Update workflow API for new references, fix search engine, add export…

… as TSV of tables

QBiCMainPortlet/src/de/uni_tuebingen/qbic/qbicmainportlet/BiologicalSamplesComponent.java

@@ -1,6 +1,6 @@
 /*******************************************************************************
- * QBiC Project qNavigator enables users to manage their projects. Copyright (C) "2016”
- * Christopher Mohr, David Wojnar, Andreas Friedrich
+ * QBiC Project qNavigator enables users to manage their projects. Copyright (C) "2016” Christopher
+ * Mohr, David Wojnar, Andreas Friedrich
  * 
  * This program is free software: you can redistribute it and/or modify it under the terms of the
  * GNU General Public License as published by the Free Software Foundation, either version 3 of the
@@ -20,14 +20,6 @@
 import java.util.List;
 import java.util.Map;
 
-import logging.Log4j2Logger;
-import logging.Logger;
-import model.BiologicalEntitySampleBean;
-import model.BiologicalSampleBean;
-import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Sample;
-import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Vocabulary;
-import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.VocabularyTerm;
-
 import com.vaadin.data.Item;
 import com.vaadin.data.util.BeanItem;
 import com.vaadin.data.util.BeanItemContainer;
@@ -37,9 +29,12 @@
 import com.vaadin.event.ItemClickEvent.ItemClickListener;
 import com.vaadin.event.SelectionEvent;
 import com.vaadin.event.SelectionEvent.SelectionListener;
+import com.vaadin.server.FileDownloader;
 import com.vaadin.server.FontAwesome;
+import com.vaadin.server.StreamResource;
 import com.vaadin.shared.ui.MarginInfo;
 import com.vaadin.shared.ui.label.ContentMode;
+import com.vaadin.ui.Button;
 import com.vaadin.ui.CustomComponent;
 import com.vaadin.ui.Grid;
 import com.vaadin.ui.HorizontalLayout;
@@ -55,6 +50,15 @@
 import com.vaadin.ui.renderers.ClickableRenderer.RendererClickListener;
 import com.vaadin.ui.renderers.HtmlRenderer;
 
+import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Sample;
+import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Vocabulary;
+import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.VocabularyTerm;
+import helpers.Utils;
+import logging.Log4j2Logger;
+import logging.Logger;
+import model.BiologicalEntitySampleBean;
+import model.BiologicalSampleBean;
+
 
 public class BiologicalSamplesComponent extends CustomComponent {
 
@@ -81,6 +85,12 @@ private enum propertyTypes {
   private BeanItemContainer<BiologicalSampleBean> samplesBio;
   private BeanItemContainer<BiologicalEntitySampleBean> samplesEntity;
   private String currentID;
+  private Button exportSources = new Button("Export as TSV");
+  private Button exportSamples = new Button("Export as TSV");
+  private FileDownloader fileDownloaderSources;
+  private FileDownloader fileDownloaderSamples;
+
+
 
   /**
    * 
@@ -89,7 +99,8 @@ private enum propertyTypes {
    * @param resourceurl
    * @param caption
    */
-  public BiologicalSamplesComponent(DataHandler dh, State state, String resourceurl, String caption) {
+  public BiologicalSamplesComponent(DataHandler dh, State state, String resourceurl,
+      String caption) {
     this.datahandler = dh;
     this.resourceUrl = resourceurl;
     this.state = state;
@@ -136,6 +147,9 @@ public void select(SelectionEvent event) {
     mainLayout.setResponsive(true);
     setResponsive(true);
 
+    exportSources.setIcon(FontAwesome.DOWNLOAD);
+    exportSamples.setIcon(FontAwesome.DOWNLOAD);
+
     // this.setWidth(Page.getCurrent().getBrowserWindowWidth() * 0.8f, Unit.PIXELS);
     this.setCompositionRoot(mainLayout);
   }
@@ -288,12 +302,10 @@ public Class<String> getType() {
 
       @Override
       public String getValue(Item item, Object itemId, Object propertyId) {
-        String ncbi =
-            String
-                .format(
-                    "http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Undef&name=%s&lvl=0&srchmode=1&keep=1&unlock' target='_blank'>%s</a>",
-                    item.getItemProperty("organism").getValue(),
-                    item.getItemProperty("organismName").getValue());
+        String ncbi = String.format(
+            "http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Undef&name=%s&lvl=0&srchmode=1&keep=1&unlock' target='_blank'>%s</a>",
+            item.getItemProperty("organism").getValue(),
+            item.getItemProperty("organismName").getValue());
         String link = String.format("<a href='%s", ncbi);
 
         return link;
@@ -432,8 +444,8 @@ public void click(RendererClickEvent event) {
 
           subWindow.addCloseListener(new CloseListener() {
             /**
-           * 
-           */
+            * 
+            */
             private static final long serialVersionUID = -1329152609834711109L;
 
