Merge pull request #491 from axlbonnet/improvements

small improvement
virtual-imaging-platform · Oct 2, 2024 · 2030acb · 2030acb
2 parents c038308 + a97aecd
commit 2030acb
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Showing 11 changed files with 35 additions and 152 deletions.
diff --git a/...va/fr/insalyon/creatis/vip/applicationimporter/client/rpc/ApplicationImporterService.java b/...va/fr/insalyon/creatis/vip/applicationimporter/client/rpc/ApplicationImporterService.java
@@ -55,7 +55,7 @@ public static ApplicationImporterServiceAsync getInstance() {
 
     String readAndValidateBoutiquesFile(String fileLFN) throws ApplicationImporterException;
 
-    void createApplication(BoutiquesApplication bt, String type, String tag, boolean isRunOnGrid, boolean overwriteVersion, String fileAccessProtocol) throws ApplicationImporterException;
+    void createApplication(BoutiquesApplication bt, String tag, boolean isRunOnGrid, boolean overwriteVersion, String fileAccessProtocol) throws ApplicationImporterException;
 
     String getApplicationImporterRootFolder() throws ApplicationImporterException;
 

diff --git a/.../insalyon/creatis/vip/applicationimporter/client/rpc/ApplicationImporterServiceAsync.java b/.../insalyon/creatis/vip/applicationimporter/client/rpc/ApplicationImporterServiceAsync.java
@@ -40,7 +40,7 @@ public interface ApplicationImporterServiceAsync {
 
     public void readAndValidateBoutiquesFile(String fileLFN, AsyncCallback<String> callback);
 
-    public void createApplication(BoutiquesApplication bt, String type, String tag, boolean isRunOnGrid, boolean overwriteVersion, String fileAccessProtocol, AsyncCallback<Void> callback);
+    public void createApplication(BoutiquesApplication bt, String tag, boolean isRunOnGrid, boolean overwriteVersion, String fileAccessProtocol, AsyncCallback<Void> callback);
 
     public void getApplicationImporterRootFolder(AsyncCallback<String> asyncCallback);
 

diff --git a/...rter/src/main/java/fr/insalyon/creatis/vip/applicationimporter/client/view/Constants.java b/...rter/src/main/java/fr/insalyon/creatis/vip/applicationimporter/client/view/Constants.java
@@ -70,13 +70,6 @@ public class Constants {
     public static final String APP_IMG_IMPORTER = IMG_FOLDER + "importer.png";
     //Group
     public static final String APPLICATION_IMPORTER_GROUP = "Application Importer";
-    //vm files
-    public static final String VM_GASW = "gasw.vm";
-    //LFN access to SegPerfAnalyzer
-    public static final String LNF_PATH = "";
-    // Application Importer types
-    public static final String APP_IMPORTER_STANDALONE_TYPE = "app-importer-standalone-type";
-    public static final String APP_IMPORTER_DOT_INPUTS_TYPE = "app-importer-dot-inputs-type";
     //Execution type
     public static final String APP_IMPORTER_FILE_PROTOCOL = "file";
     public static final String APP_IMPORTER_LFN_PROTOCOL = "lfn";

diff --git a/...r/insalyon/creatis/vip/applicationimporter/client/view/applicationdisplay/DisplayTab.java b/...r/insalyon/creatis/vip/applicationimporter/client/view/applicationdisplay/DisplayTab.java
@@ -110,8 +110,8 @@ private void configure() {
         createApplicationButton = WidgetUtil.getIButton("Create application", Constants.ICON_LAUNCH, new ClickHandler() {
             @Override
             public void onClick(ClickEvent event) {
-                if (vipLayout.getApplicationType() == null){
-                    Layout.getInstance().setWarningMessage("Select type of Application is empty, please choose one.");
+                if (vipLayout.getFileAccessProtocol() == null){
+                    Layout.getInstance().setWarningMessage("Select file access protocol.");
                 } else {
                     boutiquesTool.setApplicationLFN(vipLayout.getApplicationLocation() + "/" + boutiquesTool.getName());
                     createApplication();
@@ -215,7 +215,6 @@ public void onSuccess(Void result) {
         modal.show("Creating application...", true);
         ApplicationImporterService.Util.getInstance().createApplication(
             boutiquesTool,
-            vipLayout.getApplicationType(),
             vipLayout.getTag(),
             vipLayout.getIsRunOnGrid(),
             vipLayout.getOverwrite(),

