toolfactory: fubar-galaxytoolfactory-9603e5fd1d9a/rgToolFactory.py annotate

author	fubar
date	Mon, 02 Jul 2012 00:51:18 -0400
parents
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rev	line source
15 764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	1 # rgToolFactory.py
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	2 # see https://bitbucket.org/fubar/galaxytoolfactory/wiki/Home
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	3 #
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	4 # copyright ross lazarus (ross stop lazarus at gmail stop com) May 2012
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	5 #
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	6 # all rights reserved
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	7 # Licensed under the LGPL
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	8 # suggestions for improvement and bug fixes welcome at https://bitbucket.org/fubar/galaxytoolfactory/wiki/Home
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	9
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	10 # This is a Galaxy tool factory for simple scripts in python, R or whatever ails ye.
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	11 # It also serves as the wrapper for the new tool.
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	12 #
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	13 # you paste and run your script
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	14 # Only works for simple scripts that read one input from the history.
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	15 # Optionally can write one new history dataset,
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	16 # and optionally collect any number of outputs into links on an autogenerated HTML page.
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	17
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	18 # DO NOT install on a public or important site - please.
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	19
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	20 # installed generated tools are fine if the script is safe.
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	21 # They just run normally and their user cannot do anything unusually insecure
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	22 # but please, practice safe toolshed.
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	23 # Read the fucking code before you install any tool
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	24 # especially this one
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	25
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	26 # After you get the script working on some test data, you can
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	27 # optionally generate a toolshed compatible gzip file
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	28 # containing your script safely wrapped as an ordinary Galaxy script in your local toolshed for
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	29 # safe and largely automated installation in a production Galaxy.
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	30
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	31 # If you opt for an HTML output, you get all the script outputs arranged
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	32 # as a single Html history item - all output files are linked, thumbnails for all the pdfs.
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	33 # Ugly but really inexpensive.
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	34 #
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	35 # Patches appreciated please.
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	36 #
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	37 #
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	38 # long route to June 2012 product
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	39 # Behold the awesome power of Galaxy and the toolshed with the tool factory binds to bind them
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	40 # derived from an integrated script model
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	41 # called rgBaseScriptWrapper.py
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	42 # Note to the unwary:
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	43 # This tool allows arbitrary scripting on your Galaxy as the Galaxy user
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	44 # There is nothing stopping a malicious user doing whatever they choose
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	45 # Extremely dangerous!!
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	46 # Totally insecure. So, trusted users only
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	47 #
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	48 # preferred model is a developer using their throw away workstation instance - ie a private site.
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	49 # no real risk. The universe_wsgi.ini admin_users string is checked - only admin users are permitted to run this tool.
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	50 #
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	51
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	52 import sys
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	53 import shutil
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	54 import subprocess
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	55 import os
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	56 import time
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	57 import tempfile
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	58 import optparse
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	59 import tarfile
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	60 import re
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	61 import shutil
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	62 import math
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	63
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	64 progname = os.path.split(sys.argv[0])[1]
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	65 myversion = 'V000.2 June 2012'
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	66 verbose = False
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	67 debug = False
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	68 toolFactoryURL = 'https://bitbucket.org/fubar/galaxytoolfactory'
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	69
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	70 def timenow():
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	71 """return current time as a string
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	72 """
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	73 return time.strftime('%d/%m/%Y %H:%M:%S', time.localtime(time.time()))
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	74
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	75
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	76 class ScriptRunner:
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	77 """class is a wrapper for an arbitrary script
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	78 """
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	79
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	80 def __init__(self,opts=None):
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	81 """
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	82 cleanup inputs, setup some outputs
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	83
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	84 """
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	85 if opts.output_dir: # simplify for the tool tarball
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	86 os.chdir(opts.output_dir)
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	87 self.thumbformat = 'jpg'
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	88 self.opts = opts
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	89 self.toolname = re.sub('[^a-zA-Z0-9_]+', '', opts.tool_name) # a sanitizer now does this but..
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	90 self.toolid = self.toolname
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	91 s = open(self.opts.script_path,'r').readlines()
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	92 self.script = ''.join(s)
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	93 self.indentedScript = ''.join([' %s' % x for x in s]) # for restructured text in help
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	94 self.myname = sys.argv[0] # get our name because we write ourselves out as a tool later
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	95 self.pyfile = self.myname # crude but efficient - the cruft won't hurt much
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	96 self.xmlfile = '%s.xml' % self.toolname
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	97 self.sfile = '%s.%s' % (self.toolname,opts.interpreter)
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	98 if opts.output_dir: # may not want these complexities
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	99 self.tlog = os.path.join(opts.output_dir,"%s_runner.log" % self.toolname)
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	100 artifactpath = os.path.join(opts.output_dir,'%s_run.script' % self.toolname)
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	101 artifact = open(artifactpath,'w')
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	102 artifact.write(self.script)
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	103 artifact.write('\n')
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	104 artifact.close()
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	105 if opts.make_Tool: # need this code and the user script for the tarball
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	106 localscript = open(self.sfile,'w')
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	107 localscript.write(self.script)
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	108 localscript.close()
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	109 self.cl = []
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	110 self.html = []
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	111 a = self.cl.append
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	112 a(opts.interpreter)
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	113 a('-') # use stdin
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	114 a(opts.input_tab)
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	115 a(opts.output_tab)
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	116 self.outFormats = 'tabular' # TODO make this an option at tool generation time
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	117 self.inputFormats = 'tabular' # TODO make this an option at tool generation time
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	118 self.test1Input = '%s_test1_input.xls' % self.toolname
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	119 self.test1Output = '%s_test1_output.xls' % self.toolname
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	120 self.test1HTML = '%s_test1_output.html' % self.toolname
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	121
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	122 def makeXML(self):
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	123 """
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	124 Create a Galaxy xml tool wrapper for the new script as a string to write out
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	125 fixme - use templating or something less fugly than this example of what we produce
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	126
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	127 <tool id="reverse" name="reverse" version="0.01">
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	128 <description>a tabular file</description>
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	129 <command interpreter="python">
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	130 reverse.py --script_path "$runMe" --interpreter "python"
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	131 --tool_name "reverse" --input_tab "$input1" --output_tab "$tab_file"
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	132 </command>
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	133 <inputs>
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	134 <param name="input1" type="data" format="tabular" label="Select a suitable input file from your history"/><param name="job_name" type="text" label="Supply a name for the outputs to remind you what they contain" value="reverse"/>
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	135
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	136 </inputs>
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	137 <outputs>
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	138 <data format="tabular" name="tab_file" label="${job_name}"/>
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	139
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	140 </outputs>
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	141 <help>
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	142
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	143 What it Does
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	144
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	145 Reverse the columns in a tabular file
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	146
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	147 </help>
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	148 <configfiles>
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	149 <configfile name="runMe">
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	150
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	151 # reverse order of columns in a tabular file
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	152 import sys
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	153 inp = sys.argv[1]
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	154 outp = sys.argv[2]
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	155 i = open(inp,'r')
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	156 o = open(outp,'w')
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	157 for row in i:
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	158 rs = row.rstrip().split('\t')
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	159 rs.reverse()
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	160 o.write('\t'.join(rs))
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	161 o.write('\n')
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	162 i.close()
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	163 o.close()
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	164
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	165
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	166 </configfile>
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	167 </configfiles>
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	168 </tool>
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	169
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	170 """
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	171 newXML="""<tool id="%(toolid)s" name="%(toolname)s" version="%(tool_version)s">
