comparison rgToolFactory.py @ 9:e09c76551bed

Can run without input or output or either.. random heatmap (no inputs) example added to docs

8:220885b2d7ee

def timenow():
    """return current time as a string
    """
    return time.strftime('%d/%m/%Y %H:%M:%S', time.localtime(time.time()))
# characters that are allowed but need to be escaped
mapped_chars = { '>' :'__gt__',
                 '<' :'__lt__',
                 "'" :'__sq__',
                 '"' :'__dq__',
                 '{' :'__oc__',
                 '}' :'__cc__',
                 '@' : '__at__', 
                 '\n' : '__cn__',
                 '\r' : '__cr__',
                 '\t' : '__tc__',
                 '#' : '__pd__',
                 '[' :'__ob__',
                 ']' :'__cb__',
                 '\t' : 'Xt', 
                 'systemCallsAreNotAllowed' : 'system'
                 }

def restore_text(text):
    """Restores sanitized text"""  
    if not text:
        return text
    for key, value in mapped_chars.items():
        text = text.replace(value, key)
    return text
    
class ScriptRunner:
    """class is a wrapper for an arbitrary script
    """

    def __init__(self,opts=None):
        """
        run the script
        cheetah/galaxy will provide an escaped string so
        __pd__ your script goes here
        __cr____cn__ourargs __lt__- commandArgs(TRUE)
        __cr____cn__inf = ourargs[1]
        __cr____cn__outf = ourargs[2]
        __cr____cn__inp = read.table(inf,head=T,rownames=F,sep=__sq__Xt__sq__)
        __cr____cn__ write.table(inp,outf, quote=FALSE, sep=__dq__Xt__dq__,row.names=F)
        __cr____cn__sessionInfo()
        __cr____cn__
        """
        if opts.output_dir: # simplify for the tool tarball
            os.chdir(opts.output_dir)
        self.thumbformat = 'jpg'
        self.opts = opts
        self.toolname = re.sub('[^a-zA-Z0-9_]+', '', opts.tool_name)
        self.toolid = self.toolname
        s = open(self.opts.script_path,'r').read()
        self.script = restore_text(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)
        localscript = open(self.sfile,'w')
        localscript.write(self.script)
        localscript.close()
        if opts.output_dir or self.opts.make_Tool: # may not want these complexities if a simple script
            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()
        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):
        """
        Create a Galaxy xml tool wrapper for the new script as a string to write out
        """    
        newXML="""<tool id="%(toolid)s" name="%(toolname)s" version="0.01">
            %(tooldesc)s
            %(command)s
            <inputs>

            %(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
            
        xdict = {}
        xdict['script'] = self.script # we pass this as a configfile because it's less painful that galaxy_tool_data_dir
                                      # embed script in tool - remove dependence on something else outside in the wilds
        if self.opts.help_text:
            h = open(self.opts.help_text,'r').read()
            xdict['help'] = restore_text(h)
        else:
            xdict['help'] = 'Please ask the tool author for help as none was supplied at tool generation'
        if self.opts.tool_desc:
            xdict['tooldesc'] = '<description>%s</description>' % self.opts.tool_desc
        else:
            xdict['tooldesc'] = ''
        xdict['command_outputs'] = '' # will probably be some!
        xdict['outputs'] = '' # will probably be some!
        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['toolname'] = self.toolname
        xdict['toolid'] = self.toolid
        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"'
            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

                else:
                    fhtml.append('<li><a href="%s">%s %s</a></li>' % (fname,fname,sfsize))
            html.append('</table>\n')
        if len(fhtml) > 0:
           fhtml.insert(0,'<ul>')
           fhtml.append('</ul>')
           html += fhtml # add all non-pdf files to the end of the display
        else:
            html.append('<h2>### Error - %s returned no files - please confirm that parameters are sane</h1>' % self.opts.interpreter)
            html.append('<h3>%s log follows below</h3><hr/><pre>\n' % self.opts.interpreter)
        rlog = open(self.tlog,'r').readlines()
        html += rlog
        html.append('%s CL = %s<br/>\n' % (self.toolname,' '.join(sys.argv)))
        html.append('</pre>\n')
        html.append(galhtmlattr % (progname,timenow()))
        html.append(galhtmlpostfix)
        htmlf = file(self.opts.output_html,'w')
        htmlf.write('\n'.join(html))

9:e09c76551bed

def timenow():
    """return current time as a string
    """
    return time.strftime('%d/%m/%Y %H:%M:%S', time.localtime(time.time()))
# characters that are allowed but need to be escaped

class ScriptRunner:
    """class is a wrapper for an arbitrary script
    """

    def __init__(self,opts=None):
        """
        run the script
        
        """
        if opts.output_dir: # simplify for the tool tarball
            os.chdir(opts.output_dir)
        self.thumbformat = 'jpg'
        self.opts = opts
        self.toolname = re.sub('[^a-zA-Z0-9_]+', '', opts.tool_name)
        self.toolid = self.toolname
        s = open(self.opts.script_path,'r').read()
        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):
        """
        Create a Galaxy xml tool wrapper for the new script as a string to write out
        fixme - use templating or something less fugly than this
        """    
        newXML="""<tool id="%(toolid)s" name="%(toolname)s" version="0.01">
            %(tooldesc)s
            %(command)s
            <inputs>

            %(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
            
        xdict = {}
        xdict['script'] = self.script # configfile is least painful way to embed script to avoid external dependencies
        if self.opts.help_text:
            xdict['help'] = open(self.opts.help_text,'r').read()
        else:
            xdict['help'] = 'Please ask the tool author for help as none was supplied at tool generation'
        if self.opts.tool_desc:
            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['toolname'] = self.toolname
        xdict['toolid'] = self.toolid
        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

                else:
                    fhtml.append('<li><a href="%s">%s %s</a></li>' % (fname,fname,sfsize))
            html.append('</table>\n')
        if len(fhtml) > 0:
           fhtml.insert(0,'<ul>')
           fhtml.append('</ul><br/>')
           html += fhtml # add all non-pdf files to the end of the display
        else:
            html.append('<h2>### Error - %s returned no files - please confirm that parameters are sane</h1>' % self.opts.interpreter)
            html.append('<h3>%s log follows below</h3><hr/><pre><br/>\n' % self.opts.interpreter)
        rlog = open(self.tlog,'r').readlines()
        html += rlog
        html.append('<br/>%s CL = %s<br/>\n' % (self.toolname,' '.join(sys.argv)))
        html.append('</pre>\n')
        html.append(galhtmlattr % (progname,timenow()))
        html.append(galhtmlpostfix)
        htmlf = file(self.opts.output_html,'w')
        htmlf.write('\n'.join(html))