             @Override
@@ -445,7 +457,8 @@ public void windowClose(CloseEvent e) {
           QbicmainportletUI ui = (QbicmainportletUI) UI.getCurrent();
           ui.addWindow(subWindow);
         } catch (NullPointerException e) {
-          System.err.println("NullPointerException while trying to set metadata: " + e.getMessage());
+          System.err
+              .println("NullPointerException while trying to set metadata: " + e.getMessage());
 
         }
       }
@@ -460,6 +473,23 @@ public void windowClose(CloseEvent e) {
 
     helpers.GridFunctions.addColumnFilters(sampleBioGrid, gpcBio);
     helpers.GridFunctions.addColumnFilters(sampleEntityGrid, gpcEntity);
+
+
+    if (fileDownloaderSources != null)
+      exportSources.removeExtension(fileDownloaderSources);
+    StreamResource srSource = Utils.getTSVStream(Utils.containerToString(samplesEntityContainer),
+        String.format("%s_%s_", id.substring(1).replace("/", "_"), "sample_sources"));
+    fileDownloaderSources = new FileDownloader(srSource);
+    fileDownloaderSources.extend(exportSources);
+
+
+    if (fileDownloaderSamples != null)
+      exportSamples.removeExtension(fileDownloaderSamples);
+    StreamResource srSamples = Utils.getTSVStream(Utils.containerToString(samplesBioContainer),
+        String.format("%s_%s_", id.substring(1).replace("/", "_"), "extracted_samples"));
+    fileDownloaderSamples = new FileDownloader(srSamples);
+    fileDownloaderSamples.extend(exportSamples);
+
     this.buildLayout();
   }
 
@@ -481,30 +511,29 @@ private void buildLayout() {
     tableSectionContent.setResponsive(true);
     sampletableSectionContent.setResponsive(true);
 
-    tableSectionContent.setMargin(new MarginInfo(true, false, true, false));
+    tableSectionContent.setMargin(new MarginInfo(true, false, false, false));
     sampletableSectionContent.setMargin(new MarginInfo(true, false, false, false));
 
     // tableSectionContent.setCaption("Datasets");
     // tableSectionContent.setIcon(FontAwesome.FLASK);
-    tableSection
-        .addComponent(new Label(
-            String
-                .format(
-                    "This view shows the sample sources (e.g., human, mouse) to be studied and the corresponding extracted samples. With sample sources, information specific to the subject (e.g., age or BMI in the case of patient data) can be stored. The extracted sample is a sample which has been extracted from the corresponding sample source. This is the raw sample material that can be later prepared for specific analytical methods such as MS or NGS.<br> "
-                        + "\n\n There are %s extracted  samples coming from %s distinct sample sources in this study.",
-                    numberOfBioSamples, numberOfEntitySamples), ContentMode.HTML));
+    tableSection.addComponent(new Label(String.format(
+        "This view shows the sample sources (e.g., human, mouse) to be studied and the corresponding extracted samples. With sample sources, information specific to the subject (e.g., age or BMI in the case of patient data) can be stored. The extracted sample is a sample which has been extracted from the corresponding sample source. This is the raw sample material that can be later prepared for specific analytical methods such as MS or NGS.<br> "
+            + "\n\n There are %s extracted  samples coming from %s distinct sample sources in this study.",
+        numberOfBioSamples, numberOfEntitySamples), ContentMode.HTML));
 
     tableSectionContent.addComponent(sampleBioGrid);
     sampletableSectionContent.addComponent(sampleEntityGrid);
 
     sampleEntityGrid.setCaption("Sample Sources");
     sampleBioGrid.setCaption("Extracted Samples");
 
-    tableSection.setMargin(new MarginInfo(true, false, false, true));
+    tableSection.setMargin(new MarginInfo(true, false, true, true));
     tableSection.setSpacing(true);
 
     tableSection.addComponent(sampletableSectionContent);
+    tableSection.addComponent(exportSources);
     tableSection.addComponent(tableSectionContent);
+    tableSection.addComponent(exportSamples);
     this.vert.addComponent(tableSection);
 
     sampleBioGrid.setWidth(100, Unit.PERCENTAGE);