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	172 %(tooldesc)s
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	173 %(command)s
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	174 <inputs>
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	175 %(inputs)s
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	176 </inputs>
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	177 <outputs>
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	178 %(outputs)s
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	179 </outputs>
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	180 <configfiles>
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	181 <configfile name="runMe">
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	182 %(script)s
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	183 </configfile>
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	184 </configfiles>
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	185 %(tooltests)s
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	186 <help>
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	187 %(help)s
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	188 </help>
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	189 </tool>""" # needs a dict with toolname, toolid, interpreter, scriptname, command, inputs as a multi line string ready to write, outputs ditto, help ditto
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	190
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	191 newCommand="""<command interpreter="python">
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	192 %(toolname)s.py --script_path "$runMe" --interpreter "%(interpreter)s"
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	193 --tool_name "%(toolname)s" %(command_inputs)s %(command_outputs)s
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	194 </command>""" # may NOT be an input or htmlout
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	195 tooltestsTabOnly = """<tests><test>
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	196 <param name="input1" value="%(test1Input)s" ftype="tabular"/>
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	197 <param name="job_name" value="test1"/>
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	198 <param name="runMe" value="$runMe"/>
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	199 <output name="tab_file" file="%(test1Output)s" ftype="tabular"/>
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	200 </test></tests>"""
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	201 tooltestsHTMLOnly = """<tests><test>
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	202 <param name="input1" value="%(test1Input)s" ftype="tabular"/>
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	203 <param name="job_name" value="test1"/>
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	204 <param name="runMe" value="$runMe"/>
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	205 <output name="html_file" file="%(test1HTML)s" ftype="html" lines_diff="5"/>
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	206 </test></tests>"""
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	207 tooltestsBoth = """<tests><test>
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	208 <param name="input1" value="%(test1Input)s" ftype="tabular"/>
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	209 <param name="job_name" value="test1"/>
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	210 <param name="runMe" value="$runMe"/>
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	211 <output name="tab_file" file="%(test1Output)s" ftype="tabular" />
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	212 <output name="html_file" file="%(test1HTML)s" ftype="html" lines_diff="10"/>
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	213 </test></tests>"""
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	214 xdict = {}
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	215 xdict['tool_version'] = self.opts.tool_version
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	216 xdict['test1Input'] = self.test1Input
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	217 xdict['test1HTML'] = self.test1HTML
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	218 xdict['test1Output'] = self.test1Output
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	219 if self.opts.make_HTML and self.opts.output_tab <> 'None':
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	220 xdict['tooltests'] = tooltestsBoth % xdict
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	221 elif self.opts.make_HTML:
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	222 xdict['tooltests'] = tooltestsHTMLOnly % xdict
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	223 else:
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	224 xdict['tooltests'] = tooltestsTabOnly % xdict
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	225 xdict['script'] = self.script # configfile is least painful way to embed script to avoid external dependencies
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	226 if self.opts.help_text:
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	227 xdict['help'] = open(self.opts.help_text,'r').read()
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	228 else:
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	229 xdict['help'] = 'Please ask the tool author for help as none was supplied at tool generation'
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	230 coda = ['Script','Pressing execute will run the following code over your input file and generate some outputs in your history::']
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	231 coda.append(self.indentedScript)
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	232 coda.append('Attribution This Galaxy tool was created by %s at %s\nusing the Galaxy Tool Factory.' % (self.opts.user_email,timenow()))
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	233 coda.append('See %s for details of that project' % (toolFactoryURL))
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	234 xdict['help'] = '%s\n%s' % (xdict['help'],'\n'.join(coda))
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	235 if self.opts.tool_desc:
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	236 xdict['tooldesc'] = '<description>%s</description>' % self.opts.tool_desc
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	237 else:
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	238 xdict['tooldesc'] = ''
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	239 xdict['command_outputs'] = ''
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	240 xdict['outputs'] = ''
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	241 if self.opts.input_tab <> 'None':
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	242 xdict['command_inputs'] = '--input_tab "$input1" ' # the space may matter a lot if we append something
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	243 xdict['inputs'] = '<param name="input1" type="data" format="%s" label="Select a suitable input file from your history"/> \n' % self.inputFormats
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	244 else:
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	245 xdict['command_inputs'] = '' # assume no input - eg a random data generator
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	246 xdict['inputs'] = ''
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	247 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
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	248 xdict['toolname'] = self.toolname
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	249 xdict['toolid'] = self.toolid
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	250 xdict['interpreter'] = self.opts.interpreter
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	251 xdict['scriptname'] = self.sfile
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	252 if self.opts.make_HTML:
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	253 xdict['command_outputs'] += ' --output_dir "$html_file.files_path" --output_html "$html_file" --make_HTML "yes" '
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	254 xdict['outputs'] += ' <data format="html" name="html_file" label="${job_name}.html"/>\n'
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	255 if self.opts.output_tab <> 'None':
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	256 xdict['command_outputs'] += ' --output_tab "$tab_file"'
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	257 xdict['outputs'] += ' <data format="%s" name="tab_file" label="${job_name}"/>\n' % self.outFormats
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	258 xdict['command'] = newCommand % xdict
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	259 xmls = newXML % xdict
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	260 xf = open(self.xmlfile,'w')
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	261 xf.write(xmls)
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	262 xf.write('\n')
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	263 xf.close()
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	264 # ready for the tarball
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	265
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	266
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	267 def makeTooltar(self):
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	268 """
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	269 a tool is a gz tarball with eg
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	270 /toolname/tool.xml /toolname/tool.py /toolname/test-data/test1_in.foo ...
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	271 """
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	272 retval = self.run()
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	273 if retval:
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	274 print >> sys.stderr,'## Run failed. Cannot build yet. Please fix and retry'
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	275 sys.exit(1)
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	276 self.makeXML()
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	277 tdir = self.toolname
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	278 os.mkdir(tdir)
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	279 if self.opts.input_tab <> 'None': # no reproducible test otherwise? TODO: maybe..
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	280 testdir = os.path.join(tdir,'test-data')
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	281 os.mkdir(testdir) # make tests directory
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	282 shutil.copyfile(self.opts.input_tab,os.path.join(testdir,self.test1Input))
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	283 if self.opts.output_tab <> 'None':
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	284 shutil.copyfile(self.opts.output_tab,os.path.join(testdir,self.test1Output))
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	285 if self.opts.make_HTML:
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	286 shutil.copyfile(self.opts.output_html,os.path.join(testdir,self.test1HTML))
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	287 if self.opts.output_dir:
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	288 shutil.copyfile(self.tlog,os.path.join(testdir,'test1_out.log'))
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	289 op = '%s.py' % self.toolname # new name
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	290 outpiname = os.path.join(tdir,op) # path for the tool tarball
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	291 pyin = os.path.basename(self.pyfile) # our name - we rewrite ourselves (TM)
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	292 notes = ['# %s - a self annotated version of %s generated by running %s\n' % (op,pyin,pyin),]
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	293 notes.append('# to make a new Galaxy tool called %s\n' % self.toolname)
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	294 notes.append('# User %s at %s\n' % (self.opts.user_email,timenow()))
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	295 pi = open(self.pyfile,'r').readlines() # our code becomes new tool wrapper (!) - first Galaxy worm
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	296 notes += pi
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	297 outpi = open(outpiname,'w')
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	298 outpi.write(''.join(notes))
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	299 outpi.write('\n')
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	300 outpi.close()
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	301 shutil.copyfile(self.sfile,os.path.join(tdir,self.sfile))
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	302 shutil.copyfile(self.xmlfile,os.path.join(tdir,self.xmlfile))
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	303 tarpath = "%s.gz" % self.toolname
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	304 tar = tarfile.open(tarpath, "w:gz")
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	305 tar.add(tdir,arcname=self.toolname)
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	306 tar.close()
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	307 shutil.copyfile(tarpath,self.opts.new_tool)
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	308 shutil.rmtree(tdir)
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	309 ## TODO: replace with optional direct upload to local toolshed?
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	310 return retval
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	311
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	312 def compressPDF(self,inpdf=None,thumbformat='png'):
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	313 """need absolute path to pdf
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	314 """
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	315 assert os.path.isfile(inpdf), "## Input %s supplied to %s compressPDF not found" % (inpdf,self.myName)
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	316 hf,hlog = tempfile.mkstemp(suffix="%s.log" % self.toolname)
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	317 sto = open(hlog,'w')
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	318 outpdf = '%s_compressed' % inpdf
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	319 cl = ["gs", "-sDEVICE=pdfwrite", "-dNOPAUSE", "-dBATCH", "-sOutputFile=%s" % outpdf,inpdf]
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	320 x = subprocess.Popen(cl,stdout=sto,stderr=sto,cwd=self.opts.output_dir)
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	321 retval1 = x.wait()
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	322 if retval1 == 0:
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	323 os.unlink(inpdf)
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	324 shutil.move(outpdf,inpdf)
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	325 outpng = '%s.%s' % (os.path.splitext(inpdf)[0],thumbformat)
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	326 cl2 = ['convert', inpdf, outpng]
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	327 x = subprocess.Popen(cl2,stdout=sto,stderr=sto,cwd=self.opts.output_dir)
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	328 retval2 = x.wait()
