fubar/brokenandnotdeletablebyowneroradmin: rgToolFactory.py annotate

annotate rgToolFactory.py @ 20:3f58115c6c5b

Getting ready to implement the test generator. Brainfuck is easier.

author	ross lazarus ross.lazarus@gmail.com
date	Tue, 05 Jun 2012 22:15:31 +1000
parents	a87a262220a4
children	0ee2b06ea304

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.
a87a262220a4 Adding proof of concept for optional output formats. ross lazarus ross.lazarus@gmail.com parents: 15 diff changeset	41 # no real risk.
a87a262220a4 Adding proof of concept for optional output formats. ross lazarus ross.lazarus@gmail.com parents: 15 diff changeset	42 # a list in the xml source file is searched for users permitted to run this tool.
a87a262220a4 Adding proof of concept for optional output formats. ross lazarus ross.lazarus@gmail.com parents: 15 diff changeset	43 # PUT some IDs in the list in the XML before you restart Galaxy to load this new tool please
a87a262220a4 Adding proof of concept for optional output formats. ross lazarus ross.lazarus@gmail.com parents: 15 diff changeset	44 # otherwise, the tool won't run for anybody.
a87a262220a4 Adding proof of concept for optional output formats. ross lazarus ross.lazarus@gmail.com parents: 15 diff changeset	45 #
a87a262220a4 Adding proof of concept for optional output formats. ross lazarus ross.lazarus@gmail.com parents: 15 diff changeset	46
a87a262220a4 Adding proof of concept for optional output formats. ross lazarus ross.lazarus@gmail.com parents: 15 diff changeset	47 #
a87a262220a4 Adding proof of concept for optional output formats. ross lazarus ross.lazarus@gmail.com parents: 15 diff changeset	48 # 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	49 #
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	50 # all rights reserved
19 a87a262220a4 Adding proof of concept for optional output formats. ross lazarus ross.lazarus@gmail.com parents: 15 diff changeset	51 # 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	52
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	53 import sys
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	54 import shutil
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	55 import subprocess
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	56 import os
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	57 import time
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	58 import tempfile
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	59 import optparse
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	60 import tarfile
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	61 import re
8 220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	62 import shutil
220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	63
7 7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	64 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	65 myversion = 'V000.1 May 2012'
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	66 verbose = False
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	67 debug = False
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	68
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 def timenow():
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	71 """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	72 """
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	73 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	74 # 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	75
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	76 class ScriptRunner:
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	77 """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	78 """
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	79
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	80 def __init__(self,opts=None):
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	81 """
19 a87a262220a4 Adding proof of concept for optional output formats. ross lazarus ross.lazarus@gmail.com parents: 15 diff changeset	82 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	83
7 7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	84 """
8 220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	85 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	86 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	87 self.thumbformat = 'jpg'
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	88 self.opts = opts
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	89 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	90 self.toolid = self.toolname
7 7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	91 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	92 self.script = s
8 220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	93 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	94 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	95 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	96 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	97 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	98 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	99 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	100 artifact = open(artifactpath,'w')
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	101 artifact.write(self.script)
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	102 artifact.write('\n')
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	103 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	104 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	105 localscript = open(self.sfile,'w')
e09c76551bed Can run without input or output or either.. ross lazarus ross.lazarus@gmail.com parents: 8 diff changeset	106 localscript.write(self.script)
e09c76551bed Can run without input or output or either.. ross lazarus ross.lazarus@gmail.com parents: 8 diff changeset	107 localscript.close()
e09c76551bed Can run without input or output or either.. ross lazarus ross.lazarus@gmail.com parents: 8 diff changeset	108 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	109 self.cl = []
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	110 self.html = []
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	111 a = self.cl.append
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	112 a(opts.interpreter)
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	113 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	114 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	115 a(opts.output_tab)
8 220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	116 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	117 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	118 self.test1Input = 'test1_input.xls'
3f58115c6c5b Getting ready to implement the test generator. ross lazarus ross.lazarus@gmail.com parents: 19 diff changeset	119 self.test1Output = 'test1_output.xls'
3f58115c6c5b Getting ready to implement the test generator. ross lazarus ross.lazarus@gmail.com parents: 19 diff changeset	120 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	121
220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	122 def makeXML(self):
220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	123 """
220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	124 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	125 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	126
7725e4ab27e1 Adding tests - problem to find the script - needs a fixed string somewhere. ross lazarus ross.lazarus@gmail.com parents: 12 diff changeset	127 <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	128 <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	129 <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	130 reverse.py --script_path "$runMe" --interpreter "python"
7725e4ab27e1 Adding tests - problem to find the script - needs a fixed string somewhere. ross lazarus ross.lazarus@gmail.com parents: 12 diff changeset	131 --tool_name "reverse" --input_tab "$input1" --output_tab "$tab_file"
7725e4ab27e1 Adding tests - problem to find the script - needs a fixed string somewhere. ross lazarus ross.lazarus@gmail.com parents: 12 diff changeset	132 </command>
7725e4ab27e1 Adding tests - problem to find the script - needs a fixed string somewhere. ross lazarus ross.lazarus@gmail.com parents: 12 diff changeset	133 <inputs>