QBiCMainPortlet/src/de/uni_tuebingen/qbic/qbicmainportlet/DatasetComponent.java

@@ -35,10 +35,12 @@
 
 import com.vaadin.data.Property.ValueChangeEvent;
 import com.vaadin.data.Property.ValueChangeListener;
+import com.vaadin.data.util.BeanItemContainer;
 import com.vaadin.data.util.HierarchicalContainer;
 import com.vaadin.event.ItemClickEvent;
 import com.vaadin.event.ItemClickEvent.ItemClickListener;
 import com.vaadin.server.ExternalResource;
+import com.vaadin.server.FileDownloader;
 import com.vaadin.server.FontAwesome;
 import com.vaadin.server.Resource;
 import com.vaadin.server.StreamResource;
@@ -62,6 +64,7 @@
 import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Sample;
 import de.uni_tuebingen.qbic.util.DashboardUtil;
 import helpers.UglyToPrettyNameMapper;
+import helpers.Utils;
 import logging.Log4j2Logger;
 import logging.Logger;
 import model.DatasetBean;
@@ -87,6 +90,9 @@ public class DatasetComponent extends CustomComponent {
   private final ButtonLink download =
       new ButtonLink(DOWNLOAD_BUTTON_CAPTION, new ExternalResource(""));
 
+  private Button export = new Button("Export as TSV");
+  private FileDownloader fileDownloader;
+
   private final String[] FILTER_TABLE_COLUMNS =
       new String[] {"Select", "File Name", "Dataset Type", "Registration Date", "File Size"};
 
@@ -189,6 +195,8 @@ public void updateUI(String type, String id) {
       }
 
       numberOfDatasets = retrievedDatasets.size();
+
+      BeanItemContainer<DatasetBean> forExport = new BeanItemContainer(DatasetBean.class);
       if (numberOfDatasets == 0) {
 
         if (type.equals("project")) {
@@ -240,14 +248,24 @@ public void updateUI(String type, String id) {
           String dateString = sd.format(date);
           // Timestamp ts = Timestamp.valueOf(dateString);
           String sampleID = samples.get(d.getCode());
+          forExport.addBean(d);
 
           registerDatasetInTable(d, datasetContainer, projectCode, sampleID, dateString, null);
         }
       }
 
       this.setContainerDataSource(datasetContainer);
 
-    } catch (Exception e) {
+      if (fileDownloader != null)
+        this.export.removeExtension(fileDownloader);
+      StreamResource sr = Utils.getTSVStream(Utils.containerToString(forExport),
+          String.format("%s_%s_", id.substring(1).replace("/", "_"), "registered_datasets"));
+      fileDownloader = new FileDownloader(sr);
+      fileDownloader.extend(export);
+
+    } catch (
+
+    Exception e) {
       e.printStackTrace();
       LOGGER.error(String.format("getting dataset failed for dataset %s %s", type, id),
           e.getStackTrace());
@@ -355,6 +373,9 @@ public void buttonClick(ClickEvent event) {
             + "<p> You need to use command tar. The tar is the GNU version of tar archiving utility. <br> "
             + "To extract/unpack a tar file, type: $ tar -xvf file.tar</p>";
 
+
+    export.setIcon(FontAwesome.DOWNLOAD);
+
     PopupView tooltip = new PopupView(new helpers.ToolTip(content));
     tooltip.setHeight("44px");
 
@@ -373,6 +394,7 @@ public void buttonClick(ClickEvent event) {
     help.addComponent(helpContent);
     help.setComponentAlignment(helpContent, Alignment.TOP_CENTER);
 
+    buttonLayout.addComponent(export);
     buttonLayout.addComponent(checkAll);
     buttonLayout.addComponent(uncheckAll);
     // buttonLayout.addComponent(visualize);

QBiCMainPortlet/src/de/uni_tuebingen/qbic/qbicmainportlet/ExperimentComponent.java

@@ -1,6 +1,6 @@
 /*******************************************************************************
- * QBiC Project qNavigator enables users to manage their projects. Copyright (C) "2016”
- * Christopher Mohr, David Wojnar, Andreas Friedrich
+ * QBiC Project qNavigator enables users to manage their projects. Copyright (C) "2016” Christopher
+ * Mohr, David Wojnar, Andreas Friedrich
  * 
  * This program is free software: you can redistribute it and/or modify it under the terms of the
  * GNU General Public License as published by the Free Software Foundation, either version 3 of the
@@ -15,17 +15,10 @@
  *******************************************************************************/
 package de.uni_tuebingen.qbic.qbicmainportlet;
 
