 # 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	36 # Optionally can write one new history dataset,
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	37 # 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	38
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	39 # DO NOT install on a public or important site - please.
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 # installed generated tools are fine if the script is safe.
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	42 # 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	43 # but please, practice safe toolshed.
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	44 # Read the fucking code before you install any tool
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	45 # especially this one
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	46
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	47 # 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	48 # optionally generate a toolshed compatible gzip file
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	49 # 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	50 # safe and largely automated installation in a production Galaxy.
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	51
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	52 # 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	53 # 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	54 # Ugly but really inexpensive.
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	55 #
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	56 # Patches appreciated please.
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 #
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	59 # long route to June 2012 product
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	60 # 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	61 # derived from an integrated script model
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	62 # called rgBaseScriptWrapper.py
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	63 # Note to the unwary:
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	64 # 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	65 # There is nothing stopping a malicious user doing whatever they choose
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	66 # Extremely dangerous!!
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	67 # Totally insecure. So, trusted users only
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	68 #
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	69 # 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	70 # 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	71 #
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	72
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	73 import sys
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	74 import shutil
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	75 import subprocess
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	76 import os
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	77 import time
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	78 import tempfile
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	79 import optparse
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	80 import tarfile
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	81 import re
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	82 import shutil
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	83 import math
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	84
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	85 progname = os.path.split(sys.argv[0])[1]
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	86 myversion = 'V001.1 March 2014'
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	87 verbose = False
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	88 debug = False
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	89 toolFactoryURL = 'https://bitbucket.org/fubar/galaxytoolfactory'
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	90
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	91 def timenow():
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	92 """return current time as a string
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	93 """
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	94 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	95
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	96 html_escape_table = {
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	97 "&": "&",
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	98 ">": ">",
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	99 "<": "<",
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	100 "$": "\$"
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	101 }
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	102
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	103 def html_escape(text):
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	104 """Produce entities within text."""
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	105 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	106
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	107 def cmd_exists(cmd):
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	108 return subprocess.call("type " + cmd, shell=True,
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	109 stdout=subprocess.PIPE, stderr=subprocess.PIPE) == 0
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	110
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	111
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	112 class ScriptRunner:
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	113 """class is a wrapper for an arbitrary script
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	114 """
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	115
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	116 def __init__(self,opts=None,treatbashSpecial=True):
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	117 """
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	118 cleanup inputs, setup some outputs
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	119
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 self.useGM = cmd_exists('gm')
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	122 self.useIM = cmd_exists('convert')
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	123 self.useGS = cmd_exists('gs')
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	124 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	125 self.treatbashSpecial = treatbashSpecial
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	126 if opts.output_dir: # simplify for the tool tarball
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	127 os.chdir(opts.output_dir)
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	128 self.thumbformat = 'png'
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	129 self.opts = opts
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	130 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	131 self.toolid = self.toolname
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	132 self.myname = sys.argv[0] # get our name because we write ourselves out as a tool later
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	133 self.pyfile = self.myname # crude but efficient - the cruft won't hurt much
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	134 self.xmlfile = '%s.xml' % self.toolname
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	135 s = open(self.opts.script_path,'r').readlines()
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	136 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	137 self.script = '\n'.join(s)
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	138 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	139 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	140 tscript.write(self.script)
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	141 tscript.close()
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	142 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	143 self.escapedScript = '\n'.join([html_escape(x) for x in s])
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	144 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	145 if opts.output_dir: # may not want these complexities
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	146 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	147 art = '%s.%s' % (self.toolname,opts.interpreter)
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	148 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	149 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	150 artifact.write(self.script)
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	151 artifact.close()
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	152 self.cl = []
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	153 self.html = []
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	154 a = self.cl.append
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	155 a(opts.interpreter)
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	156 if self.treatbashSpecial and opts.interpreter in ['bash','sh']:
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	157 a(self.sfile)
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	158 else:
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	159 a('-') # stdin
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	160 a(opts.input_tab)
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	161 a(opts.output_tab)
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	162 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	163 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	164 self.test1Input = '%s_test1_input.xls' % self.toolname
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	165 self.test1Output = '%s_test1_output.xls' % self.toolname
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	166 self.test1HTML = '%s_test1_output.html' % self.toolname
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	167
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	168 def makeXML(self):
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	169 """
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	170 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	171 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	172
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	173 <tool id="reverse" name="reverse" version="0.01">
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	174 <description>a tabular file</description>
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	175 <command interpreter="python">
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	176 reverse.py --script_path "$runMe" --interpreter "python"
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	177 --tool_name "reverse" --input_tab "$input1" --output_tab "$tab_file"
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	178 </command>
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	179 <inputs>
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	180 <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	181
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	182 </inputs>
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	183 <outputs>
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	184 <data format="tabular" name="tab_file" label="${job_name}"/>
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	185
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	186 </outputs>
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	187 <help>
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	188
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	189 What it Does
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 Reverse the columns in a tabular file
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 </help>
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	194 <configfiles>
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	195 <configfile name="runMe">
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	196
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	197 # reverse order of columns in a tabular file
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	198 import sys
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	199 inp = sys.argv[1]
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	200 outp = sys.argv[2]
