Upgrade to 1.6.1

Upgraded to use version 1.7.6 of ISAcreator. Fixed issues with ontology browsing.
ISA-tools · Feb 6, 2014 · 95ca865 · 95ca865
1 parent c842367
commit 95ca865
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Showing 10 changed files with 56 additions and 90 deletions.
diff --git a/Settings/settings.properties b/Settings/settings.properties
@@ -1,8 +1,3 @@
 #settings
-#Fri Oct 05 14:24:11 BST 2012
-httpProxy.portNumber=
-httpProxy.hostname=ASDA
-httpProxy.usedLast=true
-httpProxy.password=
-httpProxy.useAuth=false
-httpProxy.login=
+#Thu Feb 06 17:12:39 GMT 2014
+java.version=1.6.0_65
diff --git a/pom.xml b/pom.xml
@@ -4,7 +4,7 @@
     <groupId>org.isatools</groupId>
     <artifactId>ISACreatorConfigurator</artifactId>
     <packaging>jar</packaging>
-    <version>1.6</version>
+    <version>1.6.1</version>
     <name>ISACreator Configurator</name>
     <url>http://isa-tools.org/isaconfig.html</url>
 
@@ -263,9 +263,11 @@
         <dependency>
             <groupId>org.isatools</groupId>
             <artifactId>ISAcreator</artifactId>
-            <version>1.7.3</version>
+            <version>1.7.6</version>
+
         </dependency>
 
+
         <dependency>
             <groupId>org.apache.poi</groupId>
             <artifactId>poi</artifactId>

diff --git a/src/main/java/org/isatools/isacreatorconfigurator/configui/FieldInterface.java b/src/main/java/org/isatools/isacreatorconfigurator/configui/FieldInterface.java
@@ -47,13 +47,11 @@ the UK BBSRC (http://www.bbsrc.ac.uk), the UK NERC-NEBC (http://nebc.nerc.ac.uk)
 import org.isatools.isacreator.effects.components.RoundedFormattedTextField;
 import org.isatools.isacreator.effects.components.RoundedJTextArea;
 import org.isatools.isacreator.effects.components.RoundedJTextField;
-import org.isatools.isacreator.ontologymanager.BioPortalClient;
-import org.isatools.isacreator.ontologymanager.OLSClient;
+import org.isatools.isacreator.ontologymanager.BioPortal4Client;
 import org.isatools.isacreator.ontologymanager.OntologyService;
 import org.isatools.isacreator.ontologyselectiontool.OntologySelectionTool;
 import org.isatools.isacreatorconfigurator.ontologyconfigurationtool.OntologyConfigUI;
-import org.isatools.isatab.configurator.schema.UnitFieldType;
-import org.isatools.isatab.configurator.schema.impl.UnitFieldTypeImpl;
+
 import org.jdesktop.fuse.InjectedResource;
 import org.jdesktop.fuse.ResourceInjector;
 
@@ -131,15 +129,12 @@ public class FieldInterface extends JLayeredPane implements ActionListener,
     private FieldElement field;
 
     static {
-        OntologyService bpc = new BioPortalClient();
+        OntologyService bpc = new BioPortal4Client();
         ontologiesToQuery = new ArrayList<Ontology>();
         if (bpc.getAllOntologies() != null) {
             ontologiesToQuery.addAll(bpc.getAllOntologies());
         }
 
-        OntologyService olsClient = new OLSClient();
-
-        ontologiesToQuery.addAll(olsClient.getAllOntologies());
         ontologyColumnHeaders = new String[]{"ontology", "search under"};
     }
 

diff --git a/...n/java/org/isatools/isacreatorconfigurator/ontologyconfigurationtool/OntologyBrowser.java b/...n/java/org/isatools/isacreatorconfigurator/ontologyconfigurationtool/OntologyBrowser.java
@@ -5,13 +5,13 @@ ISAconfigurator is a component of the ISA software suite (http://www.isa-tools.o
  ISAconfigurator is licensed under the Common Public Attribution License version 1.0 (CPAL)
 
  EXHIBIT A. CPAL version 1.0
- ÒThe contents of this file are subject to the CPAL version 1.0 (the ÒLicenseÓ); you may not use this file except
+ �The contents of this file are subject to the CPAL version 1.0 (the �License�); you may not use this file except
  in compliance with the License. You may obtain a copy of the License at http://isa-tools.org/licenses/ISAconfigurator-license.html.
  The License is based on the Mozilla Public License version 1.1 but Sections 14 and 15 have been added to cover use of software over
  a computer network and provide for limited attribution for the Original Developer. In addition, Exhibit A has been modified to be
  consistent with Exhibit B.
 
