toolfactory: fubar-galaxytoolfactory-f726a966e35d/rgToolFactory.py annotate

annotate fubar-galaxytoolfactory-f726a966e35d/rgToolFactory.py @ 20:b9892d7f0983 draft default tip

USE MAIN TOOLSHED PLEASE I keep forgetting to update this one

author	fubar
date	Fri, 08 Mar 2013 01:50:14 -0500
parents	f1dae673ec8b
children

rev	line source
19 f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	1 # rgToolFactory.py
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	2 # see https://bitbucket.org/fubar/galaxytoolfactory/wiki/Home
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	3 #
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	4 # copyright ross lazarus (ross stop lazarus at gmail stop com) May 2012
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	5 #
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	6 # all rights reserved
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	7 # Licensed under the LGPL
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	8 # suggestions for improvement and bug fixes welcome at https://bitbucket.org/fubar/galaxytoolfactory/wiki/Home
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	9
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	10 # August 11 2012
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	11 # changed to use shell=False and cl as a sequence
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	12
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	13 # This is a Galaxy tool factory for simple scripts in python, R or whatever ails ye.
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	14 # It also serves as the wrapper for the new tool.
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	15 #
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	16 # you paste and run your script
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	17 # Only works for simple scripts that read one input from the history.
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	18 # Optionally can write one new history dataset,
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	19 # and optionally collect any number of outputs into links on an autogenerated HTML page.
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	20
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	21 # DO NOT install on a public or important site - please.
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	22
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	23 # installed generated tools are fine if the script is safe.
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	24 # They just run normally and their user cannot do anything unusually insecure
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	25 # but please, practice safe toolshed.
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	26 # Read the fucking code before you install any tool
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	27 # especially this one
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	28
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	29 # After you get the script working on some test data, you can
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	30 # optionally generate a toolshed compatible gzip file
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	31 # containing your script safely wrapped as an ordinary Galaxy script in your local toolshed for
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	32 # safe and largely automated installation in a production Galaxy.
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	33
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	34 # If you opt for an HTML output, you get all the script outputs arranged
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	35 # as a single Html history item - all output files are linked, thumbnails for all the pdfs.
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	36 # Ugly but really inexpensive.
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	37 #
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	38 # Patches appreciated please.
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	39 #
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	40 #
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	41 # long route to June 2012 product
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	42 # Behold the awesome power of Galaxy and the toolshed with the tool factory binds to bind them
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	43 # derived from an integrated script model
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	44 # called rgBaseScriptWrapper.py
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	45 # Note to the unwary:
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	46 # This tool allows arbitrary scripting on your Galaxy as the Galaxy user
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	47 # There is nothing stopping a malicious user doing whatever they choose
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	48 # Extremely dangerous!!
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	49 # Totally insecure. So, trusted users only
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	50 #
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	51 # preferred model is a developer using their throw away workstation instance - ie a private site.
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	52 # no real risk. The universe_wsgi.ini admin_users string is checked - only admin users are permitted to run this tool.
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	53 #
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	54
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	55 import sys
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	56 import shutil
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	57 import subprocess
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	58 import os
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	59 import time
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	60 import tempfile
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	61 import optparse
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	62 import tarfile
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	63 import re
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	64 import shutil
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	65 import math
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	66
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	67 progname = os.path.split(sys.argv[0])[1]
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	68 myversion = 'V000.2 June 2012'
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	69 verbose = False
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	70 debug = False
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	71 toolFactoryURL = 'https://bitbucket.org/fubar/galaxytoolfactory'
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	72
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	73 def timenow():
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	74 """return current time as a string
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	75 """
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	76 return time.strftime('%d/%m/%Y %H:%M:%S', time.localtime(time.time()))
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	77
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	78
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	79 class ScriptRunner:
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	80 """class is a wrapper for an arbitrary script
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	81 """
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	82
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	83 def __init__(self,opts=None,treatbashSpecial=True):
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	84 """
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	85 cleanup inputs, setup some outputs
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	86
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	87 """
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	88 self.treatbashSpecial = treatbashSpecial
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	89 if opts.output_dir: # simplify for the tool tarball
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	90 os.chdir(opts.output_dir)
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	91 self.thumbformat = 'jpg'
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	92 self.opts = opts
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	93 self.toolname = re.sub('[^a-zA-Z0-9_]+', '', opts.tool_name) # a sanitizer now does this but..
