Mercurial > repos > fubar > brokenandnotdeletablebyowneroradmin
diff rgToolFactory.py @ 8:220885b2d7ee
End to end test works. Add tests next
| author | ross lazarus ross.lazarus@gmail.com |
|---|---|
| date | Sat, 02 Jun 2012 20:02:11 +1000 |
| parents | 7221619caefa |
| children | e09c76551bed |
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--- a/rgToolFactory.py Sat Jun 02 10:43:08 2012 +1000 +++ b/rgToolFactory.py Sat Jun 02 20:02:11 2012 +1000 @@ -30,26 +30,14 @@ import optparse import tarfile import re +import shutil + progname = os.path.split(sys.argv[0])[1] myversion = 'V000.1 May 2012' verbose = False debug = False -galhtmlprefix = """<?xml version="1.0" encoding="utf-8" ?> -<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd"> -<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en"> -<head> <meta http-equiv="Content-Type" content="text/html; charset=utf-8" /> -<meta name="generator" content="Galaxy %s tool output - see http://g2.trac.bx.psu.edu/" /> -<title></title> -<link rel="stylesheet" href="/static/style/base.css" type="text/css" /> -</head> -<body> -<div class="document"> -""" -galhtmlattr = """<b><a href="http://rgenetics.org">Galaxy Rgenetics Base Script Wrapper based </a> tool output %s run at %s</b><br/>""" -galhtmlpostfix = """</div></body></html>\n""" - def timenow(): """return current time as a string """ @@ -97,19 +85,22 @@ __cr____cn__sessionInfo() __cr____cn__ """ - self.myname = sys.argv[0] # get our name because we write ourselves out as a tool later + 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.pyfile = self.myname - self.xmlfile = '%s.xml' % os.path.splitext(self.pyfile)[0] # punt + 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.makeTool: # may not want these complexities if a simple script + 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') @@ -123,6 +114,77 @@ 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> + %(inputs)s + </inputs> + <outputs> + %(outputs)s + </outputs> + <help> + %(help)s + </help> + <configfiles> + <configfile name="runMe"> + %(script)s + </configfile> + </configfiles> + </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 "$runMe" --interpreter "%(interpreter)s" + --tool_name "%(toolname)s" %(command_inputs)s %(command_outputs)s + </command>""" # may NOT be an input or htmlout + + xdict = {} + xdict['script'] = self.script # we pass this as a configfile because it's less painful that galaxy_tool_data_dir + # embed script in tool - remove dependence on something else outside in the wilds + if self.opts.help_text: + h = open(self.opts.help_text,'r').read() + xdict['help'] = restore_text(h) + else: + xdict['help'] = 'Please ask the tool author for help as none was supplied at tool generation' + if self.opts.tool_desc: + xdict['tooldesc'] = '<description>%s</description>' % self.opts.tool_desc + else: + xdict['tooldesc'] = '' + xdict['command_outputs'] = '' # will probably be some! + xdict['outputs'] = '' # will probably be some! + if self.opts.input_tab: + xdict['command_inputs'] = '--input_tab "$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['inputs'] = '' + xdict['inputs'] += '<param name="job_name" type="text" label="Supply a name for the outputs to remind you what they contain" value="%s"/>\n' % self.toolname + 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 + xmls = newXML % xdict + xf = open(self.xmlfile,'w') + xf.write(xmls) + xf.write('\n') + xf.close() + # ready for the tarball + def makeTooltar(self): """ @@ -133,13 +195,19 @@ if retval: print >> sys.stderr,'## Run failed. Cannot build yet. Please fix and retry' sys.exit(1) - tarpath = os.path.join(self.opts.output_dir,"%s.gz" % self.toolname) + self.makeXML() + tdir = self.toolname + os.mkdir(tdir) + 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(self.xmlfile,arcname='%s.xml' % self.toolname) - tar.add(self.pyfile,arcname=os.path.basename(self.pyfile)) - tar.add(self.sfile,arcname=self.sfile) + tar.add(tdir,arcname=self.toolname) tar.close() - self.makeHtml() + 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'): @@ -181,17 +249,32 @@ return size def makeHtml(self): - """ - """ - flist = os.listdir(self.opts.output_dir) - flist = [x for x in flist if x <> 'Rplots.pdf'] - flist.sort() - html = [galhtmlprefix % progname,] - html.append('<h2>Galaxy %s outputs run at %s</h2><br/>\n' % (self.toolname,timenow())) - fhtml = [] - if len(flist) > 0: - html.append('<table cellpadding="3" cellspacing="3">\n') - for fname in flist: + """ Create an HTML file content to list all the artefacts found in the output_dir + """ + + galhtmlprefix = """<?xml version="1.0" encoding="utf-8" ?> + <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd"> + <html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en"> + <head> <meta http-equiv="Content-Type" content="text/html; charset=utf-8" /> + <meta name="generator" content="Galaxy %s tool output - see http://g2.trac.bx.psu.edu/" /> + <title></title> + <link rel="stylesheet" href="/static/style/base.css" type="text/css" /> + </head> + <body> + <div class="document"> + """ + galhtmlattr = """<hr/><b><a href="http://rgenetics.org">Galaxy Tool Factory Script Wrapper</a> tool output %s run at %s</b><br/>""" + galhtmlpostfix = """</div></body></html>\n""" + + flist = os.listdir(self.opts.output_dir) + flist = [x for x in flist if x <> 'Rplots.pdf'] + flist.sort() + html = [galhtmlprefix % progname,] + html.append('<h2>Galaxy %s outputs run at %s</h2><br/>\n' % (self.toolname,timenow())) + fhtml = [] + if len(flist) > 0: + html.append('<table cellpadding="3" cellspacing="3">\n') + for fname in flist: dname,e = os.path.splitext(fname) sfsize = self.getfSize(fname,self.opts.output_dir) if e.lower() == '.pdf' : # compress and make a thumbnail @@ -204,32 +287,31 @@ fhtml.append('<li><a href="%s">%s %s</a></li>' % (fname,fname,sfsize)) 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('CL = %s</br>\n' % (' '.join(self.cl))) - html.append('</pre>\n') - html.append(galhtmlattr % (progname,timenow())) - html.append(galhtmlpostfix) - htmlf = file(self.opts.output_html,'w') - htmlf.write('\n'.join(html)) - htmlf.write('\n') - htmlf.close() - self.html = html + 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)) + htmlf.write('\n') + htmlf.close() + self.html = html def run(self): """ """ - if self.opts.output_dir or self.opts.makeTool: + 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: @@ -237,7 +319,7 @@ p.stdin.write(self.script) p.stdin.close() retval = p.wait() - if self.opts.output_dir or self.opts.makeTool: + if self.opts.make_HTML or self.opts.make_Tool: sto.close() self.makeHtml() return retval @@ -256,11 +338,14 @@ 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('--input_tab',default=None) + a('--output_tab',default=None) a('--user_email',default=None) a('--bad_user',default=None) - a('--makeTool',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' @@ -272,7 +357,7 @@ except: pass r = ScriptRunner(opts) - if opts.makeTool: + if opts.make_Tool: retcode = r.makeTooltar() else: retcode = r.run()