Merge pull request #62 from qbicsoftware/hotfix/maxquant-download

Hotfix/maxquant download

CHANGELOG.rst

@@ -2,6 +2,18 @@
 Changelog
 ==========
 
+1.12.9 (2022-02-01)
+-------------------
+
+**Added**
+
+**Fixed**
+
+* Fix dataset table pagelength which was missing from some views
+* Selected entries are now no longer removed from the download list if a different subfolder in the same dataset is deselected
+
+**Dependencies**
+
 1.12.8 (2022-01-28)
 -------------------
 

pom.xml

@@ -8,7 +8,7 @@
 		<version>1.7.1</version>
 	</parent>
 	<artifactId>projectbrowser-portlet</artifactId>
-	<version>1.12.8</version>
+	<version>1.12.9</version>
 	<name>ProjectBrowser Portlet</name>
 	<url>http://github.com/qbicsoftware/projectbrowser-portlet</url>
 	<description>Browse and manage biomedical projects</description>

src/main/java/life/qbic/projectbrowser/components/DatasetComponent.java

@@ -337,7 +337,7 @@ private synchronized void prepareTSVExportFile(final BeanItemContainer<DatasetBe
   public void setContainerDataSource(HierarchicalContainer newDataSource) {
     datasets = (HierarchicalContainer) newDataSource;
     table.setContainerDataSource(this.datasets);
-    table.setPageLength(Math.max(3, Math.min(numberOfDatasets, 10)));
+    table.setPageLength(Math.max(10, Math.min(numberOfDatasets, 15)));
 
     table.setVisibleColumns((Object[]) FILTER_TABLE_COLUMNS);
 
@@ -698,7 +698,8 @@ public void deselectAllUnrelated(Set<Object> blackList) {
     }
   }
 
-  // if users don't click on a checkbox, but it needs to be selected or unselected due to parent items etc. we don't want to call the listeners
+  // if users don't click on a checkbox, but it needs to be selected or unselected due to parent
+  // items etc. we don't want to call the listeners
   private void changeCheckBoxValueSilently(CheckBox checkbox, boolean value) {
     Collection<ValueChangeListener> listeners =
         (Collection<ValueChangeListener>) checkbox.getListeners(ValueChangeEvent.class);
@@ -738,23 +739,26 @@ public void valueChange(ValueChangeEvent event) {
 
       boolean itemSelected = (Boolean) event.getProperty().getValue();
 
-      // find all rows of the dataset we performed changes on - important because sibling files can stay selected!
+      // find all rows of the dataset we performed changes on - important because sibling files can
+      // stay selected!
       Set<Object> rowsForDataset = getAllDatasetRows(folderToDatasetCode(itemFolderName));
 
-      // propagates selection or deselection of subfolders and files and adds/removes their paths to/from download
+      // propagates selection or deselection of subfolders and files and adds/removes their paths
+      // to/from download
       valueChange(itemId, itemSelected, entries, itemFolderName);
 
       // now we deselect all unrelated data - that means rows belonging to other datasets
       deselectAllUnrelated(rowsForDataset);
 
       // now that selections have been fixed, we remove all files from the download list that
-      // do not start with this listener's folder name (ds code), since we only allow downloads of
+      // do not start with this listener's ds code, since we only allow downloads of
       // single datasets
 
       Set<String> toRemove = new HashSet<>();
 
       for (String fileName : entries.keySet()) {
-        if (!fileName.startsWith(itemFolderName)) {
+        String datasetCode = folderToDatasetCode(itemFolderName);
+        if (!fileName.startsWith(datasetCode)) {
           toRemove.add(fileName);
         }
       }

src/main/java/life/qbic/projectbrowser/components/LevelComponent.java

@@ -357,7 +357,7 @@ public void windowClose(CloseEvent e) {
             this.datasetTable.setCaption("Raw Data");
 
             numberOfDatasets = retrievedDatasets.size();
-            this.datasetTable.setPageLength(10);
+            datasetTable.setPageLength(Math.max(10, Math.min(numberOfDatasets, 15)));
           } else if (filterFor.equals("results")) {
             BeanItemContainer<TestSampleBean> samplesContainer =
                 new BeanItemContainer<TestSampleBean>(TestSampleBean.class);
@@ -441,8 +441,7 @@ public void itemClick(ItemClickEvent event) {
             });
 
             numberOfDatasets = retrievedDatasets.size();
-            this.datasetTable.setPageLength(10);
-
+            datasetTable.setPageLength(Math.max(10, Math.min(numberOfDatasets, 15)));
           }
           break;
 
@@ -984,7 +983,8 @@ public void registerDatasetInTable(DatasetBean d, HierarchicalContainer dataset_
     }
   }
 
-  // if users don't click on a checkbox, but it needs to be selected or unselected due to parent items etc. we don't want to call the listeners
+  // if users don't click on a checkbox, but it needs to be selected or unselected due to parent
+  // items etc. we don't want to call the listeners
   private void changeCheckBoxValueSilently(CheckBox checkbox, boolean value) {
     Collection<ValueChangeListener> listeners =
         (Collection<ValueChangeListener>) checkbox.getListeners(ValueChangeEvent.class);
@@ -999,7 +999,7 @@ private void changeCheckBoxValueSilently(CheckBox checkbox, boolean value) {
       checkbox.addValueChangeListener(l);
     }
   }
-  
+
   // deselects all checkboxes but the ones provided
   public void deselectAllUnrelated(Set<Object> blackList) {
     for (Object rowId : datasetTable.getItemIds()) {
@@ -1035,23 +1035,26 @@ public void valueChange(ValueChangeEvent event) {
 
       boolean itemSelected = (Boolean) event.getProperty().getValue();
 
-      // find all rows of the dataset we performed changes on - important because sibling files can stay selected!
+      // find all rows of the dataset we performed changes on - important because sibling files can
+      // stay selected!
       Set<Object> rowsForDataset = getAllDatasetRows(folderToDatasetCode(itemFolderName));
 
-      // propagates selection or deselection of subfolders and files and adds/removes their paths to/from download
+      // propagates selection or deselection of subfolders and files and adds/removes their paths
+      // to/from download
       valueChange(itemId, itemSelected, entries, itemFolderName);
 
       // now we deselect all unrelated data - that means rows belonging to other datasets
       deselectAllUnrelated(rowsForDataset);
 
       // now that selections have been fixed, we remove all files from the download list that
-      // do not start with this listener's folder name (ds code), since we only allow downloads of
+      // do not start with this listener's ds code, since we only allow downloads of
       // single datasets
 
       Set<String> toRemove = new HashSet<>();
 
       for (String fileName : entries.keySet()) {
-        if (!fileName.startsWith(itemFolderName)) {
+        String datasetCode = folderToDatasetCode(itemFolderName);
+        if (!fileName.startsWith(datasetCode)) {
           toRemove.add(fileName);
         }
       }
@@ -1072,7 +1075,7 @@ public void valueChange(ValueChangeEvent event) {
       }
 
     }
-    
+
     private String folderToDatasetCode(String folderName) {
       try {
         return folderName.split("/")[0];
@@ -1090,7 +1093,7 @@ private Set<Object> getAllDatasetRows(String datasetCode) {
       }
       return res;
     }
-    
+
     /**
      * updates entries (puts and removes) for selected table item and all its children. Means
      * Checkbox is updated. And in case download button is clicked all checked items will be