- Software distributed under the License is distributed on an ÒAS ISÓ basis, WITHOUT WARRANTY OF ANY KIND, either express
+ Software distributed under the License is distributed on an �AS IS� basis, WITHOUT WARRANTY OF ANY KIND, either express
  or implied. See the License for the specific language governing rights and limitations under the License.
 
  The Original Code is ISAconfigurator.
@@ -87,7 +87,7 @@ public class OntologyBrowser extends JPanel implements TreeObserver, TreeSubject
      *
      * @param ontologyToQuery - the Ontology object representing the Ontology to be queried
      */
-    public OntologyBrowser(Ontology ontologyToQuery, OntologyService ontologyClient, Dimension browserSize) {
+    public OntologyBrowser(Ontology ontologyToQuery, Dimension browserSize) {
         this.ontologyToQuery = ontologyToQuery;
         this.browserSize = browserSize;
         this.observers = new ArrayList<TreeObserver>();
@@ -99,8 +99,7 @@ private void instantiate() {
         // add event change listener to detect when nodes are being selected in the tree. we can then update the definition in
         // the ViewTermDefinitionUI to show the currently selected term.
 
-        ontologyTreeCreator = ontologyToQuery.getFormat() == OntologyFormats.OBO ? new WSOntologyTreeCreator(this, ontologyTree) :
-                new WSOntologyTreeCreator(this, ontologyTree);
+        ontologyTreeCreator = new WSOntologyTreeCreator(this, ontologyTree);
 
         ((WSOntologyTreeCreator) ontologyTreeCreator).registerObserver(this);
 
@@ -116,6 +115,12 @@ private void createGUI() {
         DefaultMutableTreeNode root;
 
         try {
+            System.out.println("Querying... ");
+            System.out.println(ontologyToQuery.getOntologyAbbreviation());
+            System.out.println(ontologyToQuery.getOntologyID());
+
+            System.out.println();
+            ontologyToQuery.setOntologyVersion(ontologyToQuery.getOntologyAbbreviation());
             root = ontologyTreeCreator.createTree(Collections.singletonMap(ontologyToQuery.getOntologyAbbreviation(), new RecommendedOntology(ontologyToQuery, null)));
             ontologyTree.setModel(new DefaultTreeModel(root));
         } catch (FileNotFoundException e) {
@@ -124,8 +129,6 @@ private void createGUI() {
             log.error(re.getMessage());
         }
 
-
-
         ontologyTree.setCellRenderer(new OntologyTreeRenderer());
         ontologyTree.setShowsRootHandles(false);
 
@@ -167,7 +170,6 @@ public void mousePressed(MouseEvent mouseEvent) {
                     }
                 }
             }
-
         });
 
         JScrollPane ontologyTreeScroller = new JScrollPane(ontologyTree, JScrollPane.VERTICAL_SCROLLBAR_AS_NEEDED, JScrollPane.HORIZONTAL_SCROLLBAR_AS_NEEDED);
@@ -184,8 +186,6 @@ public void mousePressed(MouseEvent mouseEvent) {
         selectedTreePartInfo = UIHelper.createLabel("", UIHelper.VER_11_PLAIN, UIHelper.DARK_GREEN_COLOR, SwingConstants.LEFT);
         selectedTreePartInfoCont.add(selectedTreePartInfo);
         add(selectedTreePartInfoCont, BorderLayout.SOUTH);
-
-
     }
 
     private JPanel createInfoPanel() {

diff --git a/.../java/org/isatools/isacreatorconfigurator/ontologyconfigurationtool/OntologyConfigUI.java b/.../java/org/isatools/isacreatorconfigurator/ontologyconfigurationtool/OntologyConfigUI.java
@@ -5,13 +5,13 @@ ISAconfigurator is a component of the ISA software suite (http://www.isa-tools.o
  ISAconfigurator is licensed under the Common Public Attribution License version 1.0 (CPAL)
 
