fubar/brokenandnotdeletablebyowneroradmin: rgToolFactory.py annotate

annotate rgToolFactory.py @ 8:220885b2d7ee

End to end test works. Add tests next

author	ross lazarus ross.lazarus@gmail.com
date	Sat, 02 Jun 2012 20:02:11 +1000
parents	7221619caefa
children	e09c76551bed

rev	line source
7 7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	1 # rgDynamicScriptWrapper.py
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	2 # derived from
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	3 # rgBaseScriptWrapper.py
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	4 # to run some user supplied code
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	5 # extremely dangerous
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	6 # trusted users only - private site only
7221619caefa Updated name and added crude gzip generator for toolshed 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.
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	8 #
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	9 # copyright ross lazarus (ross.lazarus@gmail.com) May 2012
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	10 #
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	11 # all rights reserved
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	12 # Licensed under the LGPL for your pleasure
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	13 # Derived from rgDGE.py in May 2012
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	14 # generalized to run required interpreter
7221619caefa Updated name and added crude gzip generator for toolshed 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
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	16 # clone this and the corresponding xml wrapper
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	17 # replace the parameters/inputs/outputs and the configfile contents with your script
7221619caefa Updated name and added crude gzip generator for toolshed 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
7221619caefa Updated name and added crude gzip generator for toolshed 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.
7221619caefa Updated name and added crude gzip generator for toolshed 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
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	21 # after this generic script runner runs your script with the specified interpreter,
7221619caefa Updated name and added crude gzip generator for toolshed 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.
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	23
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	24 import sys
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	25 import shutil
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	26 import subprocess
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	27 import os
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	28 import time
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	29 import tempfile
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	30 import optparse
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	31 import tarfile
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	32 import re
8 220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	33 import shutil
220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	34
7 7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	35 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	36 myversion = 'V000.1 May 2012'
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	37 verbose = False
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	38 debug = False
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	39
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	40
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	41 def timenow():
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	42 """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	43 """
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	44 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	45 # 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	46 mapped_chars = { '>' :'__gt__',
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	47 '<' :'__lt__',
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	48 "'" :'__sq__',
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	49 '"' :'__dq__',
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	50 '{' :'__oc__',
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	51 '}' :'__cc__',
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	52 '@' : '__at__',
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	53 '\n' : '__cn__',
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	54 '\r' : '__cr__',
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	55 '\t' : '__tc__',
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	56 '#' : '__pd__',
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	57 '[' :'__ob__',
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	58 ']' :'__cb__',
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	59 '\t' : 'Xt',
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	60 'systemCallsAreNotAllowed' : 'system'
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	61 }
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	62
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	63 def restore_text(text):
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	64 """Restores sanitized text"""
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	65 if not text:
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	66 return text
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	67 for key, value in mapped_chars.items():
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	68 text = text.replace(value, key)
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	69 return text
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	70
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	71 class ScriptRunner:
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	72 """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	73 """
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	74
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	75 def __init__(self,opts=None):
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	76 """
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	77 run the script
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	78 cheetah/galaxy will provide an escaped string so
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	79 __pd__ your script goes here
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	80 __cr____cn__ourargs __lt__- commandArgs(TRUE)
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	81 __cr____cn__inf = ourargs[1]
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	82 __cr____cn__outf = ourargs[2]
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	83 __cr____cn__inp = read.table(inf,head=T,rownames=F,sep=__sq__Xt__sq__)
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	84 __cr____cn__ write.table(inp,outf, quote=FALSE, sep=__dq__Xt__dq__,row.names=F)
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	85 __cr____cn__sessionInfo()
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	86 __cr____cn__
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	87 """
8 220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	88 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	89 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	90 self.thumbformat = 'jpg'
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	91 self.opts = opts
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	92 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	93 self.toolid = self.toolname
7 7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	94 s = open(self.opts.script_path,'r').read()
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	95 self.script = restore_text(s)
8 220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	96 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	97 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	98 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	99 self.sfile = '%s.%s' % (self.toolname,opts.interpreter)
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	100 localscript = open(self.sfile,'w')
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	101 localscript.write(self.script)
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	102 localscript.close()
8 220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	103 if opts.output_dir or self.opts.make_Tool: # may not want these complexities if a simple script
7 7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	104 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	105 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	106 artifact = open(artifactpath,'w')
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	107 artifact.write(self.script)
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	108 artifact.write('\n')
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	109 artifact.close()
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	110 self.cl = []
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	111 self.html = []
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	112 a = self.cl.append
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	113 a(opts.interpreter)
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	114 a('-') # use stdin
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	115 a(opts.input_tab)
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	116 a(opts.output_tab)
8 220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	117 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	118 self.inputFormats = '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	119
