up from home

.classpath

@@ -8,17 +8,17 @@
  </attributes>
  </classpathentry>
  <classpathentry combineaccessrules="false" exported="true" kind="src" path="/phenOwl"/>
- <classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER">
+ <classpathentry kind="con" path="org.eclipse.jst.j2ee.internal.web.container"/>
+ <classpathentry kind="con" path="org.eclipse.jst.j2ee.internal.module.container"/>
+ <classpathentry kind="con" path="org.eclipse.jst.server.core.container/org.eclipse.jst.server.tomcat.runtimeTarget/Apache Tomcat v9.0">
  <attributes>
- <attribute name="owner.project.facets" value="java"/>
+ <attribute name="owner.project.facets" value="jst.web"/>
  </attributes>
  </classpathentry>
- <classpathentry kind="con" path="org.eclipse.jst.server.core.container/org.eclipse.jst.server.tomcat.runtimeTarget/Apache Tomcat v8.0">
+ <classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.launching.macosx.MacOSXType/Java SE 8 [1.8.0_161]">
  <attributes>
- <attribute name="owner.project.facets" value="jst.web"/>
+ <attribute name="owner.project.facets" value="java"/>
  </attributes>
  </classpathentry>
- <classpathentry kind="con" path="org.eclipse.jst.j2ee.internal.web.container"/>
- <classpathentry kind="con" path="org.eclipse.jst.j2ee.internal.module.container"/>
  <classpathentry kind="output" path="build/classes"/>
 </classpath>

.project

@@ -32,11 +32,6 @@
  <arguments>
  </arguments>
  </buildCommand>
- <buildCommand>
- <name>com.vaadin.integration.eclipse.addonStylesBuilder</name>
- <arguments>
- </arguments>
- </buildCommand>
  <buildCommand>
  <name>org.eclipse.m2e.core.maven2Builder</name>
  <arguments>

.settings/org.apache.ivyde.eclipse.prefs

@@ -0,0 +1,2 @@
+eclipse.preferences.version=1
+org.apache.ivyde.eclipse.standaloneretrieve=<?xml version\="1.0" encoding\="UTF-8" standalone\="no"?><setuplist/>

.settings/org.eclipse.wst.common.project.facet.core.xml

@@ -1,6 +1,6 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <faceted-project>
- <runtime name="Apache Tomcat v8.0"/>
+ <runtime name="Apache Tomcat v9.0"/>
  <fixed facet="jst.web"/>
  <fixed facet="java"/>
  <fixed facet="wst.jsdt.web"/>

ivy.xml

@@ -40,5 +40,7 @@
  <dependency org="org.vaadin.addons" name="googleanalyticstracker" rev="2.1.0" />
  <dependency org="com.github.vaadin4qbanos" name="jsclipboard" rev="1.0.2" />
  <dependency org="com.sebworks" name="vaadstrap" rev="0.1.2" /> 
+ <dependency org="net.sourceforge.owlapi" name="owlapi-distribution" rev="4.1.3"/>
+
  </dependencies> 
 </ivy-module>

src/hpoweb/HpowebUI.java

@@ -20,7 +20,6 @@
 import com.vaadin.event.FieldEvents.FocusEvent;
 import com.vaadin.event.FieldEvents.FocusListener;
 import com.vaadin.jsclipboard.JSClipboard;
-import com.vaadin.server.ExternalResource;
 import com.vaadin.server.Page;
 import com.vaadin.server.VaadinRequest;
 import com.vaadin.server.VaadinServlet;
@@ -142,13 +141,11 @@ protected void init(VaadinRequest request) {
  hpoClassTabFactory.addTermInfoElements(gridContainer, (IHpClassDataProvider) dataProvider);
 
  addExtraButtons(gridContainer, (IHpClassDataProvider) dataProvider);
- }
- else if (dataProvider instanceof IDiseaseDataProvider) {
+ } else if (dataProvider instanceof IDiseaseDataProvider) {
 
  DiseaseTabFactory diseaseTabFactory = new DiseaseTabFactory(tableUtils);
  diseaseTabFactory.addDiseaseInfoElements(gridContainer, (IDiseaseDataProvider) dataProvider);
- }
- else if (dataProvider instanceof IGeneDataProvider) {
+ } else if (dataProvider instanceof IGeneDataProvider) {
 
