fubar/brokenandnotdeletablebyowneroradmin: rgToolFactory.py annotate

annotate rgToolFactory.py @ 25:8cc3f3c0e539 default tip

Now uses admin_users to check that the user is authorized to run this tool Docs adjusted.

author	Ross Lazarus <ross.lazarus@gmail.com>
date	Wed, 06 Jun 2012 14:16:25 +1000
parents	0ee2b06ea304
children

rev	line source
10 71f2ac0eee95 Updated tarball with some test material - still need code generated... ross lazarus ross.lazarus@gmail.com parents: 9 diff changeset	1 # rgToolFactory.py
19 a87a262220a4 Adding proof of concept for optional output formats. ross lazarus ross.lazarus@gmail.com parents: 15 diff changeset	2 # https://bitbucket.org/fubar/galaxytoolfactory/wiki/Home
a87a262220a4 Adding proof of concept for optional output formats. ross lazarus ross.lazarus@gmail.com parents: 15 diff changeset	3
a87a262220a4 Adding proof of concept for optional output formats. ross lazarus ross.lazarus@gmail.com parents: 15 diff changeset	4 # this is a tool factory for simple scripts in python, R or whatever ails ye.
a87a262220a4 Adding proof of concept for optional output formats. ross lazarus ross.lazarus@gmail.com parents: 15 diff changeset	5 # you paste and run your script
a87a262220a4 Adding proof of concept for optional output formats. ross lazarus ross.lazarus@gmail.com parents: 15 diff changeset	6 # Only works for simple scripts that read one input from the history.
a87a262220a4 Adding proof of concept for optional output formats. ross lazarus ross.lazarus@gmail.com parents: 15 diff changeset	7 # Optionally can write one new history dataset,
a87a262220a4 Adding proof of concept for optional output formats. ross lazarus ross.lazarus@gmail.com parents: 15 diff changeset	8 # and optionally collect any number of outputs into links on an autogenerated HTML page.
a87a262220a4 Adding proof of concept for optional output formats. ross lazarus ross.lazarus@gmail.com parents: 15 diff changeset	9
a87a262220a4 Adding proof of concept for optional output formats. ross lazarus ross.lazarus@gmail.com parents: 15 diff changeset	10 # DO NOT install on a public or important site - please.
a87a262220a4 Adding proof of concept for optional output formats. ross lazarus ross.lazarus@gmail.com parents: 15 diff changeset	11
a87a262220a4 Adding proof of concept for optional output formats. ross lazarus ross.lazarus@gmail.com parents: 15 diff changeset	12 # installed generated tools are fine if the script is safe.
a87a262220a4 Adding proof of concept for optional output formats. ross lazarus ross.lazarus@gmail.com parents: 15 diff changeset	13 # They just run normally and their user cannot do anything unusually insecure
a87a262220a4 Adding proof of concept for optional output formats. ross lazarus ross.lazarus@gmail.com parents: 15 diff changeset	14 # but please, practice safe toolshed.
a87a262220a4 Adding proof of concept for optional output formats. ross lazarus ross.lazarus@gmail.com parents: 15 diff changeset	15 # Read the fucking code before you install any tool
a87a262220a4 Adding proof of concept for optional output formats. ross lazarus ross.lazarus@gmail.com parents: 15 diff changeset	16 # especially this one
a87a262220a4 Adding proof of concept for optional output formats. ross lazarus ross.lazarus@gmail.com parents: 15 diff changeset	17
a87a262220a4 Adding proof of concept for optional output formats. ross lazarus ross.lazarus@gmail.com parents: 15 diff changeset	18 # After you get the script working on some test data, you can
a87a262220a4 Adding proof of concept for optional output formats. ross lazarus ross.lazarus@gmail.com parents: 15 diff changeset	19 # optionally generate a toolshed compatible gzip file
a87a262220a4 Adding proof of concept for optional output formats. ross lazarus ross.lazarus@gmail.com parents: 15 diff changeset	20 # containing your script safely wrapped as an ordinary Galaxy script in your local toolshed for
a87a262220a4 Adding proof of concept for optional output formats. ross lazarus ross.lazarus@gmail.com parents: 15 diff changeset	21 # safe and largely automated installation in a production Galaxy.
a87a262220a4 Adding proof of concept for optional output formats. ross lazarus ross.lazarus@gmail.com parents: 15 diff changeset	22
a87a262220a4 Adding proof of concept for optional output formats. ross lazarus ross.lazarus@gmail.com parents: 15 diff changeset	23 # If you opt for an HTML output, you get all the script outputs arranged
a87a262220a4 Adding proof of concept for optional output formats. ross lazarus ross.lazarus@gmail.com parents: 15 diff changeset	24 # as a single Html history item - all output files are linked, thumbnails for all the pdfs.
a87a262220a4 Adding proof of concept for optional output formats. ross lazarus ross.lazarus@gmail.com parents: 15 diff changeset	25 # Ugly but really inexpensive.
a87a262220a4 Adding proof of concept for optional output formats. ross lazarus ross.lazarus@gmail.com parents: 15 diff changeset	26 #
a87a262220a4 Adding proof of concept for optional output formats. ross lazarus ross.lazarus@gmail.com parents: 15 diff changeset	27 # Patches appreciated please.
