fubar/brokenandnotdeletablebyowneroradmin: rgDynamicScriptWrapper.py annotate

annotate rgDynamicScriptWrapper.py @ 2:d95513e50c92

Add README.txt for bitbucket

author	ross lazarus ross.lazarus@gmail.com
date	Thu, 31 May 2012 09:35:18 +1000
parents	0133b97e477e
children

rev	line source
0 fda8032fe989 Initial checkin of dynamic script runner. Goal is to add code to generate a new toolshed entry once the script works correctly ross lazarus ross.lazarus@gmail.com parents: diff changeset	1 # rgDynamicScriptWrapper.py
fda8032fe989 Initial checkin of dynamic script runner. Goal is to add code to generate a new toolshed entry once the script works correctly ross lazarus ross.lazarus@gmail.com parents: diff changeset	2 # derived from
fda8032fe989 Initial checkin of dynamic script runner. Goal is to add code to generate a new toolshed entry once the script works correctly ross lazarus ross.lazarus@gmail.com parents: diff changeset	3 # rgBaseScriptWrapper.py
fda8032fe989 Initial checkin of dynamic script runner. Goal is to add code to generate a new toolshed entry once the script works correctly ross lazarus ross.lazarus@gmail.com parents: diff changeset	4 # to run some user supplied code
fda8032fe989 Initial checkin of dynamic script runner. Goal is to add code to generate a new toolshed entry once the script works correctly ross lazarus ross.lazarus@gmail.com parents: diff changeset	5 # extremely dangerous
fda8032fe989 Initial checkin of dynamic script runner. Goal is to add code to generate a new toolshed entry once the script works correctly ross lazarus ross.lazarus@gmail.com parents: diff changeset	6 # trusted users only - private site only
fda8032fe989 Initial checkin of dynamic script runner. Goal is to add code to generate a new toolshed entry once the script works correctly ross lazarus ross.lazarus@gmail.com parents: diff changeset	7 # a list in the xml is searched - only users in the list can run this tool.
fda8032fe989 Initial checkin of dynamic script runner. Goal is to add code to generate a new toolshed entry once the script works correctly ross lazarus ross.lazarus@gmail.com parents: diff changeset	8 #
fda8032fe989 Initial checkin of dynamic script runner. Goal is to add code to generate a new toolshed entry once the script works correctly ross lazarus ross.lazarus@gmail.com parents: diff changeset	9 # copyright ross lazarus (ross.lazarus@gmail.com) May 2012
fda8032fe989 Initial checkin of dynamic script runner. Goal is to add code to generate a new toolshed entry once the script works correctly ross lazarus ross.lazarus@gmail.com parents: diff changeset	10 #
fda8032fe989 Initial checkin of dynamic script runner. Goal is to add code to generate a new toolshed entry once the script works correctly ross lazarus ross.lazarus@gmail.com parents: diff changeset	11 # all rights reserved
fda8032fe989 Initial checkin of dynamic script runner. Goal is to add code to generate a new toolshed entry once the script works correctly ross lazarus ross.lazarus@gmail.com parents: diff changeset	12 # Licensed under the LGPL for your pleasure
fda8032fe989 Initial checkin of dynamic script runner. Goal is to add code to generate a new toolshed entry once the script works correctly ross lazarus ross.lazarus@gmail.com parents: diff changeset	13 # Derived from rgDGE.py in May 2012
fda8032fe989 Initial checkin of dynamic script runner. Goal is to add code to generate a new toolshed entry once the script works correctly ross lazarus ross.lazarus@gmail.com parents: diff changeset	14 # generalized to run required interpreter
fda8032fe989 Initial checkin of dynamic script runner. Goal is to add code to generate a new toolshed entry once the script works correctly ross lazarus ross.lazarus@gmail.com parents: diff changeset	15 # to make your own tools based on a given script and interpreter such as perl or python
fda8032fe989 Initial checkin of dynamic script runner. Goal is to add code to generate a new toolshed entry once the script works correctly ross lazarus ross.lazarus@gmail.com parents: diff changeset	16 # clone this and the corresponding xml wrapper
fda8032fe989 Initial checkin of dynamic script runner. Goal is to add code to generate a new toolshed entry once the script works correctly ross lazarus ross.lazarus@gmail.com parents: diff changeset	17 # replace the parameters/inputs/outputs and the configfile contents with your script
fda8032fe989 Initial checkin of dynamic script runner. Goal is to add code to generate a new toolshed entry once the script works correctly ross lazarus ross.lazarus@gmail.com parents: diff changeset	18 # Use the $foo syntax to place your parameter values inside the script to assign them - at run time, the script will be used as a template
fda8032fe989 Initial checkin of dynamic script runner. Goal is to add code to generate a new toolshed entry once the script works correctly ross lazarus ross.lazarus@gmail.com parents: diff changeset	19 # and returned as part of the output to the user - with the right values for all the parameters.
fda8032fe989 Initial checkin of dynamic script runner. Goal is to add code to generate a new toolshed entry once the script works correctly ross lazarus ross.lazarus@gmail.com parents: diff changeset	20 # Note that this assumes you want all the outputs arranged as a single Html file output
fda8032fe989 Initial checkin of dynamic script runner. Goal is to add code to generate a new toolshed entry once the script works correctly ross lazarus ross.lazarus@gmail.com parents: diff changeset	21 # after this generic script runner runs your script with the specified interpreter,
fda8032fe989 Initial checkin of dynamic script runner. Goal is to add code to generate a new toolshed entry once the script works correctly ross lazarus ross.lazarus@gmail.com parents: diff changeset	22 # it will collect all output files into the specified output_html, making thumbnails for all the pdfs it finds and making links for all the other files.
