From 72795d4e018b932a831b4ef6b82aea77fef0382c Mon Sep 17 00:00:00 2001
From: Sandesh Patil <99490622+sandepat@users.noreply.github.com>
Date: Mon, 1 Jul 2024 14:55:37 +0200
Subject: [PATCH] Update gwendia-standalone.vm

intelligence to put result dir in dot or cross
---
 .../main/resources/vm/gwendia-standalone.vm   | 158 ++++++++++--------
 1 file changed, 85 insertions(+), 73 deletions(-)

diff --git a/vip-portal/src/main/resources/vm/gwendia-standalone.vm b/vip-portal/src/main/resources/vm/gwendia-standalone.vm
index ce289c99d..36c49bbfa 100644
--- a/vip-portal/src/main/resources/vm/gwendia-standalone.vm
+++ b/vip-portal/src/main/resources/vm/gwendia-standalone.vm
@@ -5,87 +5,99 @@
     <source name="results-directory" type="URI" optional="false" default="/vip/Home" pretty-name="Results directory">
         <source-comment>Directory where the results will be stored.</source-comment>
     </source>
-#foreach( $input in $tool.getInputs() )
-  #set($type="string")
-  #if($input.getType().getCamelName()=="File")
-    #set($type="URI")
-  #end
-  #if($input.getType().getCamelName()=="Flag")
-    #if($input.getDefaultValue() && $input.getDefaultValue()!="")
-      <source name="$input.getId()" type="string" optional="$input.isOptional()" default="$input.getDefaultValue()" vip-type-restriction="flag" pretty-name="$input.getName()">
-    #else
-      <source name="$input.getId()" type="string" optional="$input.isOptional()" default="false" vip-type-restriction="flag" pretty-name="$input.getName()">
+    #foreach( $input in $tool.getInputs() )
+        #set($type="string")
+        #if($input.getType().getCamelName()=="File")
+            #set($type="URI")
+        #end
+        #if($input.getType().getCamelName()=="Flag")
+            #if($input.getDefaultValue() && $input.getDefaultValue()!="")
+                <source name="$input.getId()" type="string" optional="$input.isOptional()" default="$input.getDefaultValue()" vip-type-restriction="flag" pretty-name="$input.getName()">
+            #else
+                <source name="$input.getId()" type="string" optional="$input.isOptional()" default="false" vip-type-restriction="flag" pretty-name="$input.getName()">
+            #end
+        #else
+            #if($input.getDefaultValue() && $input.getDefaultValue()!="")
+                #if($input.getType().getCamelName()=="Number" && $input.isInteger())
+                    <source name="$input.getId()" type="$type" optional="$input.isOptional()" default="$input.getDefaultValue().intValue()" pretty-name="$input.getName()">
+                #else
+                    <source name="$input.getId()" type="$type" optional="$input.isOptional()" default="$input.getDefaultValue()" pretty-name="$input.getName()">
+                #end
+            #else
+                #if($input.isOptional()==true)
+                    <source name="$input.getId()" type="$type" optional="$input.isOptional()" default="No_value_provided" pretty-name="$input.getName()">
+                #else
+                    <source name="$input.getId()" type="$type" optional="$input.isOptional()" pretty-name="$input.getName()">
+                #end
+            #end
+        #end
+        #if($input.getDescription())
+            <source-comment>$esc.xml($input.getDescription())</source-comment>
+        #else
+            <source-comment></source-comment>
+        #end
+    </source>
     #end
-  #else
-    #if($input.getDefaultValue() && $input.getDefaultValue()!="")
-       #if($input.getType().getCamelName()=="Number" && $input.isInteger())
-           <source name="$input.getId()" type="$type" optional="$input.isOptional()" default="$input.getDefaultValue().intValue()" pretty-name="$input.getName()">
-       #else
-           <source name="$input.getId()" type="$type" optional="$input.isOptional()" default="$input.getDefaultValue()" pretty-name="$input.getName()">
-       #end
-    #else
-      #if($input.isOptional()==true)
-    <source name="$input.getId()" type="$type" optional="$input.isOptional()" default="No_value_provided" pretty-name="$input.getName()">
-      #else
-    <source name="$input.getId()" type="$type" optional="$input.isOptional()" pretty-name="$input.getName()">
-      #end
+    #foreach($output in $tool.getOutputFiles())
+        <sink name="$output.getId()" type="URI" />
     #end
-  #end
-  #if($input.getDescription())
-      <source-comment>$esc.xml($input.getDescription())</source-comment>
-  #else
-      <source-comment></source-comment>
-  #end
-    </source>
-#end
-#foreach($output in $tool.getOutputFiles())
-    <sink name="$output.getId()" type="URI" />
-#end
   </interface>
   <processors>
     <processor name="append-date" >
       <in name="dir" type="URI" depth="0" />
       <out name="result" type="string" depth="0" />
-      <beanshell>/*----------Beginning of Beanshell------------*/
-import java.text.DateFormat;
-import java.text.SimpleDateFormat;
-import java.util.Date;
+      <beanshell>
+        /*----------Beginning of Beanshell------------*/
+        import java.text.DateFormat;
+        import java.text.SimpleDateFormat;
+        import java.util.Date;
 