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	201 i = open(inp,'r')
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	202 o = open(outp,'w')
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	203 for row in i:
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	204 rs = row.rstrip().split('\t')
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	205 rs.reverse()
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	206 o.write('\t'.join(rs))
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	207 o.write('\n')
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	208 i.close()
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	209 o.close()
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	210
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 </configfile>
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	213 </configfiles>
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	214 </tool>
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 """
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	217 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	218 %(tooldesc)s
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	219 %(command)s
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	220 <inputs>
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	221 %(inputs)s
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	222 </inputs>
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	223 <outputs>
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	224 %(outputs)s
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	225 </outputs>
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	226 <configfiles>
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	227 <configfile name="runMe">
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	228 %(script)s
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	229 </configfile>
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	230 </configfiles>
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	231 %(tooltests)s
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	232 <help>
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	233 %(help)s
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	234 </help>
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	235 </tool>""" # needs a dict with toolname, toolid, interpreter, scriptname, command, inputs as a multi line string ready to write, outputs ditto, help ditto
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	236
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	237 newCommand="""<command interpreter="python">
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	238 %(toolname)s.py --script_path "$runMe" --interpreter "%(interpreter)s"
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	239 --tool_name "%(toolname)s" %(command_inputs)s %(command_outputs)s
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	240 </command>""" # may NOT be an input or htmlout
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	241 tooltestsTabOnly = """<tests><test>
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	242 <param name="input1" value="%(test1Input)s" ftype="tabular"/>
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	243 <param name="job_name" value="test1"/>
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	244 <param name="runMe" value="$runMe"/>
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	245 <output name="tab_file" file="%(test1Output)s" ftype="tabular"/>
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	246 </test></tests>"""
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	247 tooltestsHTMLOnly = """<tests><test>
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	248 <param name="input1" value="%(test1Input)s" ftype="tabular"/>
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	249 <param name="job_name" value="test1"/>
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	250 <param name="runMe" value="$runMe"/>
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	251 <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	252 </test></tests>"""
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	253 tooltestsBoth = """<tests><test>
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	254 <param name="input1" value="%(test1Input)s" ftype="tabular"/>
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	255 <param name="job_name" value="test1"/>
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	256 <param name="runMe" value="$runMe"/>
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	257 <output name="tab_file" file="%(test1Output)s" ftype="tabular" />
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	258 <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	259 </test></tests>"""
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	260 xdict = {}
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	261 xdict['tool_version'] = self.opts.tool_version
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	262 xdict['test1Input'] = self.test1Input
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	263 xdict['test1HTML'] = self.test1HTML
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	264 xdict['test1Output'] = self.test1Output
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	265 if self.opts.make_HTML and self.opts.output_tab <> 'None':
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	266 xdict['tooltests'] = tooltestsBoth % xdict
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	267 elif self.opts.make_HTML:
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	268 xdict['tooltests'] = tooltestsHTMLOnly % xdict
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	269 else:
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	270 xdict['tooltests'] = tooltestsTabOnly % xdict
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	271 xdict['script'] = self.escapedScript
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	272 # 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	273 # but requires escaping of <, > and $ to avoid Mako parsing
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	274 if self.opts.help_text:
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	275 xdict['help'] = open(self.opts.help_text,'r').read()
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	276 else:
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	277 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	278 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	279 coda.append(self.indentedScript)
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	280 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	281 coda.append('See %s for details of that project' % (toolFactoryURL))
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	282 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	283 coda.append('Bioinformatics 2012; doi: 10.1093/bioinformatics/bts573')
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	284 xdict['help'] = '%s\n%s' % (xdict['help'],'\n'.join(coda))
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	285 if self.opts.tool_desc:
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	286 xdict['tooldesc'] = '<description>%s</description>' % self.opts.tool_desc
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	287 else:
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	288 xdict['tooldesc'] = ''
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	289 xdict['command_outputs'] = ''
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	290 xdict['outputs'] = ''
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	291 if self.opts.input_tab <> 'None':
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	292 xdict['command_inputs'] = '--input_tab "$input1" ' # the space may matter a lot if we append something
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	293 xdict['inputs'] = '<param name="input1" type="data" format="%s" label="Select a suitable input file from your history"/> \n' % self.inputFormats
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	294 else:
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	295 xdict['command_inputs'] = '' # assume no input - eg a random data generator
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	296 xdict['inputs'] = ''
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	297 xdict['inputs'] += '<param name="job_name" type="text" label="Supply a name for the outputs to remind you what they contain" value="%s"/> \n' % self.toolname
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	298 xdict['toolname'] = self.toolname
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	299 xdict['toolid'] = self.toolid
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	300 xdict['interpreter'] = self.opts.interpreter
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	301 xdict['scriptname'] = self.sfile
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	302 if self.opts.make_HTML:
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	303 xdict['command_outputs'] += ' --output_dir "$html_file.files_path" --output_html "$html_file" --make_HTML "yes" '
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	304 xdict['outputs'] += ' <data format="html" name="html_file" label="${job_name}.html"/>\n'
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	305 if self.opts.output_tab <> 'None':
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	306 xdict['command_outputs'] += ' --output_tab "$tab_file"'
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	307 xdict['outputs'] += ' <data format="%s" name="tab_file" label="${job_name}"/>\n' % self.outFormats
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	308 xdict['command'] = newCommand % xdict
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	309 xmls = newXML % xdict
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	310 xf = open(self.xmlfile,'w')
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	311 xf.write(xmls)
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	312 xf.write('\n')
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	313 xf.close()
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	314 # ready for the tarball
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	315
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	316
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	317 def makeTooltar(self):
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	318 """
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	319 a tool is a gz tarball with eg
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	320 /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	321 """
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	322 retval = self.run()
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	323 if retval:
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	324 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	325 sys.exit(1)
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	326 self.makeXML()
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	327 tdir = self.toolname
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	328 os.mkdir(tdir)
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	329 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	330 testdir = os.path.join(tdir,'test-data')
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	331 os.mkdir(testdir) # make tests directory
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	332 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	333 if self.opts.output_tab <> 'None':
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	334 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	335 if self.opts.make_HTML:
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	336 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	337 if self.opts.output_dir:
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	338 shutil.copyfile(self.tlog,os.path.join(testdir,'test1_out.log'))
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	339 op = '%s.py' % self.toolname # new name
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	340 outpiname = os.path.join(tdir,op) # path for the tool tarball
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	341 pyin = os.path.basename(self.pyfile) # our name - we rewrite ourselves (TM)
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	342 notes = ['# %s - a self annotated version of %s generated by running %s\n' % (op,pyin,pyin),]
