update to be in sync

with new data
with new libs

src/hpoweb/HpowebUI.java

@@ -37,7 +37,7 @@
 import com.vaadin.ui.Window;
 import com.vaadin.ui.themes.ValoTheme;
 
-import hpo.DiseaseId;
+import hpo.ItemId;
 import hpoweb.data.HpData;
 import hpoweb.data.dataprovider.IDiseaseDataProvider;
 import hpoweb.data.dataprovider.IEntityDataProvider;
@@ -286,7 +286,7 @@ else if (parameterMap.containsKey(CONSTANTS.geneRequestId)) {
  }
  else if (parameterMap.containsKey(CONSTANTS.diseaseRequestId)) {
 
- DiseaseId diseaseId = parseDiseaseId(request);
+ ItemId 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) + "'",
@@ -433,12 +433,12 @@ private Integer parseGeneId(VaadinRequest request) {
  return geneIdInt;
  }
 
- private DiseaseId parseDiseaseId(VaadinRequest request) {
+ private ItemId parseDiseaseId(VaadinRequest request) {
  if (!doParseHpo)
  return null;
  String diseaseIdStr = request.getParameter(CONSTANTS.diseaseRequestId);
 
- DiseaseId diseaseId = new DiseaseId(diseaseIdStr);
+ ItemId diseaseId = new ItemId(diseaseIdStr);
  if (!hpData.getAnnotationUtils().getDiseaseId2entry().containsKey(diseaseId)) {
  return null;
  }

src/hpoweb/data/dataprovider/LazySearchbarService.java

@@ -10,9 +10,9 @@
 
 import de.charite.phenowl.annotations.AnnotationUtils;
 import de.charite.phenowl.hpowl.util.OboUtil;
-import hpo.DiseaseEntry;
 import hpo.DiseaseGeneMapper;
-import hpo.DiseaseId;
+import hpo.Item;
+import hpo.ItemId;
 import hpoweb.data.HpData;
 import hpoweb.data.entities.SearchableEntity;
 import hpoweb.data.entities.SearchableEntity.SearchableEntityType;
@@ -89,8 +89,8 @@ public LazySearchbarService(HpData hpdata) {
  * Diseases
  */
  AnnotationUtils annotationUtils = hpdata.getAnnotationUtils();
- for (DiseaseId id : annotationUtils.getDiseaseId2entry().keySet()) {
- DiseaseEntry diseaseEntry = annotationUtils.getDiseaseId2entry().get(id);
+ for (ItemId id : annotationUtils.getDiseaseId2entry().keySet()) {
+ Item diseaseEntry = annotationUtils.getDiseaseId2entry().get(id);
  String diseaseId = diseaseEntry.getDiseaseIdAsString();
  String searchAble = diseaseId + " " + diseaseEntry.getName();
 

src/hpoweb/data/dataprovider/impl/DiseaseDataProvider.java

@@ -14,7 +14,7 @@
 import de.charite.phenowl.annotations.HPOAnnotation;
 import de.charite.phenowl.annotations.OwlAnnotatedDiseaseEntry;
 import de.charite.phenowl.hpowl.util.OboUtil;
-import hpo.DiseaseId;
+import hpo.ItemId;
 import hpoweb.data.HpData;
 import hpoweb.data.dataprovider.IDiseaseDataProvider;
 import hpoweb.data.entities.DiseaseGene;
@@ -24,13 +24,13 @@ public class DiseaseDataProvider implements IDiseaseDataProvider {
 
  private HpData hpData;
  private AnnotationUtils annotationUtils;
- private DiseaseId diseaseId;
+ private ItemId diseaseId;
  private OwlAnnotatedDiseaseEntry diseaseEntry;
  private ArrayList<HPOAnnotation> annotations;
  private HashSet<Integer> diseaseGeneIds;
  private HashSet<DiseaseGene> diseaseGenes;
 
- public DiseaseDataProvider(DiseaseId diseaseId, HpData hpData) {
+ public DiseaseDataProvider(ItemId diseaseId, HpData hpData) {
  this.hpData = hpData;
  this.diseaseId = diseaseId;
  this.annotationUtils = hpData.getAnnotationUtils();

src/hpoweb/data/dataprovider/impl/FakeGeneDataProvider.java

@@ -9,7 +9,7 @@
 import com.google.gwt.thirdparty.guava.common.collect.Lists;
 
 import de.charite.phenowl.annotations.OwlAnnotatedDiseaseEntry;
-import hpo.DiseaseId;
+import hpo.ItemId;
 import hpoweb.data.dataprovider.IGeneDataProvider;
 import hpoweb.uicontent.table.HpoClassTableEntry;
 
@@ -54,7 +54,7 @@ public List<HpoClassTableEntry> getAssociatedHpoClasses() {
  @Override
  public Collection<OwlAnnotatedDiseaseEntry> getAssociatedDiseases() {
 