fda8032fe989 Initial checkin of dynamic script runner. Goal is to add code to generate a new toolshed entry once the script works correctly ross lazarus ross.lazarus@gmail.com parents: diff changeset	23
fda8032fe989 Initial checkin of dynamic script runner. Goal is to add code to generate a new toolshed entry once the script works correctly ross lazarus ross.lazarus@gmail.com parents: diff changeset	24 import sys
fda8032fe989 Initial checkin of dynamic script runner. Goal is to add code to generate a new toolshed entry once the script works correctly ross lazarus ross.lazarus@gmail.com parents: diff changeset	25 import shutil
fda8032fe989 Initial checkin of dynamic script runner. Goal is to add code to generate a new toolshed entry once the script works correctly ross lazarus ross.lazarus@gmail.com parents: diff changeset	26 import subprocess
fda8032fe989 Initial checkin of dynamic script runner. Goal is to add code to generate a new toolshed entry once the script works correctly ross lazarus ross.lazarus@gmail.com parents: diff changeset	27 import os
fda8032fe989 Initial checkin of dynamic script runner. Goal is to add code to generate a new toolshed entry once the script works correctly ross lazarus ross.lazarus@gmail.com parents: diff changeset	28 import time
fda8032fe989 Initial checkin of dynamic script runner. Goal is to add code to generate a new toolshed entry once the script works correctly ross lazarus ross.lazarus@gmail.com parents: diff changeset	29 import tempfile
fda8032fe989 Initial checkin of dynamic script runner. Goal is to add code to generate a new toolshed entry once the script works correctly ross lazarus ross.lazarus@gmail.com parents: diff changeset	30 import optparse
fda8032fe989 Initial checkin of dynamic script runner. Goal is to add code to generate a new toolshed entry once the script works correctly ross lazarus ross.lazarus@gmail.com parents: diff changeset	31
fda8032fe989 Initial checkin of dynamic script runner. Goal is to add code to generate a new toolshed entry once the script works correctly ross lazarus ross.lazarus@gmail.com parents: diff changeset	32 progname = os.path.split(sys.argv[0])[1]
fda8032fe989 Initial checkin of dynamic script runner. Goal is to add code to generate a new toolshed entry once the script works correctly ross lazarus ross.lazarus@gmail.com parents: diff changeset	33 myversion = 'V000.1 May 2012'
fda8032fe989 Initial checkin of dynamic script runner. Goal is to add code to generate a new toolshed entry once the script works correctly ross lazarus ross.lazarus@gmail.com parents: diff changeset	34 verbose = False
fda8032fe989 Initial checkin of dynamic script runner. Goal is to add code to generate a new toolshed entry once the script works correctly ross lazarus ross.lazarus@gmail.com parents: diff changeset	35 debug = False
fda8032fe989 Initial checkin of dynamic script runner. Goal is to add code to generate a new toolshed entry once the script works correctly ross lazarus ross.lazarus@gmail.com parents: diff changeset	36
fda8032fe989 Initial checkin of dynamic script runner. Goal is to add code to generate a new toolshed entry once the script works correctly ross lazarus ross.lazarus@gmail.com parents: diff changeset	37 # characters that are allowed but need to be escaped
fda8032fe989 Initial checkin of dynamic script runner. Goal is to add code to generate a new toolshed entry once the script works correctly ross lazarus ross.lazarus@gmail.com parents: diff changeset	38 # also a test sandboxing of any R system commands
fda8032fe989 Initial checkin of dynamic script runner. Goal is to add code to generate a new toolshed entry once the script works correctly ross lazarus ross.lazarus@gmail.com parents: diff changeset	39 # ultimately futile - we need to generate a new tool
fda8032fe989 Initial checkin of dynamic script runner. Goal is to add code to generate a new toolshed entry once the script works correctly ross lazarus ross.lazarus@gmail.com parents: diff changeset	40 # which will have no new security problems!
fda8032fe989 Initial checkin of dynamic script runner. Goal is to add code to generate a new toolshed entry once the script works correctly ross lazarus ross.lazarus@gmail.com parents: diff changeset	41 mapped_chars = { '>' :'__gt__',
fda8032fe989 Initial checkin of dynamic script runner. Goal is to add code to generate a new toolshed entry once the script works correctly ross lazarus ross.lazarus@gmail.com parents: diff changeset	42 '<' :'__lt__',
fda8032fe989 Initial checkin of dynamic script runner. Goal is to add code to generate a new toolshed entry once the script works correctly ross lazarus ross.lazarus@gmail.com parents: diff changeset	43 "'" :'__sq__',
fda8032fe989 Initial checkin of dynamic script runner. Goal is to add code to generate a new toolshed entry once the script works correctly ross lazarus ross.lazarus@gmail.com parents: diff changeset	44 '"' :'__dq__',
fda8032fe989 Initial checkin of dynamic script runner. Goal is to add code to generate a new toolshed entry once the script works correctly ross lazarus ross.lazarus@gmail.com parents: diff changeset	45 '{' :'__oc__',
fda8032fe989 Initial checkin of dynamic script runner. Goal is to add code to generate a new toolshed entry once the script works correctly ross lazarus ross.lazarus@gmail.com parents: diff changeset	46 '}' :'__cc__',
fda8032fe989 Initial checkin of dynamic script runner. Goal is to add code to generate a new toolshed entry once the script works correctly ross lazarus ross.lazarus@gmail.com parents: diff changeset	47 '@' : '__at__',
fda8032fe989 Initial checkin of dynamic script runner. Goal is to add code to generate a new toolshed entry once the script works correctly ross lazarus ross.lazarus@gmail.com parents: diff changeset	48 '\n' : '__cn__',
fda8032fe989 Initial checkin of dynamic script runner. Goal is to add code to generate a new toolshed entry once the script works correctly ross lazarus ross.lazarus@gmail.com parents: diff changeset	49 '\r' : '__cr__',
fda8032fe989 Initial checkin of dynamic script runner. Goal is to add code to generate a new toolshed entry once the script works correctly ross lazarus ross.lazarus@gmail.com parents: diff changeset	50 '\t' : '__tc__',
fda8032fe989 Initial checkin of dynamic script runner. Goal is to add code to generate a new toolshed entry once the script works correctly ross lazarus ross.lazarus@gmail.com parents: diff changeset	51 '#' : '__pd__',
fda8032fe989 Initial checkin of dynamic script runner. Goal is to add code to generate a new toolshed entry once the script works correctly ross lazarus ross.lazarus@gmail.com parents: diff changeset	52 '[' :'__ob__',
fda8032fe989 Initial checkin of dynamic script runner. Goal is to add code to generate a new toolshed entry once the script works correctly ross lazarus ross.lazarus@gmail.com parents: diff changeset	53 ']' :'__cb__',
fda8032fe989 Initial checkin of dynamic script runner. Goal is to add code to generate a new toolshed entry once the script works correctly ross lazarus ross.lazarus@gmail.com parents: diff changeset	54 '\t' : 'Xt',
fda8032fe989 Initial checkin of dynamic script runner. Goal is to add code to generate a new toolshed entry once the script works correctly ross lazarus ross.lazarus@gmail.com parents: diff changeset	55 'systemCallsAreNotAllowed' : 'system'
fda8032fe989 Initial checkin of dynamic script runner. Goal is to add code to generate a new toolshed entry once the script works correctly ross lazarus ross.lazarus@gmail.com parents: diff changeset	56 }
fda8032fe989 Initial checkin of dynamic script runner. Goal is to add code to generate a new toolshed entry once the script works correctly ross lazarus ross.lazarus@gmail.com parents: diff changeset	57