220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	120
220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	121 def makeXML(self):
220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	122 """
220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	123 Create a Galaxy xml tool wrapper for the new script as a string to write out
220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	124 """
220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	125 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	126 %(tooldesc)s
220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	127 %(command)s
220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	128 <inputs>
220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	129 %(inputs)s
220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	130 </inputs>
220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	131 <outputs>
220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	132 %(outputs)s
220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	133 </outputs>
220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	134 <help>
220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	135 %(help)s
220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	136 </help>
220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	137 <configfiles>
220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	138 <configfile name="runMe">
220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	139 %(script)s
220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	140 </configfile>
220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	141 </configfiles>
220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	142 </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	143
220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	144 newCommand="""<command interpreter="python">
220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	145 %(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	146 --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	147 </command>""" # may NOT be an input or htmlout
220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	148
220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	149 xdict = {}
220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	150 xdict['script'] = self.script # we pass this as a configfile because it's less painful that galaxy_tool_data_dir
220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	151 # embed script in tool - remove dependence on something else outside in the wilds
220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	152 if self.opts.help_text:
220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	153 h = open(self.opts.help_text,'r').read()
220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	154 xdict['help'] = restore_text(h)
220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	155 else:
220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	156 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	157 if self.opts.tool_desc:
220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	158 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	159 else:
220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	160 xdict['tooldesc'] = ''
220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	161 xdict['command_outputs'] = '' # will probably be some!
220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	162 xdict['outputs'] = '' # will probably be some!
220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	163 if self.opts.input_tab:
220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	164 xdict['command_inputs'] = '--input_tab "$input1"'
220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	165 xdict['inputs'] = '<param name="input1" type="data" format="%s" label="Select a suitable input file from your history"/>' % self.inputFormats
220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	166 else:
220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	167 xdict['command_inputs'] = '' # assume no input - eg a random data generator
220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	168 xdict['inputs'] = ''
220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	169 xdict['inputs'] += '<param name="job_name" type="text" label="Supply a name for the outputs to remind you what they contain" value="%s"/>\n' % self.toolname
220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	170 xdict['toolname'] = self.toolname
220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	171 xdict['toolid'] = self.toolid
220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	172 xdict['interpreter'] = self.opts.interpreter
220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	173 xdict['scriptname'] = self.sfile
220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	174 if self.opts.make_HTML:
220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	175 xdict['command_outputs'] += '--output_dir "$html_file.files_path" --output_html "$html_file"'
220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	176 xdict['outputs'] += '<data format="html" name="html_file" label="${job_name}.html"/>\n'
220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	177 if self.opts.output_tab:
220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	178 xdict['command_outputs'] += '--output_tab "$tab_file"'
220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	179 xdict['outputs'] += '<data format="%s" name="tab_file" label="${job_name}"/>\n' % self.outFormats
220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	180 xdict['command'] = newCommand % xdict
220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	181 xmls = newXML % xdict
220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	182 xf = open(self.xmlfile,'w')
220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	183 xf.write(xmls)
220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	184 xf.write('\n')
220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	185 xf.close()
220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	186 # ready for the tarball
220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	187
7 7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	188
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	189 def makeTooltar(self):
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	190 """
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	191 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	192 /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	193 """
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	194 retval = self.run()
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	195 if retval:
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	196 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	197 sys.exit(1)
8 220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	198 self.makeXML()
220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	199 tdir = self.toolname
220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	200 os.mkdir(tdir)
220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	201 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	202 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	203 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	204 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	205 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	206 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	207 tar.close()
8 220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	208 shutil.rmtree(tdir)
220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	209 self.makeHtml() # call this to return the new gzip inside the autogenerated html file
220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	210 ## 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	211 return retval
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	212
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	213 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	214 """need absolute path to pdf
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	215 """
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	216 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	217 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	218 sto = open(hlog,'w')
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	219 outpdf = '%s_compressed' % inpdf
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	220 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	221 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	222 retval1 = x.wait()
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	223 if retval1 == 0:
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	224 os.unlink(inpdf)
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	225 shutil.move(outpdf,inpdf)
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	226 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	227 cl2 = ['convert', inpdf, outpng]
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	228 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	229 retval2 = x.wait()
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	230 sto.close()
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	231 retval = retval1 or retval2
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	232 return retval
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	233
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	234
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	235 def getfSize(self,fpath,outpath):
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 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	238 """
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	239 size = ''
