diff --git a/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/bioEntities/elements/ElementsRestImpl.java b/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/bioEntities/elements/ElementsRestImpl.java
index 087f49f4b5dc44ead6eebba48b8767b657f6d372..996005a94edd4b316c0a0302dc97f7665ed93d69 100644
--- a/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/bioEntities/elements/ElementsRestImpl.java
+++ b/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/bioEntities/elements/ElementsRestImpl.java
@@ -13,12 +13,16 @@ import org.springframework.transaction.annotation.Transactional;
import lcsb.mapviewer.api.BaseRestImpl;
import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.species.AntisenseRna;
import lcsb.mapviewer.model.map.species.Element;
+import lcsb.mapviewer.model.map.species.Protein;
+import lcsb.mapviewer.model.map.species.Rna;
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.services.SecurityException;
import lcsb.mapviewer.services.UserAccessException;
-import lcsb.mapviewer.services.interfaces.IModelService;
-import lcsb.mapviewer.services.view.AnnotationViewFactory;
import lcsb.mapviewer.services.view.OverviewImageViewFactory;
@Transactional(value = "txManager")
@@ -30,9 +34,6 @@ public class ElementsRestImpl extends BaseRestImpl {
@SuppressWarnings("unused")
private Logger logger = Logger.getLogger(ElementsRestImpl.class);
- @Autowired
- private IModelService modelService;
-
@Autowired
private OverviewImageViewFactory factory;
@@ -109,6 +110,8 @@ public class ElementsRestImpl extends BaseRestImpl {
value = element.getFormula();
} else if (column.equals("notes")) {
value = element.getNotes();
+ } else if (column.equals("others")) {
+ value = getOthersForElement(element);
} else if (column.equals("formersymbols")) {
value = element.getFormerSymbols();
} else if (column.equals("hierarchyvisibilitylevel")) {
@@ -127,6 +130,41 @@ public class ElementsRestImpl extends BaseRestImpl {
return result;
}
+ protected Map<String, Object> getOthersForElement(Element element) {
+ Map<String, Object> result = new HashMap<>();
+ List<Map<String, Object>> modifications = new ArrayList<>();
+ String structuralState = null;
+ if (element instanceof Protein) {
+ Protein protein = ((Protein) element);
+ modifications = getModifications(protein.getModificationResidues());
+ structuralState = protein.getStructuralState();
+ } else if (element instanceof Rna) {
+ Rna rna = ((Rna) element);
+ modifications = getModifications(((Rna) element).getRegions());
+ structuralState = rna.getState();
+ } else if (element instanceof AntisenseRna) {
+ AntisenseRna antisenseRna = ((AntisenseRna) element);
+ modifications = getModifications(((AntisenseRna) element).getRegions());
+ structuralState = antisenseRna.getState();
+ }
+ result.put("modifications", modifications);
+ result.put("structuralState", structuralState);
+
+ return result;
+ }
+
+ private List<Map<String, Object>> getModifications(List<? extends ElementModification> elements) {
+ List<Map<String, Object>> result = new ArrayList<>();
+ for (ElementModification region : elements) {
+ Map<String, Object> row = new HashMap<>();
+ row.put("name", region.getName());
+ row.put("state", region.getState().name());
+ result.add(row);
+ }
+ return result;
+ }
+
+
private Map<String, Object> createBounds(Double x, Double y, Double width, Double height) {
Map<String, Object> result = new HashMap<>();
result.put("x", x);
@@ -159,6 +197,7 @@ public class ElementsRestImpl extends BaseRestImpl {
columnsSet.add("bounds");
columnsSet.add("hierarchyVisibilityLevel");
columnsSet.add("linkedSubmodel");
+ columnsSet.add("others");
} else {
for (String str : columns.split(",")) {
columnsSet.add(str);
@@ -167,23 +206,6 @@ public class ElementsRestImpl extends BaseRestImpl {
return columnsSet;
}
- /**
- * @return the modelService
- * @see #modelService
- */
- public IModelService getModelService() {
- return modelService;
- }
-
- /**
- * @param modelService
- * the modelService to set
- * @see #modelService
- */
- public void setModelService(IModelService modelService) {
- this.modelService = modelService;
- }
-
/**
* @return the factory
* @see #factory
diff --git a/rest-api/src/test/java/lcsb/mapviewer/api/projects/models/bioEntities/elements/ElementRestImplTest.java b/rest-api/src/test/java/lcsb/mapviewer/api/projects/models/bioEntities/elements/ElementRestImplTest.java
index 8cc6d689ba44e9c600f646ff1290167135c709d9..91127938e5a200c328337136d6265bbb86f3c96b 100644
