comparison rgToolFactory.py @ 11:704ccaade924 draft

Uploaded

10:59bce2efadfe

# all rights reserved
# Licensed under the LGPL
# suggestions for improvement and bug fixes welcome at https://bitbucket.org/fubar/galaxytoolfactory/wiki/Home
#
# march 2014
# added ghostscript and graphicsmagick as dependencies 
# fixed a wierd problem where gs was trying to use the new_files_path from universe (database/tmp) as ./database/tmp
# errors ensued
#
# august 2013

progname = os.path.split(sys.argv[0])[1] 
myversion = 'V001.1 March 2014' 
verbose = False 
debug = False
toolFactoryURL = 'https://bitbucket.org/fubar/galaxytoolfactory'

def timenow():
    """return current time as a string
    """
    return time.strftime('%d/%m/%Y %H:%M:%S', time.localtime(time.time()))

        self.thumbformat = 'png'
        self.opts = opts
        self.toolname = re.sub('[^a-zA-Z0-9_]+', '', opts.tool_name) # a sanitizer now does this but..
        self.toolid = self.toolname
        self.myname = sys.argv[0] # get our name because we write ourselves out as a tool later
        self.pyfile = self.myname # crude but efficient - the cruft won't hurt much
        self.xmlfile = '%s.xml' % self.toolname
        s = open(self.opts.script_path,'r').readlines()
        s = [x.rstrip() for x in s] # remove pesky dos line endings if needed
        self.script = '\n'.join(s)
        fhandle,self.sfile = tempfile.mkstemp(prefix=self.toolname,suffix=".%s" % (opts.interpreter))

            %(tooltests)s
            <help>
            %(help)s
            </help>
            </tool>""" # needs a dict with toolname, toolid, interpreter, scriptname, command, inputs as a multi line string ready to write, outputs ditto, help ditto
               
        newCommand="""<command interpreter="python">
            %(toolname)s.py --script_path "$runMe" --interpreter "%(interpreter)s" 
            --tool_name "%(toolname)s" %(command_inputs)s %(command_outputs)s 
            </command>""" # may NOT be an input or htmlout
        tooltestsTabOnly = """<tests><test>

        """
        retval = self.run()
        if retval:
            print >> sys.stderr,'## Run failed. Cannot build yet. Please fix and retry'
            sys.exit(1)
        self.makeXML()
        tdir = self.toolname
        os.mkdir(tdir)
        if self.opts.input_tab <> 'None': # no reproducible test otherwise? TODO: maybe..
            testdir = os.path.join(tdir,'test-data')
            os.mkdir(testdir) # make tests directory
            shutil.copyfile(self.opts.input_tab,os.path.join(testdir,self.test1Input))
            if self.opts.output_tab <> 'None':

11:704ccaade924

# all rights reserved
# Licensed under the LGPL
# suggestions for improvement and bug fixes welcome at https://bitbucket.org/fubar/galaxytoolfactory/wiki/Home
#
# march 2014
# added dependencies to a tool_dependencies.xml if html page generated so generated tool is properly portable
#
# added ghostscript and graphicsmagick as dependencies 
# fixed a wierd problem where gs was trying to use the new_files_path from universe (database/tmp) as ./database/tmp
# errors ensued
#
# august 2013

progname = os.path.split(sys.argv[0])[1] 
myversion = 'V001.1 March 2014' 
verbose = False 
debug = False
toolFactoryURL = 'https://bitbucket.org/fubar/galaxytoolfactory'

# if we do html we need these dependencies
toolhtmldep = """<?xml version="1.0"?>
<tool_dependency>
    <package name="ghostscript" version="9.10">
        <repository name="package_ghostscript_9_10" owner="devteam" prior_installation_required="True" toolshed="http://toolshed.g2.bx.psu.edu/" />
    </package>
    <package name="graphicsmagick" version="1.3.18">
        <repository name="package_graphicsmagick_1_3" owner="iuc" prior_installation_required="True" toolshed="http://toolshed.g2.bx.psu.edu/" />
    </package>
        <readme>
           %s
       </readme>
</tool_dependency>
"""

def timenow():
    """return current time as a string
    """
    return time.strftime('%d/%m/%Y %H:%M:%S', time.localtime(time.time()))

        self.thumbformat = 'png'
        self.opts = opts
        self.toolname = re.sub('[^a-zA-Z0-9_]+', '', opts.tool_name) # a sanitizer now does this but..
        self.toolid = self.toolname
        self.myname = sys.argv[0] # get our name because we write ourselves out as a tool later
        self.pyfile = self.myname # crude but efficient - the cruft won't hurt muchself.tooldepfile)
        self.xmlfile = '%s.xml' % self.toolname
        s = open(self.opts.script_path,'r').readlines()
        s = [x.rstrip() for x in s] # remove pesky dos line endings if needed
        self.script = '\n'.join(s)
        fhandle,self.sfile = tempfile.mkstemp(prefix=self.toolname,suffix=".%s" % (opts.interpreter))

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

        newCommand="""<command interpreter="python">
            %(toolname)s.py --script_path "$runMe" --interpreter "%(interpreter)s" 
            --tool_name "%(toolname)s" %(command_inputs)s %(command_outputs)s 
            </command>""" # may NOT be an input or htmlout
        tooltestsTabOnly = """<tests><test>

        """
        retval = self.run()
        if retval:
            print >> sys.stderr,'## Run failed. Cannot build yet. Please fix and retry'
            sys.exit(1)
        tdir = self.toolname
        os.mkdir(tdir)
        self.makeXML()
        if self.opts.make_HTML:
            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'
            tooldeps = toolhtmldep % hlp
            depf = open('tool_dependencies.xml','w')
            depf.write(hlp)
            depf.write('\n')
            depf.close()
        if self.opts.input_tab <> 'None': # no reproducible test otherwise? TODO: maybe..
            testdir = os.path.join(tdir,'test-data')
            os.mkdir(testdir) # make tests directory
            shutil.copyfile(self.opts.input_tab,os.path.join(testdir,self.test1Input))
            if self.opts.output_tab <> 'None':