fda8032fe989 Initial checkin of dynamic script runner. Goal is to add code to generate a new toolshed entry once the script works correctly ross lazarus ross.lazarus@gmail.com parents: diff changeset	58 galhtmlprefix = """<?xml version="1.0" encoding="utf-8" ?>
fda8032fe989 Initial checkin of dynamic script runner. Goal is to add code to generate a new toolshed entry once the script works correctly ross lazarus ross.lazarus@gmail.com parents: diff changeset	59 <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
fda8032fe989 Initial checkin of dynamic script runner. Goal is to add code to generate a new toolshed entry once the script works correctly ross lazarus ross.lazarus@gmail.com parents: diff changeset	60 <html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
fda8032fe989 Initial checkin of dynamic script runner. Goal is to add code to generate a new toolshed entry once the script works correctly ross lazarus ross.lazarus@gmail.com parents: diff changeset	61 <head> <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
fda8032fe989 Initial checkin of dynamic script runner. Goal is to add code to generate a new toolshed entry once the script works correctly ross lazarus ross.lazarus@gmail.com parents: diff changeset	62 <meta name="generator" content="Galaxy %s tool output - see http://g2.trac.bx.psu.edu/" />
fda8032fe989 Initial checkin of dynamic script runner. Goal is to add code to generate a new toolshed entry once the script works correctly ross lazarus ross.lazarus@gmail.com parents: diff changeset	63 <title></title>
fda8032fe989 Initial checkin of dynamic script runner. Goal is to add code to generate a new toolshed entry once the script works correctly ross lazarus ross.lazarus@gmail.com parents: diff changeset	64 <link rel="stylesheet" href="/static/style/base.css" type="text/css" />
fda8032fe989 Initial checkin of dynamic script runner. Goal is to add code to generate a new toolshed entry once the script works correctly ross lazarus ross.lazarus@gmail.com parents: diff changeset	65 </head>
fda8032fe989 Initial checkin of dynamic script runner. Goal is to add code to generate a new toolshed entry once the script works correctly ross lazarus ross.lazarus@gmail.com parents: diff changeset	66 <body>
fda8032fe989 Initial checkin of dynamic script runner. Goal is to add code to generate a new toolshed entry once the script works correctly ross lazarus ross.lazarus@gmail.com parents: diff changeset	67 <div class="document">
fda8032fe989 Initial checkin of dynamic script runner. Goal is to add code to generate a new toolshed entry once the script works correctly ross lazarus ross.lazarus@gmail.com parents: diff changeset	68 """
fda8032fe989 Initial checkin of dynamic script runner. Goal is to add code to generate a new toolshed entry once the script works correctly ross lazarus ross.lazarus@gmail.com parents: diff changeset	69 galhtmlattr = """<b><a href="http://rgenetics.org">Galaxy Rgenetics Base Script Wrapper based </a> tool output %s run at %s</b><br/>"""
fda8032fe989 Initial checkin of dynamic script runner. Goal is to add code to generate a new toolshed entry once the script works correctly ross lazarus ross.lazarus@gmail.com parents: diff changeset	70 galhtmlpostfix = """</div></body></html>\n"""
fda8032fe989 Initial checkin of dynamic script runner. Goal is to add code to generate a new toolshed entry once the script works correctly ross lazarus ross.lazarus@gmail.com parents: diff changeset	71
fda8032fe989 Initial checkin of dynamic script runner. Goal is to add code to generate a new toolshed entry once the script works correctly ross lazarus ross.lazarus@gmail.com parents: diff changeset	72 def timenow():
fda8032fe989 Initial checkin of dynamic script runner. Goal is to add code to generate a new toolshed entry once the script works correctly ross lazarus ross.lazarus@gmail.com parents: diff changeset	73 """return current time as a string
fda8032fe989 Initial checkin of dynamic script runner. Goal is to add code to generate a new toolshed entry once the script works correctly ross lazarus ross.lazarus@gmail.com parents: diff changeset	74 """
fda8032fe989 Initial checkin of dynamic script runner. Goal is to add code to generate a new toolshed entry once the script works correctly ross lazarus ross.lazarus@gmail.com parents: diff changeset	75 return time.strftime('%d/%m/%Y %H:%M:%S', time.localtime(time.time()))
fda8032fe989 Initial checkin of dynamic script runner. Goal is to add code to generate a new toolshed entry once the script works correctly ross lazarus ross.lazarus@gmail.com parents: diff changeset	76
fda8032fe989 Initial checkin of dynamic script runner. Goal is to add code to generate a new toolshed entry once the script works correctly ross lazarus ross.lazarus@gmail.com parents: diff changeset	77 def restore_text(text):
fda8032fe989 Initial checkin of dynamic script runner. Goal is to add code to generate a new toolshed entry once the script works correctly ross lazarus ross.lazarus@gmail.com parents: diff changeset	78 """Restores sanitized text"""
fda8032fe989 Initial checkin of dynamic script runner. Goal is to add code to generate a new toolshed entry once the script works correctly ross lazarus ross.lazarus@gmail.com parents: diff changeset	79 if not text:
fda8032fe989 Initial checkin of dynamic script runner. Goal is to add code to generate a new toolshed entry once the script works correctly ross lazarus ross.lazarus@gmail.com parents: diff changeset	80 return text
fda8032fe989 Initial checkin of dynamic script runner. Goal is to add code to generate a new toolshed entry once the script works correctly ross lazarus ross.lazarus@gmail.com parents: diff changeset	81 for key, value in mapped_chars.items():
fda8032fe989 Initial checkin of dynamic script runner. Goal is to add code to generate a new toolshed entry once the script works correctly ross lazarus ross.lazarus@gmail.com parents: diff changeset	82 text = text.replace(value, key)
fda8032fe989 Initial checkin of dynamic script runner. Goal is to add code to generate a new toolshed entry once the script works correctly ross lazarus ross.lazarus@gmail.com parents: diff changeset	83 return text
fda8032fe989 Initial checkin of dynamic script runner. Goal is to add code to generate a new toolshed entry once the script works correctly ross lazarus ross.lazarus@gmail.com parents: diff changeset	84
fda8032fe989 Initial checkin of dynamic script runner. Goal is to add code to generate a new toolshed entry once the script works correctly ross lazarus ross.lazarus@gmail.com parents: diff changeset	85 class ScriptRunner:
fda8032fe989 Initial checkin of dynamic script runner. Goal is to add code to generate a new toolshed entry once the script works correctly ross lazarus ross.lazarus@gmail.com parents: diff changeset	86 """class is a wrapper for an arbitrary script
fda8032fe989 Initial checkin of dynamic script runner. Goal is to add code to generate a new toolshed entry once the script works correctly ross lazarus ross.lazarus@gmail.com parents: diff changeset	87 """
fda8032fe989 Initial checkin of dynamic script runner. Goal is to add code to generate a new toolshed entry once the script works correctly ross lazarus ross.lazarus@gmail.com parents: diff changeset	88
fda8032fe989 Initial checkin of dynamic script runner. Goal is to add code to generate a new toolshed entry once the script works correctly ross lazarus ross.lazarus@gmail.com parents: diff changeset	89 def __init__(self,opts=None):
fda8032fe989 Initial checkin of dynamic script runner. Goal is to add code to generate a new toolshed entry once the script works correctly ross lazarus ross.lazarus@gmail.com parents: diff changeset	90 """