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	94 self.toolid = self.toolname
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	95 self.myname = sys.argv[0] # get our name because we write ourselves out as a tool later
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	96 self.pyfile = self.myname # crude but efficient - the cruft won't hurt much
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	97 self.xmlfile = '%s.xml' % self.toolname
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	98 s = open(self.opts.script_path,'r').readlines()
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	99 s = [x.rstrip() for x in s] # remove pesky dos line endings if needed
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	100 self.script = '\n'.join(s)
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	101 fhandle,self.sfile = tempfile.mkstemp(prefix=self.toolname,suffix=".%s" % (opts.interpreter))
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	102 tscript = open(self.sfile,'w') # use self.sfile as script source for Popen
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	103 tscript.write(self.script)
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	104 tscript.close()
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	105 self.indentedScript = ''.join([' %s' % x for x in s]) # for restructured text in help
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	106 if opts.output_dir: # may not want these complexities
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	107 self.tlog = os.path.join(opts.output_dir,"%s_runner.log" % self.toolname)
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	108 art = '%s.%s' % (self.toolname,opts.interpreter)
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	109 artpath = os.path.join(self.opts.output_dir,art) # need full path
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	110 artifact = open(artpath,'w') # use self.sfile as script source for Popen
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	111 artifact.write(self.script)
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	112 artifact.close()
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	113 self.cl = []
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	114 self.html = []
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	115 a = self.cl.append
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	116 a(opts.interpreter)
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	117 if self.treatbashSpecial and opts.interpreter in ['bash','sh']:
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	118 a(self.sfile)
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	119 else:
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	120 a('-') # stdin
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	121 a(opts.input_tab)
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	122 a(opts.output_tab)
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	123 self.outFormats = 'tabular' # TODO make this an option at tool generation time
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	124 self.inputFormats = 'tabular' # TODO make this an option at tool generation time
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	125 self.test1Input = '%s_test1_input.xls' % self.toolname
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	126 self.test1Output = '%s_test1_output.xls' % self.toolname
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	127 self.test1HTML = '%s_test1_output.html' % self.toolname
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	128
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	129 def makeXML(self):
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	130 """
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	131 Create a Galaxy xml tool wrapper for the new script as a string to write out
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	132 fixme - use templating or something less fugly than this example of what we produce
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	133
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	134 <tool id="reverse" name="reverse" version="0.01">
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	135 <description>a tabular file</description>
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	136 <command interpreter="python">
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	137 reverse.py --script_path "$runMe" --interpreter "python"
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	138 --tool_name "reverse" --input_tab "$input1" --output_tab "$tab_file"
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	139 </command>
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	140 <inputs>
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	141 <param name="input1" type="data" format="tabular" label="Select a suitable input file from your history"/><param name="job_name" type="text" label="Supply a name for the outputs to remind you what they contain" value="reverse"/>
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	142
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	143 </inputs>
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	144 <outputs>
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	145 <data format="tabular" name="tab_file" label="${job_name}"/>
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	146
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	147 </outputs>
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	148 <help>
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	149
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	150 What it Does
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	151
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	152 Reverse the columns in a tabular file
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	153
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	154 </help>
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	155 <configfiles>
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	156 <configfile name="runMe">
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	157
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	158 # reverse order of columns in a tabular file
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	159 import sys
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	160 inp = sys.argv[1]
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	161 outp = sys.argv[2]
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	162 i = open(inp,'r')
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	163 o = open(outp,'w')
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	164 for row in i:
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	165 rs = row.rstrip().split('\t')
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	166 rs.reverse()
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	167 o.write('\t'.join(rs))
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	168 o.write('\n')
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	169 i.close()
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	170 o.close()
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	171
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	172