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	343 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	344 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	345 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	346 notes += pi
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	347 outpi = open(outpiname,'w')
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	348 outpi.write(''.join(notes))
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	349 outpi.write('\n')
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	350 outpi.close()
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	351 stname = os.path.join(tdir,self.sfile)
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	352 if not os.path.exists(stname):
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	353 shutil.copyfile(self.sfile, stname)
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	354 xtname = os.path.join(tdir,self.xmlfile)
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	355 if not os.path.exists(xtname):
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	356 shutil.copyfile(self.xmlfile,xtname)
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	357 tarpath = "%s.gz" % self.toolname
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	358 tar = tarfile.open(tarpath, "w:gz")
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	359 tar.add(tdir,arcname=self.toolname)
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	360 tar.close()
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	361 shutil.copyfile(tarpath,self.opts.new_tool)
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	362 shutil.rmtree(tdir)
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	363 ## TODO: replace with optional direct upload to local toolshed?
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	364 return retval
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	365
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	366
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	367 def compressPDF(self,inpdf=None,thumbformat='png'):
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	368 """need absolute path to pdf
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	369 note that GS gets confoozled if no $TMP or $TEMP
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	370 so we set it
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	371 """
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	372 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	373 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	374 sto = open(hlog,'a')
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	375 our_env = os.environ.copy()
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	376 our_tmp = our_env.get('TMP',None)
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	377 if not our_tmp:
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	378 our_tmp = our_env.get('TEMP',None)
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	379 if not (our_tmp and os.path.exists(our_tmp)):
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	380 newtmp = os.path.join(self.opts.output_dir,'tmp')
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	381 try:
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	382 os.mkdir(newtmp)
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	383 except:
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	384 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	385 our_env['TEMP'] = newtmp
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	386 if not self.temp_warned:
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	387 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	388 self.temp_warned = True
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	389 outpdf = '%s_compressed' % inpdf
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	390 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	391 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	392 retval1 = x.wait()
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	393 sto.close()
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	394 if retval1 == 0:
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	395 os.unlink(inpdf)
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	396 shutil.move(outpdf,inpdf)
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	397 os.unlink(hlog)
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	398 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	399 sto = open(hlog,'w')
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	400 outpng = '%s.%s' % (os.path.splitext(inpdf)[0],thumbformat)
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	401 if self.useGM:
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	402 cl2 = ['gm', 'convert', inpdf, outpng]
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	403 else: # assume imagemagick
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	404 cl2 = ['convert', inpdf, outpng]
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	405 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	406 retval2 = x.wait()
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	407 sto.close()
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	408 if retval2 == 0:
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	409 os.unlink(hlog)
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	410 retval = retval1 or retval2
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	411 return retval
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	412
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	413
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	414 def getfSize(self,fpath,outpath):
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	415 """
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	416 format a nice file size string
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	417 """
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	418 size = ''
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	419 fp = os.path.join(outpath,fpath)
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	420 if os.path.isfile(fp):
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	421 size = '0 B'
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	422 n = float(os.path.getsize(fp))
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	423 if n > 2**20:
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	424 size = '%1.1f MB' % (n/2**20)
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	425 elif n > 2**10:
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	426 size = '%1.1f KB' % (n/2**10)
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	427 elif n > 0:
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	428 size = '%d B' % (int(n))
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	429 return size
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	430
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	431 def makeHtml(self):
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	432 """ 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	433 """
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	434
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	435 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	436 <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	437 <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	438 <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	439 <title></title>
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	440 <link rel="stylesheet" href="/static/style/base.css" type="text/css" />
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	441 </head>
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	442 <body>
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	443 <div class="toolFormBody">
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	444 """
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	445 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	446 galhtmlpostfix = """</div></body></html>\n"""
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	447
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	448 flist = os.listdir(self.opts.output_dir)
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	449 flist = [x for x in flist if x <> 'Rplots.pdf']
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	450 flist.sort()
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	451 html = []
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	452 html.append(galhtmlprefix % progname)
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	453 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	454 fhtml = []
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	455 if len(flist) > 0:
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	456 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	457 logfiles.sort()
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	458 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	459 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	460 pdflist = []
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	461 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	462 for rownum,fname in enumerate(flist):
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	463 dname,e = os.path.splitext(fname)
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	464 sfsize = self.getfSize(fname,self.opts.output_dir)
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	465 if e.lower() == '.pdf' : # compress and make a thumbnail
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	466 thumb = '%s.%s' % (dname,self.thumbformat)
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	467 pdff = os.path.join(self.opts.output_dir,fname)
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	468 retval = self.compressPDF(inpdf=pdff,thumbformat=self.thumbformat)
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	469 if retval == 0:
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	470 pdflist.append((fname,thumb))
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	471 else:
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	472 pdflist.append((fname,fname))
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	473 if (rownum+1) % 2 == 0:
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	474 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	475 else:
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	476 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	477 for logfname in logfiles: # expect at least tlog - if more
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	478 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	479 sectionname = 'All tool run'
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	480 if (len(logfiles) > 1):
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	481 sectionname = 'Other'
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	482 ourpdfs = pdflist
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	483 else:
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	484 realname = os.path.basename(logfname)
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	485 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	486 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	487 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	488 nacross = 1
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	489 npdf = len(ourpdfs)
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	490
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	491 if npdf > 0:
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	492 nacross = math.sqrt(npdf) ## int(round(math.log(npdf,2)))
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	493 if int(nacross)**2 != npdf:
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	494 nacross += 1
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	495 nacross = int(nacross)
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	496 width = min(400,int(1200/nacross))
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	497 html.append('<div class="toolFormTitle">%s images and outputs</div>' % sectionname)
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	498 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	499 ntogo = nacross # counter for table row padding with empty cells
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	500 html.append('<div><table class="simple" cellpadding="2" cellspacing="2">\n<tr>')