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	329 sto.close()
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	330 retval = retval1 or retval2
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	331 return retval
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	332
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	333
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	334 def getfSize(self,fpath,outpath):
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	335 """
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	336 format a nice file size string
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	337 """
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	338 size = ''
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	339 fp = os.path.join(outpath,fpath)
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	340 if os.path.isfile(fp):
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	341 n = float(os.path.getsize(fp))
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	342 if n > 2**20:
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	343 size = '%1.1f MB' % (n/2**20)
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	344 elif n > 2**10:
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	345 size = '%1.1f KB)' % (n/2**10)
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	346 elif n > 0:
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	347 size = '%d B' % (int(n))
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	348 return size
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	349
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	350 def makeHtml(self):
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	351 """ Create an HTML file content to list all the artefacts found in the output_dir
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	352 """
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	353
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	354 galhtmlprefix = """<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	355 <html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	356 <head> <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	357 <meta name="generator" content="Galaxy %s tool output - see http://g2.trac.bx.psu.edu/" />
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	358 <title></title>
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	359 <link rel="stylesheet" href="/static/style/base.css" type="text/css" />
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	360 </head>
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	361 <body>
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	362 <div class="toolFormBody">
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	363 """
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	364 galhtmlattr = """<hr/><div class="infomessage">This tool (%s) was generated by the <a href="https://bitbucket.org/fubar/galaxytoolfactory/overview">Galaxy Tool Factory</a></div><br/>"""
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	365 galhtmlpostfix = """</div></body></html>\n"""
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	366
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	367 flist = os.listdir(self.opts.output_dir)
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	368 flist = [x for x in flist if x <> 'Rplots.pdf']
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	369 flist.sort()
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	370 html = []
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	371 html.append(galhtmlprefix % progname)
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	372 html.append('<div class="infomessage">Galaxy Tool "%s" run at %s</div><br/>' % (self.toolname,timenow()))
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	373 fhtml = []
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	374 if len(flist) > 0:
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	375 pdflist = []
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	376 npdf = len([x for x in flist if os.path.splitext(x)[-1].lower() == '.pdf'])
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	377 nacross = 1
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	378 if npdf > 0:
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	379 nacross = int(round(math.log(npdf,2)))
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	380 nacross = max(1,nacross)
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	381 width = min(400,int(1200/nacross))
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	382 html.append('<div><table class="colored" cellpadding="3" cellspacing="3">\n<tr>')
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	383 for rownum,fname in enumerate(flist):
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	384 dname,e = os.path.splitext(fname)
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	385 sfsize = self.getfSize(fname,self.opts.output_dir)
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	386 if e.lower() == '.pdf' : # compress and make a thumbnail
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	387 thumb = '%s.%s' % (dname,self.thumbformat)
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	388 pdff = os.path.join(self.opts.output_dir,fname)
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	389 retval = self.compressPDF(inpdf=pdff,thumbformat=self.thumbformat)
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	390 if retval == 0:
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	391 pdflist.append((fname,thumb))
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	392 if (rownum+1) % 2 == 0:
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	393 fhtml.append('<tr class="odd_row"><td><a href="%s">%s</a></td><td>%s</td></tr>' % (fname,fname,sfsize))
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	394 else:
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	395 fhtml.append('<tr><td><a href="%s">%s</a></td><td>%s</td></tr>' % (fname,fname,sfsize))
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	396 ntogo = nacross # counter for table row padding with empty cells
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	397 for i,paths in enumerate(pdflist):
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	398 fname,thumb = paths
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	399 s= """<td><a href="%s"><img src="%s" title="Click to download a PDF of %s" hspace="5" width="%d"
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	400 alt="Image called %s"/></a></td>\n""" % (fname,thumb,fname,width,fname)
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	401 if ((i+1) % nacross == 0):
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	402 s += '</tr>\n'
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	403 ntogo = 0
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	404 if i < (npdf - 1): # more to come
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	405 s += '<tr>'
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	406 ntogo = nacross
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	407 else:
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	408 ntogo -= 1
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	409 html.append(s)
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	410 if html[-1].strip().endswith('</tr>'):
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	411 html.append('</table></div>\n')
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	412 else:
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	413 if ntogo > 0: # pad
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	414 html.append('<td> </td>'*ntogo)
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	415 html.append('</tr></table></div>\n')
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	416 if len(fhtml) > 0:
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	417 fhtml.insert(0,'<div><table class="colored" cellpadding="3" cellspacing="3"><tr><th>Output File Name (click to view)</th><th>Size</th></tr>\n')
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	418 fhtml.append('</table></div><br/>')
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	419 html += fhtml # add all non-pdf files to the end of the display
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	420 else:
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	421 html.append('<div class="warningmessagelarge">### Error - %s returned no files - please confirm that parameters are sane</div>' % self.opts.interpreter)
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	422 rlog = open(self.tlog,'r').readlines()
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	423 rlog = [x for x in rlog if x.strip() > '']
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	424 if len(rlog) > 1:
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	425 html.append('<div class="toolFormTitle">%s log</div><pre>\n' % self.opts.interpreter)
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	426 html += rlog
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	427 html.append('</pre>\n')
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	428 html.append(galhtmlattr % (self.toolname))
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	429 html.append(galhtmlpostfix)
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	430 htmlf = file(self.opts.output_html,'w')
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	431 htmlf.write('\n'.join(html))
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	432 htmlf.write('\n')
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	433 htmlf.close()
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	434 self.html = html
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	435
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	436
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	437 def run(self):
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	438 """
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	439 """
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	440 if self.opts.output_dir:
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	441 sto = open(self.tlog,'w')
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	442 p = subprocess.Popen(' '.join(self.cl),shell=True,stdout=sto,stderr=sto,stdin=subprocess.PIPE,cwd=self.opts.output_dir)
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	443 else:
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	444 p = subprocess.Popen(' '.join(self.cl),shell=True,stdin=subprocess.PIPE)
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	445 p.stdin.write(self.script)
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	446 p.stdin.close()
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	447 retval = p.wait()
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	448 if self.opts.output_dir:
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	449 sto.close()
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	450 if self.opts.make_HTML:
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	451 self.makeHtml()
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	452 return retval
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	453
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	454
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	455 def main():
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	456 u = """
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	457 This is a Galaxy wrapper. It expects to be called by a special purpose tool.xml as:
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	458 <command interpreter="python">rgBaseScriptWrapper.py --script_path "$scriptPath" --tool_name "foo" --interpreter "Rscript"
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	459 </command>
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	460 """
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	461 op = optparse.OptionParser()
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	462 a = op.add_option
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	463 a('--script_path',default=None)
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	464 a('--tool_name',default=None)
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	465 a('--interpreter',default=None)
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	466 a('--output_dir',default=None)
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	467 a('--output_html',default=None)
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	468 a('--input_tab',default="None")
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	469 a('--output_tab',default="None")
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	470 a('--user_email',default='Unknown')
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	471 a('--bad_user',default=None)
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	472 a('--make_Tool',default=None)
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	473 a('--make_HTML',default=None)
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	474 a('--help_text',default=None)
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	475 a('--tool_desc',default=None)
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	476 a('--new_tool',default=None)
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	477 a('--tool_version',default=None)
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	478 opts, args = op.parse_args()
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	479 assert not opts.bad_user,'UNAUTHORISED: %s is NOT authorized to use this tool until Galaxy admin adds %s to admin_users in universe_wsgi.ini' % (opts.bad_user,opts.bad_user)
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	480 assert opts.tool_name,'## Tool Factory expects a tool name - eg --tool_name=DESeq'
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	481 assert opts.interpreter,'## Tool Factory wrapper expects an interpreter - eg --interpreter=Rscript'
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	482 assert os.path.isfile(opts.script_path),'## Tool Factory wrapper expects a script path - eg --script_path=foo.R'
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	483 if opts.output_dir:
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	484 try:
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	485 os.makedirs(opts.output_dir)
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	486 except:
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	487 pass
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	488 r = ScriptRunner(opts)
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	489 if opts.make_Tool:
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	490 retcode = r.makeTooltar()
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	491 else:
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	492 retcode = r.run()
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	493 if retcode:
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	494 sys.exit(retcode) # indicate failure to job runner
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	495
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	496
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	497 if __name__ == "__main__":
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	498 main()
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	499
764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows fubar parents: diff changeset	500