10 71f2ac0eee95 Updated tarball with some test material - still need code generated... ross lazarus ross.lazarus@gmail.com parents: 9 diff changeset	28 #
19 a87a262220a4 Adding proof of concept for optional output formats. ross lazarus ross.lazarus@gmail.com parents: 15 diff changeset	29 #
a87a262220a4 Adding proof of concept for optional output formats. ross lazarus ross.lazarus@gmail.com parents: 15 diff changeset	30 # long route to June 2012 product
a87a262220a4 Adding proof of concept for optional output formats. ross lazarus ross.lazarus@gmail.com parents: 15 diff changeset	31 # Behold the awesome power of Galaxy and the toolshed with the tool factory binds to bind them
a87a262220a4 Adding proof of concept for optional output formats. ross lazarus ross.lazarus@gmail.com parents: 15 diff changeset	32 # derived from an integrated script model
a87a262220a4 Adding proof of concept for optional output formats. ross lazarus ross.lazarus@gmail.com parents: 15 diff changeset	33 # called rgBaseScriptWrapper.py
a87a262220a4 Adding proof of concept for optional output formats. ross lazarus ross.lazarus@gmail.com parents: 15 diff changeset	34 # Note to the unwary:
a87a262220a4 Adding proof of concept for optional output formats. ross lazarus ross.lazarus@gmail.com parents: 15 diff changeset	35 # This tool allows arbitrary scripting on your Galaxy as the Galaxy user
a87a262220a4 Adding proof of concept for optional output formats. ross lazarus ross.lazarus@gmail.com parents: 15 diff changeset	36 # There is nothing stopping a malicious user doing whatever they choose
a87a262220a4 Adding proof of concept for optional output formats. ross lazarus ross.lazarus@gmail.com parents: 15 diff changeset	37 # Extremely dangerous!!
a87a262220a4 Adding proof of concept for optional output formats. ross lazarus ross.lazarus@gmail.com parents: 15 diff changeset	38 # Totally insecure. So, trusted users only
a87a262220a4 Adding proof of concept for optional output formats. ross lazarus ross.lazarus@gmail.com parents: 15 diff changeset	39 #
a87a262220a4 Adding proof of concept for optional output formats. ross lazarus ross.lazarus@gmail.com parents: 15 diff changeset	40 # preferred model is a developer using their throw away workstation instance - ie a private site.
25 8cc3f3c0e539 Now uses admin_users to check that the user is authorized to run this tool Ross Lazarus <ross.lazarus@gmail.com> parents: 21 diff changeset	41 # no real risk. The universe_wsgi.ini admin_users string is checked - only admin users are permitted to run this tool.
19 a87a262220a4 Adding proof of concept for optional output formats. ross lazarus ross.lazarus@gmail.com parents: 15 diff changeset	42 #
a87a262220a4 Adding proof of concept for optional output formats. ross lazarus ross.lazarus@gmail.com parents: 15 diff changeset	43
a87a262220a4 Adding proof of concept for optional output formats. ross lazarus ross.lazarus@gmail.com parents: 15 diff changeset	44 #
a87a262220a4 Adding proof of concept for optional output formats. ross lazarus ross.lazarus@gmail.com parents: 15 diff changeset	45 # copyright ross lazarus (ross stop lazarus at gmail stop com) May 2012
7 7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	46 #
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	47 # all rights reserved
19 a87a262220a4 Adding proof of concept for optional output formats. ross lazarus ross.lazarus@gmail.com parents: 15 diff changeset	48 # Licensed under the LGPL if you want to improve it, feel free https://bitbucket.org/fubar/galaxytoolfactory/wiki/Home
7 7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	49
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	50 import sys
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	51 import shutil
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	52 import subprocess
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	53 import os
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	54 import time
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	55 import tempfile
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	56 import optparse
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	57 import tarfile
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	58 import re
8 220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	59 import shutil
220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	60
7 7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	61 progname = os.path.split(sys.argv[0])[1]
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	62 myversion = 'V000.1 May 2012'
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	63 verbose = False
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	64 debug = False
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	65
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	66
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	67 def timenow():
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	68 """return current time as a string
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	69 """
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	70 return time.strftime('%d/%m/%Y %H:%M:%S', time.localtime(time.time()))
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	71 # characters that are allowed but need to be escaped
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	72
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	73 class ScriptRunner:
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	74 """class is a wrapper for an arbitrary script
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	75 """
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	76
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	77 def __init__(self,opts=None):
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	78 """
19 a87a262220a4 Adding proof of concept for optional output formats. ross lazarus ross.lazarus@gmail.com parents: 15 diff changeset	79 cleanup inputs, setup some outputs
9 e09c76551bed Can run without input or output or either.. ross lazarus ross.lazarus@gmail.com parents: 8 diff changeset	80
7 7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	81 """