7

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1 # rgToolFactory.py

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

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3 #

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

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5 #

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1fcf3fda325f major fixes with GS and graphicsmagick dependencies included

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7 # Licensed under the LGPL

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

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9 #

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10 # march 2014

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11 # added ghostscript and graphicsmagick as dependencies

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

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13 # errors ensued

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14 #

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15 # august 2013

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

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17 #

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18 # july 2013

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

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

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

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22 # otherwise old format for html

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23 #

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24 # January 2013

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25 # problem pointed out by Carlos Borroto

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

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27 #

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28 # August 11 2012

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

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30

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

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

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33 #

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34 # you paste and run your script

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

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36 # Optionally can write one new history dataset,

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

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38

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

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40

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

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

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43 # but please, practice safe toolshed.

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44 # Read the fucking code before you install any tool

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45 # especially this one

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46

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

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48 # optionally generate a toolshed compatible gzip file

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

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

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51

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

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

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54 # Ugly but really inexpensive.

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55 #

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56 # Patches appreciated please.

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57 #

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58 #

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59 # long route to June 2012 product

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

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61 # derived from an integrated script model

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62 # called rgBaseScriptWrapper.py

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63 # Note to the unwary:

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

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

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66 # Extremely dangerous!!

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67 # Totally insecure. So, trusted users only

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68 #

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

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

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71 #

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72

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73 import sys

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74 import shutil

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75 import subprocess

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76 import os

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77 import time

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78 import tempfile

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79 import optparse

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80 import tarfile

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81 import re

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82 import shutil

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83 import math

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84

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

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86 myversion = 'V001.1 March 2014'

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87 verbose = False

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88 debug = False

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

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90

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91 def timenow():

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92 """return current time as a string

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93 """

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

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95

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96 html_escape_table = {

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97 "&": "&",

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98 ">": ">",

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99 "<": "<",

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100 "$": "\$"

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101 }

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102

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103 def html_escape(text):

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104 """Produce entities within text."""

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

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106

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107 def cmd_exists(cmd):

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

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

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110

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111

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112 class ScriptRunner:

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

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114 """

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115

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

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117 """

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118 cleanup inputs, setup some outputs

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119

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120 """

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121 self.useGM = cmd_exists('gm')

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122 self.useIM = cmd_exists('convert')

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123 self.useGS = cmd_exists('gs')

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

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125 self.treatbashSpecial = treatbashSpecial

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

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127 os.chdir(opts.output_dir)

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128 self.thumbformat = 'png'

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129 self.opts = opts

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

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131 self.toolid = self.toolname

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

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

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

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

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

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

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

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

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140 tscript.write(self.script)

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141 tscript.close()

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

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

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

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

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

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

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

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

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150 artifact.write(self.script)

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151 artifact.close()

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152 self.cl = []

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153 self.html = []

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154 a = self.cl.append

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155 a(opts.interpreter)

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

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157 a(self.sfile)

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158 else:

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159 a('-') # stdin

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160 a(opts.input_tab)

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161 a(opts.output_tab)

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162 self.outFormats = 'tabular' # TODO make this an option at tool generation time

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163 self.inputFormats = 'tabular' # TODO make this an option at tool generation time

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164 self.test1Input = '%s_test1_input.xls' % self.toolname