--- a/rest-api/src/test/java/lcsb/mapviewer/api/projects/models/bioEntities/elements/ElementRestImplTest.java
+++ b/rest-api/src/test/java/lcsb/mapviewer/api/projects/models/bioEntities/elements/ElementRestImplTest.java
@@ -21,7 +21,13 @@ import com.fasterxml.jackson.databind.ObjectMapper;
import lcsb.mapviewer.api.RestTestFunctions;
import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.species.AntisenseRna;
import lcsb.mapviewer.model.map.species.GenericProtein;
+import lcsb.mapviewer.model.map.species.Rna;
+import lcsb.mapviewer.model.map.species.field.AntisenseRnaRegion;
+import lcsb.mapviewer.model.map.species.field.ModificationResidue;
+import lcsb.mapviewer.model.map.species.field.ModificationState;
+import lcsb.mapviewer.model.map.species.field.RnaRegion;
import lcsb.mapviewer.services.interfaces.IModelService;
public class ElementRestImplTest extends RestTestFunctions {
@@ -47,7 +53,7 @@ public class ElementRestImplTest extends RestTestFunctions {
@Test
public void testGetElementsProcessAllColumns() throws Exception {
try {
- ElementsRestImpl projectRest = createMockProjectRest("testFiles/model/sample.xml");
+ ElementsRestImpl projectRest = createMockElementRest("testFiles/model/sample.xml");
List<Map<String, Object>> result = projectRest.getElements("sample", "", "", "*", token.getId(), "");
for (Map<String, Object> element : result) {
for (String paramName : element.keySet()) {
@@ -72,8 +78,8 @@ public class ElementRestImplTest extends RestTestFunctions {
public void testGetElementsByType() throws Exception {
try {
String proteinType = new GenericProtein("1").getStringType();
- ElementsRestImpl projectRest = createMockProjectRest("testFiles/model/sample.xml");
- List<Map<String, Object>> result = projectRest.getElements("sample", "", "", "*", token.getId(), proteinType);
+ ElementsRestImpl elementRest = createMockElementRest("testFiles/model/sample.xml");
+ List<Map<String, Object>> result = elementRest.getElements("sample", "", "", "*", token.getId(), proteinType);
assertEquals(12, result.size());
} catch (Exception e) {
@@ -82,7 +88,70 @@ public class ElementRestImplTest extends RestTestFunctions {
}
}
- private ElementsRestImpl createMockProjectRest(String string) throws Exception {
+ @Test
+ public void testGetModificationsForProtein() throws Exception {
+ try {
+ String state = "asd";
+ GenericProtein protein = new GenericProtein("s1");
+ ModificationResidue mr = new ModificationResidue();
+ mr.setState(ModificationState.ACETYLATED);
+ mr.setName("S250");
+ protein.addModificationResidue(mr);
+ protein.setStructuralState(state);
+ Map<String, Object> result = _elementsRestImpl.getOthersForElement(protein);
+ assertNotNull(result.get("modifications"));
+ assertEquals(state, result.get("structuralState"));
+ List<Map<String, Object>> modifications = (List<Map<String, Object>>) result.get("modifications");
+ assertEquals(1, modifications.size());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetModificationsForRna() throws Exception {
+ try {
+ String state = "asd";
+ Rna rna = new Rna("s1");
+ RnaRegion mr = new RnaRegion();
+ mr.setState(ModificationState.ACETYLATED);
+ mr.setName("S250");
+ rna.addRegion(mr);
+ rna.setState(state);
+ Map<String, Object> result = _elementsRestImpl.getOthersForElement(rna);
+ assertNotNull(result.get("modifications"));
+ assertEquals(state, result.get("structuralState"));
+ List<Map<String, Object>> modifications = (List<Map<String, Object>>) result.get("modifications");
+ assertEquals(1, modifications.size());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetModificationsForAntisenseRna() throws Exception {
+ try {
+ String state = "asd";
+ AntisenseRna antisenseRna = new AntisenseRna("s1");
+ AntisenseRnaRegion mr = new AntisenseRnaRegion();
+ mr.setState(ModificationState.ACETYLATED);
+ mr.setName("S250");
+ antisenseRna.addRegion(mr);
+ antisenseRna.setState(state);
+ Map<String, Object> result = _elementsRestImpl.getOthersForElement(antisenseRna);
+ assertNotNull(result.get("modifications"));
+ assertEquals(state, result.get("structuralState"));
+ List<Map<String, Object>> modifications = (List<Map<String, Object>>) result.get("modifications");
+ assertEquals(1, modifications.size());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ private ElementsRestImpl createMockElementRest(String string) throws Exception {
Model model = super.getModelForFile(string, true);
IModelService mockModelService = Mockito.mock(IModelService.class);
Mockito.when(mockModelService.getLastModelByProjectId(anyString(), any())).thenReturn(model);