Merge branch 'development'

qbicsoftware-archive · Apr 18, 2018 · a0261c1 · a0261c1
2 parents da6891a + 4120df6
commit a0261c1
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Showing 9 changed files with 111 additions and 441 deletions.
diff --git a/QBiCMainPortlet/ivy.xml b/QBiCMainPortlet/ivy.xml
@@ -57,7 +57,7 @@
   		<dependency org="org.apache.logging.log4j" name="log4j-core" rev="2.2" />
   		<!--DocX4J -->
   		<dependency org="org.slf4j" name ="slf4j-api" rev="1.7.5" />
-  		<dependency org="org.docx4j" name ="docx4j" rev="3.3.1" />
+  		<dependency org="org.docx4j" name ="docx4j" rev="3.3.2" />
   		<!--upload -->
   		<dependency org="com.github.lookfirst" name="sardine" rev="5.5" />
   		<dependency org="commons-io" name="commons-io" rev="2.4" />

diff --git a/QBiCMainPortlet/src/de/uni_tuebingen/qbic/qbicmainportlet/PatientView.java b/QBiCMainPortlet/src/de/uni_tuebingen/qbic/qbicmainportlet/PatientView.java
@@ -1006,8 +1006,9 @@ public VerticalLayout initProjectStatus() {
     return projectStatus;
   }
 
-  void resetGraph() {
+  void resetGraphs() {
     graphSectionContent.removeAllComponents();
+    newGraphContent.removeAllComponents();
     // VerticalLayout graphSection = (VerticalLayout) graphSectionContent.getParent();
     // graphSection.getComponent(1).setVisible(true);
     // graphSection.getComponent(1).setEnabled(true);
@@ -1217,7 +1218,7 @@ public void enter(ViewChangeEvent event) {
       ProjectBean pbean = datahandler.getProject2(currentValue);
       // if the new project bean is different than reset the graph.
       if (currentBean != null && !pbean.getId().equals(currentBean.getId())) {
-        resetGraph();
+        resetGraphs();
         patientViewTab.setSelectedTab(0);
       }
       this.currentBean = pbean;

diff --git a/QBiCMainPortlet/src/de/uni_tuebingen/qbic/qbicmainportlet/ProjectView.java b/QBiCMainPortlet/src/de/uni_tuebingen/qbic/qbicmainportlet/ProjectView.java
@@ -529,8 +529,9 @@ void updateContentTable() {
   /**
    * 
    */
-  void resetGraph() {
+  void resetGraphs() {
     graphSectionContent.removeAllComponents();
+    newGraphContent.removeAllComponents();
     // VerticalLayout graphSection = (VerticalLayout) graphSectionContent.getParent();
     // graphSection.getComponent(1).setVisible(true);
     // graphSection.getComponent(1).setEnabled(true);
@@ -957,7 +958,7 @@ public void enter(ViewChangeEvent event) {
       ProjectBean pbean = datahandler.getProject2(currentValue);
       // if the new project bean is different than reset the graph.
       if (currentBean != null && !pbean.getId().equals(currentBean.getId())) {
-        resetGraph();
+        resetGraphs();
         projectview_tab.setSelectedTab(0);
       }
       this.currentBean = pbean;

diff --git a/QBiCMainPortlet/src/helpers/SummaryFetcher.java b/QBiCMainPortlet/src/helpers/SummaryFetcher.java
@@ -17,16 +17,12 @@
 import model.notes.Note;
 import model.notes.Notes;
 
-import org.docx4j.jaxb.Context;
-import org.docx4j.model.datastorage.XPathEnhancerParser.main_return;
 import org.docx4j.openpackaging.exceptions.Docx4JException;
 import org.docx4j.openpackaging.exceptions.InvalidFormatException;
 import org.docx4j.openpackaging.packages.WordprocessingMLPackage;
 import org.docx4j.openpackaging.parts.WordprocessingML.MainDocumentPart;
 import org.docx4j.wml.Br;
-import org.docx4j.wml.ObjectFactory;
 import org.docx4j.wml.P;
-import org.docx4j.wml.R;
 
