comparison rgToolFactory.py @ 12:d12728e33c3d

Changed to deliver a gz file - requires a new datatypes_conf.xml entry: <datatype extension="gz" type="galaxy.datatypes.binary:Binary" mimetype="multipart/x-gzip" subclass="True" /> There's some wierd shit going on with filter values and such but it now all appears to be working ok

11:a0a5d0757e39

        self.script = s
        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
        self.sfile = '%s.%s' % (self.toolname,opts.interpreter)
        if opts.output_dir or self.opts.make_Tool: # may not want these complexities 
            self.tlog = os.path.join(opts.output_dir,"%s_runner.log" % self.toolname)
            artifactpath = os.path.join(opts.output_dir,'%s_run.script' % self.toolname) 
            artifact = open(artifactpath,'w')
            artifact.write(self.script)
            artifact.write('\n')
            artifact.close()
            localscript = open(self.sfile,'w')
            localscript.write(self.script)
            localscript.close()
            shutil.copyfile(self.myname,'%s.py' % self.toolname) # for tool and for user 
            localpy = open('%s.py' % self.toolname,'w')
            localpy.write(open(self.myname,'r').read())
        self.cl = []
        self.html = []
        a = self.cl.append
        a(opts.interpreter)
        a('-') # use stdin
        if opts.input_tab:
            a(opts.input_tab)
        if opts.output_tab:
            a(opts.output_tab)
        self.outFormats = 'tabular' # TODO make this an option at tool generation time
        self.inputFormats = 'tabular' # TODO make this an option at tool generation time


    def makeXML(self):

            xdict['tooldesc'] = '<description>%s</description>' % self.opts.tool_desc
        else:
            xdict['tooldesc'] = ''
        xdict['command_outputs'] = '' 
        xdict['outputs'] = '' 
        if self.opts.input_tab:
            xdict['command_inputs'] = '--input_tab "$input1"'
            xdict['inputs'] = '<param name="input1"  type="data" format="%s" label="Select a suitable input file from your history"/>' % self.inputFormats
        else:
            xdict['command_inputs'] = '' # assume no input - eg a random data generator          
            xdict['inputs'] = ''

        xdict['interpreter'] = self.opts.interpreter
        xdict['scriptname'] = self.sfile
        if self.opts.make_HTML:
            xdict['command_outputs'] += '--output_dir "$html_file.files_path" --output_html "$html_file" --make_HTML "yes"'
            xdict['outputs'] +=  '<data format="html" name="html_file" label="${job_name}.html"/>\n'
        if self.opts.output_tab:
            xdict['command_outputs'] += '--output_tab "$tab_file"'
            xdict['outputs'] += '<data format="%s" name="tab_file" label="${job_name}"/>\n' % self.outFormats
        xdict['command'] = newCommand % xdict
        xmls = newXML % xdict
        xf = open(self.xmlfile,'w')

            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: # we may have test data?
            testdir = os.path.join(tdir,'test-data')
            os.mkdir(testdir) # make tests directory
            shutil.copyfile(self.opts.input_tab,os.path.join(testdir,'test1_in.tab'))
            if self.opts.output_tab:
                shutil.copyfile(self.opts.output_tab,os.path.join(testdir,'test1_out.tab'))
            if self.opts.make_HTML:
                shutil.copyfile(self.opts.output_html,os.path.join(testdir,'test1_out.html'))
                shutil.copyfile(self.opts.tlog,os.path.join(testdir,'test1_out.log'))
        shutil.copyfile(self.xmlfile,os.path.join(tdir,self.xmlfile))
        shutil.copyfile(self.pyfile,os.path.join(tdir,'%s.py' % self.toolname))
        shutil.copyfile(self.sfile,os.path.join(tdir,self.sfile))
        tarpath = "%s.gz" % self.toolname
        tar = tarfile.open(tarpath, "w:gz")
        tar.add(tdir,arcname=self.toolname)
        tar.close()
        shutil.rmtree(tdir)
        self.makeHtml() # call this to return the new gzip inside the autogenerated html file
        ## TODO: replace with optional direct upload to local toolshed?
        return retval

    def compressPDF(self,inpdf=None,thumbformat='png'):
        """need absolute path to pdf

    def run(self):
        """
        """
        if self.opts.output_dir or self.opts.make_Tool:
            sto = open(self.tlog,'w')
            p = subprocess.Popen(' '.join(self.cl),shell=True,stdout=sto,stderr=sto,stdin=subprocess.PIPE,cwd=self.opts.output_dir)
        else:
            p = subprocess.Popen(' '.join(self.cl),shell=True,stdin=subprocess.PIPE)            
        p.stdin.write(self.script)
        p.stdin.close()
        retval = p.wait()
        if self.opts.make_HTML or self.opts.make_Tool:
            sto.close()
            self.makeHtml()
        return retval
  

def main():

    a('--script_path',default=None)
    a('--tool_name',default=None)
    a('--interpreter',default=None)
    a('--output_dir',default=None)
    a('--output_html',default=None)
    a('--input_tab',default=None)
    a('--output_tab',default=None)
    a('--user_email',default=None)
    a('--bad_user',default=None)
    a('--make_Tool',default=None)
    a('--make_HTML',default=None)
    a('--help_text',default=None)
    a('--tool_desc',default=None)
    opts, args = op.parse_args()
    assert not opts.bad_user,'%s is NOT authorized to use this tool. Please ask your friendly admin' % opts.bad_user
    assert opts.tool_name,'## Tool Factory expects a tool name - eg --tool_name=DESeq'
    assert opts.interpreter,'## Tool Factory wrapper expects an interpreter - eg --interpreter=Rscript'
    assert os.path.isfile(opts.script_path),'## Tool Factory wrapper expects a script path - eg --script_path=foo.R'