  EXHIBIT A. CPAL version 1.0
- ÒThe contents of this file are subject to the CPAL version 1.0 (the ÒLicenseÓ); you may not use this file except
+ �The contents of this file are subject to the CPAL version 1.0 (the �License�); you may not use this file except
  in compliance with the License. You may obtain a copy of the License at http://isa-tools.org/licenses/ISAconfigurator-license.html.
  The License is based on the Mozilla Public License version 1.1 but Sections 14 and 15 have been added to cover use of software over
  a computer network and provide for limited attribution for the Original Developer. In addition, Exhibit A has been modified to be
  consistent with Exhibit B.
 
- Software distributed under the License is distributed on an ÒAS ISÓ basis, WITHOUT WARRANTY OF ANY KIND, either express
+ Software distributed under the License is distributed on an �AS IS� basis, WITHOUT WARRANTY OF ANY KIND, either express
  or implied. See the License for the specific language governing rights and limitations under the License.
 
  The Original Code is ISAconfigurator.
@@ -39,6 +39,7 @@ the UK BBSRC (http://www.bbsrc.ac.uk), the UK NERC-NEBC (http://nebc.nerc.ac.uk)
 import com.explodingpixels.macwidgets.IAppWidgetFactory;
 import org.apache.commons.collections15.map.ListOrderedMap;
 import org.isatools.isacreator.autofilteringlist.ExtendedJList;
+import org.isatools.isacreator.common.CommonMouseAdapter;
 import org.isatools.isacreator.common.UIHelper;
 import org.isatools.isacreator.configuration.Ontology;
 import org.isatools.isacreator.configuration.RecommendedOntology;
@@ -47,11 +48,8 @@ the UK BBSRC (http://www.bbsrc.ac.uk), the UK NERC-NEBC (http://nebc.nerc.ac.uk)
 import org.isatools.isacreator.effects.InfiniteProgressPanel;
 import org.isatools.isacreator.effects.borders.RoundedBorder;
 import org.isatools.isacreator.ontologybrowsingutils.TreeObserver;
-import org.isatools.isacreator.ontologymanager.BioPortalClient;
-import org.isatools.isacreator.ontologymanager.OLSClient;
+import org.isatools.isacreator.ontologymanager.BioPortal4Client;
 import org.isatools.isacreator.ontologymanager.OntologyService;
-import org.isatools.isacreator.ontologymanager.bioportal.model.OntologyPortal;
-import org.isatools.isacreator.ontologymanager.utils.OntologyUtils;
 import org.isatools.isacreatorconfigurator.configui.notifications.NotificationWindow;
 import org.jdesktop.fuse.InjectedResource;
 import org.jdesktop.fuse.ResourceInjector;
@@ -80,8 +78,7 @@ the UK BBSRC (http://www.bbsrc.ac.uk), the UK NERC-NEBC (http://nebc.nerc.ac.uk)
 
 public class OntologyConfigUI extends JFrame {
 
-    private static final BioPortalClient bioportalClient = new BioPortalClient();
-    private static final OLSClient olsClient = new OLSClient();
+    private static final BioPortal4Client bioportalClient = new BioPortal4Client();
 
     @InjectedResource
     private ImageIcon infoImage, confirmButton, confirmButtonOver, addOntologyButtonIcon, addOntologyButtonIconOver,
@@ -328,7 +325,7 @@ public void mousePressed(MouseEvent mouseEvent) {
 
                 if (!selectedOntologyList.isSelectionEmpty()) {
                     String ontologyToRemove = selectedOntologyList.getSelectedValue().toString();
-                    System.out.println("Removing  " + ontologyToRemove);
+
                     selectedOntologies.remove(ontologyToRemove);
                     setOntologySelectionPanelPlaceholder(infoImage);
 
@@ -352,20 +349,23 @@ public void mouseExited(MouseEvent mouseEvent) {
         removeOntologyButton.setVisible(false);
 
         viewOntologyButton = new JLabel(browseOntologyButtonIcon);
-        viewOntologyButton.addMouseListener(new MouseAdapter() {
+        viewOntologyButton.addMouseListener(new CommonMouseAdapter() {
             @Override
             public void mousePressed(MouseEvent mouseEvent) {
-                performTransition();
+                super.mousePressed(mouseEvent);
+                doOntologyDisplay();
                 viewOntologyButton.setIcon(browseOntologyButtonIcon);
             }
 