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	240 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	241 if os.path.isfile(fp):
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	242 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	243 if n > 2**20:
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	244 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	245 elif n > 2**10:
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	246 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	247 elif n > 0:
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	248 size = ' (%d B)' % (int(n))
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	249 return size
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	250
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	251 def makeHtml(self):
8 220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	252 """ 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	253 """
220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	254
220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	255 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	256 <!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	257 <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	258 <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	259 <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	260 <title></title>
220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	261 <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	262 </head>
220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	263 <body>
220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	264 <div class="document">
220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	265 """
220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	266 galhtmlattr = """<hr/><b><a href="http://rgenetics.org">Galaxy Tool Factory Script Wrapper</a> tool output %s run at %s</b><br/>"""
220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	267 galhtmlpostfix = """</div></body></html>\n"""
220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	268
220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	269 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	270 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	271 flist.sort()
220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	272 html = [galhtmlprefix % progname,]
220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	273 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	274 fhtml = []
220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	275 if len(flist) > 0:
220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	276 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	277 for fname in flist:
7 7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	278 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	279 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	280 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	281 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	282 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	283 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	284 if retval == 0:
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	285 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	286 html.append(s)
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	287 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	288 else:
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	289 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	290 html.append('</table>\n')
220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	291 if len(fhtml) > 0:
220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	292 fhtml.insert(0,'<ul>')
220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	293 fhtml.append('</ul>')
220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	294 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	295 else:
220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	296 html.append('<h2>### Error - %s returned no files - please confirm that parameters are sane</h1>' % self.opts.interpreter)
220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	297 html.append('<h3>%s log follows below</h3><hr/><pre>\n' % self.opts.interpreter)
220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	298 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	299 html += rlog
220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	300 html.append('%s CL = %s<br/>\n' % (self.toolname,' '.join(sys.argv)))
220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	301 html.append('</pre>\n')
220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	302 html.append(galhtmlattr % (progname,timenow()))
220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	303 html.append(galhtmlpostfix)
220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	304 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	305 htmlf.write('\n'.join(html))
220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	306 htmlf.write('\n')
220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	307 htmlf.close()
220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	308 self.html = html
7 7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	309
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	310
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	311 def run(self):
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	312 """
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	313 """
8 220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	314 if self.opts.output_dir or self.opts.make_Tool:
7 7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	315 sto = open(self.tlog,'w')
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	316 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	317 else:
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	318 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	319 p.stdin.write(self.script)
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	320 p.stdin.close()
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	321 retval = p.wait()
8 220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	322 if self.opts.make_HTML or self.opts.make_Tool:
7 7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	323 sto.close()
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	324 self.makeHtml()
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	325 return retval
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	326
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	327
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	328 def main():
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	329 u = """
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	330 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	331 <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	332 </command>
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	333 """
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	334 op = optparse.OptionParser()
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	335 a = op.add_option
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	336 a('--script_path',default=None)
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	337 a('--tool_name',default=None)
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	338 a('--interpreter',default=None)
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	339 a('--output_dir',default=None)
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	340 a('--output_html',default=None)
8 220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	341 a('--input_tab',default=None)
220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	342 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	343 a('--user_email',default=None)
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	344 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	345 a('--make_Tool',default=None)
220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	346 a('--make_HTML',default=None)
220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	347 a('--help_text',default=None)
220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	348 a('--tool_desc',default=None)
7 7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	349 opts, args = op.parse_args()
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	350 assert not opts.bad_user,'%s is NOT authorized to use this tool. Please ask your friendly admin' % opts.bad_user
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	351 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	352 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	353 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	354 if opts.output_dir:
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	355 try:
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	356 os.makedirs(opts.output_dir)
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	357 except:
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	358 pass
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	359 r = ScriptRunner(opts)
8 220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	360 if opts.make_Tool:
7 7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	361 retcode = r.makeTooltar()
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	362 else:
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	363 retcode = r.run()
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	364 if retcode:
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	365 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	366
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 if __name__ == "__main__":
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	369 main()
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

Mercurial > repos > fubar > brokenandnotdeletablebyowneroradmin

annotate rgToolFactory.py @ 8:220885b2d7ee