8 220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	82 if opts.output_dir: # simplify for the tool tarball
220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	83 os.chdir(opts.output_dir)
7 7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	84 self.thumbformat = 'jpg'
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	85 self.opts = opts
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	86 self.toolname = re.sub('[^a-zA-Z0-9_]+', '', opts.tool_name)
8 220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	87 self.toolid = self.toolname
7 7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	88 s = open(self.opts.script_path,'r').read()
9 e09c76551bed Can run without input or output or either.. ross lazarus ross.lazarus@gmail.com parents: 8 diff changeset	89 self.script = s
8 220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	90 self.myname = sys.argv[0] # get our name because we write ourselves out as a tool later
220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	91 self.pyfile = self.myname # crude but efficient - the cruft won't hurt much
220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	92 self.xmlfile = '%s.xml' % self.toolname
7 7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	93 self.sfile = '%s.%s' % (self.toolname,opts.interpreter)
12 d12728e33c3d Changed to deliver a gz file - requires a new datatypes_conf.xml entry: ross lazarus ross.lazarus@gmail.com parents: 10 diff changeset	94 if opts.output_dir: # may not want these complexities
7 7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	95 self.tlog = os.path.join(opts.output_dir,"%s_runner.log" % self.toolname)
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	96 artifactpath = os.path.join(opts.output_dir,'%s_run.script' % self.toolname)
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	97 artifact = open(artifactpath,'w')
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	98 artifact.write(self.script)
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	99 artifact.write('\n')
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	100 artifact.close()
12 d12728e33c3d Changed to deliver a gz file - requires a new datatypes_conf.xml entry: ross lazarus ross.lazarus@gmail.com parents: 10 diff changeset	101 if opts.make_Tool: # need this code and the user script for the tarball
9 e09c76551bed Can run without input or output or either.. ross lazarus ross.lazarus@gmail.com parents: 8 diff changeset	102 localscript = open(self.sfile,'w')
e09c76551bed Can run without input or output or either.. ross lazarus ross.lazarus@gmail.com parents: 8 diff changeset	103 localscript.write(self.script)
e09c76551bed Can run without input or output or either.. ross lazarus ross.lazarus@gmail.com parents: 8 diff changeset	104 localscript.close()
e09c76551bed Can run without input or output or either.. ross lazarus ross.lazarus@gmail.com parents: 8 diff changeset	105 shutil.copyfile(self.myname,'%s.py' % self.toolname) # for tool and for user
7 7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	106 self.cl = []
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	107 self.html = []
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	108 a = self.cl.append
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	109 a(opts.interpreter)
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	110 a('-') # use stdin
12 d12728e33c3d Changed to deliver a gz file - requires a new datatypes_conf.xml entry: ross lazarus ross.lazarus@gmail.com parents: 10 diff changeset	111 a(opts.input_tab)
d12728e33c3d Changed to deliver a gz file - requires a new datatypes_conf.xml entry: ross lazarus ross.lazarus@gmail.com parents: 10 diff changeset	112 a(opts.output_tab)
8 220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	113 self.outFormats = 'tabular' # TODO make this an option at tool generation time
220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	114 self.inputFormats = 'tabular' # TODO make this an option at tool generation time
20 3f58115c6c5b Getting ready to implement the test generator. ross lazarus ross.lazarus@gmail.com parents: 19 diff changeset	115 self.test1Input = 'test1_input.xls'
3f58115c6c5b Getting ready to implement the test generator. ross lazarus ross.lazarus@gmail.com parents: 19 diff changeset	116 self.test1Output = 'test1_output.xls'
3f58115c6c5b Getting ready to implement the test generator. ross lazarus ross.lazarus@gmail.com parents: 19 diff changeset	117 self.test1HTML = 'test1_output.html'
8 220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	118
220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	119 def makeXML(self):
220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	120 """
220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	121 Create a Galaxy xml tool wrapper for the new script as a string to write out
19 a87a262220a4 Adding proof of concept for optional output formats. ross lazarus ross.lazarus@gmail.com parents: 15 diff changeset	122 fixme - use templating or something less fugly than this example of what we produce
13 7725e4ab27e1 Adding tests - problem to find the script - needs a fixed string somewhere. ross lazarus ross.lazarus@gmail.com parents: 12 diff changeset	123
7725e4ab27e1 Adding tests - problem to find the script - needs a fixed string somewhere. ross lazarus ross.lazarus@gmail.com parents: 12 diff changeset	124 <tool id="reverse" name="reverse" version="0.01">
7725e4ab27e1 Adding tests - problem to find the script - needs a fixed string somewhere. ross lazarus ross.lazarus@gmail.com parents: 12 diff changeset	125 <description>a tabular file</description>
7725e4ab27e1 Adding tests - problem to find the script - needs a fixed string somewhere. ross lazarus ross.lazarus@gmail.com parents: 12 diff changeset	126 <command interpreter="python">
7725e4ab27e1 Adding tests - problem to find the script - needs a fixed string somewhere. ross lazarus ross.lazarus@gmail.com parents: 12 diff changeset	127 reverse.py --script_path "$runMe" --interpreter "python"
7725e4ab27e1 Adding tests - problem to find the script - needs a fixed string somewhere. ross lazarus ross.lazarus@gmail.com parents: 12 diff changeset	128 --tool_name "reverse" --input_tab "$input1" --output_tab "$tab_file"