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	173 </configfile>
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	174 </configfiles>
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	175 </tool>
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	176
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	177 """
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	178 newXML="""<tool id="%(toolid)s" name="%(toolname)s" version="%(tool_version)s">
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	179 %(tooldesc)s
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	180 %(command)s
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	181 <inputs>
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	182 %(inputs)s
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	183 </inputs>
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	184 <outputs>
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	185 %(outputs)s
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	186 </outputs>
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	187 <configfiles>
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	188 <configfile name="runMe">
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	189 %(script)s
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	190 </configfile>
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	191 </configfiles>
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	192 %(tooltests)s
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	193 <help>
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	194 %(help)s
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	195 </help>
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	196 </tool>""" # needs a dict with toolname, toolid, interpreter, scriptname, command, inputs as a multi line string ready to write, outputs ditto, help ditto
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	197
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	198 newCommand="""<command interpreter="python">
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	199 %(toolname)s.py --script_path "$runMe" --interpreter "%(interpreter)s"
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	200 --tool_name "%(toolname)s" %(command_inputs)s %(command_outputs)s
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	201 </command>""" # may NOT be an input or htmlout
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	202 tooltestsTabOnly = """<tests><test>
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	203 <param name="input1" value="%(test1Input)s" ftype="tabular"/>
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	204 <param name="job_name" value="test1"/>
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	205 <param name="runMe" value="$runMe"/>
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	206 <output name="tab_file" file="%(test1Output)s" ftype="tabular"/>
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	207 </test></tests>"""
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	208 tooltestsHTMLOnly = """<tests><test>
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	209 <param name="input1" value="%(test1Input)s" ftype="tabular"/>
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	210 <param name="job_name" value="test1"/>
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	211 <param name="runMe" value="$runMe"/>
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	212 <output name="html_file" file="%(test1HTML)s" ftype="html" lines_diff="5"/>
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	213 </test></tests>"""
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	214 tooltestsBoth = """<tests><test>
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	215 <param name="input1" value="%(test1Input)s" ftype="tabular"/>
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	216 <param name="job_name" value="test1"/>
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	217 <param name="runMe" value="$runMe"/>
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	218 <output name="tab_file" file="%(test1Output)s" ftype="tabular" />
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	219 <output name="html_file" file="%(test1HTML)s" ftype="html" lines_diff="10"/>
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	220 </test></tests>"""
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	221 xdict = {}
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	222 xdict['tool_version'] = self.opts.tool_version
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	223 xdict['test1Input'] = self.test1Input
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	224 xdict['test1HTML'] = self.test1HTML
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	225 xdict['test1Output'] = self.test1Output
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	226 if self.opts.make_HTML and self.opts.output_tab <> 'None':
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	227 xdict['tooltests'] = tooltestsBoth % xdict
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	228 elif self.opts.make_HTML:
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	229 xdict['tooltests'] = tooltestsHTMLOnly % xdict
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	230 else:
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	231 xdict['tooltests'] = tooltestsTabOnly % xdict
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	232 xdict['script'] = self.script # configfile is least painful way to embed script to avoid external dependencies
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	233 if self.opts.help_text:
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	234 xdict['help'] = open(self.opts.help_text,'r').read()
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	235 else:
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	236 xdict['help'] = 'Please ask the tool author for help as none was supplied at tool generation'
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	237 coda = ['Script','Pressing execute will run the following code over your input file and generate some outputs in your history::']
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	238 coda.append(self.indentedScript)
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	239 coda.append('Attribution This Galaxy tool was created by %s at %s\nusing the Galaxy Tool Factory.' % (self.opts.user_email,timenow()))
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	240 coda.append('See %s for details of that project' % (toolFactoryURL))
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	241 xdict['help'] = '%s\n%s' % (xdict['help'],'\n'.join(coda))
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	242 if self.opts.tool_desc:
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	243 xdict['tooldesc'] = '<description>%s</description>' % self.opts.tool_desc
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	244 else:
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	245 xdict['tooldesc'] = ''
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	246 xdict['command_outputs'] = ''
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	247 xdict['outputs'] = ''
