tool_factory_2: rgToolFactory2.py comparison

comparison rgToolFactory2.py @ 14:3635f4518c4d draft

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author	fubar
date	Tue, 20 Jan 2015 19:03:18 -0500
parents	00777b83aaca
children	dd6cf2ddaac7

comparison

equal deleted inserted replaced

-:00777b83aaca
+:3635f4518c4d
 # suggestions for improvement and bug fixes welcome at https://bitbucket.org/fubar/galaxytoolfactory/wiki/Home
 #
 # January 2015
 # in the process of building a complex tool
 # added ability to choose one of the current toolshed package_r or package_perl or package_python dependencies and source that package
-# need to add that package to tool_dependencies
+# add that package to tool_dependencies
+# Note that once the generated tool is loaded, it will have that package's env.sh loaded automagically so there is no
+# --envshpath in the parameters for the generated tool and it uses the system one which will be first on the adjusted path.
 #
 # sept 2014 added additional params from
 # https://bitbucket.org/mvdbeek/dockertoolfactory/src/d4863bcf7b521532c7e8c61b6333840ba5393f73/DockerToolFactory.py?at=default
 # passing them is complex
 # and they are restricted to NOT contain commas or double quotes to ensure that they can be safely passed together on
 <repository name="%(interpreter_pack)s" owner="%(interpreter_owner)s" prior_installation_required="True" />
 </package>
 <readme>
 %(readme)s
+This file was autogenerated by the Galaxy Tool Factory 2
 </readme>
 </tool_dependency>
 """
 self.toolhtmldepskel = """<?xml version="1.0"?>
 <package name="graphicsmagick" version="1.3.18">
 <repository name="package_graphicsmagick_1_3" owner="iuc" prior_installation_required="True" />
 </package>
 <readme>
 %(readme)s
+This file was autogenerated by the Galaxy Tool Factory 2
 </readme>
 </tool_dependency>
 """
 self.emptytoolhtmldepskel = """<?xml version="1.0"?>
 <tool_dependency>
 <readme>
 %(readme)s
+This file was autogenerated by the Galaxy Tool Factory 2
 </readme>
 </tool_dependency>
 """
 self.protorequirements = """<requirements>
 </tests>
 <help>
 %(help)s
+This tool was autogenerated from a user provided script using the Galaxy Tool Factory 2
+https://toolshed.g2.bx.psu.edu/view/fubar/tool_factory_2
 </help>
 <citations>
 %(citations)s
 <citation type="doi">10.1093/bioinformatics/bts573</citation>
 </citations>
 self.interp_owner = None
 self.interp_pack = None
 self.interp_revision = None
 self.interp_version = None
 if opts.envshpath <> 'system': # need to parse out details for our tool_dependency
-try:
+try: # fragile - depends on common naming convention as at jan 2015 = package_[interp]_v0_v1_v2... = version v0.v1.v2.. is in play
 packdetails = opts.envshpath.split(os.path.sep)[-4:-1]  # eg ['fubar', 'package_r_3_1_1', '63cdb9b2234c']
 self.interpreter_owner = packdetails[0]
 self.interpreter_pack = packdetails[1]
 self.interpreter_name = packdetails[1].split('_')[1].upper()
 self.interpreter_revision = packdetails[2]
-self.interpreter_version =  '.'.join(self.interpreter_pack.split('_')[2:])
+self.interpreter_version =  '.'.join(packdetails[1].split('_')[2:])
-# hope our naming convention as at jan 2015 = package_[interp]_v0_v1_v2... = version v0.v1.v2.. is in play
 except:
 pass
 self.outFormats = opts.output_format
 self.inputFormats = opts.input_formats
 self.test1Output = '%s_test1_output.xls' % self.toolname
 if self.opts.help_text:
 hlp = open(self.opts.help_text,'r').read()
 else:
 hlp = 'Please ask the tool author for help as none was supplied at tool generation\n'
 readme_dict = {'readme':hlp,'interpreter':self.opts.interpreter,'interpreter_version':self.interpreter_version,'interpreter_name':self.interpreter_name,
-'interpreter_owner':self.interpreter_owner}
+'interpreter_owner':self.interpreter_owner,'interpreter_pack':self.interpreter_pack}
 if self.opts.include_dependencies == "yes":
 if self.opts.envshpath == 'system':
 tooldepcontent = self.toolhtmldepskel % readme_dict
 else:
 tooldepcontent = self.toolhtmldepinterpskel % readme_dict
 tooldepcontent = self.emptytoolhtmldepskel  % readme_dictls -l
 depf = open(os.path.join(tdir,'tool_dependencies.xml'),'w')
 depf.write(tooldepcontent)
 depf.write('\n')
 depf.close()
-if self.opts.input_tab: # no reproducible test otherwise? TODO: maybe..
+testdir = os.path.join(tdir,'test-data')
-testdir = os.path.join(tdir,'test-data')
+os.mkdir(testdir) # make tests directory
-os.mkdir(testdir) # make tests directory
+for i,intab in enumerate(self.opts.input_tab):
-for i,intab in enumerate(self.opts.input_tab):
+si = self.opts.input_tab[i]
-si = self.opts.input_tab[i]
+if si.find(',') <> -1:
-if si.find(',') <> -1:
+s = si.split(',')[0]
-s = si.split(',')[0]
+si = s
-si = s
+dest = os.path.join(testdir,os.path.basename(si))
-dest = os.path.join(testdir,os.path.basename(si))
+if si <> dest:
-if si <> dest:
+shutil.copyfile(si,dest)
-shutil.copyfile(si,dest)
+if self.opts.output_tab:
-if self.opts.output_tab:
+shutil.copyfile(self.opts.output_tab,os.path.join(testdir,self.test1Output))
-shutil.copyfile(self.opts.output_tab,os.path.join(testdir,self.test1Output))
+if self.opts.make_HTML:
-if self.opts.make_HTML:
+shutil.copyfile(self.opts.output_html,os.path.join(testdir,self.test1HTML))
-shutil.copyfile(self.opts.output_html,os.path.join(testdir,self.test1HTML))
+if self.opts.output_dir:
-if self.opts.output_dir:
+shutil.copyfile(self.tlog,os.path.join(testdir,'test1_out.log'))
-shutil.copyfile(self.tlog,os.path.join(testdir,'test1_out.log'))
 outpif = '%s.py' % self.toolname # new name
 outpiname = os.path.join(tdir,outpif) # path for the tool tarball
 pyin = os.path.basename(self.pyfile) # our name - we rewrite ourselves (TM)
 notes = ['# %s - a self annotated version of %s generated by running %s\n' % (outpiname,pyin,pyin),]
 notes.append('# to make a new Galaxy tool called %s\n' % self.toolname)

Mercurial > repos > fubar > tool_factory_2

comparison rgToolFactory2.py @ 14:3635f4518c4d draft