7725e4ab27e1 Adding tests - problem to find the script - needs a fixed string somewhere. ross lazarus ross.lazarus@gmail.com parents: 12 diff changeset	129 </command>
7725e4ab27e1 Adding tests - problem to find the script - needs a fixed string somewhere. ross lazarus ross.lazarus@gmail.com parents: 12 diff changeset	130 <inputs>
7725e4ab27e1 Adding tests - problem to find the script - needs a fixed string somewhere. ross lazarus ross.lazarus@gmail.com parents: 12 diff changeset	131 <param name="input1" type="data" format="tabular" label="Select a suitable input file from your history"/><param name="job_name" type="text" label="Supply a name for the outputs to remind you what they contain" value="reverse"/>
7725e4ab27e1 Adding tests - problem to find the script - needs a fixed string somewhere. ross lazarus ross.lazarus@gmail.com parents: 12 diff changeset	132
7725e4ab27e1 Adding tests - problem to find the script - needs a fixed string somewhere. ross lazarus ross.lazarus@gmail.com parents: 12 diff changeset	133 </inputs>
7725e4ab27e1 Adding tests - problem to find the script - needs a fixed string somewhere. ross lazarus ross.lazarus@gmail.com parents: 12 diff changeset	134 <outputs>
7725e4ab27e1 Adding tests - problem to find the script - needs a fixed string somewhere. ross lazarus ross.lazarus@gmail.com parents: 12 diff changeset	135 <data format="tabular" name="tab_file" label="${job_name}"/>
7725e4ab27e1 Adding tests - problem to find the script - needs a fixed string somewhere. ross lazarus ross.lazarus@gmail.com parents: 12 diff changeset	136
7725e4ab27e1 Adding tests - problem to find the script - needs a fixed string somewhere. ross lazarus ross.lazarus@gmail.com parents: 12 diff changeset	137 </outputs>
7725e4ab27e1 Adding tests - problem to find the script - needs a fixed string somewhere. ross lazarus ross.lazarus@gmail.com parents: 12 diff changeset	138 <help>
7725e4ab27e1 Adding tests - problem to find the script - needs a fixed string somewhere. ross lazarus ross.lazarus@gmail.com parents: 12 diff changeset	139
7725e4ab27e1 Adding tests - problem to find the script - needs a fixed string somewhere. ross lazarus ross.lazarus@gmail.com parents: 12 diff changeset	140 What it Does
7725e4ab27e1 Adding tests - problem to find the script - needs a fixed string somewhere. ross lazarus ross.lazarus@gmail.com parents: 12 diff changeset	141
7725e4ab27e1 Adding tests - problem to find the script - needs a fixed string somewhere. ross lazarus ross.lazarus@gmail.com parents: 12 diff changeset	142 Reverse the columns in a tabular file
7725e4ab27e1 Adding tests - problem to find the script - needs a fixed string somewhere. ross lazarus ross.lazarus@gmail.com parents: 12 diff changeset	143
7725e4ab27e1 Adding tests - problem to find the script - needs a fixed string somewhere. ross lazarus ross.lazarus@gmail.com parents: 12 diff changeset	144 </help>
7725e4ab27e1 Adding tests - problem to find the script - needs a fixed string somewhere. ross lazarus ross.lazarus@gmail.com parents: 12 diff changeset	145 <configfiles>
7725e4ab27e1 Adding tests - problem to find the script - needs a fixed string somewhere. ross lazarus ross.lazarus@gmail.com parents: 12 diff changeset	146 <configfile name="runMe">
7725e4ab27e1 Adding tests - problem to find the script - needs a fixed string somewhere. ross lazarus ross.lazarus@gmail.com parents: 12 diff changeset	147
7725e4ab27e1 Adding tests - problem to find the script - needs a fixed string somewhere. ross lazarus ross.lazarus@gmail.com parents: 12 diff changeset	148 # reverse order of columns in a tabular file
7725e4ab27e1 Adding tests - problem to find the script - needs a fixed string somewhere. ross lazarus ross.lazarus@gmail.com parents: 12 diff changeset	149 import sys
7725e4ab27e1 Adding tests - problem to find the script - needs a fixed string somewhere. ross lazarus ross.lazarus@gmail.com parents: 12 diff changeset	150 inp = sys.argv[1]
7725e4ab27e1 Adding tests - problem to find the script - needs a fixed string somewhere. ross lazarus ross.lazarus@gmail.com parents: 12 diff changeset	151 outp = sys.argv[2]
7725e4ab27e1 Adding tests - problem to find the script - needs a fixed string somewhere. ross lazarus ross.lazarus@gmail.com parents: 12 diff changeset	152 i = open(inp,'r')
7725e4ab27e1 Adding tests - problem to find the script - needs a fixed string somewhere. ross lazarus ross.lazarus@gmail.com parents: 12 diff changeset	153 o = open(outp,'w')
7725e4ab27e1 Adding tests - problem to find the script - needs a fixed string somewhere. ross lazarus ross.lazarus@gmail.com parents: 12 diff changeset	154 for row in i:
7725e4ab27e1 Adding tests - problem to find the script - needs a fixed string somewhere. ross lazarus ross.lazarus@gmail.com parents: 12 diff changeset	155 rs = row.rstrip().split('\t')
7725e4ab27e1 Adding tests - problem to find the script - needs a fixed string somewhere. ross lazarus ross.lazarus@gmail.com parents: 12 diff changeset	156 rs.reverse()
7725e4ab27e1 Adding tests - problem to find the script - needs a fixed string somewhere. ross lazarus ross.lazarus@gmail.com parents: 12 diff changeset	157 o.write('\t'.join(rs))
7725e4ab27e1 Adding tests - problem to find the script - needs a fixed string somewhere. ross lazarus ross.lazarus@gmail.com parents: 12 diff changeset	158 o.write('\n')
7725e4ab27e1 Adding tests - problem to find the script - needs a fixed string somewhere. ross lazarus ross.lazarus@gmail.com parents: 12 diff changeset	159 i.close()
7725e4ab27e1 Adding tests - problem to find the script - needs a fixed string somewhere. ross lazarus ross.lazarus@gmail.com parents: 12 diff changeset	160 o.close()
7725e4ab27e1 Adding tests - problem to find the script - needs a fixed string somewhere. ross lazarus ross.lazarus@gmail.com parents: 12 diff changeset	161
7725e4ab27e1 Adding tests - problem to find the script - needs a fixed string somewhere. ross lazarus ross.lazarus@gmail.com parents: 12 diff changeset	162
7725e4ab27e1 Adding tests - problem to find the script - needs a fixed string somewhere. ross lazarus ross.lazarus@gmail.com parents: 12 diff changeset	163 </configfile>
