update on disease-gene associations

closes #17 closes #9
drseb · Apr 22, 2016 · 52f6cd6 · 52f6cd6
1 parent 610c984
commit 52f6cd6
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Showing 3 changed files with 39 additions and 49 deletions.
diff --git a/.settings/com.vaadin.integration.eclipse.prefs b/.settings/com.vaadin.integration.eclipse.prefs
@@ -1,5 +1,5 @@
-com.vaadin.integration.eclipse.previousCompileAction=theme
+com.vaadin.integration.eclipse.previousCompileAction=both
 com.vaadin.integration.eclipse.useLatestNightly=false
-com.vaadin.integration.eclipse.widgetsetCompilationEta=41585
-com.vaadin.integration.eclipse.widgetsetDirty=true
+com.vaadin.integration.eclipse.widgetsetCompilationEta=190643
+com.vaadin.integration.eclipse.widgetsetDirty=false
 eclipse.preferences.version=1
diff --git a/src/hpoweb/HpowebUI.java b/src/hpoweb/HpowebUI.java
@@ -1,5 +1,25 @@
 package hpoweb;
 
+import hpoweb.data.HpData;
+import hpoweb.data.dataprovider.IDiseaseDataProvider;
+import hpoweb.data.dataprovider.IEntityDataProvider;
+import hpoweb.data.dataprovider.IGeneDataProvider;
+import hpoweb.data.dataprovider.IHpClassDataProvider;
+import hpoweb.data.dataprovider.impl.DiseaseDataProvider;
+import hpoweb.data.dataprovider.impl.FakeDiseaseDataProvider;
+import hpoweb.data.dataprovider.impl.FakeGeneDataProvider;
+import hpoweb.data.dataprovider.impl.FakeHpClassDataProvider;
+import hpoweb.data.dataprovider.impl.GeneDataProvider;
+import hpoweb.data.dataprovider.impl.HpClassDataProvider;
+import hpoweb.data.entities.SearchableEntity;
+import hpoweb.uicontent.SearchBarFactory;
+import hpoweb.uicontent.graph.GraphtestUI;
+import hpoweb.uicontent.tabs.disease.DiseaseTabFactory;
+import hpoweb.uicontent.tabs.gene.GeneTabFactory;
+import hpoweb.uicontent.tabs.hpoclass.HpoClassTabFactory;
+import hpoweb.util.CONSTANTS;
+import hpoweb.util.TableUtils;
+
 import java.util.Map;
 
 import javax.servlet.annotation.WebServlet;
@@ -38,25 +58,6 @@
 import com.vaadin.ui.themes.ValoTheme;
 
 import de.charite.phenowl.annotations.DiseaseId;
-import hpoweb.data.HpData;
-import hpoweb.data.dataprovider.IDiseaseDataProvider;
-import hpoweb.data.dataprovider.IEntityDataProvider;
-import hpoweb.data.dataprovider.IGeneDataProvider;
-import hpoweb.data.dataprovider.IHpClassDataProvider;
-import hpoweb.data.dataprovider.impl.DiseaseDataProvider;
-import hpoweb.data.dataprovider.impl.FakeDiseaseDataProvider;
-import hpoweb.data.dataprovider.impl.FakeGeneDataProvider;
-import hpoweb.data.dataprovider.impl.FakeHpClassDataProvider;
-import hpoweb.data.dataprovider.impl.GeneDataProvider;
-import hpoweb.data.dataprovider.impl.HpClassDataProvider;
-import hpoweb.data.entities.SearchableEntity;
-import hpoweb.uicontent.SearchBarFactory;
-import hpoweb.uicontent.graph.GraphtestUI;
-import hpoweb.uicontent.tabs.disease.DiseaseTabFactory;
-import hpoweb.uicontent.tabs.gene.GeneTabFactory;
-import hpoweb.uicontent.tabs.hpoclass.HpoClassTabFactory;
-import hpoweb.util.CONSTANTS;
-import hpoweb.util.TableUtils;
 
 @SuppressWarnings("serial")
 @Theme("hpoweb")
@@ -142,13 +143,11 @@ 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 +160,7 @@ else if (dataProvider instanceof IGeneDataProvider) {
  String ontologyVersion;
  if (doParseHpo) {
  ontologyVersion = hpData.getExtOwlOntology().getOntologyVersionIri().toString();
- }
- else
+ } else
 
  {
  ontologyVersion = "some ontology version here";
@@ -259,52 +257,44 @@ private IEntityDataProvider setupDataProvider(VaadinRequest request, Map<String,
 
  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());
+ 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());
  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)) {
 
  DiseaseId diseaseId = parseDiseaseId(request);
  if (diseaseId == null && doParseHpo) {
- new Notification("Invalid disease id input",
- "<br/><br/>Can't parse disease id from '" + request.getParameter(CONSTANTS.geneRequestId) + "'",
- Notification.Type.ERROR_MESSAGE, true).show(Page.getCurrent());
+ new Notification("Invalid disease id input", "<br/><br/>Can't parse disease id from '"
+ + request.getParameter(CONSTANTS.geneRequestId) + "'", Notification.Type.ERROR_MESSAGE, true).show(Page.getCurrent());
  return null;
  }
 
  if (doParseHpo) {
  dataProvider = new DiseaseDataProvider(diseaseId, hpData);
- }
- else {
+ } else {
  dataProvider = new FakeDiseaseDataProvider();
  }
- }
- else {
+ } 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());
+ + CONSTANTS.geneRequestId + ", or " + CONSTANTS.diseaseRequestId + ") ! ", Notification.Type.WARNING_MESSAGE, true).show(Page
+ .getCurrent());
  return null;
  }
  return dataProvider;

diff --git a/src/hpoweb/data/HpData.java b/src/hpoweb/data/HpData.java
@@ -44,7 +44,7 @@ public HpData() {
  DiseaseGeneMapper.setOrphanetPath(datapath);
  annotationUtils.setDataPath(datapath);
  annotationUtils.parseAssociation();
-
+ annotationUtils.getDiseaseGeneMapper().addCancerGeneAssociationsToDiseaseGenes();
  }
 
  public ExtendedOwlOntology getExtOwlOntology() {