15

764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows

fubar

parents:

diff changeset

1 # rgToolFactory.py

764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows

fubar

parents:

diff changeset

2 # see https://bitbucket.org/fubar/galaxytoolfactory/wiki/Home

764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows

fubar

parents:

diff changeset

3 #

764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows

fubar

parents:

diff changeset

4 # copyright ross lazarus (ross stop lazarus at gmail stop com) May 2012

764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows

fubar

parents:

diff changeset

5 #

764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows

fubar

parents:

diff changeset

764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows

fubar

parents:

diff changeset

7 # Licensed under the LGPL

764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows

fubar

parents:

diff changeset

8 # suggestions for improvement and bug fixes welcome at https://bitbucket.org/fubar/galaxytoolfactory/wiki/Home

764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows

fubar

parents:

diff changeset

9

764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows

fubar

parents:

diff changeset

10 # This is a Galaxy tool factory for simple scripts in python, R or whatever ails ye.

764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows

fubar

parents:

diff changeset

11 # It also serves as the wrapper for the new tool.

764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows

fubar

parents:

diff changeset

12 #

764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows

fubar

parents:

diff changeset

13 # you paste and run your script

764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows

fubar

parents:

diff changeset

14 # Only works for simple scripts that read one input from the history.

764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows

fubar

parents:

diff changeset

15 # Optionally can write one new history dataset,

764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows

fubar

parents:

diff changeset

16 # and optionally collect any number of outputs into links on an autogenerated HTML page.

764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows

fubar

parents:

diff changeset

17

764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows

fubar

parents:

diff changeset

18 # DO NOT install on a public or important site - please.

764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows

fubar

parents:

diff changeset

19

764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows

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20 # installed generated tools are fine if the script is safe.

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21 # They just run normally and their user cannot do anything unusually insecure

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22 # but please, practice safe toolshed.

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23 # Read the fucking code before you install any tool

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24 # especially this one

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25

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26 # After you get the script working on some test data, you can

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27 # optionally generate a toolshed compatible gzip file

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28 # containing your script safely wrapped as an ordinary Galaxy script in your local toolshed for

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29 # safe and largely automated installation in a production Galaxy.

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30

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31 # If you opt for an HTML output, you get all the script outputs arranged

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32 # as a single Html history item - all output files are linked, thumbnails for all the pdfs.

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33 # Ugly but really inexpensive.

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34 #

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35 # Patches appreciated please.