-String result = dir.toString();
-if ( result.startsWith("/") || result.startsWith("lfn:") ) {
-  DateFormat dateFormat = new SimpleDateFormat("dd-MM-yyyy_HH:mm:ss");
-  result = result + "/" + (dateFormat.format(System.currentTimeMillis()));
-}
-/*------------End of Beanshell------------*/
+        String result = dir.toString();
+        if ( result.startsWith("/") || result.startsWith("lfn:") ) {
+          DateFormat dateFormat = new SimpleDateFormat("dd-MM-yyyy_HH:mm:ss");
+          result = result + "/" + (dateFormat.format(System.currentTimeMillis()));
+        }
+        /*------------End of Beanshell------------*/
       </beanshell>
     </processor>
     <processor name="$tool.getName()" >
         <in name="results-directory" type="string" depth="0"/>
-#foreach($input in $tool.getInputs())
-  #if($input.getType().getCamelName()=="File" )
-        <in name="$input.getId()" type="URI" depth="0"/>
-  #else
-        <in name="$input.getId()" type="string" depth="0"/>
-  #end
-#end
-#foreach( $output in $tool.getOutputFiles() )
-        <out name="$output.getId()" type="URI" depth="0"/>
-#end
+        #foreach($input in $tool.getInputs())
+            #if($input.getType().getCamelName()=="File" )
+                <in name="$input.getId()" type="URI" depth="0"/>
+            #else
+                <in name="$input.getId()" type="string" depth="0"/>
+            #end
+        #end
+        #foreach( $output in $tool.getOutputFiles() )
+            <out name="$output.getId()" type="URI" depth="0"/>
+        #end
         <iterationstrategy>
           <cross>
-            <port name="results-directory" />
-#foreach($input in $tool.getInputs()) 
-  #if(!$tool.getVipDotInputIds().contains($input.getId()))
-            <port name="$input.getId()"/>
-  #end
-#end
-#if($tool.getVipDotInputIds() && !$tool.getVipDotInputIds().isEmpty())
-            <dot>
-#foreach($dotInput in $tool.getVipDotInputIds())
-                <port name="$dotInput"/>
-#end
-            </dot>
-#end
+            #if($tools.getVipDotResultDirs)
+                <dot>
+                    <port name="results-directory" />
+                    #foreach($input in $tool.getInputs()) 
+                        #if($tool.getVipDotInputIds().contains($input.getId()))
+                            <port name="$input.getId()"/>
+                        #end
+                    #end
+                </dot>
+            #else
+                <port name="results-directory" />
+                #foreach($input in $tool.getInputs()) 
+                    #if(!$tool.getVipDotInputIds().contains($input.getId()))
+                        <port name="$input.getId()"/>
+                    #end
+                #end
+            #end
+            #if($tool.getVipDotInputIds() && !$tool.getVipDotInputIds().isEmpty() && !$tools.getVipDotResultDirs)
+                <dot>
+                    #foreach($dotInput in $tool.getVipDotInputIds())
+                        <port name="$dotInput"/>
+                    #end
+                </dot>
+            #end
           </cross>
         </iterationstrategy>
         <gasw descriptor="$fileAccessProtocol:$tool.getGASWLFN()"/>
@@ -94,11 +106,11 @@ if ( result.startsWith("/") || result.startsWith("lfn:") ) {
   <links>
     <link from="results-directory" to="append-date:dir" />
     <link from="append-date:result" to="$tool.getName():results-directory" />
-#foreach( $input in $tool.getInputs() )
-    <link from="$input.getId()" to="$tool.getName():$input.getId()" />
-#end
-#foreach($output in $tool.getOutputFiles())
-    <link from="$tool.getName():$output.getId()" to="$output.getId()" />
-#end
+    #foreach( $input in $tool.getInputs() )
+        <link from="$input.getId()" to="$tool.getName():$input.getId()" />
+    #end
+    #foreach($output in $tool.getOutputFiles())
+        <link from="$tool.getName():$output.getId()" to="$output.getId()" />
+    #end
   </links>
 </workflow>