7725e4ab27e1 Adding tests - problem to find the script - needs a fixed string somewhere. ross lazarus ross.lazarus@gmail.com parents: 12 diff changeset	164 </configfiles>
7725e4ab27e1 Adding tests - problem to find the script - needs a fixed string somewhere. ross lazarus ross.lazarus@gmail.com parents: 12 diff changeset	165 </tool>
7725e4ab27e1 Adding tests - problem to find the script - needs a fixed string somewhere. ross lazarus ross.lazarus@gmail.com parents: 12 diff changeset	166
8 220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	167 """
220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	168 newXML="""<tool id="%(toolid)s" name="%(toolname)s" version="0.01">
220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	169 %(tooldesc)s
220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	170 %(command)s
220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	171 <inputs>
220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	172 %(inputs)s
220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	173 </inputs>
220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	174 <outputs>
220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	175 %(outputs)s
220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	176 </outputs>
220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	177 <help>
220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	178 %(help)s
220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	179 </help>
220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	180 <configfiles>
220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	181 <configfile name="runMe">
220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	182 %(script)s
220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	183 </configfile>
220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	184 </configfiles>
220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	185 </tool>""" # needs a dict with toolname, toolid, interpreter, scriptname, command, inputs as a multi line string ready to write, outputs ditto, help ditto
220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	186
220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	187 newCommand="""<command interpreter="python">
220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	188 %(toolname)s.py --script_path "$runMe" --interpreter "%(interpreter)s"
220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	189 --tool_name "%(toolname)s" %(command_inputs)s %(command_outputs)s
220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	190 </command>""" # may NOT be an input or htmlout
13 7725e4ab27e1 Adding tests - problem to find the script - needs a fixed string somewhere. ross lazarus ross.lazarus@gmail.com parents: 12 diff changeset	191 tooltests = """<tests><test>
7725e4ab27e1 Adding tests - problem to find the script - needs a fixed string somewhere. ross lazarus ross.lazarus@gmail.com parents: 12 diff changeset	192 <param name="input1" value="%s" ftype="%s"/>
7725e4ab27e1 Adding tests - problem to find the script - needs a fixed string somewhere. ross lazarus ross.lazarus@gmail.com parents: 12 diff changeset	193 <param name="job_name" value="test1"/>
7725e4ab27e1 Adding tests - problem to find the script - needs a fixed string somewhere. ross lazarus ross.lazarus@gmail.com parents: 12 diff changeset	194 <param name="runMe" value="$runMe"/>
7725e4ab27e1 Adding tests - problem to find the script - needs a fixed string somewhere. ross lazarus ross.lazarus@gmail.com parents: 12 diff changeset	195 </test><tests>"""
8 220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	196 xdict = {}
9 e09c76551bed Can run without input or output or either.. ross lazarus ross.lazarus@gmail.com parents: 8 diff changeset	197 xdict['script'] = self.script # configfile is least painful way to embed script to avoid external dependencies
8 220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	198 if self.opts.help_text:
9 e09c76551bed Can run without input or output or either.. ross lazarus ross.lazarus@gmail.com parents: 8 diff changeset	199 xdict['help'] = open(self.opts.help_text,'r').read()
8 220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	200 else:
220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	201 xdict['help'] = 'Please ask the tool author for help as none was supplied at tool generation'
220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	202 if self.opts.tool_desc:
220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	203 xdict['tooldesc'] = '<description>%s</description>' % self.opts.tool_desc
220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	204 else:
220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	205 xdict['tooldesc'] = ''
9 e09c76551bed Can run without input or output or either.. ross lazarus ross.lazarus@gmail.com parents: 8 diff changeset	206 xdict['command_outputs'] = ''
e09c76551bed Can run without input or output or either.. ross lazarus ross.lazarus@gmail.com parents: 8 diff changeset	207 xdict['outputs'] = ''
12 d12728e33c3d Changed to deliver a gz file - requires a new datatypes_conf.xml entry: ross lazarus ross.lazarus@gmail.com parents: 10 diff changeset	208 if self.opts.input_tab <> 'None':
8 220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	209 xdict['command_inputs'] = '--input_tab "$input1"'
220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	210 xdict['inputs'] = '<param name="input1" type="data" format="%s" label="Select a suitable input file from your history"/>' % self.inputFormats
220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	211 else:
220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	212 xdict['command_inputs'] = '' # assume no input - eg a random data generator
220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	213 xdict['inputs'] = ''
220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	214 xdict['inputs'] += '<param name="job_name" type="text" label="Supply a name for the outputs to remind you what they contain" value="%s"/>\n' % self.toolname
220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	215 xdict['toolname'] = self.toolname
