Custom properties vip:dot

coverage/src/test/java/Coverage/Coverage.java

@@ -1,4 +1,4 @@
-package coverage;
+package Coverage;
 
 import org.junit.jupiter.api.Test;
 

vip-application-importer/src/main/java/fr/insalyon/creatis/vip/applicationimporter/client/view/applicationdisplay/DisplayTab.java

@@ -31,6 +31,9 @@
  */
 package fr.insalyon.creatis.vip.applicationimporter.client.view.applicationdisplay;
 
+import java.util.HashSet;
+import java.util.Set;
+
 import com.google.gwt.user.client.rpc.AsyncCallback;
 import com.smartgwt.client.widgets.Canvas;
 import com.smartgwt.client.widgets.IButton;
@@ -39,6 +42,7 @@
 import com.smartgwt.client.widgets.layout.HLayout;
 import com.smartgwt.client.widgets.layout.VLayout;
 import com.smartgwt.client.widgets.tab.Tab;
+
 import fr.insalyon.creatis.vip.application.client.bean.boutiquesTools.BoutiquesApplication;
 import fr.insalyon.creatis.vip.application.client.view.boutiquesParsing.BoutiquesParser;
 import fr.insalyon.creatis.vip.application.client.view.boutiquesParsing.InvalidBoutiquesDescriptorException;
@@ -49,6 +53,7 @@
 import fr.insalyon.creatis.vip.core.client.view.layout.Layout;
 import fr.insalyon.creatis.vip.core.client.view.util.WidgetUtil;
 
+
 public class DisplayTab extends Tab {
 
     // Layouts
@@ -158,6 +163,34 @@ private static void verifyBoutiquesTool(BoutiquesApplication boutiquesTool)
         if (boutiquesTool.getAuthor() == null) {
             throw new ApplicationImporterException("Boutiques file must have an author");
         }
+         checkvipdot(boutiquesTool);
+    }
+
+    /**
+     * display warning message if any.
+     *
+     * @param application BoutiquesApplication object to cehck warning message 
+     * @throws ApplicationImporterException 
+     * **/
+    private static void checkvipdot(BoutiquesApplication application) throws ApplicationImporterException {
+        Set<String> commandLineFlags = application.getCommandLineFlag();
+        Set<String> vipDotInputIds = application.getVipDotInputIds();
+        Set<String> inputIds = application.getinputIds();
+        Set<String> commonValues = new HashSet<>(vipDotInputIds);
+
+        commonValues.retainAll(commandLineFlags);
+
+        if (!commonValues.isEmpty()) {
+            String warningMessage = "<b>" + String.join(", ", commonValues) + "</b> appears as command-line flag input(s), it should not be included in Dot iteration. Importing it may cause functionality issues, although the application will still be imported.";
+            Layout.getInstance().setWarningMessage(warningMessage);
+        }
+        // Check if all vipDotInputIds are in inputs
+        if (!inputIds.containsAll(vipDotInputIds)) {
+            Set<String> incorrectInputs = new HashSet<>(vipDotInputIds);
+            incorrectInputs.removeAll(inputIds);
+            String errorMessage = "<b>" + String.join(", ", incorrectInputs) + "</b> appears in vipDotInputIds but not in inputs. Please ensure all ids are correct.";
+            throw new ApplicationImporterException(errorMessage);
+    }
     }
 
     /**

vip-application-importer/src/main/java/fr/insalyon/creatis/vip/applicationimporter/client/view/applicationdisplay/GeneralLayout.java

@@ -46,7 +46,8 @@ public class GeneralLayout extends AbstractFormLayout {
             version,
             schemaVersion,
             description,
-            vipContainer;
+            vipContainer,
+            dotInputs;
 
     public GeneralLayout(String width, String height) {
         super(width, height);
@@ -63,8 +64,9 @@ public GeneralLayout(String width, String height) {
         schemaVersion = new LocalTextField("Schema Version", false, false);
         description = new LocalTextField("Description", false, false);
         vipContainer = new LocalTextField("VIP Container", false, false);
+        dotInputs = new LocalTextField("DOT Inputs", false, false);
 
-        this.addMembers(name, commandLine, dockerImage, dockerIndex, version, schemaVersion, description, vipContainer);
+        this.addMembers(name, commandLine, dockerImage, dockerIndex, version, schemaVersion, description, vipContainer, dotInputs);
     }
 
     public void setTool(BoutiquesApplication bt) {
@@ -76,5 +78,7 @@ public void setTool(BoutiquesApplication bt) {
         dockerIndex.setValue(bt.getContainerIndex());
         schemaVersion.setValue(bt.getSchemaVersion());
         vipContainer.setValue(bt.getVipContainer());
+        String dotInputsValue = String.join(", ", bt.getVipDotInputIds());
+        dotInputs.setValue(dotInputsValue + (bt.getVipDotIncludesResultsDir() ? (dotInputsValue.isEmpty() ? "results-directory" : ", results-directory") : ""));
     }
 }

vip-application/src/main/java/fr/insalyon/creatis/vip/application/client/bean/boutiquesTools/BoutiquesApplication.java