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	248 if self.opts.input_tab <> 'None':
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	249 xdict['command_inputs'] = '--input_tab "$input1" ' # the space may matter a lot if we append something
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	250 xdict['inputs'] = '<param name="input1" type="data" format="%s" label="Select a suitable input file from your history"/> \n' % self.inputFormats
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	251 else:
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	252 xdict['command_inputs'] = '' # assume no input - eg a random data generator
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	253 xdict['inputs'] = ''
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	254 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
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	255 xdict['toolname'] = self.toolname
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	256 xdict['toolid'] = self.toolid
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	257 xdict['interpreter'] = self.opts.interpreter
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	258 xdict['scriptname'] = self.sfile
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	259 if self.opts.make_HTML:
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	260 xdict['command_outputs'] += ' --output_dir "$html_file.files_path" --output_html "$html_file" --make_HTML "yes" '
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	261 xdict['outputs'] += ' <data format="html" name="html_file" label="${job_name}.html"/>\n'
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	262 if self.opts.output_tab <> 'None':
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	263 xdict['command_outputs'] += ' --output_tab "$tab_file"'
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	264 xdict['outputs'] += ' <data format="%s" name="tab_file" label="${job_name}"/>\n' % self.outFormats
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	265 xdict['command'] = newCommand % xdict
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	266 xmls = newXML % xdict
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	267 xf = open(self.xmlfile,'w')
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	268 xf.write(xmls)
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	269 xf.write('\n')
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	270 xf.close()
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	271 # ready for the tarball
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	272
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	273
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	274 def makeTooltar(self):
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	275 """
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	276 a tool is a gz tarball with eg
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	277 /toolname/tool.xml /toolname/tool.py /toolname/test-data/test1_in.foo ...
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	278 """
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	279 retval = self.run()
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	280 if retval:
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	281 print >> sys.stderr,'## Run failed. Cannot build yet. Please fix and retry'
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	282 sys.exit(1)
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	283 self.makeXML()
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	284 tdir = self.toolname
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	285 os.mkdir(tdir)
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	286 if self.opts.input_tab <> 'None': # no reproducible test otherwise? TODO: maybe..
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	287 testdir = os.path.join(tdir,'test-data')
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	288 os.mkdir(testdir) # make tests directory
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	289 shutil.copyfile(self.opts.input_tab,os.path.join(testdir,self.test1Input))
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	290 if self.opts.output_tab <> 'None':
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	291 shutil.copyfile(self.opts.output_tab,os.path.join(testdir,self.test1Output))
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	292 if self.opts.make_HTML:
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	293 shutil.copyfile(self.opts.output_html,os.path.join(testdir,self.test1HTML))
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	294 if self.opts.output_dir:
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	295 shutil.copyfile(self.tlog,os.path.join(testdir,'test1_out.log'))
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	296 op = '%s.py' % self.toolname # new name
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	297 outpiname = os.path.join(tdir,op) # path for the tool tarball
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	298 pyin = os.path.basename(self.pyfile) # our name - we rewrite ourselves (TM)
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	299 notes = ['# %s - a self annotated version of %s generated by running %s\n' % (op,pyin,pyin),]
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	300 notes.append('# to make a new Galaxy tool called %s\n' % self.toolname)
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	301 notes.append('# User %s at %s\n' % (self.opts.user_email,timenow()))
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	302 pi = open(self.pyfile,'r').readlines() # our code becomes new tool wrapper (!) - first Galaxy worm
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	303 notes += pi
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	304 outpi = open(outpiname,'w')
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	305 outpi.write(''.join(notes))
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	306 outpi.write('\n')
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	307 outpi.close()
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	308 stname = os.path.join(tdir,self.sfile)
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	309 if not os.path.exists(stname):
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	310 shutil.copyfile(self.sfile, stname)
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	311 xtname = os.path.join(tdir,self.xmlfile)
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	312 if not os.path.exists(xtname):
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	313 shutil.copyfile(self.xmlfile,xtname)
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	314 tarpath = "%s.gz" % self.toolname
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	315 tar = tarfile.open(tarpath, "w:gz")
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	316 tar.add(tdir,arcname=self.toolname)
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	317 tar.close()
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	318 shutil.copyfile(tarpath,self.opts.new_tool)
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	319 shutil.rmtree(tdir)
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	320 ## TODO: replace with optional direct upload to local toolshed?