             @Override
             public void mouseEntered(MouseEvent mouseEvent) {
+                super.mouseEntered(mouseEvent);
                 viewOntologyButton.setIcon(browseOntologyButtonIconOver);
             }
 
             @Override
             public void mouseExited(MouseEvent mouseEvent) {
+                super.mouseExited(mouseEvent);
                 viewOntologyButton.setIcon(browseOntologyButtonIcon);
             }
         });
@@ -464,11 +464,10 @@ public void propertyChange(PropertyChangeEvent propertyChangeEvent) {
 
         if (ontologiesToBrowseOn == null) {
             ontologiesToBrowseOn = new ArrayList<Ontology>();
-            List<Ontology> bioportalQueryResult = bioportalClient.getAllOntologies();
+            Collection<Ontology> bioportalQueryResult = bioportalClient.getAllOntologies();
             if (bioportalQueryResult != null) {
                 ontologiesToBrowseOn.addAll(bioportalQueryResult);
             }
-            ontologiesToBrowseOn.addAll(olsClient.getAllOntologies());
         }
 
         // precautionary check in case of having no ontologies available to search on.
@@ -527,7 +526,7 @@ private void updateSelectedOntologies() {
         repaint();
     }
 
-    private void performTransition() {
+    private void doOntologyDisplay() {
 
         Thread performer = new Thread(new Runnable() {
             public void run() {
@@ -553,15 +552,10 @@ public void run() {
                             ontology.setSubsectionToQuery(selectedOntologies.get(ontology.getOntologyDisplayLabel()).getBranchToSearchUnder());
                         }
 
-                        if (OntologyUtils.getSourceOntologyPortal(ontology) == OntologyPortal.BIOPORTAL) {
-                            currentlyActiveBrowser = new OntologyBrowser(ontology, bioportalClient, getMaxBrowserSize());
-                            configureSearchAndTermDefinitionPanel(ontology, bioportalClient);
-                            ontologyViewContainer.add(currentlyActiveBrowser);
-                        } else {
-                            currentlyActiveBrowser = new OntologyBrowser(ontology, olsClient, getMaxBrowserSize());
-                            configureSearchAndTermDefinitionPanel(ontology, olsClient);
-                            ontologyViewContainer.add(currentlyActiveBrowser);
-                        }
+
+                        currentlyActiveBrowser = new OntologyBrowser(ontology, getMaxBrowserSize());
+                        configureSearchAndTermDefinitionPanel(ontology, bioportalClient);
+                        ontologyViewContainer.add(currentlyActiveBrowser);
 
                         currentlyActiveBrowser.setPreferredSize(getMaxBrowserSize());
                         glassPane.stop();

diff --git a/...a/org/isatools/isacreatorconfigurator/ontologyconfigurationtool/OntologyListRenderer.java b/...a/org/isatools/isacreatorconfigurator/ontologyconfigurationtool/OntologyListRenderer.java
@@ -5,13 +5,13 @@ ISAconfigurator is a component of the ISA software suite (http://www.isa-tools.o
  ISAconfigurator is licensed under the Common Public Attribution License version 1.0 (CPAL)
 
  EXHIBIT A. CPAL version 1.0
- ÒThe contents of this file are subject to the CPAL version 1.0 (the ÒLicenseÓ); you may not use this file except
+ �The contents of this file are subject to the CPAL version 1.0 (the �License�); you may not use this file except
  in compliance with the License. You may obtain a copy of the License at http://isa-tools.org/licenses/ISAconfigurator-license.html.
  The License is based on the Mozilla Public License version 1.1 but Sections 14 and 15 have been added to cover use of software over
  a computer network and provide for limited attribution for the Original Developer. In addition, Exhibit A has been modified to be
  consistent with Exhibit B.
 
- Software distributed under the License is distributed on an ÒAS ISÓ basis, WITHOUT WARRANTY OF ANY KIND, either express
+ Software distributed under the License is distributed on an �AS IS� basis, WITHOUT WARRANTY OF ANY KIND, either express
  or implied. See the License for the specific language governing rights and limitations under the License.
 