12:d12728e33c3d

        self.script = s
        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
        self.sfile = '%s.%s' % (self.toolname,opts.interpreter)
        if opts.output_dir: # may not want these complexities 
            self.tlog = os.path.join(opts.output_dir,"%s_runner.log" % self.toolname)
            artifactpath = os.path.join(opts.output_dir,'%s_run.script' % self.toolname) 
            artifact = open(artifactpath,'w')
            artifact.write(self.script)
            artifact.write('\n')
            artifact.close()
        if opts.make_Tool: # need this code and the user script for the tarball 
            localscript = open(self.sfile,'w')
            localscript.write(self.script)
            localscript.close()
            shutil.copyfile(self.myname,'%s.py' % self.toolname) # for tool and for user 
        self.cl = []
        self.html = []
        a = self.cl.append
        a(opts.interpreter)
        a('-') # use stdin
        a(opts.input_tab)
        a(opts.output_tab)
        self.outFormats = 'tabular' # TODO make this an option at tool generation time
        self.inputFormats = 'tabular' # TODO make this an option at tool generation time


    def makeXML(self):

            xdict['tooldesc'] = '<description>%s</description>' % self.opts.tool_desc
        else:
            xdict['tooldesc'] = ''
        xdict['command_outputs'] = '' 
        xdict['outputs'] = '' 
        if self.opts.input_tab <> 'None':
            xdict['command_inputs'] = '--input_tab "$input1"'
            xdict['inputs'] = '<param name="input1"  type="data" format="%s" label="Select a suitable input file from your history"/>' % self.inputFormats
        else:
            xdict['command_inputs'] = '' # assume no input - eg a random data generator          
            xdict['inputs'] = ''

        xdict['interpreter'] = self.opts.interpreter
        xdict['scriptname'] = self.sfile
        if self.opts.make_HTML:
            xdict['command_outputs'] += '--output_dir "$html_file.files_path" --output_html "$html_file" --make_HTML "yes"'
            xdict['outputs'] +=  '<data format="html" name="html_file" label="${job_name}.html"/>\n'
        if self.opts.output_tab <> 'None':
            xdict['command_outputs'] += '--output_tab "$tab_file"'
            xdict['outputs'] += '<data format="%s" name="tab_file" label="${job_name}"/>\n' % self.outFormats
        xdict['command'] = newCommand % xdict
        xmls = newXML % xdict
        xf = open(self.xmlfile,'w')

            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': # we may have test data?
            testdir = os.path.join(tdir,'test-data')
            os.mkdir(testdir) # make tests directory
            shutil.copyfile(self.opts.input_tab,os.path.join(testdir,'test1_in.tab'))
            if self.opts.output_tab <> 'None':
                shutil.copyfile(self.opts.output_tab,os.path.join(testdir,'test1_out.tab'))
            if self.opts.make_HTML:
                shutil.copyfile(self.opts.output_html,os.path.join(testdir,'test1_out.html'))
            if self.opts.output_dir:
                shutil.copyfile(self.tlog,os.path.join(testdir,'test1_out.log'))
        shutil.copyfile(self.xmlfile,os.path.join(tdir,self.xmlfile))
        shutil.copyfile(self.pyfile,os.path.join(tdir,'%s.py' % self.toolname))
        shutil.copyfile(self.sfile,os.path.join(tdir,self.sfile))
        tarpath = "%s.gz" % self.toolname
        tar = tarfile.open(tarpath, "w:gz")
        tar.add(tdir,arcname=self.toolname)
        tar.close()
        shutil.copy(tarpath,self.opts.new_tool)
        shutil.rmtree(tdir)
        ## TODO: replace with optional direct upload to local toolshed?
        return retval

    def compressPDF(self,inpdf=None,thumbformat='png'):
        """need absolute path to pdf

    def run(self):
        """
        """
        if self.opts.output_dir:
            sto = open(self.tlog,'w')
            p = subprocess.Popen(' '.join(self.cl),shell=True,stdout=sto,stderr=sto,stdin=subprocess.PIPE,cwd=self.opts.output_dir)
        else:
            p = subprocess.Popen(' '.join(self.cl),shell=True,stdin=subprocess.PIPE)            
        p.stdin.write(self.script)
        p.stdin.close()
        retval = p.wait()
        if self.opts.output_dir:
            sto.close()
        if self.opts.make_HTML:
            self.makeHtml()
        return retval
  

def main():

    a('--script_path',default=None)
    a('--tool_name',default=None)
    a('--interpreter',default=None)
    a('--output_dir',default=None)
    a('--output_html',default=None)
    a('--input_tab',default="None")
    a('--output_tab',default="None")
    a('--user_email',default=None)
    a('--bad_user',default=None)
    a('--make_Tool',default=None)
    a('--make_HTML',default=None)
    a('--help_text',default=None)
    a('--tool_desc',default=None)
    a('--new_tool',default=None)
    opts, args = op.parse_args()
    assert not opts.bad_user,'%s is NOT authorized to use this tool. Please ask your friendly admin' % opts.bad_user
    assert opts.tool_name,'## Tool Factory expects a tool name - eg --tool_name=DESeq'
    assert opts.interpreter,'## Tool Factory wrapper expects an interpreter - eg --interpreter=Rscript'
    assert os.path.isfile(opts.script_path),'## Tool Factory wrapper expects a script path - eg --script_path=foo.R'