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

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

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167

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168 def makeXML(self):

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169 """

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

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

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172

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

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174 <description>a tabular file</description>

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175 <command interpreter="python">

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

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

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178 </command>

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179 <inputs>

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180 <param name="input1" type="data" format="tabular" label="Select a suitable input file from your history"/><param name="job_name" type="text" label="Supply a name for the outputs to remind you what they contain" value="reverse"/>

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181

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182 </inputs>

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183 <outputs>

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

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185

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186 </outputs>

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187 <help>

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188

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189 **What it Does**

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190

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191 Reverse the columns in a tabular file

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192

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193 </help>

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194 <configfiles>

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195 <configfile name="runMe">

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196

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197 # reverse order of columns in a tabular file

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198 import sys

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199 inp = sys.argv[1]

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200 outp = sys.argv[2]

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201 i = open(inp,'r')

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202 o = open(outp,'w')

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203 for row in i:

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

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205 rs.reverse()

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

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207 o.write('\n')

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208 i.close()

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209 o.close()

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210

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211

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212 </configfile>

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213 </configfiles>

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214 </tool>

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215

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216 """

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

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218 %(tooldesc)s

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219 %(command)s

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220 <inputs>

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221 %(inputs)s

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222 </inputs>

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223 <outputs>

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224 %(outputs)s

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225 </outputs>

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226 <configfiles>

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227 <configfile name="runMe">

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228 %(script)s

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229 </configfile>

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230 </configfiles>

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231 %(tooltests)s

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232 <help>

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233 %(help)s

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234 </help>

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

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236

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237 newCommand="""<command interpreter="python">

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238 %(toolname)s.py --script_path "$runMe" --interpreter "%(interpreter)s"

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239 --tool_name "%(toolname)s" %(command_inputs)s %(command_outputs)s

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240 </command>""" # may NOT be an input or htmlout

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241 tooltestsTabOnly = """<tests><test>

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242 <param name="input1" value="%(test1Input)s" ftype="tabular"/>

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

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

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

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246 </test></tests>"""

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247 tooltestsHTMLOnly = """<tests><test>

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248 <param name="input1" value="%(test1Input)s" ftype="tabular"/>

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

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

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

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252 </test></tests>"""

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253 tooltestsBoth = """<tests><test>

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254 <param name="input1" value="%(test1Input)s" ftype="tabular"/>

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

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

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

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

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259 </test></tests>"""

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260 xdict = {}

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

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262 xdict['test1Input'] = self.test1Input

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263 xdict['test1HTML'] = self.test1HTML

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264 xdict['test1Output'] = self.test1Output

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

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266 xdict['tooltests'] = tooltestsBoth % xdict

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267 elif self.opts.make_HTML:

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268 xdict['tooltests'] = tooltestsHTMLOnly % xdict

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269 else:

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270 xdict['tooltests'] = tooltestsTabOnly % xdict

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271 xdict['script'] = self.escapedScript

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diff changeset

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

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

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274 if self.opts.help_text:

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275 xdict['help'] = open(self.opts.help_text,'r').read()

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276 else:

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277 xdict['help'] = 'Please ask the tool author for help as none was supplied at tool generation'

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

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279 coda.append(self.indentedScript)

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

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

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

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283 coda.append('Bioinformatics 2012; doi: 10.1093/bioinformatics/bts573')

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

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285 if self.opts.tool_desc:

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

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287 else:

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288 xdict['tooldesc'] = ''

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289 xdict['command_outputs'] = ''

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290 xdict['outputs'] = ''

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

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292 xdict['command_inputs'] = '--input_tab "$input1" ' # the space may matter a lot if we append something

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293 xdict['inputs'] = '<param name="input1" type="data" format="%s" label="Select a suitable input file from your history"/> \n' % self.inputFormats

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294 else:

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

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296 xdict['inputs'] = ''

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297 xdict['inputs'] += '<param name="job_name" type="text" label="Supply a name for the outputs to remind you what they contain" value="%s"/> \n' % self.toolname

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298 xdict['toolname'] = self.toolname

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299 xdict['toolid'] = self.toolid

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

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301 xdict['scriptname'] = self.sfile

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302 if self.opts.make_HTML:

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

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

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

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

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

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308 xdict['command'] = newCommand % xdict

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309 xmls = newXML % xdict

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

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311 xf.write(xmls)

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312 xf.write('\n')

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313 xf.close()

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diff changeset

314 # ready for the tarball

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315

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316

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317 def makeTooltar(self):

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318 """

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319 a tool is a gz tarball with eg

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

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321 """

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322 retval = self.run()

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323 if retval:

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

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325 sys.exit(1)

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326 self.makeXML()

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327 tdir = self.toolname

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328 os.mkdir(tdir)

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

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

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331 os.mkdir(testdir) # make tests directory

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332 shutil.copyfile(self.opts.input_tab,os.path.join(testdir,self.test1Input))

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

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

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335 if self.opts.make_HTML:

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

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337 if self.opts.output_dir:

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

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339 op = '%s.py' % self.toolname # new name

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340 outpiname = os.path.join(tdir,op) # path for the tool tarball

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

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

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

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

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

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346 notes += pi

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347 outpi = open(outpiname,'w')

