# HG changeset patch # User ross lazarus ross.lazarus@gmail.com # Date 1338631331 -36000 # Node ID 220885b2d7eebaac73d5f38449bb929ca08004dd # Parent 7221619caefa0554e01f69d19af7d407b626fec2 End to end test works. Add tests next diff -r 7221619caefa -r 220885b2d7ee rgToolFactory.py --- 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 = """ - - - - - - - - -
-""" -galhtmlattr = """Galaxy Rgenetics Base Script Wrapper based tool output %s run at %s
""" -galhtmlpostfix = """
\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=""" + %(tooldesc)s + %(command)s + + %(inputs)s + + + %(outputs)s + + + %(help)s + + + + %(script)s + + + """ # needs a dict with toolname, toolid, interpreter, scriptname, command, inputs as a multi line string ready to write, outputs ditto, help ditto + + newCommand=""" + %(toolname)s.py --script_path "$runMe" --interpreter "%(interpreter)s" + --tool_name "%(toolname)s" %(command_inputs)s %(command_outputs)s + """ # may NOT be an input or htmlout + + xdict = {} + xdict['script'] = self.script # we pass this as a configfile because it's less painful that galaxy_tool_data_dir + # embed script in tool - remove dependence on something else outside in the wilds + if self.opts.help_text: + h = open(self.opts.help_text,'r').read() + xdict['help'] = restore_text(h) + else: + xdict['help'] = 'Please ask the tool author for help as none was supplied at tool generation' + if self.opts.tool_desc: + xdict['tooldesc'] = '%s' % self.opts.tool_desc + else: + xdict['tooldesc'] = '' + xdict['command_outputs'] = '' # will probably be some! + xdict['outputs'] = '' # will probably be some! + if self.opts.input_tab: + xdict['command_inputs'] = '--input_tab "$input1"' + xdict['inputs'] = '' % self.inputFormats + else: + xdict['command_inputs'] = '' # assume no input - eg a random data generator + xdict['inputs'] = '' + xdict['inputs'] += '\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'] += '\n' + if self.opts.output_tab: + xdict['command_outputs'] += '--output_tab "$tab_file"' + xdict['outputs'] += '\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('

Galaxy %s outputs run at %s


\n' % (self.toolname,timenow())) - fhtml = [] - if len(flist) > 0: - html.append('\n') - for fname in flist: + """ Create an HTML file content to list all the artefacts found in the output_dir + """ + + galhtmlprefix = """ + + + + + + + + +
+ """ + galhtmlattr = """
Galaxy Tool Factory Script Wrapper tool output %s run at %s
""" + galhtmlpostfix = """
\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('

Galaxy %s outputs run at %s


\n' % (self.toolname,timenow())) + fhtml = [] + if len(flist) > 0: + html.append('
\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('
  • %s %s
    • ' % (fname,fname,sfsize)) else: fhtml.append('
  • %s %s
    • ' % (fname,fname,sfsize)) - html.append('
    \n') - if len(fhtml) > 0: - fhtml.insert(0,'') - html += fhtml # add all non-pdf files to the end of the display - else: - html.append('

    ### Error - %s returned no files - please confirm that parameters are sane

    ' % self.opts.interpreter) - html.append('

    %s log follows below

    \n' % self.opts.interpreter)
-       rlog = open(self.tlog,'r').readlines()
-       html += rlog
-       html.append('%s CL = %s
    \n' % (self.toolname,' '.join(sys.argv)))
-       html.append('CL = %s
    \n' % (' '.join(self.cl)))
-       html.append('
    \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('\n') + if len(fhtml) > 0: + fhtml.insert(0,'') + html += fhtml # add all non-pdf files to the end of the display + else: + html.append('

    ### Error - %s returned no files - please confirm that parameters are sane

    ' % self.opts.interpreter) + html.append('

    %s log follows below

    \n' % self.opts.interpreter)
+        rlog = open(self.tlog,'r').readlines()
+        html += rlog
+        html.append('%s CL = %s
    \n' % (self.toolname,' '.join(sys.argv)))
+        html.append('
    \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() diff -r 7221619caefa -r 220885b2d7ee rgToolFactory.xml --- a/rgToolFactory.xml Sat Jun 02 10:43:08 2012 +1000 +++ b/rgToolFactory.xml Sat Jun 02 20:02:11 2012 +1000 @@ -5,15 +5,20 @@ rgToolFactory.py --bad_user $__user_email__ #else: rgToolFactory.py --script_path "$runme" --interpreter "$interpreter" - --tool_name "$tool_name" --input_tab "$input1" --user_email "${__user_email__}" - #if $makeHTML.value=="yes" or $makeTool.value=="yes": + --tool_name "$tool_name" --input_tab "$input1" + #if $make_HTML.value=="yes" or $factory.make_Tool=="yes": --output_dir "$html_file.files_path" --output_html "$html_file" #end if - #if $makeTAB.value=="yes": + #if $make_HTML.value=="yes": + --make_HTML "yes" + #end if + #if $make_TAB.value=="yes": --output_tab "$tab_file" #end if - #if $makeTool.value=="yes": - --makeTool "$makeTool" + #if $factory.make_Tool=="yes": + --make_Tool "$factory.make_Tool" + --help_text "$helpme" + --tool_desc "$factory.tool_desc" #end if #end if @@ -21,17 +26,28 @@ - + + - - + + + + + + + + + + + + - @@ -42,20 +58,32 @@ + help="Expect FIRST CL parameter = the optional input tabular file path (or NONE if not specified). Ensure your script writes tabular output to the path in the SECOND command line parameter it gets."> + + + + + + - makeTAB=="yes" + make_TAB=="yes" - makeHTML=="yes" or makeTool=="yes" + make_HTML=="yes" or make_Tool=="yes" ${dynScript} +#if $factory.make_Tool == "yes": + +$factory.help_text + +#end if + **What it does**