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36 #

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37 #

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38 # long route to June 2012 product

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39 # Behold the awesome power of Galaxy and the toolshed with the tool factory binds to bind them

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40 # derived from an integrated script model

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41 # called rgBaseScriptWrapper.py

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42 # Note to the unwary:

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43 # This tool allows arbitrary scripting on your Galaxy as the Galaxy user

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44 # There is nothing stopping a malicious user doing whatever they choose

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45 # Extremely dangerous!!

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46 # Totally insecure. So, trusted users only

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47 #

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48 # preferred model is a developer using their throw away workstation instance - ie a private site.

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49 # no real risk. The universe_wsgi.ini admin_users string is checked - only admin users are permitted to run this tool.

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50 #

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51

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52 import sys

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53 import shutil

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54 import subprocess

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55 import os

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56 import time

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57 import tempfile

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58 import optparse

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59 import tarfile

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60 import re

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61 import shutil

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62 import math

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63

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64 progname = os.path.split(sys.argv[0])[1]

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65 myversion = 'V000.2 June 2012'

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66 verbose = False

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67 debug = False

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68 toolFactoryURL = 'https://bitbucket.org/fubar/galaxytoolfactory'

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69

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70 def timenow():

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71 """return current time as a string

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72 """

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73 return time.strftime('%d/%m/%Y %H:%M:%S', time.localtime(time.time()))

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74

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75

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76 class ScriptRunner:

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77 """class is a wrapper for an arbitrary script

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78 """

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79

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80 def __init__(self,opts=None):

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81 """

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82 cleanup inputs, setup some outputs

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83

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84 """

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85 if opts.output_dir: # simplify for the tool tarball

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86 os.chdir(opts.output_dir)

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87 self.thumbformat = 'jpg'

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88 self.opts = opts

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89 self.toolname = re.sub('[^a-zA-Z0-9_]+', '', opts.tool_name) # a sanitizer now does this but..

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90 self.toolid = self.toolname

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91 s = open(self.opts.script_path,'r').readlines()

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92 self.script = ''.join(s)

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93 self.indentedScript = ''.join([' %s' % x for x in s]) # for restructured text in help

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94 self.myname = sys.argv[0] # get our name because we write ourselves out as a tool later

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95 self.pyfile = self.myname # crude but efficient - the cruft won't hurt much

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96 self.xmlfile = '%s.xml' % self.toolname

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97 self.sfile = '%s.%s' % (self.toolname,opts.interpreter)

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98 if opts.output_dir: # may not want these complexities

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99 self.tlog = os.path.join(opts.output_dir,"%s_runner.log" % self.toolname)

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100 artifactpath = os.path.join(opts.output_dir,'%s_run.script' % self.toolname)

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101 artifact = open(artifactpath,'w')

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102 artifact.write(self.script)

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103 artifact.write('\n')

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104 artifact.close()

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105 if opts.make_Tool: # need this code and the user script for the tarball

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106 localscript = open(self.sfile,'w')

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107 localscript.write(self.script)

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108 localscript.close()

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109 self.cl = []

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110 self.html = []

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111 a = self.cl.append

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112 a(opts.interpreter)

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113 a('-') # use stdin

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114 a(opts.input_tab)

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115 a(opts.output_tab)

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116 self.outFormats = 'tabular' # TODO make this an option at tool generation time

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117 self.inputFormats = 'tabular' # TODO make this an option at tool generation time

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118 self.test1Input = '%s_test1_input.xls' % self.toolname

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119 self.test1Output = '%s_test1_output.xls' % self.toolname

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120 self.test1HTML = '%s_test1_output.html' % self.toolname

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121

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122 def makeXML(self):

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123 """

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124 Create a Galaxy xml tool wrapper for the new script as a string to write out

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125 fixme - use templating or something less fugly than this example of what we produce

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126

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127 <tool id="reverse" name="reverse" version="0.01">

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128 <description>a tabular file</description>

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129 <command interpreter="python">

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130 reverse.py --script_path "$runMe" --interpreter "python"

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131 --tool_name "reverse" --input_tab "$input1" --output_tab "$tab_file"

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132 </command>

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133 <inputs>

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134 <param name="input1" type="data" format="tabular" label="Select a suitable input file from your history"/><param name="job_name" type="text" label="Supply a name for the outputs to remind you what they contain" value="reverse"/>

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135

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136 </inputs>

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137 <outputs>

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138 <data format="tabular" name="tab_file" label="${job_name}"/>

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139

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140 </outputs>

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141 <help>

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142

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143 **What it Does**

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144

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145 Reverse the columns in a tabular file

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146

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147 </help>

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148 <configfiles>

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149 <configfile name="runMe">

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150

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151 # reverse order of columns in a tabular file

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152 import sys

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153 inp = sys.argv[1]

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154 outp = sys.argv[2]

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155 i = open(inp,'r')

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156 o = open(outp,'w')

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157 for row in i:

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158 rs = row.rstrip().split('\t')

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159 rs.reverse()

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160 o.write('\t'.join(rs))

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161 o.write('\n')

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162 i.close()

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163 o.close()

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164

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165

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166 </configfile>

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167 </configfiles>

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168 </tool>

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169

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170 """

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171 newXML="""<tool id="%(toolid)s" name="%(toolname)s" version="%(tool_version)s">

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172 %(tooldesc)s

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173 %(command)s

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174 <inputs>

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175 %(inputs)s

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176 </inputs>

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177 <outputs>

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178 %(outputs)s

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179 </outputs>

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180 <configfiles>

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181 <configfile name="runMe">

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182 %(script)s

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183 </configfile>

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184 </configfiles>

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185 %(tooltests)s

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186 <help>

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187 %(help)s

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188 </help>

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189 </tool>""" # needs a dict with toolname, toolid, interpreter, scriptname, command, inputs as a multi line string ready to write, outputs ditto, help ditto

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190

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191 newCommand="""<command interpreter="python">

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192 %(toolname)s.py --script_path "$runMe" --interpreter "%(interpreter)s"

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193 --tool_name "%(toolname)s" %(command_inputs)s %(command_outputs)s

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194 </command>""" # may NOT be an input or htmlout

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195 tooltestsTabOnly = """<tests><test>

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196 <param name="input1" value="%(test1Input)s" ftype="tabular"/>

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197 <param name="job_name" value="test1"/>

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198 <param name="runMe" value="$runMe"/>

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199 <output name="tab_file" file="%(test1Output)s" ftype="tabular"/>

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200 </test></tests>"""

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201 tooltestsHTMLOnly = """<tests><test>

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202 <param name="input1" value="%(test1Input)s" ftype="tabular"/>

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203 <param name="job_name" value="test1"/>

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204 <param name="runMe" value="$runMe"/>

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205 <output name="html_file" file="%(test1HTML)s" ftype="html" lines_diff="5"/>

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206 </test></tests>"""