diff --git a/...fr/insalyon/creatis/vip/applicationimporter/client/view/applicationdisplay/VIPLayout.java b/...fr/insalyon/creatis/vip/applicationimporter/client/view/applicationdisplay/VIPLayout.java
@@ -52,7 +52,6 @@ public class VIPLayout extends AbstractFormLayout {
     private final LocalTextField applicationLocation;
     private final CheckboxItem isRunOnGrid; // And not locally.
     private final CheckboxItem overwriteIfexists;
-    private final SelectItem appCbItem;
     private final SelectItem tagsCbItem;
     private final SelectItem fileAccessProtocolItem;
 
@@ -72,15 +71,6 @@ public VIPLayout(String width, String height) {
         isRunOnGrid = new CheckboxItem("ckbox_isRunOnGrid", "Application must run on grid, and not locally");
         isRunOnGrid.setAlign(Alignment.LEFT);
 
-        //ComboBox to select type of application
-        appCbItem = new SelectItem();
-        appCbItem.setTitle("<b>Select type of application</b>");
-        appCbItem.setType("comboBox");
-        LinkedHashMap<String, String> valueMap = new LinkedHashMap<>();
-        valueMap.put(Constants.APP_IMPORTER_STANDALONE_TYPE, "standalone");
-        valueMap.put(Constants.APP_IMPORTER_DOT_INPUTS_TYPE, "Dot inputs (Challenge)");
-        appCbItem.setValueMap(valueMap);
-
         tagsCbItem = createTagsSelect();
 
         //select list to choose the execution type
@@ -92,7 +82,6 @@ public VIPLayout(String width, String height) {
         fileAccessProtocolValueMap.put(Constants.APP_IMPORTER_LFN_PROTOCOL, "Grid (lfn)");
         fileAccessProtocolItem.setValueMap(fileAccessProtocolValueMap);
 
-        this.addMember(FieldUtil.getForm(appCbItem));
         this.addMember(FieldUtil.getForm(isRunOnGrid));
         this.addMember(FieldUtil.getForm(overwriteIfexists));
         this.addMember(FieldUtil.getForm(tagsCbItem));
@@ -141,19 +130,6 @@ public boolean getIsRunOnGrid() {
         return this.isRunOnGrid.getValueAsBoolean();
     }
 
-    /**
-     * Get the type of application (standalone or challenge)
-     *
-     * @return the type
-     */
-    public String getApplicationType() {
-        if (appCbItem._getValue() == null){
-            return null;
-        } else {
-            return appCbItem._getValue().toString();
-        }
-    }
-
     private SelectItem createTagsSelect() {
         // ComboBox to select tags.
         SelectItem tagsCb = new SelectItem();
@@ -192,6 +168,7 @@ public void onSuccess(List<String> result) {
     public String getTag() {
         return tagsCbItem._getValue().toString();
     }
+
     public String getFileAccessProtocol(){
         return fileAccessProtocolItem._getValue().toString();
     }

diff --git a/...insalyon/creatis/vip/applicationimporter/server/business/ApplicationImporterBusiness.java b/...insalyon/creatis/vip/applicationimporter/server/business/ApplicationImporterBusiness.java
@@ -104,20 +104,13 @@ public String readAndValidationBoutiquesFile(String fileLFN, User user)
     }
 
     public void createApplication(
-            BoutiquesApplication bt, String type, String tag, boolean isRunOnGrid, boolean overwriteApplicationVersion, String fileAccessProtocol, User user)
+            BoutiquesApplication bt, String tag, boolean isRunOnGrid, boolean overwriteApplicationVersion, String fileAccessProtocol, User user)
             throws BusinessException {
 
         try {
             String wrapperTemplate = "vm/wrapper.vm";
             String gaswTemplate = "vm/gasw.vm";
-
             String gwendiaTemplate = "vm/gwendia-standalone.vm";
-            if (Constants.APP_IMPORTER_DOT_INPUTS_TYPE.equals(type)) {
-                gwendiaTemplate = "vm/gwendia-dot-inputs.vm";
-            } else if ( ! Constants.APP_IMPORTER_STANDALONE_TYPE.equals(type)) {
-                logger.error("Cannot import pipeline : unknown importer type : {}", type);
-                throw new BusinessException("Cannot import pipeline : unknown importer type");
-            }
 