-import helpers.Utils;
-
 import java.text.SimpleDateFormat;
 import java.util.ArrayList;
 import java.util.Date;
 
-import logging.Log4j2Logger;
-import logging.Logger;
-import model.ExperimentBean;
-import model.ProjectBean;
-
 import com.vaadin.data.Item;
 import com.vaadin.data.util.BeanItem;
 import com.vaadin.data.util.GeneratedPropertyContainer;
@@ -49,6 +42,12 @@
 import com.vaadin.ui.renderers.ClickableRenderer.RendererClickEvent;
 import com.vaadin.ui.renderers.ClickableRenderer.RendererClickListener;
 
+import helpers.Utils;
+import logging.Log4j2Logger;
+import logging.Logger;
+import model.ExperimentBean;
+import model.ProjectBean;
+
 public class ExperimentComponent extends CustomComponent {
   /**
    * 
@@ -89,6 +88,7 @@ private void initUI() {
     expSteps.setSpacing(true);
 
     export = new Button("Export as TSV");
+    export.setIcon(FontAwesome.DOWNLOAD);
     VerticalLayout buttonLayoutSection = new VerticalLayout();
     HorizontalLayout buttonLayout = new HorizontalLayout();
     buttonLayout.setHeight(null);
@@ -107,10 +107,9 @@ private void initUI() {
     // experiments.setContainerDataSource(new
     // BeanItemContainer<ExperimentBean>(ExperimentBean.class));
 
-    expSteps
-        .addComponent(new Label(
-            "This view shows the experimental steps which have been registered for this project. Experimental steps contain real biological experiments as well as executed computational workflows on project data",
-            ContentMode.HTML));
+    expSteps.addComponent(new Label(
+        "This view shows the experimental steps which have been registered for this project. Experimental steps contain real biological experiments as well as executed computational workflows on project data",
+        ContentMode.HTML));
 
     expSteps.addComponent(experiments);
     expSteps.addComponent(buttonLayoutSection);
@@ -251,8 +250,8 @@ public void click(RendererClickEvent event) {
     if (fileDownloader != null)
       this.export.removeExtension(fileDownloader);
     StreamResource sr =
-        Utils.getTSVStream(Utils.containerToString(projectBean.getExperiments()),
-            projectBean.getId());
+        Utils.getTSVStream(Utils.containerToString(projectBean.getExperiments()), String.format(
+            "%s_%s_", projectBean.getId().substring(1).replace("/", "_"), "experimental_steps"));
     fileDownloader = new FileDownloader(sr);
     fileDownloader.extend(export);
   }

QBiCMainPortlet/src/de/uni_tuebingen/qbic/qbicmainportlet/HomeView.java

@@ -269,7 +269,7 @@ private void setExportButton() {
     buttonLayout.addComponent(this.export);
 
     StreamResource sr =
-        Utils.getTSVStream(Utils.containerToString(currentBean.getProjects()), this.caption);
+        Utils.getTSVStream(Utils.containerToString(currentBean.getProjects()), "project_overview");
     FileDownloader fileDownloader = new FileDownloader(sr);
     fileDownloader.extend(this.export);
   }
@@ -311,6 +311,7 @@ void buildLayout(int browserHeight, int browserWidth, WebBrowser browser) {
     // clean up first
     // homeview_content.removeAllComponents();
     removeAllComponents();
+    setSpacing(true);
 
     // updateView(browserWidth, browserWidth, browser);
 
@@ -339,6 +340,8 @@ void buildLayout(int browserHeight, int browserWidth, WebBrowser browser) {
     // tableSectionContent.setIcon(FontAwesome.TABLE);
     // tableSectionContent.addComponent(this.table);
     addComponent(projectGrid);
+    addComponent(buttonLayoutSection);
+    setExportButton();
 
     setCaption("Sub-Projects");
     setIcon(FontAwesome.TABLE);
@@ -349,6 +352,8 @@ void buildLayout(int browserHeight, int browserWidth, WebBrowser browser) {
     projectGrid.setSelectionMode(SelectionMode.SINGLE);
     projectGrid.setResponsive(true);
 
+    export.setIcon(FontAwesome.DOWNLOAD);
+
     // tableSection.setWidth("100%");
     // tableSectionContent.setWidth("100%");