7725e4ab27e1 Adding tests - problem to find the script - needs a fixed string somewhere. ross lazarus ross.lazarus@gmail.com parents: 12 diff changeset	134 <param name="input1" type="data" format="tabular" label="Select a suitable input file from your history"/><param name="job_name" type="text" label="Supply a name for the outputs to remind you what they contain" value="reverse"/>
7725e4ab27e1 Adding tests - problem to find the script - needs a fixed string somewhere. ross lazarus ross.lazarus@gmail.com parents: 12 diff changeset	135
7725e4ab27e1 Adding tests - problem to find the script - needs a fixed string somewhere. ross lazarus ross.lazarus@gmail.com parents: 12 diff changeset	136 </inputs>
7725e4ab27e1 Adding tests - problem to find the script - needs a fixed string somewhere. ross lazarus ross.lazarus@gmail.com parents: 12 diff changeset	137 <outputs>
7725e4ab27e1 Adding tests - problem to find the script - needs a fixed string somewhere. ross lazarus ross.lazarus@gmail.com parents: 12 diff changeset	138 <data format="tabular" name="tab_file" label="${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	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 </outputs>
7725e4ab27e1 Adding tests - problem to find the script - needs a fixed string somewhere. ross lazarus ross.lazarus@gmail.com parents: 12 diff changeset	141 <help>
7725e4ab27e1 Adding tests - problem to find the script - needs a fixed string somewhere. ross lazarus ross.lazarus@gmail.com parents: 12 diff changeset	142
7725e4ab27e1 Adding tests - problem to find the script - needs a fixed string somewhere. ross lazarus ross.lazarus@gmail.com parents: 12 diff changeset	143 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	144
7725e4ab27e1 Adding tests - problem to find the script - needs a fixed string somewhere. ross lazarus ross.lazarus@gmail.com parents: 12 diff changeset	145 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	146
7725e4ab27e1 Adding tests - problem to find the script - needs a fixed string somewhere. ross lazarus ross.lazarus@gmail.com parents: 12 diff changeset	147 </help>
7725e4ab27e1 Adding tests - problem to find the script - needs a fixed string somewhere. ross lazarus ross.lazarus@gmail.com parents: 12 diff changeset	148 <configfiles>
7725e4ab27e1 Adding tests - problem to find the script - needs a fixed string somewhere. ross lazarus ross.lazarus@gmail.com parents: 12 diff changeset	149 <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	150
7725e4ab27e1 Adding tests - problem to find the script - needs a fixed string somewhere. ross lazarus ross.lazarus@gmail.com parents: 12 diff changeset	151 # 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	152 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	153 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	154 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	155 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	156 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	157 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	158 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	159 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	160 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	161 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	162 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	163 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	164
7725e4ab27e1 Adding tests - problem to find the script - needs a fixed string somewhere. ross lazarus ross.lazarus@gmail.com parents: 12 diff changeset	165
7725e4ab27e1 Adding tests - problem to find the script - needs a fixed string somewhere. ross lazarus ross.lazarus@gmail.com parents: 12 diff changeset	166 </configfile>
7725e4ab27e1 Adding tests - problem to find the script - needs a fixed string somewhere. ross lazarus ross.lazarus@gmail.com parents: 12 diff changeset	167 </configfiles>
7725e4ab27e1 Adding tests - problem to find the script - needs a fixed string somewhere. ross lazarus ross.lazarus@gmail.com parents: 12 diff changeset	168 </tool>
7725e4ab27e1 Adding tests - problem to find the script - needs a fixed string somewhere. ross lazarus ross.lazarus@gmail.com parents: 12 diff changeset	169
8 220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	170 """
220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	171 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	172 %(tooldesc)s
220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	173 %(command)s
220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	174 <inputs>
220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	175 %(inputs)s
220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	176 </inputs>
220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	177 <outputs>
220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	178 %(outputs)s
220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	179 </outputs>
220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	180 <help>
220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	181 %(help)s
220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	182 </help>
220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	183 <configfiles>
220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	184 <configfile name="runMe">
220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	185 %(script)s
220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	186 </configfile>
220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	187 </configfiles>
220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	188 </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	189
220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	190 newCommand="""<command interpreter="python">
220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	191 %(toolname)s.py --script_path "$runMe" --interpreter "%(interpreter)s"
220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	192 --tool_name "%(toolname)s" %(command_inputs)s %(command_outputs)s
220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	193 </command>""" # may NOT be an input or htmlout
13 7725e4ab27e1 Adding tests - problem to find the script - needs a fixed string somewhere. ross lazarus ross.lazarus@gmail.com parents: 12 diff changeset	194 tooltests = """<tests><test>
7725e4ab27e1 Adding tests - problem to find the script - needs a fixed string somewhere. ross lazarus ross.lazarus@gmail.com parents: 12 diff changeset	195 <param name="input1" value="%s" ftype="%s"/>
7725e4ab27e1 Adding tests - problem to find the script - needs a fixed string somewhere. ross lazarus ross.lazarus@gmail.com parents: 12 diff changeset	196 <param name="job_name" value="test1"/>
7725e4ab27e1 Adding tests - problem to find the script - needs a fixed string somewhere. ross lazarus ross.lazarus@gmail.com parents: 12 diff changeset	197 <param name="runMe" value="$runMe"/>
7725e4ab27e1 Adding tests - problem to find the script - needs a fixed string somewhere. ross lazarus ross.lazarus@gmail.com parents: 12 diff changeset	198 </test><tests>"""
8 220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	199 xdict = {}
9 e09c76551bed Can run without input or output or either.. ross lazarus ross.lazarus@gmail.com parents: 8 diff changeset	200 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	201 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	202 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	203 else:
220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	204 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	205 if self.opts.tool_desc:
220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	206 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	207 else:
220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	208 xdict['tooldesc'] = ''
9 e09c76551bed Can run without input or output or either.. ross lazarus ross.lazarus@gmail.com parents: 8 diff changeset	209 xdict['command_outputs'] = ''
e09c76551bed Can run without input or output or either.. ross lazarus ross.lazarus@gmail.com parents: 8 diff changeset	210 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	211 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	212 xdict['command_inputs'] = '--input_tab "$input1"'
220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	213 xdict['inputs'] = '<param name="input1" type="data" format="%s" label="Select a suitable input file from your history"/>' % self.inputFormats