fda8032fe989 Initial checkin of dynamic script runner. Goal is to add code to generate a new toolshed entry once the script works correctly ross lazarus ross.lazarus@gmail.com parents: diff changeset	91 run the script
fda8032fe989 Initial checkin of dynamic script runner. Goal is to add code to generate a new toolshed entry once the script works correctly ross lazarus ross.lazarus@gmail.com parents: diff changeset	92 cheetah/galaxy will provide an escaped string so
fda8032fe989 Initial checkin of dynamic script runner. Goal is to add code to generate a new toolshed entry once the script works correctly ross lazarus ross.lazarus@gmail.com parents: diff changeset	93 __pd__ your script goes here
fda8032fe989 Initial checkin of dynamic script runner. Goal is to add code to generate a new toolshed entry once the script works correctly ross lazarus ross.lazarus@gmail.com parents: diff changeset	94 __cr____cn__ourargs __lt__- commandArgs(TRUE)
fda8032fe989 Initial checkin of dynamic script runner. Goal is to add code to generate a new toolshed entry once the script works correctly ross lazarus ross.lazarus@gmail.com parents: diff changeset	95 __cr____cn__inf = ourargs[1]
fda8032fe989 Initial checkin of dynamic script runner. Goal is to add code to generate a new toolshed entry once the script works correctly ross lazarus ross.lazarus@gmail.com parents: diff changeset	96 __cr____cn__outf = ourargs[2]
fda8032fe989 Initial checkin of dynamic script runner. Goal is to add code to generate a new toolshed entry once the script works correctly ross lazarus ross.lazarus@gmail.com parents: diff changeset	97 __cr____cn__inp = read.table(inf,head=T,rownames=F,sep=__sq__Xt__sq__)
fda8032fe989 Initial checkin of dynamic script runner. Goal is to add code to generate a new toolshed entry once the script works correctly ross lazarus ross.lazarus@gmail.com parents: diff changeset	98 __cr____cn__ write.table(inp,outf, quote=FALSE, sep=__dq__Xt__dq__,row.names=F)
fda8032fe989 Initial checkin of dynamic script runner. Goal is to add code to generate a new toolshed entry once the script works correctly ross lazarus ross.lazarus@gmail.com parents: diff changeset	99 __cr____cn__sessionInfo()
fda8032fe989 Initial checkin of dynamic script runner. Goal is to add code to generate a new toolshed entry once the script works correctly ross lazarus ross.lazarus@gmail.com parents: diff changeset	100 __cr____cn__
fda8032fe989 Initial checkin of dynamic script runner. Goal is to add code to generate a new toolshed entry once the script works correctly ross lazarus ross.lazarus@gmail.com parents: diff changeset	101 """
fda8032fe989 Initial checkin of dynamic script runner. Goal is to add code to generate a new toolshed entry once the script works correctly ross lazarus ross.lazarus@gmail.com parents: diff changeset	102 self.thumbformat = 'jpg'
fda8032fe989 Initial checkin of dynamic script runner. Goal is to add code to generate a new toolshed entry once the script works correctly ross lazarus ross.lazarus@gmail.com parents: diff changeset	103 self.opts = opts
fda8032fe989 Initial checkin of dynamic script runner. Goal is to add code to generate a new toolshed entry once the script works correctly ross lazarus ross.lazarus@gmail.com parents: diff changeset	104 self.toolname = opts.tool_name.replace(' ','_')
fda8032fe989 Initial checkin of dynamic script runner. Goal is to add code to generate a new toolshed entry once the script works correctly ross lazarus ross.lazarus@gmail.com parents: diff changeset	105 s = open(self.opts.script_path,'r').read()
fda8032fe989 Initial checkin of dynamic script runner. Goal is to add code to generate a new toolshed entry once the script works correctly ross lazarus ross.lazarus@gmail.com parents: diff changeset	106 self.script = restore_text(s)
fda8032fe989 Initial checkin of dynamic script runner. Goal is to add code to generate a new toolshed entry once the script works correctly ross lazarus ross.lazarus@gmail.com parents: diff changeset	107 if opts.output_dir: # may not want these complexities if a simple script
fda8032fe989 Initial checkin of dynamic script runner. Goal is to add code to generate a new toolshed entry once the script works correctly ross lazarus ross.lazarus@gmail.com parents: diff changeset	108 self.tlog = os.path.join(opts.output_dir,"%s_runner.log" % self.toolname)
fda8032fe989 Initial checkin of dynamic script runner. Goal is to add code to generate a new toolshed entry once the script works correctly ross lazarus ross.lazarus@gmail.com parents: diff changeset	109 artifactpath = os.path.join(opts.output_dir,'%s_run.script' % self.toolname)
fda8032fe989 Initial checkin of dynamic script runner. Goal is to add code to generate a new toolshed entry once the script works correctly ross lazarus ross.lazarus@gmail.com parents: diff changeset	110 artifact = open(artifactpath,'w')
fda8032fe989 Initial checkin of dynamic script runner. Goal is to add code to generate a new toolshed entry once the script works correctly ross lazarus ross.lazarus@gmail.com parents: diff changeset	111 artifact.write(self.script)
fda8032fe989 Initial checkin of dynamic script runner. Goal is to add code to generate a new toolshed entry once the script works correctly ross lazarus ross.lazarus@gmail.com parents: diff changeset	112 artifact.write('\n')
fda8032fe989 Initial checkin of dynamic script runner. Goal is to add code to generate a new toolshed entry once the script works correctly ross lazarus ross.lazarus@gmail.com parents: diff changeset	113 artifact.close()
fda8032fe989 Initial checkin of dynamic script runner. Goal is to add code to generate a new toolshed entry once the script works correctly ross lazarus ross.lazarus@gmail.com parents: diff changeset	114 self.cl = []
fda8032fe989 Initial checkin of dynamic script runner. Goal is to add code to generate a new toolshed entry once the script works correctly ross lazarus ross.lazarus@gmail.com parents: diff changeset	115 a = self.cl.append
fda8032fe989 Initial checkin of dynamic script runner. Goal is to add code to generate a new toolshed entry once the script works correctly ross lazarus ross.lazarus@gmail.com parents: diff changeset	116 a(opts.interpreter)
fda8032fe989 Initial checkin of dynamic script runner. Goal is to add code to generate a new toolshed entry once the script works correctly ross lazarus ross.lazarus@gmail.com parents: diff changeset	117 a('-') # use stdin
fda8032fe989 Initial checkin of dynamic script runner. Goal is to add code to generate a new toolshed entry once the script works correctly ross lazarus ross.lazarus@gmail.com parents: diff changeset	118 a(opts.input_tab)
fda8032fe989 Initial checkin of dynamic script runner. Goal is to add code to generate a new toolshed entry once the script works correctly ross lazarus ross.lazarus@gmail.com parents: diff changeset	119 a(opts.output_tab)
fda8032fe989 Initial checkin of dynamic script runner. Goal is to add code to generate a new toolshed entry once the script works correctly ross lazarus ross.lazarus@gmail.com parents: diff changeset	120
fda8032fe989 Initial checkin of dynamic script runner. Goal is to add code to generate a new toolshed entry once the script works correctly ross lazarus ross.lazarus@gmail.com parents: diff changeset	121 def compressPDF(self,inpdf=None,thumbformat='png'):
fda8032fe989 Initial checkin of dynamic script runner. Goal is to add code to generate a new toolshed entry once the script works correctly ross lazarus ross.lazarus@gmail.com parents: diff changeset	122 """need absolute path to pdf
fda8032fe989 Initial checkin of dynamic script runner. Goal is to add code to generate a new toolshed entry once the script works correctly ross lazarus ross.lazarus@gmail.com parents: diff changeset	123 """