@@ -1,5 +1,6 @@
 package fr.insalyon.creatis.vip.application.client.bean.boutiquesTools;
 
+import java.util.Collections;
 import java.util.HashMap;
 import java.util.HashSet;
 import java.util.Map;
@@ -10,6 +11,8 @@
 
 import com.google.gwt.user.client.rpc.IsSerializable;
 
+import fr.insalyon.creatis.vip.application.client.bean.boutiquesTools.BoutiquesInput.InputType;
+
 /**
  * Representation of an application Boutiques descriptor
  *
@@ -38,6 +41,8 @@ public class BoutiquesApplication implements IsSerializable {
     private Set<BoutiquesOutputFile> outputFiles = new HashSet<>();
     private Map<String, String> tags = new HashMap<>();
     private String jsonFile;
+    private Set<String> vipDotInputIds;
+    private boolean vipDotIncludesResultsDir;
 
     private BoutiquesApplicationExtensions boutiquesExtensions;
 
@@ -229,6 +234,30 @@ public String getVipContainer() {
         return vipContainer;
     }
 
+    public Set<String> getVipDotInputIds() {
+        if (vipDotInputIds == null) {
+            return Collections.emptySet();      
+            }
+            return vipDotInputIds;
+    }
+
+    public Set<String> getCommandLineFlag() {
+        return inputs.stream()
+                .filter(i -> InputType.FLAG.equals(i.getType()))
+                .map(BoutiquesInput::getId)
+                .collect(Collectors.toSet());
+    }
+
+    public Set<String> getinputIds() {
+        return this.getInputs().stream()
+                .map(BoutiquesInput::getId)
+                .collect(Collectors.toSet());
+    }
+
+    public boolean getVipDotIncludesResultsDir() {
+        return vipDotIncludesResultsDir;
+    }
+
     public void addInput(BoutiquesInput input){
         this.inputs.add(input);
     }
@@ -280,4 +309,12 @@ public void addTag(String key, String value) {
     public void setVipContainer(String vipContainer) {
         this.vipContainer = vipContainer;
     }
-}
+
+    public void setVipDotInputIds(Set<String> inputIds) {
+        this.vipDotInputIds = inputIds;
+    }
+
+    public void setVipDotIncludesResultsDir(boolean vipDotIncludesResultsDir) {
+        this.vipDotIncludesResultsDir = vipDotIncludesResultsDir;
+    }
+}

vip-application/src/main/java/fr/insalyon/creatis/vip/application/client/view/boutiquesParsing/BoutiquesParser.java

@@ -114,8 +114,9 @@ public BoutiquesApplication parseApplication(String descriptor) throws InvalidBo
         // Custom property
         JSONObject customObject = getObjectValue(parsedDescriptor, "custom", true);
         if (customObject != null) {
-            String vipImagePath = getStringValue(customObject, "vip:imagepath", true);
-            application.setVipContainer(vipImagePath);
+            application.setVipContainer(getStringValue(customObject, "vip:imagepath", true));
+            application.setVipDotInputIds(getArrayValueAsStringSet(customObject, "vip:dot", true));
+            application.setVipDotIncludesResultsDir(getBooleanValue(customObject, "vip:dot-with-results-directory", true));
         }
         // Json descriptor
         application.setJsonFile(parsedDescriptor.toString());
@@ -241,6 +242,4 @@ private BoutiquesOutputFile parseBoutiquesOutputFile(JSONObject outputFile)
         bof.setCommandLineFlag(commandLineFlag);
         return bof;
     }
-
-
 }

vip-portal/src/main/resources/vm/gwendia-standalone.vm

@@ -71,14 +71,30 @@ if ( result.startsWith("/") || result.startsWith("lfn:") ) {
 #foreach( $output in $tool.getOutputFiles() )
         <out name="$output.getId()" type="URI" depth="0"/>
 #end
-        <iterationstrategy>
-          <cross>
+      <iterationstrategy>
+        <cross>
+#if($tool.getVipDotInputIds() && !$tool.getVipDotInputIds().isEmpty())
+          <dot>
+    #if($tools.getVipDotResultDirs)
             <port name="results-directory" />
+    #end
+    #foreach($dotInput in $tool.getVipDotInputIds())
+            <port name="$dotInput"/>
+    #end
+          </dot>
+    #if( ! $tools.getVipDotResultDirs)
+          <port name="results-directory" />
+    #end
+#else
+          <port name="results-directory" />
+#end
 #foreach($input in $tool.getInputs()) 
-            <port name="$input.getId()"/>
+    #if(!$tool.getVipDotInputIds().contains($input.getId()))
+          <port name="$input.getId()"/>
+    #end
 #end
-          </cross>
-        </iterationstrategy>
+        </cross>
+      </iterationstrategy>
         <gasw descriptor="$fileAccessProtocol:$tool.getGASWLFN()"/>
     </processor>
   </processors>
@@ -92,4 +108,4 @@ if ( result.startsWith("/") || result.startsWith("lfn:") ) {
     <link from="$tool.getName():$output.getId()" to="$output.getId()" />
 #end
   </links>
-</workflow>
+</workflow>