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207 tooltestsBoth = """<tests><test>

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208 <param name="input1" value="%(test1Input)s" ftype="tabular"/>

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209 <param name="job_name" value="test1"/>

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210 <param name="runMe" value="$runMe"/>

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211 <output name="tab_file" file="%(test1Output)s" ftype="tabular" />

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212 <output name="html_file" file="%(test1HTML)s" ftype="html" lines_diff="10"/>

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213 </test></tests>"""

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214 xdict = {}

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215 xdict['tool_version'] = self.opts.tool_version

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216 xdict['test1Input'] = self.test1Input

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217 xdict['test1HTML'] = self.test1HTML

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218 xdict['test1Output'] = self.test1Output

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219 if self.opts.make_HTML and self.opts.output_tab <> 'None':

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220 xdict['tooltests'] = tooltestsBoth % xdict

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221 elif self.opts.make_HTML:

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222 xdict['tooltests'] = tooltestsHTMLOnly % xdict

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223 else:

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224 xdict['tooltests'] = tooltestsTabOnly % xdict

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225 xdict['script'] = self.script # configfile is least painful way to embed script to avoid external dependencies

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226 if self.opts.help_text:

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227 xdict['help'] = open(self.opts.help_text,'r').read()

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228 else:

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229 xdict['help'] = 'Please ask the tool author for help as none was supplied at tool generation'

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230 coda = ['**Script**','Pressing execute will run the following code over your input file and generate some outputs in your history::']

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231 coda.append(self.indentedScript)

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232 coda.append('**Attribution** This Galaxy tool was created by %s at %s\nusing the Galaxy Tool Factory.' % (self.opts.user_email,timenow()))

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233 coda.append('See %s for details of that project' % (toolFactoryURL))

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234 xdict['help'] = '%s\n%s' % (xdict['help'],'\n'.join(coda))

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235 if self.opts.tool_desc:

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236 xdict['tooldesc'] = '<description>%s</description>' % self.opts.tool_desc

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237 else:

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238 xdict['tooldesc'] = ''

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239 xdict['command_outputs'] = ''

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240 xdict['outputs'] = ''

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241 if self.opts.input_tab <> 'None':

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242 xdict['command_inputs'] = '--input_tab "$input1" ' # the space may matter a lot if we append something

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243 xdict['inputs'] = '<param name="input1" type="data" format="%s" label="Select a suitable input file from your history"/> \n' % self.inputFormats

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244 else:

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245 xdict['command_inputs'] = '' # assume no input - eg a random data generator

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246 xdict['inputs'] = ''

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247 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

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248 xdict['toolname'] = self.toolname

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249 xdict['toolid'] = self.toolid

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250 xdict['interpreter'] = self.opts.interpreter

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251 xdict['scriptname'] = self.sfile

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252 if self.opts.make_HTML:

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253 xdict['command_outputs'] += ' --output_dir "$html_file.files_path" --output_html "$html_file" --make_HTML "yes" '

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254 xdict['outputs'] += ' <data format="html" name="html_file" label="${job_name}.html"/>\n'

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255 if self.opts.output_tab <> 'None':

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256 xdict['command_outputs'] += ' --output_tab "$tab_file"'

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257 xdict['outputs'] += ' <data format="%s" name="tab_file" label="${job_name}"/>\n' % self.outFormats

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258 xdict['command'] = newCommand % xdict

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259 xmls = newXML % xdict

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260 xf = open(self.xmlfile,'w')

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261 xf.write(xmls)

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262 xf.write('\n')

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263 xf.close()

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264 # ready for the tarball

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265

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266

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267 def makeTooltar(self):

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268 """

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269 a tool is a gz tarball with eg

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270 /toolname/tool.xml /toolname/tool.py /toolname/test-data/test1_in.foo ...

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271 """

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272 retval = self.run()

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273 if retval:

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274 print >> sys.stderr,'## Run failed. Cannot build yet. Please fix and retry'

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275 sys.exit(1)

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276 self.makeXML()

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277 tdir = self.toolname

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278 os.mkdir(tdir)

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279 if self.opts.input_tab <> 'None': # no reproducible test otherwise? TODO: maybe..

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280 testdir = os.path.join(tdir,'test-data')

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281 os.mkdir(testdir) # make tests directory

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282 shutil.copyfile(self.opts.input_tab,os.path.join(testdir,self.test1Input))

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283 if self.opts.output_tab <> 'None':

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284 shutil.copyfile(self.opts.output_tab,os.path.join(testdir,self.test1Output))

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285 if self.opts.make_HTML:

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286 shutil.copyfile(self.opts.output_html,os.path.join(testdir,self.test1HTML))

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287 if self.opts.output_dir:

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288 shutil.copyfile(self.tlog,os.path.join(testdir,'test1_out.log'))

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289 op = '%s.py' % self.toolname # new name

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290 outpiname = os.path.join(tdir,op) # path for the tool tarball

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291 pyin = os.path.basename(self.pyfile) # our name - we rewrite ourselves (TM)

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292 notes = ['# %s - a self annotated version of %s generated by running %s\n' % (op,pyin,pyin),]

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293 notes.append('# to make a new Galaxy tool called %s\n' % self.toolname)

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294 notes.append('# User %s at %s\n' % (self.opts.user_email,timenow()))

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295 pi = open(self.pyfile,'r').readlines() # our code becomes new tool wrapper (!) - first Galaxy worm

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296 notes += pi

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297 outpi = open(outpiname,'w')

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298 outpi.write(''.join(notes))

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299 outpi.write('\n')

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300 outpi.close()

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301 shutil.copyfile(self.sfile,os.path.join(tdir,self.sfile))

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302 shutil.copyfile(self.xmlfile,os.path.join(tdir,self.xmlfile))

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303 tarpath = "%s.gz" % self.toolname

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304 tar = tarfile.open(tarpath, "w:gz")

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305 tar.add(tdir,arcname=self.toolname)

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306 tar.close()

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307 shutil.copyfile(tarpath,self.opts.new_tool)

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308 shutil.rmtree(tdir)

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309 ## TODO: replace with optional direct upload to local toolshed?