  GeneTabFactory geneTabFactory = new GeneTabFactory(tableUtils);
  geneTabFactory.addGeneInfoElements(gridContainer, (IGeneDataProvider) dataProvider);
@@ -161,8 +158,7 @@ else if (dataProvider instanceof IGeneDataProvider) {
  String ontologyVersion;
  if (doParseHpo) {
  ontologyVersion = hpData.getExtOwlOntology().getOntologyVersionIri().toString();
- }
- else
+ } else
 
  {
  ontologyVersion = "some ontology version here";
@@ -173,7 +169,8 @@ else if (dataProvider instanceof IGeneDataProvider) {
  */
  Label version = new Label("Ontology version: " + ontologyVersion);
  Label copyright = new Label("Copyright 2017 - Sebastian Köhler & The Human Phenotype Ontology Project");
- Link feedback = new Link("Question, Comments, Feedback: [email protected]", new ExternalResource("http:https://drseb.github.io/"));
+ Link feedback = new Link("Question, Comments, Feedback: [email protected]",
+ new com.vaadin.server.ExternalResource("http:https://drseb.github.io/"));
  addLabelRow(gridContainer, version);
  addLabelRow(gridContainer, copyright);
  addLabelRow(gridContainer, feedback);
@@ -252,39 +249,36 @@ private IEntityDataProvider setupDataProvider(VaadinRequest request, Map<String,
 
  OWLClass hpClass = parseHpId(request);
  if (hpClass == null && doParseHpo) {
- new Notification("Invalid HPO id input", "<br/><br/>Can't parse HPO id from '" + request.getParameter(CONSTANTS.hpRequestId) + "'",
+ new Notification("Invalid HPO id input",
+ "<br/><br/>Can't parse HPO id from '" + request.getParameter(CONSTANTS.hpRequestId) + "'",
  Notification.Type.ERROR_MESSAGE, true).show(Page.getCurrent());
  return null;
  }
 
  if (doParseHpo) {
  dataProvider = new HpClassDataProvider(hpClass, hpData);
- }
- else {
+ } else {
  dataProvider = new FakeHpClassDataProvider();
  }
 
- }
- else if (parameterMap.containsKey(CONSTANTS.geneRequestId)) {
+ } else if (parameterMap.containsKey(CONSTANTS.geneRequestId)) {
 
  Integer geneId = parseGeneId(request);
  if (geneId == null && doParseHpo) {
  new Notification("Invalid gene id input",
- "<br/><br/>Can't parse gene id from '" + request.getParameter(CONSTANTS.geneRequestId) + "'", Notification.Type.ERROR_MESSAGE,
- true).show(Page.getCurrent());
+ "<br/><br/>Can't parse gene id from '" + request.getParameter(CONSTANTS.geneRequestId) + "'",
+ Notification.Type.ERROR_MESSAGE, true).show(Page.getCurrent());
  return null;
  }
 
  if (doParseHpo) {
 
  dataProvider = new GeneDataProvider(geneId, hpData);
- }
- else {
+ } else {
  dataProvider = new FakeGeneDataProvider();
  }
 
- }
- else if (parameterMap.containsKey(CONSTANTS.diseaseRequestId)) {
+ } else if (parameterMap.containsKey(CONSTANTS.diseaseRequestId)) {
 
  ItemId diseaseId = parseDiseaseId(request);
  if (diseaseId == null && doParseHpo) {
@@ -296,15 +290,14 @@ else if (parameterMap.containsKey(CONSTANTS.diseaseRequestId)) {
 
  if (doParseHpo) {
  dataProvider = new DiseaseDataProvider(diseaseId, hpData);
- }
- else {
+ } else {
  dataProvider = new FakeDiseaseDataProvider();
  }
- }
- else {
- new Notification("Invalid URL", "<br/><br/>You have to provide one URL parameter (" + CONSTANTS.hpRequestId + ","
- + CONSTANTS.geneRequestId + ", or " + CONSTANTS.diseaseRequestId + ") ! ", Notification.Type.WARNING_MESSAGE, true)
-  .show(Page.getCurrent());
+ } else {
+  new Notification("Invalid URL",
+  "<br/><br/>You have to provide one URL parameter (" + CONSTANTS.hpRequestId + ","
+  + CONSTANTS.geneRequestId + ", or " + CONSTANTS.diseaseRequestId + ") ! ",
+ Notification.Type.WARNING_MESSAGE, true).show(Page.getCurrent());
  return null;
  }
  return dataProvider;

tmp

@@ -0,0 +1 @@
+page.setUriFragment("!" + SampleCrudView2.VIEW_NAME + "/" + fragmentParameter, false);