220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	214 else:
220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	215 xdict['command_inputs'] = '' # assume no input - eg a random data generator
220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	216 xdict['inputs'] = ''
220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	217 xdict['inputs'] += '<param name="job_name" type="text" label="Supply a name for the outputs to remind you what they contain" value="%s"/>\n' % self.toolname
220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	218 xdict['toolname'] = self.toolname
220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	219 xdict['toolid'] = self.toolid
220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	220 xdict['interpreter'] = self.opts.interpreter
220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	221 xdict['scriptname'] = self.sfile
220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	222 if self.opts.make_HTML:
9 e09c76551bed Can run without input or output or either.. ross lazarus ross.lazarus@gmail.com parents: 8 diff changeset	223 xdict['command_outputs'] += '--output_dir "$html_file.files_path" --output_html "$html_file" --make_HTML "yes"'
8 220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	224 xdict['outputs'] += '<data format="html" name="html_file" label="${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	225 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	226 xdict['command_outputs'] += '--output_tab "$tab_file"'
220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	227 xdict['outputs'] += '<data format="%s" name="tab_file" label="${job_name}"/>\n' % self.outFormats
220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	228 xdict['command'] = newCommand % xdict
220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	229 xmls = newXML % xdict
220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	230 xf = open(self.xmlfile,'w')
220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	231 xf.write(xmls)
220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	232 xf.write('\n')
220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	233 xf.close()
220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	234 # ready for the tarball
220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	235
7 7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	236
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	237 def makeTooltar(self):
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 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	240 /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	241 """
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	242 retval = self.run()
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	243 if retval:
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	244 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	245 sys.exit(1)
8 220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	246 self.makeXML()
220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	247 tdir = self.toolname
220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	248 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	249 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	250 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	251 os.mkdir(testdir) # make tests directory
71f2ac0eee95 Updated tarball with some test material - still need code generated... ross lazarus ross.lazarus@gmail.com parents: 9 diff changeset	252 shutil.copyfile(self.opts.input_tab,os.path.join(testdir,'test1_in.tab'))
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	253 if self.opts.output_tab <> 'None':
10 71f2ac0eee95 Updated tarball with some test material - still need code generated... ross lazarus ross.lazarus@gmail.com parents: 9 diff changeset	254 shutil.copyfile(self.opts.output_tab,os.path.join(testdir,'test1_out.tab'))
71f2ac0eee95 Updated tarball with some test material - still need code generated... ross lazarus ross.lazarus@gmail.com parents: 9 diff changeset	255 if self.opts.make_HTML:
71f2ac0eee95 Updated tarball with some test material - still need code generated... ross lazarus ross.lazarus@gmail.com parents: 9 diff changeset	256 shutil.copyfile(self.opts.output_html,os.path.join(testdir,'test1_out.html'))
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	257 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	258 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	259 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	260 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	261 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	262 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	263 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	264 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	265 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	266 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	267 shutil.rmtree(tdir)
220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	268 ## 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	269 return retval
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 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	272 """need absolute path to pdf
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	273 """
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	274 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	275 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	276 sto = open(hlog,'w')
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	277 outpdf = '%s_compressed' % inpdf
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	278 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	279 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	280 retval1 = x.wait()
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	281 if retval1 == 0:
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	282 os.unlink(inpdf)
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	283 shutil.move(outpdf,inpdf)
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	284 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	285 cl2 = ['convert', inpdf, outpng]
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	286 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	287 retval2 = x.wait()
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	288 sto.close()
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	289 retval = retval1 or retval2
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	290 return retval
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
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	293 def getfSize(self,fpath,outpath):
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	294 """
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	295 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	296 """
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	297 size = ''
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	298 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	299 if os.path.isfile(fp):
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	300 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	301 if n > 2**20:
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	302 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	303 elif n > 2**10:
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	304 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	305 elif n > 0:
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	306 size = ' (%d B)' % (int(n))
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	307 return size
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	308
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	309 def makeHtml(self):
8 220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	310 """ 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	311 """
220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	312
220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	313 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	314 <!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	315 <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	316 <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	317 <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	318 <title></title>
