workflow/odin_epi_folder.gwendia

   1 <?xml version="1.0" encoding="UTF-8"?>
   2 <workflow name="odin" version="1.0">
   3
   4   <description>This application wraps the Odin MRI simulator. The Odin code source is available at http://od1n.sourceforge.net</description>
   5
   6   <interface>
   7     <source name="ProData" type="uri">
   8       <source-comment>&lt;b&gt;&lt;font color="blue"&gt;new input&lt;/font&gt;&lt;/b&gt;: Pro file
   9       </source-comment>
  10     </source>
  11     <source name="SmpDir" type="uri">
  12       <source-comment>&lt;b&gt;&lt;font color="blue"&gt;new input&lt;/font&gt;&lt;/b&gt;: Folder containing all (and only) Smp files
  13       </source-comment>
  14     </source>
  15     <source name="ResultsDirectory" type="uri">
  16       <source-comment>&lt;b&gt;&lt;font color="blue"&gt;new input&lt;/font&gt;&lt;/b&gt;: add description here...
  17       </source-comment>
  18     </source>
  19     <constant name="OdinSeq" type="string" value="odinepiexe" cardinality="scalar" />
  20     <source name="options" type="string">
  21       <source-comment>&lt;b&gt;&lt;font color="blue"&gt;options&lt;/font&gt;&lt;/b&gt;: any option string, to be appended to the recon-all command line. For instance: '-all'. &lt;b&gt;Important:&lt;/b&gt; don't put spaces, use '_'  instead. And put 'no' in case you don't want to use any option.
  22       </source-comment>
  23     </source>
  24   </interface>
  25
  26   <processors>
  27     <processor name="odin" >
  28       <in name="input4" type="string" depth="0" />
  29       <in name="input3" type="string" depth="0" />
  30       <in name="input2" type="string" depth="0" />
  31       <in name="input1" type="string" depth="0" />
  32       <in name="input0" type="uri" depth="0" />
  33       <iterationstrategy>
  34         <cross>
  35           <port name="input0" />
  36           <port name="input1" />
  37           <port name="input2" />
  38           <port name="input3" />
  39           <port name="input4" />
  40         </cross>
  41       </iterationstrategy>
  42       <gasw descriptor="[GASW_DIR]/odin.xml"/>
  43     </processor>
  44     <processor name="append-date" >
  45       <in name="dir" type="uri" depth="0" />
  46       <out name="result" type="string" depth="0" />
  47       <beanshell>/*----------Beginning of Beanshell------------*/
  48                         import java.text.DateFormat;
  49                         import java.text.SimpleDateFormat;
  50                         import java.util.Date;
  51
  52 DateFormat dateFormat = new SimpleDateFormat("dd-MM-yyyy_HH:mm:ss");
  53 String result = dir.toString()+"/"+(dateFormat.format(System.currentTimeMillis()));
  54 /*------------End of Beanshell------------*/
  55       </beanshell>
  56     </processor>
  57     <processor name="listSmpDir" >
  58       <in name="inDir" type="uri" depth="0" />
  59       <out name="arrayLfn" type="string" depth="1" />
  60       <beanshell>
  61 String smpDir=inDir.toString();
  62 arrayLfn = new ArrayList();
  63 String smpLfn="";
  64 Runtime rt = Runtime.getRuntime();
  65 try{
  66             String [] cmd1 = new String [2];
  67             cmd1[0] = "lfc-ls";
  68             cmd1[1] = smpDir;
  69             Process p1 = rt.exec(cmd1);
  70             p1.waitFor();
  71
  72             String line ="";
  73             BufferedReader in = new BufferedReader(new InputStreamReader(p1.getInputStream()));
  74             System.out.println(" Listing directory "+smpDir);
  75             while(in.ready()){
  76         line=in.readLine();
  77         try{
  78           System.out.println(" Line is "+line);
  79           smpLfn=smpDir+"/"+line;
  80           arrayLfn.add(""+smpLfn);
  81         }catch(Exception e){
  82                                         System.out.println(" exception:"+e.getMessage());
  83                 }
  84
  85
  86                 BufferedReader err = new BufferedReader(new InputStreamReader(p1.getErrorStream()));
  87                 while(err.ready()){
  88                     line=err.readLine();
  89                     System.out.println(" error listing directory "+smpDir+": "+line);
  90                 }
  91                 p1.getErrorStream().close();
  92                 p1.getInputStream().close();
  93                 p1.getOutputStream().close();
  94             }
  95                 }
  96
  97         catch(Exception e){
  98             System.out.println(" exception:"+e.getMessage());
  99         }
 100       </beanshell>
 101     </processor>
 102   </processors>
 103
 104   <links>
 105       <link from="ProData" to="odin:input0" />
 106       <link from="ResultsDirectory" to="append-date:dir" />
 107       <link from="append-date:result" to="odin:input2" />
 108       <link from="OdinSeq" to="odin:input3" />
 109       <link from="options" to="odin:input4" />
 110       <link from="SmpDir" to="listSmpDir:inDir" />
 111       <link from="listSmpDir:arrayLfn" to="odin:input1" />
 112   </links>
 113
 114 </workflow>