             // Check rights
             checkEditionRights(bt.getName(), bt.getToolVersion(), overwriteApplicationVersion, user);

diff --git a/...r/insalyon/creatis/vip/applicationimporter/server/rpc/ApplicationImporterServiceImpl.java b/...r/insalyon/creatis/vip/applicationimporter/server/rpc/ApplicationImporterServiceImpl.java
@@ -69,12 +69,12 @@ public String readAndValidateBoutiquesFile(String fileLFN) throws ApplicationImp
 
     @Override
     public void createApplication(
-            BoutiquesApplication bt, String type, String tag, boolean isRunOnGrid, boolean overwriteVersion, String fileAccessProtocol)
+            BoutiquesApplication bt, String tag, boolean isRunOnGrid, boolean overwriteVersion, String fileAccessProtocol)
             throws ApplicationImporterException {
         try {
             trace(logger, "Creating application");
             applicationImporterBusiness.createApplication(
-                    bt, type, tag, isRunOnGrid, overwriteVersion, fileAccessProtocol, getSessionUser());
+                    bt, tag, isRunOnGrid, overwriteVersion, fileAccessProtocol, getSessionUser());
         } catch (CoreException | BusinessException ex) {
             throw new ApplicationImporterException(ex);
         }

diff --git a/...ion/src/main/java/fr/insalyon/creatis/vip/application/server/rpc/WorkflowServiceImpl.java b/...ion/src/main/java/fr/insalyon/creatis/vip/application/server/rpc/WorkflowServiceImpl.java
@@ -43,6 +43,7 @@
 import fr.insalyon.creatis.vip.application.server.dao.ApplicationInputDAO;
 import fr.insalyon.creatis.vip.core.client.bean.Group;
 import fr.insalyon.creatis.vip.core.client.bean.User;
+import fr.insalyon.creatis.vip.core.client.view.CoreConstants;
 import fr.insalyon.creatis.vip.core.client.view.CoreException;
 import fr.insalyon.creatis.vip.core.server.business.BusinessException;
 import fr.insalyon.creatis.vip.core.server.business.ConfigurationBusiness;
@@ -60,6 +61,8 @@
 import java.io.File;
 import java.io.FileReader;
 import java.io.IOException;
+import java.text.DateFormat;
+import java.text.SimpleDateFormat;
 import java.util.ArrayList;
 import java.util.Date;
 import java.util.List;
@@ -192,8 +195,9 @@ public void launchSimulation(Map<String, String> parametersMap,
             }
 
             for (Map.Entry<String,String> p : parametersMap.entrySet()) {
-                logger.info("received param {} : {}", p.getKey(), p.getValue());
+                logger.info("received param {} : {}", p.getKey(), p.getValue());
             }
+            addTimestampedSubDirectoryIfNecessary(parametersMap);
 
             String simulationID = workflowBusiness.launch(
                 user, groups,
@@ -207,6 +211,24 @@ public void launchSimulation(Map<String, String> parametersMap,
         }
     }
 
