Working REST API

model/src/main/java/lcsb/mapviewer/model/map/species/field/Structure.java

 package lcsb.mapviewer.model.map.species.field;
 
 import java.io.Serializable;
+import java.util.Map;
+import java.util.HashMap;
 
 import javax.persistence.Column;
 import javax.persistence.Entity;
@@ -12,6 +14,8 @@ import javax.persistence.JoinColumn;
 import javax.persistence.ManyToOne;
 import javax.persistence.Table;
 
+import org.apache.commons.collections.map.HashedMap;
+
 import lcsb.mapviewer.common.exception.NotImplementedException;
 
 /**
@@ -23,8 +27,8 @@ import lcsb.mapviewer.common.exception.NotImplementedException;
  * 	coverage: the percent coverage of the entire UniProt sequence
  * 	resolution: the resolution of the structure
  * 	start: the structure residue number which maps to the start of the mapped sequence
- * 	end: the structure residue number which maps to the end of the mapped sequence
  * 	unp_start: the sequence residue number which maps to the structure start
+ * 	end: the structure residue number which maps to the end of the mapped sequence
  * 	unp_end: the sequence residue number which maps to the structure end
  * 	experimental_method: type of experiment used to determine structure
  * 	tax_id: taxonomic ID of the protein's original organism 
@@ -339,6 +343,21 @@ public class Structure implements Serializable {
 				+ ", unpEnd=" + unpEnd + ", experimentalMethod=" + experimentalMethod + ", taxId=" + taxId + "]";
 	}
 	
-	
+	public Map<String, Object> toMap() {
+		Map<String, Object> result = new HashMap<>();
+		
+		result.put("pdbId", this.pdbId);
+		result.put("chainId", this.chainId);
+		result.put("coverage", this.coverage);
+		result.put("resolution", this.resolution);
+		result.put("structStart", this.structStart);
+		result.put("structEnd", this.structEnd);
+		result.put("unpStart", this.unpStart);
+		result.put("unpEnd", this.unpEnd);
+		result.put("experimentalMethod", this.experimentalMethod);
+		result.put("taxId", this.taxId);		
+		
+		return result;		
+	}	
 
 }

rest-api/src/main/java/lcsb/mapviewer/api/projects/models/bioEntities/elements/ElementsRestImpl.java

@@ -21,6 +21,8 @@ import lcsb.mapviewer.model.map.species.Species;
 import lcsb.mapviewer.model.map.species.field.ElementModification;
 import lcsb.mapviewer.model.map.species.field.ModificationResidue;
 import lcsb.mapviewer.model.map.species.field.RnaRegion;
+import lcsb.mapviewer.model.map.species.field.Structure;
+import lcsb.mapviewer.model.map.species.field.UniprotRecord;
 import lcsb.mapviewer.services.SecurityException;
 import lcsb.mapviewer.services.UserAccessException;
 import lcsb.mapviewer.services.view.OverviewImageViewFactory;
@@ -121,11 +123,7 @@ public class ElementsRestImpl extends BaseRestImpl {
 					value = element.getSubmodel().getSubmodel().getId();
 				}
 			} else if (column.equals("bounds")) {
-				value = createBounds(element.getX(), element.getY(), element.getWidth(), element.getHeight());
-			} else if (column.equals("others")) {
-				if (element instanceof Species) {
-					value = ((Species)element).getUniprots();
-				}
+				value = createBounds(element.getX(), element.getY(), element.getWidth(), element.getHeight());				
 			} 
 			else {
 				value = "Unknown column";
@@ -137,8 +135,9 @@ public class ElementsRestImpl extends BaseRestImpl {
 
 	protected Map<String, Object> getOthersForElement(Element element) {
 		Map<String, Object> result = new HashMap<>();
-		List<Map<String, Object>> modifications = new ArrayList<>();
+		List<Map<String, Object>> modifications = new ArrayList<>();		
 		String structuralState = null;
+		Map<String, Object> structures = new HashMap<>();
 		if (element instanceof Protein) {
 			Protein protein = ((Protein) element);
 			modifications = getModifications(protein.getModificationResidues());
@@ -151,9 +150,13 @@ public class ElementsRestImpl extends BaseRestImpl {
 			AntisenseRna antisenseRna = ((AntisenseRna) element);
 			modifications = getModifications(((AntisenseRna) element).getRegions());
 			structuralState = antisenseRna.getState();
+		}		
+		if (element instanceof Species) {
+			structures = getStructures(((Species)element).getUniprots());
 		}
 		result.put("modifications", modifications);
 		result.put("structuralState", structuralState);
+		result.put("structures", structures);
 
 		return result;
 	}
@@ -171,6 +174,18 @@ public class ElementsRestImpl extends BaseRestImpl {
 		}
 		return result;
 	}
+	
+	private Map<String, Object> getStructures(Set<UniprotRecord> uniprots) {
+		Map<String, Object> result = new HashMap<>();
+		for (UniprotRecord uniprotRec : uniprots) {
+			Set<Object> structs = new HashSet<>();			
+			for (Structure struct: uniprotRec.getStructures()) {
+				structs.add(struct.toMap());				
+			}			
+			result.put(uniprotRec.getUniprotId(), structs);
+		}
+		return result;
+	}
 
 	private Map<String, Object> createBounds(Double x, Double y, Double width, Double height) {
 		Map<String, Object> result = new HashMap<>();

rest-api/src/test/java/lcsb/mapviewer/api/projects/models/bioEntities/elements/ElementRestImplTest.java

@@ -156,20 +156,20 @@ public class ElementRestImplTest extends RestTestFunctions {
 		}
 	}
 
-	private ElementsRestImpl createMockElementRest(String string, Boolean annotate) throws Exception {
+	private ElementsRestImpl createMockElementRest(String string, Boolean annotate) throws Exception {		
 		Model model = super.getModelForFile(string, true);
 		if (annotate) {
-			try {
+			try {				
 				Protein protein = new GenericProtein("SNCA");
 				protein.setElementId("SNCA");
 				pdbAnnotator.annotateElement(protein);
-				model.addElement(protein);
+				model.addElement(protein);				
 			} catch (Exception e) {			
 			}
 		}
 		IModelService mockModelService = Mockito.mock(IModelService.class);
 		Mockito.when(mockModelService.getLastModelByProjectId(anyString(), any())).thenReturn(model);
-		_elementsRestImpl.setModelService(mockModelService);
+		_elementsRestImpl.setModelService(mockModelService);		
 		return _elementsRestImpl;
 	}
 }