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310 return retval

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311

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312 def compressPDF(self,inpdf=None,thumbformat='png'):

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313 """need absolute path to pdf

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314 """

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315 assert os.path.isfile(inpdf), "## Input %s supplied to %s compressPDF not found" % (inpdf,self.myName)

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316 hf,hlog = tempfile.mkstemp(suffix="%s.log" % self.toolname)

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317 sto = open(hlog,'w')

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318 outpdf = '%s_compressed' % inpdf

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319 cl = ["gs", "-sDEVICE=pdfwrite", "-dNOPAUSE", "-dBATCH", "-sOutputFile=%s" % outpdf,inpdf]

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320 x = subprocess.Popen(cl,stdout=sto,stderr=sto,cwd=self.opts.output_dir)

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321 retval1 = x.wait()

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322 if retval1 == 0:

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323 os.unlink(inpdf)

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324 shutil.move(outpdf,inpdf)

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325 outpng = '%s.%s' % (os.path.splitext(inpdf)[0],thumbformat)

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parents:

diff changeset

326 cl2 = ['convert', inpdf, outpng]

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diff changeset

327 x = subprocess.Popen(cl2,stdout=sto,stderr=sto,cwd=self.opts.output_dir)

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parents:

diff changeset

328 retval2 = x.wait()

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parents:

diff changeset

329 sto.close()

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parents:

diff changeset

330 retval = retval1 or retval2

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diff changeset

331 return retval

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diff changeset

332

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parents:

diff changeset

333

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fubar

parents:

diff changeset

334 def getfSize(self,fpath,outpath):

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fubar

parents:

diff changeset

335 """

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fubar

parents:

diff changeset

336 format a nice file size string

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fubar

parents:

diff changeset

337 """

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fubar

parents:

diff changeset

338 size = ''

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parents:

diff changeset

339 fp = os.path.join(outpath,fpath)

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fubar

parents:

diff changeset

340 if os.path.isfile(fp):

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fubar

parents:

diff changeset

341 n = float(os.path.getsize(fp))

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fubar

parents:

diff changeset

342 if n > 2**20:

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fubar

parents:

diff changeset

343 size = '%1.1f MB' % (n/2**20)

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fubar

parents:

diff changeset

344 elif n > 2**10:

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fubar

parents:

diff changeset

345 size = '%1.1f KB)' % (n/2**10)

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fubar

parents:

diff changeset

346 elif n > 0:

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parents:

diff changeset

347 size = '%d B' % (int(n))

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diff changeset

348 return size

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diff changeset

349

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fubar

parents:

diff changeset

350 def makeHtml(self):

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fubar

parents:

diff changeset

351 """ Create an HTML file content to list all the artefacts found in the output_dir

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fubar

parents:

diff changeset

352 """

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parents:

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353

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fubar

parents:

diff changeset

354 galhtmlprefix = """<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">

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parents:

diff changeset

355 <html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">

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fubar

parents:

diff changeset

356 <head> <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />

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fubar

parents:

diff changeset

357 <meta name="generator" content="Galaxy %s tool output - see http://g2.trac.bx.psu.edu/" />

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parents:

diff changeset

358 <title></title>

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fubar

parents:

diff changeset

359 <link rel="stylesheet" href="/static/style/base.css" type="text/css" />

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fubar

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diff changeset

360 </head>

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fubar

parents:

diff changeset

361 <body>

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fubar

parents:

diff changeset

362 <div class="toolFormBody">

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fubar

parents:

diff changeset

363 """

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fubar

parents:

diff changeset

364 galhtmlattr = """<hr/><div class="infomessage">This tool (%s) was generated by the <a href="https://bitbucket.org/fubar/galaxytoolfactory/overview">Galaxy Tool Factory</a></div><br/>"""

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fubar

parents:

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365 galhtmlpostfix = """</div></body></html>\n"""

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fubar

parents:

diff changeset

366

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367 flist = os.listdir(self.opts.output_dir)

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fubar

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368 flist = [x for x in flist if x <> 'Rplots.pdf']

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fubar

parents:

diff changeset

369 flist.sort()

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parents:

diff changeset

370 html = []

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fubar

parents:

diff changeset

371 html.append(galhtmlprefix % progname)

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fubar

parents:

diff changeset

372 html.append('<div class="infomessage">Galaxy Tool "%s" run at %s</div><br/>' % (self.toolname,timenow()))

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fubar

parents:

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373 fhtml = []

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fubar

parents:

diff changeset

374 if len(flist) > 0:

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parents:

diff changeset

375 pdflist = []

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parents:

diff changeset

376 npdf = len([x for x in flist if os.path.splitext(x)[-1].lower() == '.pdf'])

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fubar

parents:

diff changeset

377 nacross = 1

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fubar

parents:

diff changeset

378 if npdf > 0:

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fubar

parents:

diff changeset

379 nacross = int(round(math.log(npdf,2)))

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fubar

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diff changeset

380 nacross = max(1,nacross)

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fubar

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diff changeset

381 width = min(400,int(1200/nacross))

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fubar

parents:

diff changeset

382 html.append('<div><table class="colored" cellpadding="3" cellspacing="3">\n<tr>')

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fubar

parents:

diff changeset

383 for rownum,fname in enumerate(flist):

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fubar

parents:

diff changeset

384 dname,e = os.path.splitext(fname)

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fubar

parents:

diff changeset

385 sfsize = self.getfSize(fname,self.opts.output_dir)

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fubar

parents:

diff changeset

386 if e.lower() == '.pdf' : # compress and make a thumbnail

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fubar

parents:

diff changeset

387 thumb = '%s.%s' % (dname,self.thumbformat)

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fubar

parents:

diff changeset

388 pdff = os.path.join(self.opts.output_dir,fname)

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fubar

parents:

diff changeset

389 retval = self.compressPDF(inpdf=pdff,thumbformat=self.thumbformat)

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fubar

parents:

diff changeset

390 if retval == 0:

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fubar

parents:

diff changeset

391 pdflist.append((fname,thumb))

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fubar

parents:

diff changeset

392 if (rownum+1) % 2 == 0:

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fubar

parents:

diff changeset

393 fhtml.append('<tr class="odd_row"><td><a href="%s">%s</a></td><td>%s</td></tr>' % (fname,fname,sfsize))

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fubar

parents:

diff changeset

394 else:

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fubar

parents:

diff changeset

395 fhtml.append('<tr><td><a href="%s">%s</a></td><td>%s</td></tr>' % (fname,fname,sfsize))

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fubar

parents:

diff changeset

396 ntogo = nacross # counter for table row padding with empty cells

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fubar

parents:

diff changeset

397 for i,paths in enumerate(pdflist):

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fubar

parents:

diff changeset

398 fname,thumb = paths

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fubar

parents:

diff changeset

399 s= """<td><a href="%s"><img src="%s" title="Click to download a PDF of %s" hspace="5" width="%d"

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fubar

parents:

diff changeset

400 alt="Image called %s"/></a></td>\n""" % (fname,thumb,fname,width,fname)

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fubar

parents:

diff changeset

401 if ((i+1) % nacross == 0):

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fubar

parents:

diff changeset

402 s += '</tr>\n'

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fubar

parents:

diff changeset

403 ntogo = 0

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fubar

parents:

diff changeset

404 if i < (npdf - 1): # more to come

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fubar

parents:

diff changeset

405 s += '<tr>'

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fubar

parents:

diff changeset

406 ntogo = nacross

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fubar

parents:

diff changeset

407 else:

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fubar

parents:

diff changeset

408 ntogo -= 1

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fubar

parents:

diff changeset

409 html.append(s)

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fubar

parents:

diff changeset

410 if html[-1].strip().endswith('</tr>'):