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	321 return retval
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	322
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	323 def compressPDF(self,inpdf=None,thumbformat='png'):
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	324 """need absolute path to pdf
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	325 """
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	326 assert os.path.isfile(inpdf), "## Input %s supplied to %s compressPDF not found" % (inpdf,self.myName)
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	327 hf,hlog = tempfile.mkstemp(suffix="%s.log" % self.toolname)
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	328 sto = open(hlog,'w')
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	329 outpdf = '%s_compressed' % inpdf
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	330 cl = ["gs", "-sDEVICE=pdfwrite", "-dNOPAUSE", "-dBATCH", "-sOutputFile=%s" % outpdf,inpdf]
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	331 x = subprocess.Popen(cl,stdout=sto,stderr=sto,cwd=self.opts.output_dir)
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	332 retval1 = x.wait()
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	333 if retval1 == 0:
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	334 os.unlink(inpdf)
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	335 shutil.move(outpdf,inpdf)
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	336 outpng = '%s.%s' % (os.path.splitext(inpdf)[0],thumbformat)
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	337 cl2 = ['convert', inpdf, outpng]
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	338 x = subprocess.Popen(cl2,stdout=sto,stderr=sto,cwd=self.opts.output_dir)
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	339 retval2 = x.wait()
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	340 sto.close()
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	341 retval = retval1 or retval2
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	342 return retval
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	343
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	344
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	345 def getfSize(self,fpath,outpath):
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	346 """
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	347 format a nice file size string
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	348 """
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	349 size = ''
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	350 fp = os.path.join(outpath,fpath)
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	351 if os.path.isfile(fp):
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	352 size = '0 B'
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	353 n = float(os.path.getsize(fp))
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	354 if n > 2**20:
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	355 size = '%1.1f MB' % (n/2**20)
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	356 elif n > 2**10:
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	357 size = '%1.1f KB)' % (n/2**10)
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	358 elif n > 0:
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	359 size = '%d B' % (int(n))
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	360 return size
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	361
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	362 def makeHtml(self):
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	363 """ Create an HTML file content to list all the artifacts found in the output_dir
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	364 """
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	365
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	366 galhtmlprefix = """<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	367 <html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	368 <head> <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	369 <meta name="generator" content="Galaxy %s tool output - see http://g2.trac.bx.psu.edu/" />
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	370 <title></title>
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	371 <link rel="stylesheet" href="/static/style/base.css" type="text/css" />
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	372 </head>
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	373 <body>
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	374 <div class="toolFormBody">
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	375 """
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	376 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/>"""
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	377 galhtmlpostfix = """</div></body></html>\n"""
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	378
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	379 flist = os.listdir(self.opts.output_dir)
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	380 flist = [x for x in flist if x <> 'Rplots.pdf']
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	381 flist.sort()
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	382 html = []
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	383 html.append(galhtmlprefix % progname)
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	384 html.append('<div class="infomessage">Galaxy Tool "%s" run at %s</div><br/>' % (self.toolname,timenow()))
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	385 fhtml = []
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	386 if len(flist) > 0:
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	387 pdflist = []
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	388 npdf = len([x for x in flist if os.path.splitext(x)[-1].lower() == '.pdf'])