  The Original Code is ISAconfigurator.
@@ -58,8 +58,7 @@ public class OntologyListRenderer extends JPanel
     static Color listForeground = UIHelper.DARK_GREEN_COLOR;
 
     @InjectedResource
-    private ImageIcon olsIcon, bioPortalIcon;
-
+    private ImageIcon bioPortalIcon;
 
     private JLabel icon;
     private JLabel text;
@@ -72,7 +71,7 @@ public OntologyListRenderer() {
 
         setLayout(new BorderLayout());
 
-        icon = new JLabel(olsIcon);
+        icon = new JLabel(bioPortalIcon);
         add(icon, BorderLayout.WEST);
 
         text = UIHelper.createLabel("", UIHelper.VER_10_PLAIN, listForeground);
@@ -99,12 +98,6 @@ public Component getListCellRendererComponent(JList jList, Object val,
             Ontology o = (Ontology) val;
 
             // ols versions are now like Jun 2010 rather than their previous version format 1.26
-            if (o.getOntologyVersion().length() > 5) {
-                icon.setIcon(olsIcon);
-            } else {
-                icon.setIcon(bioPortalIcon);
-            }
-
             stringRepresentation = o.getOntologyAbbreviation() + " - " + o.getOntologyDisplayLabel();
         }
 

diff --git a/.../org/isatools/isacreatorconfigurator/ontologyconfigurationtool/SearchAndDefinitionUI.java b/.../org/isatools/isacreatorconfigurator/ontologyconfigurationtool/SearchAndDefinitionUI.java
@@ -5,13 +5,13 @@ ISAconfigurator is a component of the ISA software suite (http://www.isa-tools.o
  ISAconfigurator is licensed under the Common Public Attribution License version 1.0 (CPAL)
 
  EXHIBIT A. CPAL version 1.0
- ÒThe contents of this file are subject to the CPAL version 1.0 (the ÒLicenseÓ); you may not use this file except
+ �The contents of this file are subject to the CPAL version 1.0 (the �License�); you may not use this file except
  in compliance with the License. You may obtain a copy of the License at http://isa-tools.org/licenses/ISAconfigurator-license.html.
  The License is based on the Mozilla Public License version 1.1 but Sections 14 and 15 have been added to cover use of software over
  a computer network and provide for limited attribution for the Original Developer. In addition, Exhibit A has been modified to be
  consistent with Exhibit B.
 
- Software distributed under the License is distributed on an ÒAS ISÓ basis, WITHOUT WARRANTY OF ANY KIND, either express
+ Software distributed under the License is distributed on an �AS IS� basis, WITHOUT WARRANTY OF ANY KIND, either express
  or implied. See the License for the specific language governing rights and limitations under the License.
 
  The Original Code is ISAconfigurator.
@@ -38,13 +38,11 @@ the UK BBSRC (http://www.bbsrc.ac.uk), the UK NERC-NEBC (http://nebc.nerc.ac.uk)
 
 import org.isatools.isacreator.common.UIHelper;
 import org.isatools.isacreator.configuration.Ontology;
-import org.isatools.isacreator.configuration.OntologyBranch;
 import org.isatools.isacreator.ontologybrowsingutils.OntologyTreeCreator;
 import org.isatools.isacreator.ontologybrowsingutils.OntologyTreeItem;
 import org.isatools.isacreator.ontologybrowsingutils.TreeObserver;
 import org.isatools.isacreator.ontologybrowsingutils.WSOntologyTreeCreator;
-import org.isatools.isacreator.ontologymanager.BioPortalClient;
-import org.isatools.isacreator.ontologymanager.OLSClient;
+import org.isatools.isacreator.ontologymanager.BioPortal4Client;
 import org.isatools.isacreator.ontologymanager.OntologyService;
 import org.isatools.isacreator.ontologymanager.common.OntologyTerm;
 import org.jdesktop.fuse.InjectedResource;
@@ -254,7 +252,7 @@ public void setOntologyClient(OntologyService ontologyClient) {
 
     public OntologyService getOntologyClient() {
         if (ontologyClient == null) {
-            ontologyClient = ontologyTreeCreator instanceof WSOntologyTreeCreator ? new OLSClient() : new BioPortalClient();
+            ontologyClient = new BioPortal4Client();
         }
         return ontologyClient;
     }