diff 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

--- a/rgToolFactory.py	Sat Jun 02 22:49:40 2012 +1000
+++ b/rgToolFactory.py	Sun Jun 03 15:39:20 2012 +1000
@@ -67,28 +67,25 @@
         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 
+        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 
-            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)
+        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
 
@@ -134,7 +131,7 @@
             xdict['tooldesc'] = ''
         xdict['command_outputs'] = '' 
         xdict['outputs'] = '' 
-        if self.opts.input_tab:
+        if self.opts.input_tab <> 'None':
             xdict['command_inputs'] = '--input_tab "$input1"'
             xdict['inputs'] = '<param name="input1"  type="data" format="%s" label="Select a suitable input file from your history"/>' % self.inputFormats
         else:
@@ -148,7 +145,7 @@
         if self.opts.make_HTML:
             xdict['command_outputs'] += '--output_dir "$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:
+        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
@@ -172,15 +169,16 @@
         self.makeXML()
         tdir = self.toolname
         os.mkdir(tdir)
-        if self.opts.input_tab: # we may have test data?
+        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:
+            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'))
-                shutil.copyfile(self.opts.tlog,os.path.join(testdir,'test1_out.log'))
+            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))
@@ -188,8 +186,8 @@
         tar = tarfile.open(tarpath, "w:gz")
         tar.add(tdir,arcname=self.toolname)
         tar.close()
+        shutil.copy(tarpath,self.opts.new_tool)
         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
 
@@ -294,7 +292,7 @@
     def run(self):
         """
         """
-        if self.opts.output_dir or self.opts.make_Tool:
+        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:
@@ -302,8 +300,9 @@
         p.stdin.write(self.script)
         p.stdin.close()
         retval = p.wait()
-        if self.opts.make_HTML or self.opts.make_Tool:
+        if self.opts.output_dir:
             sto.close()
+        if self.opts.make_HTML:
             self.makeHtml()
         return retval
   
@@ -321,14 +320,15 @@
     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('--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'