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comparison rgToolFactory.py @ 11:704ccaade924 draft

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author fubar
date Thu, 20 Mar 2014 05:50:38 -0400
parents 1fcf3fda325f
children a898ba82496e
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10:59bce2efadfe 11:704ccaade924
6 # all rights reserved 6 # all rights reserved
7 # Licensed under the LGPL 7 # Licensed under the LGPL
8 # suggestions for improvement and bug fixes welcome at https://bitbucket.org/fubar/galaxytoolfactory/wiki/Home 8 # suggestions for improvement and bug fixes welcome at https://bitbucket.org/fubar/galaxytoolfactory/wiki/Home
9 # 9 #
10 # march 2014 10 # march 2014
11 # added dependencies to a tool_dependencies.xml if html page generated so generated tool is properly portable
12 #
11 # added ghostscript and graphicsmagick as dependencies 13 # added ghostscript and graphicsmagick as dependencies
12 # fixed a wierd problem where gs was trying to use the new_files_path from universe (database/tmp) as ./database/tmp 14 # fixed a wierd problem where gs was trying to use the new_files_path from universe (database/tmp) as ./database/tmp
13 # errors ensued 15 # errors ensued
14 # 16 #
15 # august 2013 17 # august 2013
85 progname = os.path.split(sys.argv[0])[1] 87 progname = os.path.split(sys.argv[0])[1]
86 myversion = 'V001.1 March 2014' 88 myversion = 'V001.1 March 2014'
87 verbose = False 89 verbose = False
88 debug = False 90 debug = False
89 toolFactoryURL = 'https://bitbucket.org/fubar/galaxytoolfactory' 91 toolFactoryURL = 'https://bitbucket.org/fubar/galaxytoolfactory'
92
93 # if we do html we need these dependencies
94 toolhtmldep = """<?xml version="1.0"?>
95 <tool_dependency>
96 <package name="ghostscript" version="9.10">
97 <repository name="package_ghostscript_9_10" owner="devteam" prior_installation_required="True" toolshed="http://toolshed.g2.bx.psu.edu/" />
98 </package>
99 <package name="graphicsmagick" version="1.3.18">
100 <repository name="package_graphicsmagick_1_3" owner="iuc" prior_installation_required="True" toolshed="http://toolshed.g2.bx.psu.edu/" />
101 </package>
102 <readme>
103 %s
104 </readme>
105 </tool_dependency>
106 """
90 107
91 def timenow(): 108 def timenow():
92 """return current time as a string 109 """return current time as a string
93 """ 110 """
94 return time.strftime('%d/%m/%Y %H:%M:%S', time.localtime(time.time())) 111 return time.strftime('%d/%m/%Y %H:%M:%S', time.localtime(time.time()))
128 self.thumbformat = 'png' 145 self.thumbformat = 'png'
129 self.opts = opts 146 self.opts = opts
130 self.toolname = re.sub('[^a-zA-Z0-9_]+', '', opts.tool_name) # a sanitizer now does this but.. 147 self.toolname = re.sub('[^a-zA-Z0-9_]+', '', opts.tool_name) # a sanitizer now does this but..
131 self.toolid = self.toolname 148 self.toolid = self.toolname
132 self.myname = sys.argv[0] # get our name because we write ourselves out as a tool later 149 self.myname = sys.argv[0] # get our name because we write ourselves out as a tool later
133 self.pyfile = self.myname # crude but efficient - the cruft won't hurt much 150 self.pyfile = self.myname # crude but efficient - the cruft won't hurt muchself.tooldepfile)
134 self.xmlfile = '%s.xml' % self.toolname 151 self.xmlfile = '%s.xml' % self.toolname
135 s = open(self.opts.script_path,'r').readlines() 152 s = open(self.opts.script_path,'r').readlines()
136 s = [x.rstrip() for x in s] # remove pesky dos line endings if needed 153 s = [x.rstrip() for x in s] # remove pesky dos line endings if needed
137 self.script = '\n'.join(s) 154 self.script = '\n'.join(s)
138 fhandle,self.sfile = tempfile.mkstemp(prefix=self.toolname,suffix=".%s" % (opts.interpreter)) 155 fhandle,self.sfile = tempfile.mkstemp(prefix=self.toolname,suffix=".%s" % (opts.interpreter))
231 %(tooltests)s 248 %(tooltests)s
232 <help> 249 <help>
233 %(help)s 250 %(help)s
234 </help> 251 </help>
235 </tool>""" # needs a dict with toolname, toolid, interpreter, scriptname, command, inputs as a multi line string ready to write, outputs ditto, help ditto 252 </tool>""" # needs a dict with toolname, toolid, interpreter, scriptname, command, inputs as a multi line string ready to write, outputs ditto, help ditto
236 253
237 newCommand="""<command interpreter="python"> 254 newCommand="""<command interpreter="python">
238 %(toolname)s.py --script_path "$runMe" --interpreter "%(interpreter)s" 255 %(toolname)s.py --script_path "$runMe" --interpreter "%(interpreter)s"
239 --tool_name "%(toolname)s" %(command_inputs)s %(command_outputs)s 256 --tool_name "%(toolname)s" %(command_inputs)s %(command_outputs)s
240 </command>""" # may NOT be an input or htmlout 257 </command>""" # may NOT be an input or htmlout
241 tooltestsTabOnly = """<tests><test> 258 tooltestsTabOnly = """<tests><test>
321 """ 338 """
322 retval = self.run() 339 retval = self.run()
323 if retval: 340 if retval:
324 print >> sys.stderr,'## Run failed. Cannot build yet. Please fix and retry' 341 print >> sys.stderr,'## Run failed. Cannot build yet. Please fix and retry'
325 sys.exit(1) 342 sys.exit(1)
326 self.makeXML()
327 tdir = self.toolname 343 tdir = self.toolname
328 os.mkdir(tdir) 344 os.mkdir(tdir)
345 self.makeXML()
346 if self.opts.make_HTML:
347 if self.opts.help_text:
348 hlp = open(self.opts.help_text,'r').read()
349 else:
350 hlp = 'Please ask the tool author for help as none was supplied at tool generation\n'
351 tooldeps = toolhtmldep % hlp
352 depf = open('tool_dependencies.xml','w')
353 depf.write(hlp)
354 depf.write('\n')
355 depf.close()
329 if self.opts.input_tab <> 'None': # no reproducible test otherwise? TODO: maybe.. 356 if self.opts.input_tab <> 'None': # no reproducible test otherwise? TODO: maybe..
330 testdir = os.path.join(tdir,'test-data') 357 testdir = os.path.join(tdir,'test-data')
331 os.mkdir(testdir) # make tests directory 358 os.mkdir(testdir) # make tests directory
332 shutil.copyfile(self.opts.input_tab,os.path.join(testdir,self.test1Input)) 359 shutil.copyfile(self.opts.input_tab,os.path.join(testdir,self.test1Input))
333 if self.opts.output_tab <> 'None': 360 if self.opts.output_tab <> 'None':