fda8032fe989 Initial checkin of dynamic script runner. Goal is to add code to generate a new toolshed entry once the script works correctly ross lazarus ross.lazarus@gmail.com parents: diff changeset	124 assert os.path.isfile(inpdf), "## Input %s supplied to %s compressPDF not found" % (inpdf,self.myName)
fda8032fe989 Initial checkin of dynamic script runner. Goal is to add code to generate a new toolshed entry once the script works correctly ross lazarus ross.lazarus@gmail.com parents: diff changeset	125 hf,hlog = tempfile.mkstemp(suffix="%s.log" % self.toolname)
fda8032fe989 Initial checkin of dynamic script runner. Goal is to add code to generate a new toolshed entry once the script works correctly ross lazarus ross.lazarus@gmail.com parents: diff changeset	126 sto = open(hlog,'w')
fda8032fe989 Initial checkin of dynamic script runner. Goal is to add code to generate a new toolshed entry once the script works correctly ross lazarus ross.lazarus@gmail.com parents: diff changeset	127 outpdf = '%s_compressed' % inpdf
fda8032fe989 Initial checkin of dynamic script runner. Goal is to add code to generate a new toolshed entry once the script works correctly ross lazarus ross.lazarus@gmail.com parents: diff changeset	128 cl = ["gs", "-sDEVICE=pdfwrite", "-dNOPAUSE", "-dBATCH", "-sOutputFile=%s" % outpdf,inpdf]
fda8032fe989 Initial checkin of dynamic script runner. Goal is to add code to generate a new toolshed entry once the script works correctly ross lazarus ross.lazarus@gmail.com parents: diff changeset	129 x = subprocess.Popen(cl,stdout=sto,stderr=sto,cwd=self.opts.output_dir)
fda8032fe989 Initial checkin of dynamic script runner. Goal is to add code to generate a new toolshed entry once the script works correctly ross lazarus ross.lazarus@gmail.com parents: diff changeset	130 retval1 = x.wait()
fda8032fe989 Initial checkin of dynamic script runner. Goal is to add code to generate a new toolshed entry once the script works correctly ross lazarus ross.lazarus@gmail.com parents: diff changeset	131 if retval1 == 0:
fda8032fe989 Initial checkin of dynamic script runner. Goal is to add code to generate a new toolshed entry once the script works correctly ross lazarus ross.lazarus@gmail.com parents: diff changeset	132 os.unlink(inpdf)
fda8032fe989 Initial checkin of dynamic script runner. Goal is to add code to generate a new toolshed entry once the script works correctly ross lazarus ross.lazarus@gmail.com parents: diff changeset	133 shutil.move(outpdf,inpdf)
fda8032fe989 Initial checkin of dynamic script runner. Goal is to add code to generate a new toolshed entry once the script works correctly ross lazarus ross.lazarus@gmail.com parents: diff changeset	134 outpng = '%s.%s' % (os.path.splitext(inpdf)[0],thumbformat)
fda8032fe989 Initial checkin of dynamic script runner. Goal is to add code to generate a new toolshed entry once the script works correctly ross lazarus ross.lazarus@gmail.com parents: diff changeset	135 cl2 = ['convert', inpdf, outpng]
fda8032fe989 Initial checkin of dynamic script runner. Goal is to add code to generate a new toolshed entry once the script works correctly ross lazarus ross.lazarus@gmail.com parents: diff changeset	136 x = subprocess.Popen(cl2,stdout=sto,stderr=sto,cwd=self.opts.output_dir)
fda8032fe989 Initial checkin of dynamic script runner. Goal is to add code to generate a new toolshed entry once the script works correctly ross lazarus ross.lazarus@gmail.com parents: diff changeset	137 retval2 = x.wait()
fda8032fe989 Initial checkin of dynamic script runner. Goal is to add code to generate a new toolshed entry once the script works correctly ross lazarus ross.lazarus@gmail.com parents: diff changeset	138 sto.close()
fda8032fe989 Initial checkin of dynamic script runner. Goal is to add code to generate a new toolshed entry once the script works correctly ross lazarus ross.lazarus@gmail.com parents: diff changeset	139 retval = retval1 or retval2
fda8032fe989 Initial checkin of dynamic script runner. Goal is to add code to generate a new toolshed entry once the script works correctly ross lazarus ross.lazarus@gmail.com parents: diff changeset	140 return retval
fda8032fe989 Initial checkin of dynamic script runner. Goal is to add code to generate a new toolshed entry once the script works correctly ross lazarus ross.lazarus@gmail.com parents: diff changeset	141
fda8032fe989 Initial checkin of dynamic script runner. Goal is to add code to generate a new toolshed entry once the script works correctly ross lazarus ross.lazarus@gmail.com parents: diff changeset	142
fda8032fe989 Initial checkin of dynamic script runner. Goal is to add code to generate a new toolshed entry once the script works correctly ross lazarus ross.lazarus@gmail.com parents: diff changeset	143 def getfSize(self,fpath,outpath):
fda8032fe989 Initial checkin of dynamic script runner. Goal is to add code to generate a new toolshed entry once the script works correctly ross lazarus ross.lazarus@gmail.com parents: diff changeset	144 """
fda8032fe989 Initial checkin of dynamic script runner. Goal is to add code to generate a new toolshed entry once the script works correctly ross lazarus ross.lazarus@gmail.com parents: diff changeset	145 format a nice file size string
fda8032fe989 Initial checkin of dynamic script runner. Goal is to add code to generate a new toolshed entry once the script works correctly ross lazarus ross.lazarus@gmail.com parents: diff changeset	146 """
fda8032fe989 Initial checkin of dynamic script runner. Goal is to add code to generate a new toolshed entry once the script works correctly ross lazarus ross.lazarus@gmail.com parents: diff changeset	147 size = ''
fda8032fe989 Initial checkin of dynamic script runner. Goal is to add code to generate a new toolshed entry once the script works correctly ross lazarus ross.lazarus@gmail.com parents: diff changeset	148 fp = os.path.join(outpath,fpath)
fda8032fe989 Initial checkin of dynamic script runner. Goal is to add code to generate a new toolshed entry once the script works correctly ross lazarus ross.lazarus@gmail.com parents: diff changeset	149 if os.path.isfile(fp):
fda8032fe989 Initial checkin of dynamic script runner. Goal is to add code to generate a new toolshed entry once the script works correctly ross lazarus ross.lazarus@gmail.com parents: diff changeset	150 n = float(os.path.getsize(fp))
fda8032fe989 Initial checkin of dynamic script runner. Goal is to add code to generate a new toolshed entry once the script works correctly ross lazarus ross.lazarus@gmail.com parents: diff changeset	151 if n > 2**20:
fda8032fe989 Initial checkin of dynamic script runner. Goal is to add code to generate a new toolshed entry once the script works correctly ross lazarus ross.lazarus@gmail.com parents: diff changeset	152 size = ' (%1.1f MB)' % (n/2**20)
fda8032fe989 Initial checkin of dynamic script runner. Goal is to add code to generate a new toolshed entry once the script works correctly ross lazarus ross.lazarus@gmail.com parents: diff changeset	153 elif n > 2**10:
fda8032fe989 Initial checkin of dynamic script runner. Goal is to add code to generate a new toolshed entry once the script works correctly ross lazarus ross.lazarus@gmail.com parents: diff changeset	154 size = ' (%1.1f KB)' % (n/2**10)
fda8032fe989 Initial checkin of dynamic script runner. Goal is to add code to generate a new toolshed entry once the script works correctly ross lazarus ross.lazarus@gmail.com parents: diff changeset	155 elif n > 0:
fda8032fe989 Initial checkin of dynamic script runner. Goal is to add code to generate a new toolshed entry once the script works correctly ross lazarus ross.lazarus@gmail.com parents: diff changeset	156 size = ' (%d B)' % (int(n))
fda8032fe989 Initial checkin of dynamic script runner. Goal is to add code to generate a new toolshed entry once the script works correctly ross lazarus ross.lazarus@gmail.com parents: diff changeset	157 return size