 import parser.XMLParser;
 import properties.Property;
@@ -95,7 +91,6 @@ public class SummaryFetcher {
       put("Q_MHC_LIGAND_EXTRACTION", "MHC Ligand Extraction");
     };
   };
-  private ObjectFactory factory;
   private WordprocessingMLPackage wordMLPackage;
   private Docx4jHelper docxHelper;
   private Component summaryComponent;
@@ -262,7 +257,6 @@ private void addSummaryDownload(VerticalLayout res) {
   }
 
   private void initDocx4J() {
-    factory = Context.getWmlObjectFactory();
     docxHelper = new Docx4jHelper();
     try {
       wordMLPackage = WordprocessingMLPackage.createPackage();

diff --git a/QBiCMainPortlet/src/samplegraph/GraphPage.java b/QBiCMainPortlet/src/samplegraph/GraphPage.java
@@ -46,11 +46,6 @@ public GraphPage(Map<String, String> taxMap, Map<String, String> tissueMap) {
         .collect(Collectors.toMap(Map.Entry::getValue, Map.Entry::getKey));
 
     parser = new ProjectParser(reverseTaxMap, reverseTissueMap);
-
-    this.factorBox = new ComboBox("Experimental Factor");
-    factorBox.setVisible(false);
-
-    addComponent(factorBox);
   }
 
   private String buildImagePath() {
@@ -74,8 +69,9 @@ private String buildImagePath() {
 
   public void loadProjectGraph(String projectIdentifier, List<Sample> samples,
       List<DataSet> datasets) {
-    factorBox.removeAllItems();
+    this.factorBox = new ComboBox("Experimental Factor");
     factorBox.setVisible(false);
+    addComponent(factorBox);
 
     currentSamples = samples;
     // openbis
@@ -87,6 +83,7 @@ public void loadProjectGraph(String projectIdentifier, List<Sample> samples,
     } else {
       // structure = parser.parseAll(currentSamples, datasets);
       try {
+        // load here
         structure = parser.parseSamplesBreadthFirst(currentSamples, datasets);
         if (!structure.getFactorsToSamples().isEmpty()) {
           factorBox.addItems(structure.getFactorsToSamples().keySet());
@@ -119,7 +116,7 @@ public void valueChange(ValueChangeEvent event) {
   }
 
   public void showDatasetsForSamples(String label, List<String> sampleCodes) {
-    Window subWindow = new Window(" " + label + " Dataset information");
+    Window subWindow = new Window(" " + label + " information");
     subWindow.setWidth("680px");
 
     VerticalLayout layout = new VerticalLayout();
@@ -135,7 +132,7 @@ public void showDatasetsForSamples(String label, List<String> sampleCodes) {
         samplesWithoutData.add(s);
     }
 
-    Table haveData = new Table("Samples with Data");
+    Table haveData = new Table("Samples/Entities with Data");
     haveData.setStyleName(ValoTheme.TABLE_SMALL);
     haveData.addContainerProperty("Sample", String.class, null);
     haveData.addContainerProperty("Secondary Name", String.class, null);
@@ -159,7 +156,7 @@ public void showDatasetsForSamples(String label, List<String> sampleCodes) {
       haveData.addItem(row.toArray(new Object[row.size()]), s);
     }
 
-    Table noData = new Table("Samples without Data");
+    Table noData = new Table("Samples/Entities without Data");
     noData.setStyleName(ValoTheme.TABLE_SMALL);
     noData.addContainerProperty("Sample", String.class, null);
     noData.addContainerProperty("Secondary Name", String.class, null);
@@ -207,25 +204,4 @@ public void buttonClick(ClickEvent event) {
     ui.addWindow(subWindow);
   }
 
-  //
-  // public void showSamples(List<String> nodeEntries) {
-  // sampleTable.setPageLength(Math.min(6, nodeEntries.size()));
-  // sampleTable.removeAllItems();
-  // sampleTable.addContainerProperty("Code", String.class, null);
-  // sampleTable.addContainerProperty("Secondary Name", String.class, null);
-  // int i = 0;
-  // for (Sample s : currentSamples) {
-  // i++;
-  // String code = s.getCode();
-  // String name = s.getProperties().get("Q_SECONDARY_NAME");
-  // if (nodeEntries.contains(code)) {
-  // List<Object> row = new ArrayList<Object>();
-  // row.add(code);
-  // row.add(name);
-  // sampleTable.addItem(row.toArray(new Object[row.size()]), i);
-  // }
-  // }
-  // sampleTable.setVisible(true);
-  // }
-
 }