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fubar

parents:

diff changeset

411 html.append('</table></div>\n')

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fubar

parents:

diff changeset

412 else:

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fubar

parents:

diff changeset

413 if ntogo > 0: # pad

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fubar

parents:

diff changeset

414 html.append('<td> </td>'*ntogo)

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fubar

parents:

diff changeset

415 html.append('</tr></table></div>\n')

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fubar

parents:

diff changeset

416 if len(fhtml) > 0:

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fubar

parents:

diff changeset

417 fhtml.insert(0,'<div><table class="colored" cellpadding="3" cellspacing="3"><tr><th>Output File Name (click to view)</th><th>Size</th></tr>\n')

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fubar

parents:

diff changeset

418 fhtml.append('</table></div><br/>')

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fubar

parents:

diff changeset

419 html += fhtml # add all non-pdf files to the end of the display

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fubar

parents:

diff changeset

420 else:

764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows

fubar

parents:

diff changeset

421 html.append('<div class="warningmessagelarge">### Error - %s returned no files - please confirm that parameters are sane</div>' % self.opts.interpreter)

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fubar

parents:

diff changeset

422 rlog = open(self.tlog,'r').readlines()

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fubar

parents:

diff changeset

423 rlog = [x for x in rlog if x.strip() > '']

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fubar

parents:

diff changeset

424 if len(rlog) > 1:

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fubar

parents:

diff changeset

425 html.append('<div class="toolFormTitle">%s log</div><pre>\n' % self.opts.interpreter)

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fubar

parents:

diff changeset

426 html += rlog

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fubar

parents:

diff changeset

427 html.append('</pre>\n')

764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows

fubar

parents:

diff changeset

428 html.append(galhtmlattr % (self.toolname))

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fubar

parents:

diff changeset

429 html.append(galhtmlpostfix)

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fubar

parents:

diff changeset

430 htmlf = file(self.opts.output_html,'w')

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fubar

parents:

diff changeset

431 htmlf.write('\n'.join(html))

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fubar

parents:

diff changeset

432 htmlf.write('\n')

764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows

fubar

parents:

diff changeset

433 htmlf.close()

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fubar

parents:

diff changeset

434 self.html = html

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fubar

parents:

diff changeset

435

764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows

fubar

parents:

diff changeset

436

764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows

fubar

parents:

diff changeset

437 def run(self):

764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows

fubar

parents:

diff changeset

438 """

764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows

fubar

parents:

diff changeset

439 """

764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows

fubar

parents:

diff changeset

440 if self.opts.output_dir:

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fubar

parents:

diff changeset

441 sto = open(self.tlog,'w')

764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows

fubar

parents:

diff changeset

442 p = subprocess.Popen(' '.join(self.cl),shell=True,stdout=sto,stderr=sto,stdin=subprocess.PIPE,cwd=self.opts.output_dir)

764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows

fubar

parents:

diff changeset

443 else:

764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows

fubar

parents:

diff changeset

444 p = subprocess.Popen(' '.join(self.cl),shell=True,stdin=subprocess.PIPE)

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fubar

parents:

diff changeset

445 p.stdin.write(self.script)

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fubar

parents:

diff changeset

446 p.stdin.close()

764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows

fubar

parents:

diff changeset

447 retval = p.wait()

764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows

fubar

parents:

diff changeset

448 if self.opts.output_dir:

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fubar

parents:

diff changeset

449 sto.close()

764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows

fubar

parents:

diff changeset

450 if self.opts.make_HTML:

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fubar

parents:

diff changeset

451 self.makeHtml()

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fubar

parents:

diff changeset

452 return retval

764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows

fubar

parents:

diff changeset

453

764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows

fubar

parents:

diff changeset

454

764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows

fubar

parents:

diff changeset

455 def main():

764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows

fubar

parents:

diff changeset

456 u = """

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fubar

parents:

diff changeset

457 This is a Galaxy wrapper. It expects to be called by a special purpose tool.xml as:

764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows

fubar

parents:

diff changeset

458 <command interpreter="python">rgBaseScriptWrapper.py --script_path "$scriptPath" --tool_name "foo" --interpreter "Rscript"

764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows

fubar

parents:

diff changeset

459 </command>

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fubar

parents:

diff changeset

460 """

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fubar

parents:

diff changeset

461 op = optparse.OptionParser()

764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows

fubar

parents:

diff changeset

462 a = op.add_option

764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows

fubar

parents:

diff changeset

463 a('--script_path',default=None)

764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows

fubar

parents:

diff changeset

464 a('--tool_name',default=None)

764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows

fubar

parents:

diff changeset

465 a('--interpreter',default=None)

764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows

fubar

parents:

diff changeset

466 a('--output_dir',default=None)

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fubar

parents:

diff changeset

467 a('--output_html',default=None)

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fubar

parents:

diff changeset

468 a('--input_tab',default="None")

764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows

fubar

parents:

diff changeset

469 a('--output_tab',default="None")

764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows

fubar

parents:

diff changeset

470 a('--user_email',default='Unknown')

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fubar

parents:

diff changeset

471 a('--bad_user',default=None)

764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows

fubar

parents:

diff changeset

472 a('--make_Tool',default=None)

764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows

fubar

parents:

diff changeset

473 a('--make_HTML',default=None)

764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows

fubar

parents:

diff changeset

474 a('--help_text',default=None)

764691bf1045 Fixes to pretty html layout of many images including proper filling of otherwise partly empty rows

fubar

parents:

diff changeset

475 a('--tool_desc',default=None)

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476 a('--new_tool',default=None)

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477 a('--tool_version',default=None)

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478 opts, args = op.parse_args()

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479 assert not opts.bad_user,'UNAUTHORISED: %s is NOT authorized to use this tool until Galaxy admin adds %s to admin_users in universe_wsgi.ini' % (opts.bad_user,opts.bad_user)

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480 assert opts.tool_name,'## Tool Factory expects a tool name - eg --tool_name=DESeq'

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481 assert opts.interpreter,'## Tool Factory wrapper expects an interpreter - eg --interpreter=Rscript'

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482 assert os.path.isfile(opts.script_path),'## Tool Factory wrapper expects a script path - eg --script_path=foo.R'

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483 if opts.output_dir:

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484 try:

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485 os.makedirs(opts.output_dir)

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486 except:

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487 pass

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488 r = ScriptRunner(opts)

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489 if opts.make_Tool:

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490 retcode = r.makeTooltar()

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491 else:

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492 retcode = r.run()

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493 if retcode:

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494 sys.exit(retcode) # indicate failure to job runner

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495

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496

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497 if __name__ == "__main__":

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498 main()

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499

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500

Mercurial > repos > fubar > toolfactory

annotate fubar-galaxytoolfactory-9603e5fd1d9a/rgToolFactory.py @ 15:764691bf1045 draft