fda8032fe989 Initial checkin of dynamic script runner. Goal is to add code to generate a new toolshed entry once the script works correctly ross lazarus ross.lazarus@gmail.com parents: diff changeset	158
fda8032fe989 Initial checkin of dynamic script runner. Goal is to add code to generate a new toolshed entry once the script works correctly ross lazarus ross.lazarus@gmail.com parents: diff changeset	159
fda8032fe989 Initial checkin of dynamic script runner. Goal is to add code to generate a new toolshed entry once the script works correctly ross lazarus ross.lazarus@gmail.com parents: diff changeset	160 def run(self):
fda8032fe989 Initial checkin of dynamic script runner. Goal is to add code to generate a new toolshed entry once the script works correctly ross lazarus ross.lazarus@gmail.com parents: diff changeset	161 """
fda8032fe989 Initial checkin of dynamic script runner. Goal is to add code to generate a new toolshed entry once the script works correctly ross lazarus ross.lazarus@gmail.com parents: diff changeset	162 """
fda8032fe989 Initial checkin of dynamic script runner. Goal is to add code to generate a new toolshed entry once the script works correctly ross lazarus ross.lazarus@gmail.com parents: diff changeset	163 if self.opts.output_dir:
fda8032fe989 Initial checkin of dynamic script runner. Goal is to add code to generate a new toolshed entry once the script works correctly ross lazarus ross.lazarus@gmail.com parents: diff changeset	164 sto = open(self.tlog,'w')
fda8032fe989 Initial checkin of dynamic script runner. Goal is to add code to generate a new toolshed entry once the script works correctly ross lazarus ross.lazarus@gmail.com parents: diff changeset	165 p = subprocess.Popen(' '.join(self.cl),shell=True,stdout=sto,stderr=sto,stdin=subprocess.PIPE,cwd=self.opts.output_dir)
fda8032fe989 Initial checkin of dynamic script runner. Goal is to add code to generate a new toolshed entry once the script works correctly ross lazarus ross.lazarus@gmail.com parents: diff changeset	166 else:
fda8032fe989 Initial checkin of dynamic script runner. Goal is to add code to generate a new toolshed entry once the script works correctly ross lazarus ross.lazarus@gmail.com parents: diff changeset	167 p = subprocess.Popen(' '.join(self.cl),shell=True,stdin=subprocess.PIPE)
fda8032fe989 Initial checkin of dynamic script runner. Goal is to add code to generate a new toolshed entry once the script works correctly ross lazarus ross.lazarus@gmail.com parents: diff changeset	168 p.stdin.write(self.script)
fda8032fe989 Initial checkin of dynamic script runner. Goal is to add code to generate a new toolshed entry once the script works correctly ross lazarus ross.lazarus@gmail.com parents: diff changeset	169 p.stdin.close()
fda8032fe989 Initial checkin of dynamic script runner. Goal is to add code to generate a new toolshed entry once the script works correctly ross lazarus ross.lazarus@gmail.com parents: diff changeset	170 retval = p.wait()
fda8032fe989 Initial checkin of dynamic script runner. Goal is to add code to generate a new toolshed entry once the script works correctly ross lazarus ross.lazarus@gmail.com parents: diff changeset	171 if self.opts.output_dir:
fda8032fe989 Initial checkin of dynamic script runner. Goal is to add code to generate a new toolshed entry once the script works correctly ross lazarus ross.lazarus@gmail.com parents: diff changeset	172 sto.close()
fda8032fe989 Initial checkin of dynamic script runner. Goal is to add code to generate a new toolshed entry once the script works correctly ross lazarus ross.lazarus@gmail.com parents: diff changeset	173 flist = os.listdir(self.opts.output_dir)
fda8032fe989 Initial checkin of dynamic script runner. Goal is to add code to generate a new toolshed entry once the script works correctly ross lazarus ross.lazarus@gmail.com parents: diff changeset	174 flist = [x for x in flist if x <> 'Rplots.pdf']
fda8032fe989 Initial checkin of dynamic script runner. Goal is to add code to generate a new toolshed entry once the script works correctly ross lazarus ross.lazarus@gmail.com parents: diff changeset	175 flist.sort()
fda8032fe989 Initial checkin of dynamic script runner. Goal is to add code to generate a new toolshed entry once the script works correctly ross lazarus ross.lazarus@gmail.com parents: diff changeset	176 html = [galhtmlprefix % progname,]
fda8032fe989 Initial checkin of dynamic script runner. Goal is to add code to generate a new toolshed entry once the script works correctly ross lazarus ross.lazarus@gmail.com parents: diff changeset	177 html.append('<h2>Galaxy %s outputs run at %s</h2></br>Click on a thumbnail below to download the original PDF</br>\n' % (self.toolname,timenow()))
fda8032fe989 Initial checkin of dynamic script runner. Goal is to add code to generate a new toolshed entry once the script works correctly ross lazarus ross.lazarus@gmail.com parents: diff changeset	178 fhtml = []
fda8032fe989 Initial checkin of dynamic script runner. Goal is to add code to generate a new toolshed entry once the script works correctly ross lazarus ross.lazarus@gmail.com parents: diff changeset	179 if len(flist) > 0:
fda8032fe989 Initial checkin of dynamic script runner. Goal is to add code to generate a new toolshed entry once the script works correctly ross lazarus ross.lazarus@gmail.com parents: diff changeset	180 html.append('<table cellpadding="3" cellspacing="3">\n')
fda8032fe989 Initial checkin of dynamic script runner. Goal is to add code to generate a new toolshed entry once the script works correctly ross lazarus ross.lazarus@gmail.com parents: diff changeset	181 for fname in flist:
fda8032fe989 Initial checkin of dynamic script runner. Goal is to add code to generate a new toolshed entry once the script works correctly ross lazarus ross.lazarus@gmail.com parents: diff changeset	182 dname,e = os.path.splitext(fname)
fda8032fe989 Initial checkin of dynamic script runner. Goal is to add code to generate a new toolshed entry once the script works correctly ross lazarus ross.lazarus@gmail.com parents: diff changeset	183 sfsize = self.getfSize(fname,self.opts.output_dir)
fda8032fe989 Initial checkin of dynamic script runner. Goal is to add code to generate a new toolshed entry once the script works correctly ross lazarus ross.lazarus@gmail.com parents: diff changeset	184 if e.lower() == '.pdf' : # compress and make a thumbnail
fda8032fe989 Initial checkin of dynamic script runner. Goal is to add code to generate a new toolshed entry once the script works correctly ross lazarus ross.lazarus@gmail.com parents: diff changeset	185 thumb = '%s.%s' % (dname,self.thumbformat)
fda8032fe989 Initial checkin of dynamic script runner. Goal is to add code to generate a new toolshed entry once the script works correctly ross lazarus ross.lazarus@gmail.com parents: diff changeset	186 pdff = os.path.join(self.opts.output_dir,fname)
fda8032fe989 Initial checkin of dynamic script runner. Goal is to add code to generate a new toolshed entry once the script works correctly ross lazarus ross.lazarus@gmail.com parents: diff changeset	187 retval = self.compressPDF(inpdf=pdff,thumbformat=self.thumbformat)
fda8032fe989 Initial checkin of dynamic script runner. Goal is to add code to generate a new toolshed entry once the script works correctly ross lazarus ross.lazarus@gmail.com parents: diff changeset	188 if retval == 0:
fda8032fe989 Initial checkin of dynamic script runner. Goal is to add code to generate a new toolshed entry once the script works correctly ross lazarus ross.lazarus@gmail.com parents: diff changeset	189 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)