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

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349 outpi.write('\n')

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350 outpi.close()

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

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

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353 shutil.copyfile(self.sfile, stname)

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

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

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356 shutil.copyfile(self.xmlfile,xtname)

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

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

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diff changeset

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

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diff changeset

360 tar.close()

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diff changeset

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

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diff changeset

362 shutil.rmtree(tdir)

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

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364 return retval

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diff changeset

365

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366

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

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diff changeset

368 """need absolute path to pdf

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

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diff changeset

370 so we set it

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371 """

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

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

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374 sto = open(hlog,'a')

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375 our_env = os.environ.copy()

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

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diff changeset

377 if not our_tmp:

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diff changeset

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

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diff changeset

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

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diff changeset

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

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diff changeset

381 try:

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diff changeset

382 os.mkdir(newtmp)

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diff changeset

383 except:

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

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385 our_env['TEMP'] = newtmp

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diff changeset

386 if not self.temp_warned:

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

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388 self.temp_warned = True

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389 outpdf = '%s_compressed' % inpdf

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

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

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diff changeset

392 retval1 = x.wait()

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diff changeset

393 sto.close()

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diff changeset

394 if retval1 == 0:

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diff changeset

395 os.unlink(inpdf)

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diff changeset

396 shutil.move(outpdf,inpdf)

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diff changeset

397 os.unlink(hlog)

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

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399 sto = open(hlog,'w')

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

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diff changeset

401 if self.useGM:

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diff changeset

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

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403 else: # assume imagemagick

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

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diff changeset

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

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parents:

diff changeset

406 retval2 = x.wait()

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parents:

diff changeset

407 sto.close()

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parents:

diff changeset

408 if retval2 == 0:

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parents:

diff changeset

409 os.unlink(hlog)

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parents:

diff changeset

410 retval = retval1 or retval2

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parents:

diff changeset

411 return retval

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parents:

diff changeset

412

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parents:

diff changeset

413

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parents:

diff changeset

414 def getfSize(self,fpath,outpath):

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parents:

diff changeset

415 """

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parents:

diff changeset

416 format a nice file size string

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parents:

diff changeset

417 """

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parents:

diff changeset

418 size = ''

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parents:

diff changeset

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

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parents:

diff changeset

420 if os.path.isfile(fp):

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parents:

diff changeset

421 size = '0 B'

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parents:

diff changeset

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

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parents:

diff changeset

423 if n > 2**20:

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parents:

diff changeset

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

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parents:

diff changeset

425 elif n > 2**10:

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parents:

diff changeset

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

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parents:

diff changeset

427 elif n > 0:

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parents:

diff changeset

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

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parents:

diff changeset

429 return size

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parents:

diff changeset

430

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parents:

diff changeset

431 def makeHtml(self):

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diff changeset

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

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diff changeset

433 """

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diff changeset

434

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diff changeset

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

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parents:

diff changeset

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

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diff changeset

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

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diff changeset

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

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diff changeset

439 <title></title>

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diff changeset

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

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parents:

diff changeset

441 </head>

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diff changeset

442 <body>

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diff changeset

443 <div class="toolFormBody">

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diff changeset

444 """

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diff changeset

445 galhtmlattr = """<hr/><div class="infomessage">This tool (%s) was generated by the <a href="https://bitbucket.org/fubar/galaxytoolfactory/overview">Galaxy Tool Factory</a></div><br/>"""

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diff changeset

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

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diff changeset

447

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diff changeset

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

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parents:

diff changeset

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

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parents:

diff changeset

450 flist.sort()

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parents:

diff changeset

451 html = []

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diff changeset

452 html.append(galhtmlprefix % progname)

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parents:

diff changeset

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

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parents:

diff changeset

454 fhtml = []

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parents:

diff changeset

455 if len(flist) > 0:

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parents:

diff changeset

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

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parents:

diff changeset

457 logfiles.sort()

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diff changeset

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

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diff changeset

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

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parents:

diff changeset

460 pdflist = []

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parents:

diff changeset

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

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parents:

diff changeset

462 for rownum,fname in enumerate(flist):

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parents:

diff changeset

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

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parents:

diff changeset

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

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parents:

diff changeset

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

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parents:

diff changeset

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

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parents:

diff changeset

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

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parents:

diff changeset

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

1fcf3fda325f major fixes with GS and graphicsmagick dependencies included

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parents:

diff changeset

469 if retval == 0:

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parents:

diff changeset

470 pdflist.append((fname,thumb))

1fcf3fda325f major fixes with GS and graphicsmagick dependencies included

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parents:

diff changeset

471 else:

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parents:

diff changeset

472 pdflist.append((fname,fname))

1fcf3fda325f major fixes with GS and graphicsmagick dependencies included

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parents:

diff changeset

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

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parents:

diff changeset

474 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

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parents:

diff changeset

475 else:

1fcf3fda325f major fixes with GS and graphicsmagick dependencies included

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parents:

diff changeset

476 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

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parents:

diff changeset

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

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parents:

diff changeset

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

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parents:

diff changeset

479 sectionname = 'All tool run'

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parents:

diff changeset

480 if (len(logfiles) > 1):

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parents:

diff changeset

481 sectionname = 'Other'