220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	216 xdict['toolid'] = self.toolid
220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	217 xdict['interpreter'] = self.opts.interpreter
220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	218 xdict['scriptname'] = self.sfile
220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	219 if self.opts.make_HTML:
9 e09c76551bed Can run without input or output or either.. ross lazarus ross.lazarus@gmail.com parents: 8 diff changeset	220 xdict['command_outputs'] += '--output_dir "$html_file.files_path" --output_html "$html_file" --make_HTML "yes"'
8 220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	221 xdict['outputs'] += '<data format="html" name="html_file" label="${job_name}.html"/>\n'
12 d12728e33c3d Changed to deliver a gz file - requires a new datatypes_conf.xml entry: ross lazarus ross.lazarus@gmail.com parents: 10 diff changeset	222 if self.opts.output_tab <> 'None':
8 220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	223 xdict['command_outputs'] += '--output_tab "$tab_file"'
220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	224 xdict['outputs'] += '<data format="%s" name="tab_file" label="${job_name}"/>\n' % self.outFormats
220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	225 xdict['command'] = newCommand % xdict
220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	226 xmls = newXML % xdict
220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	227 xf = open(self.xmlfile,'w')
220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	228 xf.write(xmls)
220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	229 xf.write('\n')
220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	230 xf.close()
220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	231 # ready for the tarball
220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	232
7 7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	233
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	234 def makeTooltar(self):
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	235 """
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	236 a tool is a gz tarball with eg
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	237 /toolname/tool.xml /toolname/tool.py /toolname/test-data/test1_in.foo ...
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	238 """
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	239 retval = self.run()
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	240 if retval:
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	241 print >> sys.stderr,'## Run failed. Cannot build yet. Please fix and retry'
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	242 sys.exit(1)
8 220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	243 self.makeXML()
220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	244 tdir = self.toolname
220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	245 os.mkdir(tdir)
12 d12728e33c3d Changed to deliver a gz file - requires a new datatypes_conf.xml entry: ross lazarus ross.lazarus@gmail.com parents: 10 diff changeset	246 if self.opts.input_tab <> 'None': # we may have test data?
10 71f2ac0eee95 Updated tarball with some test material - still need code generated... ross lazarus ross.lazarus@gmail.com parents: 9 diff changeset	247 testdir = os.path.join(tdir,'test-data')
71f2ac0eee95 Updated tarball with some test material - still need code generated... ross lazarus ross.lazarus@gmail.com parents: 9 diff changeset	248 os.mkdir(testdir) # make tests directory
21 0ee2b06ea304 fix destination names of test files to match test generator schema ross lazarus ross.lazarus@gmail.com parents: 20 diff changeset	249 shutil.copyfile(self.opts.input_tab,os.path.join(testdir,self.test1Input))
12 d12728e33c3d Changed to deliver a gz file - requires a new datatypes_conf.xml entry: ross lazarus ross.lazarus@gmail.com parents: 10 diff changeset	250 if self.opts.output_tab <> 'None':
21 0ee2b06ea304 fix destination names of test files to match test generator schema ross lazarus ross.lazarus@gmail.com parents: 20 diff changeset	251 shutil.copyfile(self.opts.output_tab,os.path.join(testdir,self.test1Output))
10 71f2ac0eee95 Updated tarball with some test material - still need code generated... ross lazarus ross.lazarus@gmail.com parents: 9 diff changeset	252 if self.opts.make_HTML:
21 0ee2b06ea304 fix destination names of test files to match test generator schema ross lazarus ross.lazarus@gmail.com parents: 20 diff changeset	253 shutil.copyfile(self.opts.output_html,os.path.join(testdir,self.test1HTML))
12 d12728e33c3d Changed to deliver a gz file - requires a new datatypes_conf.xml entry: ross lazarus ross.lazarus@gmail.com parents: 10 diff changeset	254 if self.opts.output_dir:
d12728e33c3d Changed to deliver a gz file - requires a new datatypes_conf.xml entry: ross lazarus ross.lazarus@gmail.com parents: 10 diff changeset	255 shutil.copyfile(self.tlog,os.path.join(testdir,'test1_out.log'))
8 220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	256 shutil.copyfile(self.xmlfile,os.path.join(tdir,self.xmlfile))
220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	257 shutil.copyfile(self.pyfile,os.path.join(tdir,'%s.py' % self.toolname))
220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	258 shutil.copyfile(self.sfile,os.path.join(tdir,self.sfile))
220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	259 tarpath = "%s.gz" % self.toolname
7 7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	260 tar = tarfile.open(tarpath, "w:gz")
8 220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	261 tar.add(tdir,arcname=self.toolname)
7 7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	262 tar.close()
12 d12728e33c3d Changed to deliver a gz file - requires a new datatypes_conf.xml entry: ross lazarus ross.lazarus@gmail.com parents: 10 diff changeset	263 shutil.copy(tarpath,self.opts.new_tool)
8 220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	264 shutil.rmtree(tdir)
220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	265 ## TODO: replace with optional direct upload to local toolshed?