fda8032fe989 Initial checkin of dynamic script runner. Goal is to add code to generate a new toolshed entry once the script works correctly ross lazarus ross.lazarus@gmail.com parents: diff changeset	190 html.append(s)
fda8032fe989 Initial checkin of dynamic script runner. Goal is to add code to generate a new toolshed entry once the script works correctly ross lazarus ross.lazarus@gmail.com parents: diff changeset	191 fhtml.append('<li><a href="%s">%s %s</a></li>' % (fname,fname,sfsize))
fda8032fe989 Initial checkin of dynamic script runner. Goal is to add code to generate a new toolshed entry once the script works correctly ross lazarus ross.lazarus@gmail.com parents: diff changeset	192 else:
fda8032fe989 Initial checkin of dynamic script runner. Goal is to add code to generate a new toolshed entry once the script works correctly ross lazarus ross.lazarus@gmail.com parents: diff changeset	193 fhtml.append('<li><a href="%s">%s %s</a></li>' % (fname,fname,sfsize))
fda8032fe989 Initial checkin of dynamic script runner. Goal is to add code to generate a new toolshed entry once the script works correctly ross lazarus ross.lazarus@gmail.com parents: diff changeset	194 html.append('</table>\n')
fda8032fe989 Initial checkin of dynamic script runner. Goal is to add code to generate a new toolshed entry once the script works correctly ross lazarus ross.lazarus@gmail.com parents: diff changeset	195 if len(fhtml) > 0:
fda8032fe989 Initial checkin of dynamic script runner. Goal is to add code to generate a new toolshed entry once the script works correctly ross lazarus ross.lazarus@gmail.com parents: diff changeset	196 fhtml.insert(0,'<ul>')
fda8032fe989 Initial checkin of dynamic script runner. Goal is to add code to generate a new toolshed entry once the script works correctly ross lazarus ross.lazarus@gmail.com parents: diff changeset	197 fhtml.append('</ul>')
fda8032fe989 Initial checkin of dynamic script runner. Goal is to add code to generate a new toolshed entry once the script works correctly ross lazarus ross.lazarus@gmail.com parents: diff changeset	198 html += fhtml # add all non-pdf files to the end of the display
fda8032fe989 Initial checkin of dynamic script runner. Goal is to add code to generate a new toolshed entry once the script works correctly ross lazarus ross.lazarus@gmail.com parents: diff changeset	199 else:
fda8032fe989 Initial checkin of dynamic script runner. Goal is to add code to generate a new toolshed entry once the script works correctly ross lazarus ross.lazarus@gmail.com parents: diff changeset	200 html.append('<h2>### Error - %s returned no files - please confirm that parameters are sane</h1>' % self.opts.interpreter)
fda8032fe989 Initial checkin of dynamic script runner. Goal is to add code to generate a new toolshed entry once the script works correctly ross lazarus ross.lazarus@gmail.com parents: diff changeset	201 html.append('<h3>%s log follows below</h3><hr><pre>\n' % self.opts.interpreter)
fda8032fe989 Initial checkin of dynamic script runner. Goal is to add code to generate a new toolshed entry once the script works correctly ross lazarus ross.lazarus@gmail.com parents: diff changeset	202 rlog = open(self.tlog,'r').readlines()
fda8032fe989 Initial checkin of dynamic script runner. Goal is to add code to generate a new toolshed entry once the script works correctly ross lazarus ross.lazarus@gmail.com parents: diff changeset	203 html += rlog
fda8032fe989 Initial checkin of dynamic script runner. Goal is to add code to generate a new toolshed entry once the script works correctly ross lazarus ross.lazarus@gmail.com parents: diff changeset	204 html.append('%s CL = %s</br>\n' % (self.toolname,' '.join(sys.argv)))
fda8032fe989 Initial checkin of dynamic script runner. Goal is to add code to generate a new toolshed entry once the script works correctly ross lazarus ross.lazarus@gmail.com parents: diff changeset	205 html.append('CL = %s</br>\n' % (' '.join(self.cl)))
fda8032fe989 Initial checkin of dynamic script runner. Goal is to add code to generate a new toolshed entry once the script works correctly ross lazarus ross.lazarus@gmail.com parents: diff changeset	206 html.append('</pre>\n')
fda8032fe989 Initial checkin of dynamic script runner. Goal is to add code to generate a new toolshed entry once the script works correctly ross lazarus ross.lazarus@gmail.com parents: diff changeset	207 html.append(galhtmlattr % (progname,timenow()))
fda8032fe989 Initial checkin of dynamic script runner. Goal is to add code to generate a new toolshed entry once the script works correctly ross lazarus ross.lazarus@gmail.com parents: diff changeset	208 html.append(galhtmlpostfix)
fda8032fe989 Initial checkin of dynamic script runner. Goal is to add code to generate a new toolshed entry once the script works correctly ross lazarus ross.lazarus@gmail.com parents: diff changeset	209 htmlf = file(self.opts.output_html,'w')
fda8032fe989 Initial checkin of dynamic script runner. Goal is to add code to generate a new toolshed entry once the script works correctly ross lazarus ross.lazarus@gmail.com parents: diff changeset	210 htmlf.write('\n'.join(html))
fda8032fe989 Initial checkin of dynamic script runner. Goal is to add code to generate a new toolshed entry once the script works correctly ross lazarus ross.lazarus@gmail.com parents: diff changeset	211 htmlf.write('\n')
fda8032fe989 Initial checkin of dynamic script runner. Goal is to add code to generate a new toolshed entry once the script works correctly ross lazarus ross.lazarus@gmail.com parents: diff changeset	212 htmlf.close()
fda8032fe989 Initial checkin of dynamic script runner. Goal is to add code to generate a new toolshed entry once the script works correctly ross lazarus ross.lazarus@gmail.com parents: diff changeset	213 return retval
fda8032fe989 Initial checkin of dynamic script runner. Goal is to add code to generate a new toolshed entry once the script works correctly ross lazarus ross.lazarus@gmail.com parents: diff changeset	214
fda8032fe989 Initial checkin of dynamic script runner. Goal is to add code to generate a new toolshed entry once the script works correctly ross lazarus ross.lazarus@gmail.com parents: diff changeset	215
fda8032fe989 Initial checkin of dynamic script runner. Goal is to add code to generate a new toolshed entry once the script works correctly ross lazarus ross.lazarus@gmail.com parents: diff changeset	216 def main():
fda8032fe989 Initial checkin of dynamic script runner. Goal is to add code to generate a new toolshed entry once the script works correctly ross lazarus ross.lazarus@gmail.com parents: diff changeset	217 u = """
fda8032fe989 Initial checkin of dynamic script runner. Goal is to add code to generate a new toolshed entry once the script works correctly ross lazarus ross.lazarus@gmail.com parents: diff changeset	218 This is a Galaxy wrapper. It expects to be called by a special purpose tool.xml as:
fda8032fe989 Initial checkin of dynamic script runner. Goal is to add code to generate a new toolshed entry once the script works correctly ross lazarus ross.lazarus@gmail.com parents: diff changeset	219 <command interpreter="python">rgBaseScriptWrapper.py --script_path "$scriptPath" --tool_name "foo" --interpreter "Rscript"
fda8032fe989 Initial checkin of dynamic script runner. Goal is to add code to generate a new toolshed entry once the script works correctly ross lazarus ross.lazarus@gmail.com parents: diff changeset	220 </command>
fda8032fe989 Initial checkin of dynamic script runner. Goal is to add code to generate a new toolshed entry once the script works correctly ross lazarus ross.lazarus@gmail.com parents: diff changeset	221 """
fda8032fe989 Initial checkin of dynamic script runner. Goal is to add code to generate a new toolshed entry once the script works correctly ross lazarus ross.lazarus@gmail.com parents: diff changeset	222 permitted_users = ['rlazarus@bakeridi.edu.au','akaspi@bakeridi.edu.au','mziemann@bakeridi.edu.edu']