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	389 nacross = 1
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	390 if npdf > 0:
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	391 nacross = int(round(math.log(npdf,2)))
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	392 nacross = max(1,nacross)
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	393 width = min(400,int(1200/nacross))
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	394 for rownum,fname in enumerate(flist):
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	395 dname,e = os.path.splitext(fname)
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	396 sfsize = self.getfSize(fname,self.opts.output_dir)
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	397 if e.lower() == '.pdf' : # compress and make a thumbnail
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	398 thumb = '%s.%s' % (dname,self.thumbformat)
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	399 pdff = os.path.join(self.opts.output_dir,fname)
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	400 retval = self.compressPDF(inpdf=pdff,thumbformat=self.thumbformat)
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	401 if retval == 0:
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	402 pdflist.append((fname,thumb))
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	403 if (rownum+1) % 2 == 0:
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	404 fhtml.append('<tr class="odd_row"><td><a href="%s">%s</a></td><td>%s</td></tr>' % (fname,fname,sfsize))
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	405 else:
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	406 fhtml.append('<tr><td><a href="%s">%s</a></td><td>%s</td></tr>' % (fname,fname,sfsize))
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	407 ntogo = nacross # counter for table row padding with empty cells
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	408 if len(pdflist) > 0:
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	409 html.append('<div><table class="simple" cellpadding="2" cellspacing="2">\n<tr>')
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	410 for i,paths in enumerate(pdflist):
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	411 fname,thumb = paths
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	412 s= """<td><a href="%s"><img src="%s" title="Click to download a PDF of %s" hspace="5" width="%d"
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	413 alt="Image called %s"/></a></td>\n""" % (fname,thumb,fname,width,fname)
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	414 if ((i+1) % nacross == 0):
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	415 s += '</tr>\n'
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	416 ntogo = 0
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	417 if i < (npdf - 1): # more to come
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	418 s += '<tr>'
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	419 ntogo = nacross
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	420 else:
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	421 ntogo -= 1
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	422 html.append(s)
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	423 if html[-1].strip().endswith('</tr>'):
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	424 html.append('</table></div>\n')
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	425 else:
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	426 if ntogo > 0: # pad
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	427 html.append('<td> </td>'*ntogo)
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	428 html.append('</tr></table></div>\n')
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	429 if len(fhtml) > 0:
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	430 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')
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	431 fhtml.append('</table></div><br/>')
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	432 html += fhtml # add all non-pdf files to the end of the display
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	433 else:
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	434 html.append('<div class="warningmessagelarge">### Error - %s returned no files - please confirm that parameters are sane</div>' % self.opts.interpreter)
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	435 rlog = open(self.tlog,'r').readlines()
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	436 rlog = [x for x in rlog if x.strip() > '']
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	437 if len(rlog) > 1:
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	438 html.append('<div class="toolFormTitle">%s log</div><pre>\n' % self.opts.interpreter)
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	439 html += rlog
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	440 html.append('</pre>\n')
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	441 html.append(galhtmlattr % (self.toolname))
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	442 html.append(galhtmlpostfix)
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	443 htmlf = file(self.opts.output_html,'w')
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	444 htmlf.write('\n'.join(html))
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	445 htmlf.write('\n')
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	446 htmlf.close()
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	447 self.html = html
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	448
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	449
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	450 def run(self):
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	451 """
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	452 scripts must be small enough not to fill the pipe!