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parents:

diff changeset

482 ourpdfs = pdflist

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parents:

diff changeset

483 else:

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parents:

diff changeset

484 realname = os.path.basename(logfname)

1fcf3fda325f major fixes with GS and graphicsmagick dependencies included

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parents:

diff changeset

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

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parents:

diff changeset

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

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parents:

diff changeset

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

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parents:

diff changeset

488 nacross = 1

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parents:

diff changeset

489 npdf = len(ourpdfs)

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parents:

diff changeset

490

1fcf3fda325f major fixes with GS and graphicsmagick dependencies included

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parents:

diff changeset

491 if npdf > 0:

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parents:

diff changeset

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

1fcf3fda325f major fixes with GS and graphicsmagick dependencies included

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parents:

diff changeset

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

1fcf3fda325f major fixes with GS and graphicsmagick dependencies included

fubar

parents:

diff changeset

494 nacross += 1

1fcf3fda325f major fixes with GS and graphicsmagick dependencies included

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parents:

diff changeset

495 nacross = int(nacross)

1fcf3fda325f major fixes with GS and graphicsmagick dependencies included

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parents:

diff changeset

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

1fcf3fda325f major fixes with GS and graphicsmagick dependencies included

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parents:

diff changeset

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

1fcf3fda325f major fixes with GS and graphicsmagick dependencies included

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parents:

diff changeset

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

1fcf3fda325f major fixes with GS and graphicsmagick dependencies included

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parents:

diff changeset

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

1fcf3fda325f major fixes with GS and graphicsmagick dependencies included

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parents:

diff changeset

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

1fcf3fda325f major fixes with GS and graphicsmagick dependencies included

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parents:

diff changeset

501 for i,paths in enumerate(ourpdfs):

1fcf3fda325f major fixes with GS and graphicsmagick dependencies included

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parents:

diff changeset

502 fname,thumb = paths

1fcf3fda325f major fixes with GS and graphicsmagick dependencies included

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parents:

diff changeset

503 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

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parents:

diff changeset

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

1fcf3fda325f major fixes with GS and graphicsmagick dependencies included

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parents:

diff changeset

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

1fcf3fda325f major fixes with GS and graphicsmagick dependencies included

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parents:

diff changeset

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

1fcf3fda325f major fixes with GS and graphicsmagick dependencies included

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parents:

diff changeset

507 ntogo = 0

1fcf3fda325f major fixes with GS and graphicsmagick dependencies included

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parents:

diff changeset

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

1fcf3fda325f major fixes with GS and graphicsmagick dependencies included

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parents:

diff changeset

509 s += '<tr>'

1fcf3fda325f major fixes with GS and graphicsmagick dependencies included

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parents:

diff changeset

510 ntogo = nacross

1fcf3fda325f major fixes with GS and graphicsmagick dependencies included

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parents:

diff changeset

511 else:

1fcf3fda325f major fixes with GS and graphicsmagick dependencies included

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parents:

diff changeset

512 ntogo -= 1

1fcf3fda325f major fixes with GS and graphicsmagick dependencies included

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parents:

diff changeset

513 html.append(s)

1fcf3fda325f major fixes with GS and graphicsmagick dependencies included

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parents:

diff changeset

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

1fcf3fda325f major fixes with GS and graphicsmagick dependencies included

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parents:

diff changeset

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

1fcf3fda325f major fixes with GS and graphicsmagick dependencies included

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parents:

diff changeset

516 else:

1fcf3fda325f major fixes with GS and graphicsmagick dependencies included

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parents:

diff changeset

517 if ntogo > 0: # pad

1fcf3fda325f major fixes with GS and graphicsmagick dependencies included

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parents:

diff changeset

518 html.append('<td> </td>'*ntogo)

1fcf3fda325f major fixes with GS and graphicsmagick dependencies included

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parents:

diff changeset

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

1fcf3fda325f major fixes with GS and graphicsmagick dependencies included

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parents:

diff changeset

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

1fcf3fda325f major fixes with GS and graphicsmagick dependencies included

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parents:

diff changeset

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

1fcf3fda325f major fixes with GS and graphicsmagick dependencies included

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parents:

diff changeset

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

1fcf3fda325f major fixes with GS and graphicsmagick dependencies included

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parents:

diff changeset

523 if len(logtext) > 1:

1fcf3fda325f major fixes with GS and graphicsmagick dependencies included

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parents:

diff changeset

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

1fcf3fda325f major fixes with GS and graphicsmagick dependencies included

fubar

parents:

diff changeset

525 html += logtext

1fcf3fda325f major fixes with GS and graphicsmagick dependencies included

fubar

parents:

diff changeset

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

1fcf3fda325f major fixes with GS and graphicsmagick dependencies included

fubar

parents:

diff changeset

527 else:

1fcf3fda325f major fixes with GS and graphicsmagick dependencies included

fubar

parents:

diff changeset

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

1fcf3fda325f major fixes with GS and graphicsmagick dependencies included

fubar

parents:

diff changeset

529 if len(fhtml) > 0:

1fcf3fda325f major fixes with GS and graphicsmagick dependencies included

fubar

parents:

diff changeset

530 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

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parents:

diff changeset

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

1fcf3fda325f major fixes with GS and graphicsmagick dependencies included

fubar

parents:

diff changeset

532 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

533 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

534 else:

1fcf3fda325f major fixes with GS and graphicsmagick dependencies included

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parents:

diff changeset

535 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

536 html.append(galhtmlpostfix)

1fcf3fda325f major fixes with GS and graphicsmagick dependencies included

fubar

parents:

diff changeset

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

1fcf3fda325f major fixes with GS and graphicsmagick dependencies included

fubar

parents:

diff changeset

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

1fcf3fda325f major fixes with GS and graphicsmagick dependencies included

fubar

parents:

diff changeset

539 htmlf.write('\n')

1fcf3fda325f major fixes with GS and graphicsmagick dependencies included

fubar

parents:

diff changeset

540 htmlf.close()

1fcf3fda325f major fixes with GS and graphicsmagick dependencies included

fubar

parents:

diff changeset

541 self.html = html

1fcf3fda325f major fixes with GS and graphicsmagick dependencies included

fubar

parents:

diff changeset

542

1fcf3fda325f major fixes with GS and graphicsmagick dependencies included

fubar

parents:

diff changeset

543

1fcf3fda325f major fixes with GS and graphicsmagick dependencies included

fubar

parents:

diff changeset

544 def run(self):

1fcf3fda325f major fixes with GS and graphicsmagick dependencies included

fubar

parents:

diff changeset

545 """

1fcf3fda325f major fixes with GS and graphicsmagick dependencies included

fubar

parents:

diff changeset

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

1fcf3fda325f major fixes with GS and graphicsmagick dependencies included

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parents:

diff changeset

547 """

1fcf3fda325f major fixes with GS and graphicsmagick dependencies included

fubar

parents:

diff changeset

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

1fcf3fda325f major fixes with GS and graphicsmagick dependencies included

fubar

parents:

diff changeset

549 retval = self.runBash()

1fcf3fda325f major fixes with GS and graphicsmagick dependencies included

fubar

parents:

diff changeset

550 else:

1fcf3fda325f major fixes with GS and graphicsmagick dependencies included

fubar

parents:

diff changeset

551 if self.opts.output_dir:

1fcf3fda325f major fixes with GS and graphicsmagick dependencies included

fubar

parents:

diff changeset

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

1fcf3fda325f major fixes with GS and graphicsmagick dependencies included

fubar

parents:

diff changeset

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

1fcf3fda325f major fixes with GS and graphicsmagick dependencies included

fubar

parents:

diff changeset

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

1fcf3fda325f major fixes with GS and graphicsmagick dependencies included

fubar

parents:

diff changeset

555 sto.flush()

1fcf3fda325f major fixes with GS and graphicsmagick dependencies included

fubar

parents:

diff changeset

556 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

557 else:

1fcf3fda325f major fixes with GS and graphicsmagick dependencies included

fubar

parents:

diff changeset

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

1fcf3fda325f major fixes with GS and graphicsmagick dependencies included

fubar

parents:

diff changeset

559 p.stdin.write(self.script)

1fcf3fda325f major fixes with GS and graphicsmagick dependencies included

fubar

parents:

diff changeset

560 p.stdin.close()

1fcf3fda325f major fixes with GS and graphicsmagick dependencies included

fubar

parents:

diff changeset

561 retval = p.wait()

1fcf3fda325f major fixes with GS and graphicsmagick dependencies included

fubar

parents:

diff changeset

562 if self.opts.output_dir:

1fcf3fda325f major fixes with GS and graphicsmagick dependencies included

fubar

parents:

diff changeset

563 sto.close()

1fcf3fda325f major fixes with GS and graphicsmagick dependencies included

fubar

parents:

diff changeset

564 ste.close()

1fcf3fda325f major fixes with GS and graphicsmagick dependencies included

fubar

parents:

diff changeset

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

1fcf3fda325f major fixes with GS and graphicsmagick dependencies included

fubar

parents:

diff changeset

566 if retval <> 0 and err: # problem

1fcf3fda325f major fixes with GS and graphicsmagick dependencies included

fubar

parents:

diff changeset

567 print >> sys.stderr,err

1fcf3fda325f major fixes with GS and graphicsmagick dependencies included

fubar

parents:

diff changeset

568 if self.opts.make_HTML:

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569 self.makeHtml()

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570 return retval

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571

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572 def runBash(self):

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573 """

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574 cannot use - for bash so use self.sfile

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575 """

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576 if self.opts.output_dir:

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

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

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579 sto.write(s)

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580 sto.flush()

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

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582 else:

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

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584 retval = p.wait()

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585 if self.opts.output_dir:

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586 sto.close()

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587 if self.opts.make_HTML:

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588 self.makeHtml()

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589 return retval

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590

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591

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592 def main():

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593 u = """

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

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

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596 </command>

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597 """

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598 op = optparse.OptionParser()

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599 a = op.add_option

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

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

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

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603 a('--output_dir',default=None)

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

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605 a('--input_tab',default="None")

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

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

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

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

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

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

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

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

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

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615 opts, args = op.parse_args()

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616 assert not opts.bad_user,'UNAUTHORISED: %s is NOT authorized to use this tool until Galaxy admin adds %s to admin_users in universe_wsgi.ini' % (opts.bad_user,opts.bad_user)

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

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

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