220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	319 <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	320 </head>
220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	321 <body>
220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	322 <div class="document">
220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	323 """
19 a87a262220a4 Adding proof of concept for optional output formats. ross lazarus ross.lazarus@gmail.com parents: 15 diff changeset	324 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	325 galhtmlpostfix = """</div></body></html>\n"""
220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	326
220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	327 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	328 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	329 flist.sort()
220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	330 html = [galhtmlprefix % progname,]
220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	331 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	332 fhtml = []
220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	333 if len(flist) > 0:
220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	334 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	335 for fname in flist:
7 7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	336 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	337 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	338 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	339 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	340 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	341 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	342 if retval == 0:
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	343 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	344 html.append(s)
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	345 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	346 else:
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	347 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	348 html.append('</table>\n')
220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	349 if len(fhtml) > 0:
220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	350 fhtml.insert(0,'<ul>')
9 e09c76551bed Can run without input or output or either.. ross lazarus ross.lazarus@gmail.com parents: 8 diff changeset	351 fhtml.append('</ul><br/>')
8 220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	352 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	353 else:
220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	354 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	355 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	356 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	357 html += rlog
9 e09c76551bed Can run without input or output or either.. ross lazarus ross.lazarus@gmail.com parents: 8 diff changeset	358 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	359 html.append('</pre>\n')
220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	360 html.append(galhtmlattr % (progname,timenow()))
220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	361 html.append(galhtmlpostfix)
220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	362 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	363 htmlf.write('\n'.join(html))
220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	364 htmlf.write('\n')
220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	365 htmlf.close()
220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	366 self.html = html
7 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
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	369 def run(self):
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	370 """
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	371 """
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	372 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	373 sto = open(self.tlog,'w')
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	374 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	375 else:
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	376 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	377 p.stdin.write(self.script)
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	378 p.stdin.close()
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	379 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	380 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	381 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	382 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	383 self.makeHtml()
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	384 return retval
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	385
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	386
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	387 def main():
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	388 u = """
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	389 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	390 <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	391 </command>
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	392 """
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	393 op = optparse.OptionParser()
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	394 a = op.add_option
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	395 a('--script_path',default=None)
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	396 a('--tool_name',default=None)
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	397 a('--interpreter',default=None)
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	398 a('--output_dir',default=None)
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	399 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	400 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	401 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	402 a('--user_email',default=None)
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	403 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	404 a('--make_Tool',default=None)
220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	405 a('--make_HTML',default=None)
220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	406 a('--help_text',default=None)
220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	407 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	408 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	409 opts, args = op.parse_args()
19 a87a262220a4 Adding proof of concept for optional output formats. ross lazarus ross.lazarus@gmail.com parents: 15 diff changeset	410 assert not opts.bad_user,'%s is NOT authorized to use this tool. Please ask your friendly admin to add their ID to %s.xml' % (opts.bad_user,os.path.splitext(self.myname)[0])
7 7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	411 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	412 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	413 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	414 if opts.output_dir:
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	415 try:
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	416 os.makedirs(opts.output_dir)
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	417 except:
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	418 pass
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	419 r = ScriptRunner(opts)
8 220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	420 if opts.make_Tool:
7 7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	421 retcode = r.makeTooltar()
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	422 else:
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	423 retcode = r.run()
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	424 if retcode:
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	425 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	426
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 if __name__ == "__main__":
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	429 main()
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	430
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	431

Mercurial > repos > fubar > brokenandnotdeletablebyowneroradmin

annotate rgToolFactory.py @ 20:3f58115c6c5b