- DiseaseId id = new DiseaseId("OMIM", RandomStringUtils.randomNumeric(6));
+ ItemId id = new ItemId("OMIM", RandomStringUtils.randomNumeric(6));
  OwlAnnotatedDiseaseEntry entry = new OwlAnnotatedDiseaseEntry(id, null, null);
  entry.setName(RandomStringUtils.randomAlphabetic(8) + " " + RandomStringUtils.randomAlphabetic(4) + " syndrome");
  return Lists.newArrayList(entry);

src/hpoweb/data/dataprovider/impl/FakeHpClassDataProvider.java

@@ -10,7 +10,7 @@
 import com.google.common.collect.ImmutableSet;
 
 import de.charite.phenowl.annotations.OwlAnnotatedDiseaseEntry;
-import hpo.DiseaseId;
+import hpo.ItemId;
 import hpoweb.data.dataprovider.IHpClassDataProvider;
 import hpoweb.data.entities.DiseaseGene;
 import hpoweb.uicontent.graph.GraphtestUI;
@@ -140,7 +140,7 @@ else if (Math.random() < 0.6) {
  }
 
  private OwlAnnotatedDiseaseEntry getRandomDisease() {
- DiseaseId id = new DiseaseId("OMIM", RandomStringUtils.randomNumeric(6));
+ ItemId id = new ItemId("OMIM", RandomStringUtils.randomNumeric(6));
  OwlAnnotatedDiseaseEntry entry = new OwlAnnotatedDiseaseEntry(id, null, null);
  entry.setName(RandomStringUtils.randomAlphabetic(8) + " " + RandomStringUtils.randomAlphabetic(4) + " syndrome");
  return entry;

src/hpoweb/data/dataprovider/impl/GeneDataProvider.java

@@ -11,8 +11,8 @@
 import de.charite.phenowl.annotations.AnnotationUtils;
 import de.charite.phenowl.annotations.OwlAnnotatedDiseaseEntry;
 import de.charite.phenowl.hpowl.util.OboUtil;
-import hpo.DiseaseEntry;
-import hpo.DiseaseId;
+import hpo.Item;
+import hpo.ItemId;
 import hpoweb.data.HpData;
 import hpoweb.data.dataprovider.IGeneDataProvider;
 import hpoweb.uicontent.table.HpoClassTableEntry;
@@ -34,7 +34,7 @@ public GeneDataProvider(Integer geneId, HpData hpData) {
  hpClass2annotatedDiseases = HashMultimap.create();
  associatedDiseases = new ArrayList<OwlAnnotatedDiseaseEntry>();
  if (util.getDiseaseGeneMapper().entrezId2diseaseIds.containsKey(geneId)) {
- for (DiseaseId diseaseId : util.getDiseaseGeneMapper().entrezId2diseaseIds.get(geneId)) {
+ for (ItemId diseaseId : util.getDiseaseGeneMapper().entrezId2diseaseIds.get(geneId)) {
  if (!util.getDiseaseId2entry().containsKey(diseaseId))
  continue;
  OwlAnnotatedDiseaseEntry entry = util.getDiseaseId2entry().get(diseaseId);
@@ -73,7 +73,7 @@ public List<HpoClassTableEntry> getAssociatedHpoClasses() {
  String hpoId = OboUtil.IRI2ID(cls.getIRI());
  String hpoLabel = hpData.getExtOwlOntology().getLabel(cls.getIRI());
  String description = "This annotation is supported by:<br>";
- for (DiseaseEntry e : hpClass2annotatedDiseases.get(cls)) {
+ for (Item e : hpClass2annotatedDiseases.get(cls)) {
  description += " - " + e.getName() + "<br>";
  }
  HpoClassTableEntry entry = new HpoClassTableEntry(hpoId, hpoLabel, description);

src/hpoweb/data/dataprovider/impl/HpClassDataProvider.java

@@ -14,8 +14,8 @@
 import de.charite.phenowl.annotations.OwlAnnotatedDiseaseEntry;
 import de.charite.phenowl.hpowl.util.ExtendedOwlOntology;
 import de.charite.phenowl.hpowl.util.OboUtil;
-import hpo.DiseaseEntry;
-import hpo.DiseaseId;
+import hpo.Item;
+import hpo.ItemId;
 import hpoweb.data.HpData;
 import hpoweb.data.dataprovider.IHpClassDataProvider;
 import hpoweb.data.entities.DiseaseGene;
@@ -36,7 +36,7 @@ public class HpClassDataProvider implements IHpClassDataProvider {
  private Set<String> synonyms;
  private String textdef;
  private String logicaldef;
- private HashSet<DiseaseId> associatedDiseaseIds;
+ private HashSet<ItemId> associatedDiseaseIds;
  private AnnotationUtils utils;
  private HashSet<Integer> associatedGeneIds;
 
@@ -158,8 +158,8 @@ public List<DiseaseGeneTableEntry> getDiseaseGeneTableContent() {
  if (this.associatedDiseaseIds == null)
  return tableentries;
 
- for (DiseaseId dID : this.associatedDiseaseIds) {
- DiseaseEntry entry = utils.getDiseaseId2entry().get(dID);
+ for (ItemId dID : this.associatedDiseaseIds) {
+ Item entry = utils.getDiseaseId2entry().get(dID);
  String diseaseId = dID.toString();
  String diseaseName = entry.getName();
  ArrayList<DiseaseGene> associatedGenes = new ArrayList<DiseaseGene>();
@@ -187,10 +187,10 @@ public List<GeneDiseaseTableEntry> getGeneDiseaseTableContent() {
  String geneSymbol = utils.getDiseaseGeneMapper().entrez2symbol.get(geneId);
 
  ArrayList<OwlAnnotatedDiseaseEntry> associatedDiseases = new ArrayList<OwlAnnotatedDiseaseEntry>();
- HashSet<DiseaseId> diseaseIds = utils.getDiseaseGeneMapper().entrezId2diseaseIds.get(geneId);
+ HashSet<ItemId> diseaseIds = utils.getDiseaseGeneMapper().entrezId2diseaseIds.get(geneId);
 
  if (diseaseIds != null)
- for (DiseaseId diseaseId : diseaseIds) {
+ for (ItemId diseaseId : diseaseIds) {
  if (utils.getDiseaseId2entry().containsKey(diseaseId)) {
  OwlAnnotatedDiseaseEntry diseaseentry = utils.getDiseaseId2entry().get(diseaseId);
  associatedDiseases.add(diseaseentry);