7 7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	266 return retval
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	267
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	268 def compressPDF(self,inpdf=None,thumbformat='png'):
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	269 """need absolute path to pdf
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	270 """
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	271 assert os.path.isfile(inpdf), "## Input %s supplied to %s compressPDF not found" % (inpdf,self.myName)
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	272 hf,hlog = tempfile.mkstemp(suffix="%s.log" % self.toolname)
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	273 sto = open(hlog,'w')
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	274 outpdf = '%s_compressed' % inpdf
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	275 cl = ["gs", "-sDEVICE=pdfwrite", "-dNOPAUSE", "-dBATCH", "-sOutputFile=%s" % outpdf,inpdf]
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	276 x = subprocess.Popen(cl,stdout=sto,stderr=sto,cwd=self.opts.output_dir)
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	277 retval1 = x.wait()
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	278 if retval1 == 0:
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	279 os.unlink(inpdf)
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	280 shutil.move(outpdf,inpdf)
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	281 outpng = '%s.%s' % (os.path.splitext(inpdf)[0],thumbformat)
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	282 cl2 = ['convert', inpdf, outpng]
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	283 x = subprocess.Popen(cl2,stdout=sto,stderr=sto,cwd=self.opts.output_dir)
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	284 retval2 = x.wait()
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	285 sto.close()
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	286 retval = retval1 or retval2
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	287 return retval
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	288
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	289
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	290 def getfSize(self,fpath,outpath):
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	291 """
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	292 format a nice file size string
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	293 """
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	294 size = ''
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	295 fp = os.path.join(outpath,fpath)
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	296 if os.path.isfile(fp):
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	297 n = float(os.path.getsize(fp))
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	298 if n > 2**20:
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	299 size = ' (%1.1f MB)' % (n/2**20)
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	300 elif n > 2**10:
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	301 size = ' (%1.1f KB)' % (n/2**10)
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	302 elif n > 0:
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	303 size = ' (%d B)' % (int(n))
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	304 return size
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	305
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	306 def makeHtml(self):
8 220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	307 """ Create an HTML file content to list all the artefacts found in the output_dir
220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	308 """
220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	309
220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	310 galhtmlprefix = """<?xml version="1.0" encoding="utf-8" ?>
220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	311 <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	312 <html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	313 <head> <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	314 <meta name="generator" content="Galaxy %s tool output - see http://g2.trac.bx.psu.edu/" />
220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	315 <title></title>
220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	316 <link rel="stylesheet" href="/static/style/base.css" type="text/css" />
220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	317 </head>
220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	318 <body>
220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	319 <div class="document">
220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	320 """
19 a87a262220a4 Adding proof of concept for optional output formats. ross lazarus ross.lazarus@gmail.com parents: 15 diff changeset	321 galhtmlattr = """<hr/><b><a href="https://bitbucket.org/fubar/galaxytoolfactory/overview">Galaxy Tool Factory Script Wrapper</a> tool output %s run at %s</b><br/>"""
8 220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	322 galhtmlpostfix = """</div></body></html>\n"""
220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	323
220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	324 flist = os.listdir(self.opts.output_dir)
220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	325 flist = [x for x in flist if x <> 'Rplots.pdf']
220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	326 flist.sort()
220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	327 html = [galhtmlprefix % progname,]
220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	328 html.append('<h2>Galaxy %s outputs run at %s</h2><br/>\n' % (self.toolname,timenow()))
220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	329 fhtml = []
220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	330 if len(flist) > 0:
220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	331 html.append('<table cellpadding="3" cellspacing="3">\n')
220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	332 for fname in flist:
7 7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	333 dname,e = os.path.splitext(fname)
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	334 sfsize = self.getfSize(fname,self.opts.output_dir)
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	335 if e.lower() == '.pdf' : # compress and make a thumbnail
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	336 thumb = '%s.%s' % (dname,self.thumbformat)
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	337 pdff = os.path.join(self.opts.output_dir,fname)
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	338 retval = self.compressPDF(inpdf=pdff,thumbformat=self.thumbformat)
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	339 if retval == 0:
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	340 s= '<tr><td><a href="%s"><img src="%s" title="Click to download a PDF of %s" hspace="10" width="600"></a></td></tr>\n' % (fname,thumb,fname)
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	341 html.append(s)
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	342 fhtml.append('<li><a href="%s">%s %s</a></li>' % (fname,fname,sfsize))
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	343 else:
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	344 fhtml.append('<li><a href="%s">%s %s</a></li>' % (fname,fname,sfsize))
8 220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	345 html.append('</table>\n')
220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	346 if len(fhtml) > 0:
220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	347 fhtml.insert(0,'<ul>')
9 e09c76551bed Can run without input or output or either.. ross lazarus ross.lazarus@gmail.com parents: 8 diff changeset	348 fhtml.append('</ul><br/>')
8 220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	349 html += fhtml # add all non-pdf files to the end of the display
220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	350 else:
220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	351 html.append('<h2>### Error - %s returned no files - please confirm that parameters are sane</h1>' % self.opts.interpreter)
9 e09c76551bed Can run without input or output or either.. ross lazarus ross.lazarus@gmail.com parents: 8 diff changeset	352 html.append('<h3>%s log follows below</h3><hr/><pre><br/>\n' % self.opts.interpreter)
8 220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	353 rlog = open(self.tlog,'r').readlines()
220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	354 html += rlog
9 e09c76551bed Can run without input or output or either.. ross lazarus ross.lazarus@gmail.com parents: 8 diff changeset	355 html.append('<br/>%s CL = %s<br/>\n' % (self.toolname,' '.join(sys.argv)))
8 220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	356 html.append('</pre>\n')
220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	357 html.append(galhtmlattr % (progname,timenow()))
220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	358 html.append(galhtmlpostfix)
220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	359 htmlf = file(self.opts.output_html,'w')
220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	360 htmlf.write('\n'.join(html))
220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	361 htmlf.write('\n')
220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	362 htmlf.close()
220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	363 self.html = html
7 7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	364
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	365
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	366 def run(self):
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	367 """
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	368 """
12 d12728e33c3d Changed to deliver a gz file - requires a new datatypes_conf.xml entry: ross lazarus ross.lazarus@gmail.com parents: 10 diff changeset	369 if self.opts.output_dir:
7 7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	370 sto = open(self.tlog,'w')
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	371 p = subprocess.Popen(' '.join(self.cl),shell=True,stdout=sto,stderr=sto,stdin=subprocess.PIPE,cwd=self.opts.output_dir)
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	372 else:
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	373 p = subprocess.Popen(' '.join(self.cl),shell=True,stdin=subprocess.PIPE)
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	374 p.stdin.write(self.script)
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	375 p.stdin.close()
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	376 retval = p.wait()
12 d12728e33c3d Changed to deliver a gz file - requires a new datatypes_conf.xml entry: ross lazarus ross.lazarus@gmail.com parents: 10 diff changeset	377 if self.opts.output_dir:
7 7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	378 sto.close()
12 d12728e33c3d Changed to deliver a gz file - requires a new datatypes_conf.xml entry: ross lazarus ross.lazarus@gmail.com parents: 10 diff changeset	379 if self.opts.make_HTML:
7 7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	380 self.makeHtml()
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	381 return retval
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	382
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	383
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	384 def main():
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	385 u = """
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	386 This is a Galaxy wrapper. It expects to be called by a special purpose tool.xml as:
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	387 <command interpreter="python">rgBaseScriptWrapper.py --script_path "$scriptPath" --tool_name "foo" --interpreter "Rscript"
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	388 </command>
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	389 """
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	390 op = optparse.OptionParser()
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	391 a = op.add_option
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	392 a('--script_path',default=None)
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	393 a('--tool_name',default=None)
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	394 a('--interpreter',default=None)
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	395 a('--output_dir',default=None)
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	396 a('--output_html',default=None)
12 d12728e33c3d Changed to deliver a gz file - requires a new datatypes_conf.xml entry: ross lazarus ross.lazarus@gmail.com parents: 10 diff changeset	397 a('--input_tab',default="None")
d12728e33c3d Changed to deliver a gz file - requires a new datatypes_conf.xml entry: ross lazarus ross.lazarus@gmail.com parents: 10 diff changeset	398 a('--output_tab',default="None")
7 7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	399 a('--user_email',default=None)
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	400 a('--bad_user',default=None)
8 220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	401 a('--make_Tool',default=None)
220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	402 a('--make_HTML',default=None)
220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	403 a('--help_text',default=None)
220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	404 a('--tool_desc',default=None)
12 d12728e33c3d Changed to deliver a gz file - requires a new datatypes_conf.xml entry: ross lazarus ross.lazarus@gmail.com parents: 10 diff changeset	405 a('--new_tool',default=None)
7 7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	406 opts, args = op.parse_args()
25 8cc3f3c0e539 Now uses admin_users to check that the user is authorized to run this tool Ross Lazarus <ross.lazarus@gmail.com> parents: 21 diff changeset	407 assert not opts.bad_user,'%s is NOT authorized to use this tool. Please ask your friendly admin to add their ID to admin_users in universe_wsgi.ini' % (opts.bad_user)
7 7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	408 assert opts.tool_name,'## Tool Factory expects a tool name - eg --tool_name=DESeq'
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	409 assert opts.interpreter,'## Tool Factory wrapper expects an interpreter - eg --interpreter=Rscript'
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	410 assert os.path.isfile(opts.script_path),'## Tool Factory wrapper expects a script path - eg --script_path=foo.R'
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	411 if opts.output_dir:
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	412 try:
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	413 os.makedirs(opts.output_dir)
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	414 except:
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	415 pass
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	416 r = ScriptRunner(opts)
8 220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	417 if opts.make_Tool:
7 7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	418 retcode = r.makeTooltar()
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	419 else:
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	420 retcode = r.run()
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	421 if retcode:
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	422 sys.exit(retcode) # indicate failure to job runner
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	423
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	424
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	425 if __name__ == "__main__":
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	426 main()
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	427
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	428

Mercurial > repos > fubar > brokenandnotdeletablebyowneroradmin

annotate rgToolFactory.py @ 25:8cc3f3c0e539 default tip