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	453 """
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	454 if self.treatbashSpecial and self.opts.interpreter in ['bash','sh']:
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	455 retval = self.runBash()
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	456 else:
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	457 if self.opts.output_dir:
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	458 sto = open(self.tlog,'w')
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	459 sto.write('## Toolfactory generated command line = %s\n' % ' '.join(self.cl))
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	460 sto.flush()
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	461 p = subprocess.Popen(self.cl,shell=False,stdout=sto,stderr=sto,stdin=subprocess.PIPE,cwd=self.opts.output_dir)
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	462 else:
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	463 p = subprocess.Popen(self.cl,shell=False,stdin=subprocess.PIPE)
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	464 p.stdin.write(self.script)
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	465 p.stdin.close()
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	466 retval = p.wait()
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	467 if self.opts.output_dir:
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	468 sto.close()
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	469 if self.opts.make_HTML:
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	470 self.makeHtml()
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	471 return retval
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	472
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	473 def runBash(self):
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	474 """
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	475 cannot use - for bash so use self.sfile
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	476 """
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	477 if self.opts.output_dir:
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	478 s = '## Toolfactory generated command line = %s\n' % ' '.join(self.cl)
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	479 sto = open(self.tlog,'w')
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	480 sto.write(s)
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	481 sto.flush()
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	482 p = subprocess.Popen(self.cl,shell=False,stdout=sto,stderr=sto,cwd=self.opts.output_dir)
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	483 else:
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	484 p = subprocess.Popen(self.cl,shell=False)
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	485 retval = p.wait()
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	486 if self.opts.output_dir:
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	487 sto.close()
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	488 if self.opts.make_HTML:
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	489 self.makeHtml()
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	490 return retval
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	491
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	492
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	493 def main():
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	494 u = """
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	495 This is a Galaxy wrapper. It expects to be called by a special purpose tool.xml as:
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	496 <command interpreter="python">rgBaseScriptWrapper.py --script_path "$scriptPath" --tool_name "foo" --interpreter "Rscript"
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	497 </command>
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	498 """
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	499 op = optparse.OptionParser()
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	500 a = op.add_option
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	501 a('--script_path',default=None)
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	502 a('--tool_name',default=None)
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	503 a('--interpreter',default=None)
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	504 a('--output_dir',default=None)
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	505 a('--output_html',default=None)
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	506 a('--input_tab',default="None")
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	507 a('--output_tab',default="None")
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	508 a('--user_email',default='Unknown')
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	509 a('--bad_user',default=None)
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	510 a('--make_Tool',default=None)
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	511 a('--make_HTML',default=None)
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	512 a('--help_text',default=None)
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	513 a('--tool_desc',default=None)
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	514 a('--new_tool',default=None)
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	515 a('--tool_version',default=None)
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	516 opts, args = op.parse_args()
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	517 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)
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	518 assert opts.tool_name,'## Tool Factory expects a tool name - eg --tool_name=DESeq'
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	519 assert opts.interpreter,'## Tool Factory wrapper expects an interpreter - eg --interpreter=Rscript'
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	520 assert os.path.isfile(opts.script_path),'## Tool Factory wrapper expects a script path - eg --script_path=foo.R'
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	521 if opts.output_dir:
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	522 try:
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	523 os.makedirs(opts.output_dir)
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	524 except:
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	525 pass
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	526 r = ScriptRunner(opts)
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	527 if opts.make_Tool:
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	528 retcode = r.makeTooltar()
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	529 else:
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	530 retcode = r.run()
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	531 os.unlink(r.sfile)
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	532 if retcode:
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	533 sys.exit(retcode) # indicate failure to job runner
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	534
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	535
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	536 if __name__ == "__main__":
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	537 main()
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	538
f1dae673ec8b Uploaded corrected version as 0.9 to trigger updates for those with the older version fubar parents: diff changeset	539

Mercurial > repos > fubar > toolfactory

annotate fubar-galaxytoolfactory-f726a966e35d/rgToolFactory.py @ 20:b9892d7f0983 draft default tip