+    private void addTimestampedSubDirectoryIfNecessary(Map<String, String> parametersMap) {
+        if (server.useMoteurlite()) {
+            if (parametersMap.containsKey(CoreConstants.RESULTS_DIRECTORY_PARAM_NAME)) {
+                String resultDir = parametersMap.get(CoreConstants.RESULTS_DIRECTORY_PARAM_NAME);
+                if (resultDir.startsWith("/") || resultDir.startsWith("lfn:")) {
+                    DateFormat dateFormat = new SimpleDateFormat("dd-MM-yyyy_HH:mm:ss");
+                    resultDir = resultDir + "/" + (dateFormat.format(System.currentTimeMillis()));
+                    parametersMap.put(CoreConstants.RESULTS_DIRECTORY_PARAM_NAME, resultDir);
+                    logger.info("For MoteurLite : changing results-directory to : {}", resultDir);
+                } else {
+                    logger.info("Using MoteurLite but results-directory not a LFN ({})", resultDir);
+                }
+            } else {
+                logger.info("Using MoteurLite but no results-directory given -> no subdirectory added");
+            }
+        }
+    }
+
     /**
      *
      * @param name

diff --git a/vip-portal/src/main/resources/vm/gwendia-dot-inputs.vm b/vip-portal/src/main/resources/vm/gwendia-dot-inputs.vm
diff --git a/vip-portal/src/main/resources/vm/wrapper.vm b/vip-portal/src/main/resources/vm/wrapper.vm
@@ -187,9 +187,6 @@ then
 fi
 #end
 
-# Change PYTHONPATH to make all strings unicode by default in python2 (as in python3)
-# Otherwise `bosh exec` fails on any non-ascii characters in outputs
-echo "import sys; sys.setdefaultencoding(\"UTF8\")" > sitecustomize.py
 #creating a temporary directory for bindmount /tmp of containers
 #TMP_FOLDER is created differently for execution on GRID and execution on LOCAL
 #TMP of the container is bind mounted on TMP_FOLDER to avoid creating temporary files on container.

diff --git a/vip-portal/src/test/java/fr/insalyon/creatis/applicationimporter/GwendiaTemplateTest.java b/vip-portal/src/test/java/fr/insalyon/creatis/applicationimporter/GwendiaTemplateTest.java
@@ -22,11 +22,10 @@
  */
 public class GwendiaTemplateTest {
 
-    final protected String DOT_TEMPLATE = "vm/gwendia-dot-inputs.vm";
     final protected String STANDALONE_TEMPLATE = "vm/gwendia-standalone.vm";
 
     @ParameterizedTest
-    @ValueSource(strings = {DOT_TEMPLATE, STANDALONE_TEMPLATE})
+    @ValueSource(strings = {STANDALONE_TEMPLATE})
     public void testTemplateWithNonNullDescription(String template) throws IOException, InvalidBoutiquesDescriptorException, SAXException {
         String inputDescription = "test input description";
         Descriptor gwendiaDesc = testGwendiaTemplate(
@@ -37,7 +36,7 @@ public void testTemplateWithNonNullDescription(String template) throws IOExcepti
     }
 
     @ParameterizedTest
-    @ValueSource(strings = {DOT_TEMPLATE, STANDALONE_TEMPLATE})
+    @ValueSource(strings = {STANDALONE_TEMPLATE})
     public void testTemplateWithNullDescription(String template) throws IOException, InvalidBoutiquesDescriptorException, SAXException {
         // when the description is not in boutiques, it must be an empty string in gwendia
         Descriptor gwendiaDesc = testGwendiaTemplate(
@@ -48,7 +47,7 @@ public void testTemplateWithNullDescription(String template) throws IOException,
     }
 
     @ParameterizedTest
-    @ValueSource(strings = {DOT_TEMPLATE, STANDALONE_TEMPLATE})
+    @ValueSource(strings = {STANDALONE_TEMPLATE})
     public void testTemplateWithAIntegerInput(String template) throws IOException, InvalidBoutiquesDescriptorException, SAXException {
         Descriptor gwendiaDesc = testGwendiaTemplate(
                 template,
@@ -57,7 +56,7 @@ public void testTemplateWithAIntegerInput(String template) throws IOException, I
     }
 
     @ParameterizedTest
-    @ValueSource(strings = {DOT_TEMPLATE, STANDALONE_TEMPLATE})
+    @ValueSource(strings = {STANDALONE_TEMPLATE})
     public void testTemplateWithANumberInput(String template) throws IOException, InvalidBoutiquesDescriptorException, SAXException {
         Descriptor gwendiaDesc = testGwendiaTemplate(
                 template,