fda8032fe989 Initial checkin of dynamic script runner. Goal is to add code to generate a new toolshed entry once the script works correctly ross lazarus ross.lazarus@gmail.com parents: diff changeset	223 op = optparse.OptionParser()
fda8032fe989 Initial checkin of dynamic script runner. Goal is to add code to generate a new toolshed entry once the script works correctly ross lazarus ross.lazarus@gmail.com parents: diff changeset	224 a = op.add_option
fda8032fe989 Initial checkin of dynamic script runner. Goal is to add code to generate a new toolshed entry once the script works correctly ross lazarus ross.lazarus@gmail.com parents: diff changeset	225 a('--script_path',default=None)
fda8032fe989 Initial checkin of dynamic script runner. Goal is to add code to generate a new toolshed entry once the script works correctly ross lazarus ross.lazarus@gmail.com parents: diff changeset	226 a('--tool_name',default=None)
fda8032fe989 Initial checkin of dynamic script runner. Goal is to add code to generate a new toolshed entry once the script works correctly ross lazarus ross.lazarus@gmail.com parents: diff changeset	227 a('--interpreter',default=None)
fda8032fe989 Initial checkin of dynamic script runner. Goal is to add code to generate a new toolshed entry once the script works correctly ross lazarus ross.lazarus@gmail.com parents: diff changeset	228 a('--output_dir',default=None)
fda8032fe989 Initial checkin of dynamic script runner. Goal is to add code to generate a new toolshed entry once the script works correctly ross lazarus ross.lazarus@gmail.com parents: diff changeset	229 a('--output_html',default=None)
fda8032fe989 Initial checkin of dynamic script runner. Goal is to add code to generate a new toolshed entry once the script works correctly ross lazarus ross.lazarus@gmail.com parents: diff changeset	230 a('--input_tab',default='NONE')
fda8032fe989 Initial checkin of dynamic script runner. Goal is to add code to generate a new toolshed entry once the script works correctly ross lazarus ross.lazarus@gmail.com parents: diff changeset	231 a('--output_tab',default='NONE')
fda8032fe989 Initial checkin of dynamic script runner. Goal is to add code to generate a new toolshed entry once the script works correctly ross lazarus ross.lazarus@gmail.com parents: diff changeset	232 a('--user_email',default=None)
fda8032fe989 Initial checkin of dynamic script runner. Goal is to add code to generate a new toolshed entry once the script works correctly ross lazarus ross.lazarus@gmail.com parents: diff changeset	233 a('--bad_user',default=None)
fda8032fe989 Initial checkin of dynamic script runner. Goal is to add code to generate a new toolshed entry once the script works correctly ross lazarus ross.lazarus@gmail.com parents: diff changeset	234 opts, args = op.parse_args()
fda8032fe989 Initial checkin of dynamic script runner. Goal is to add code to generate a new toolshed entry once the script works correctly ross lazarus ross.lazarus@gmail.com parents: diff changeset	235 assert not opts.bad_user,'%s is NOT authorized to use this tool. Please ask your friendly admin' % opts.bad_user
fda8032fe989 Initial checkin of dynamic script runner. Goal is to add code to generate a new toolshed entry once the script works correctly ross lazarus ross.lazarus@gmail.com parents: diff changeset	236 assert opts.tool_name,'## Dynamic script wrapper expects a tool name - eg --tool_name=DESeq'
fda8032fe989 Initial checkin of dynamic script runner. Goal is to add code to generate a new toolshed entry once the script works correctly ross lazarus ross.lazarus@gmail.com parents: diff changeset	237 assert opts.interpreter,'## Dynamic script wrapper expects an interpreter - eg --interpreter=Rscript'
fda8032fe989 Initial checkin of dynamic script runner. Goal is to add code to generate a new toolshed entry once the script works correctly ross lazarus ross.lazarus@gmail.com parents: diff changeset	238 assert os.path.isfile(opts.script_path),'## Dynamic script wrapper expects a script path - eg --script_path=foo.R'
fda8032fe989 Initial checkin of dynamic script runner. Goal is to add code to generate a new toolshed entry once the script works correctly ross lazarus ross.lazarus@gmail.com parents: diff changeset	239 if opts.output_dir:
fda8032fe989 Initial checkin of dynamic script runner. Goal is to add code to generate a new toolshed entry once the script works correctly ross lazarus ross.lazarus@gmail.com parents: diff changeset	240 try:
fda8032fe989 Initial checkin of dynamic script runner. Goal is to add code to generate a new toolshed entry once the script works correctly ross lazarus ross.lazarus@gmail.com parents: diff changeset	241 os.makedirs(opts.output_dir)
fda8032fe989 Initial checkin of dynamic script runner. Goal is to add code to generate a new toolshed entry once the script works correctly ross lazarus ross.lazarus@gmail.com parents: diff changeset	242 except:
fda8032fe989 Initial checkin of dynamic script runner. Goal is to add code to generate a new toolshed entry once the script works correctly ross lazarus ross.lazarus@gmail.com parents: diff changeset	243 pass
fda8032fe989 Initial checkin of dynamic script runner. Goal is to add code to generate a new toolshed entry once the script works correctly ross lazarus ross.lazarus@gmail.com parents: diff changeset	244 r = ScriptRunner(opts)
fda8032fe989 Initial checkin of dynamic script runner. Goal is to add code to generate a new toolshed entry once the script works correctly ross lazarus ross.lazarus@gmail.com parents: diff changeset	245 retcode = r.run()
fda8032fe989 Initial checkin of dynamic script runner. Goal is to add code to generate a new toolshed entry once the script works correctly ross lazarus ross.lazarus@gmail.com parents: diff changeset	246 if retcode:
1 0133b97e477e Write to stderr to force job runner to realise that the tool failed - it ignores return codes :( ross lazarus ross.lazarus@gmail.com parents: 0 diff changeset	247 print >> sys.stderr,'Executing your script %s failed - return code was %d' % (opts.tool_name,retcode)
0 fda8032fe989 Initial checkin of dynamic script runner. Goal is to add code to generate a new toolshed entry once the script works correctly ross lazarus ross.lazarus@gmail.com parents: diff changeset	248 sys.exit(retcode) # indicate failure to job runner
fda8032fe989 Initial checkin of dynamic script runner. Goal is to add code to generate a new toolshed entry once the script works correctly ross lazarus ross.lazarus@gmail.com parents: diff changeset	249
fda8032fe989 Initial checkin of dynamic script runner. Goal is to add code to generate a new toolshed entry once the script works correctly ross lazarus ross.lazarus@gmail.com parents: diff changeset	250
fda8032fe989 Initial checkin of dynamic script runner. Goal is to add code to generate a new toolshed entry once the script works correctly ross lazarus ross.lazarus@gmail.com parents: diff changeset	251 if __name__ == "__main__":
fda8032fe989 Initial checkin of dynamic script runner. Goal is to add code to generate a new toolshed entry once the script works correctly ross lazarus ross.lazarus@gmail.com parents: diff changeset	252 main()
fda8032fe989 Initial checkin of dynamic script runner. Goal is to add code to generate a new toolshed entry once the script works correctly ross lazarus ross.lazarus@gmail.com parents: diff changeset	253
fda8032fe989 Initial checkin of dynamic script runner. Goal is to add code to generate a new toolshed entry once the script works correctly ross lazarus ross.lazarus@gmail.com parents: diff changeset	254

Mercurial > repos > fubar > brokenandnotdeletablebyowneroradmin

annotate rgDynamicScriptWrapper.py @ 2:d95513e50c92