From 86d82b99c0ed26296a34f0dd16058f8000ca6bc8 Mon Sep 17 00:00:00 2001
From: Piotr Gawron <piotr.gawron@uni.lu>
Date: Wed, 26 Jul 2017 12:08:14 +0200
Subject: [PATCH] serialization issue when chemical didn't have casId defined
---
.../java/lcsb/mapviewer/api/BaseRestImpl.java | 6 +-
.../projects/chemicals/ChemicalRestImpl.java | 12 ++--
.../chemicals/ChemicalRestImplTest.java | 67 +++++++++++++++++++
.../api/projects/drugs/DrugRestImplTest.java | 2 +-
4 files changed, 80 insertions(+), 7 deletions(-)
create mode 100644 rest-api/src/test/java/lcsb/mapviewer/api/projects/chemicals/ChemicalRestImplTest.java
diff --git a/rest-api/src/main/java/lcsb/mapviewer/api/BaseRestImpl.java b/rest-api/src/main/java/lcsb/mapviewer/api/BaseRestImpl.java
index 635f9985de..57882b3194 100644
--- a/rest-api/src/main/java/lcsb/mapviewer/api/BaseRestImpl.java
+++ b/rest-api/src/main/java/lcsb/mapviewer/api/BaseRestImpl.java
@@ -75,8 +75,8 @@ public abstract class BaseRestImpl {
};
protected Map<String, Object> createAnnotation(MiriamData annotation) {
- Map<String, Object> result = new HashMap<>();
if (annotation != null && annotation.getDataType() != null) {
+ Map<String, Object> result = new HashMap<>();
if (annotation.getDataType().getUris().size() > 0) {
try {
result.put("link", miriamConnector.getUrlString(annotation));
@@ -95,8 +95,10 @@ public abstract class BaseRestImpl {
result.put("type", annotation.getDataType().name());
result.put("resource", annotation.getResource());
result.put("id", annotation.getId());
+ return result;
+ } else {
+ throw new InvalidArgumentException("invalid miriam data: " + annotation);
}
- return result;
};
protected Map<String, Object> createAnnotation(AnnotationView annotation) {
diff --git a/rest-api/src/main/java/lcsb/mapviewer/api/projects/chemicals/ChemicalRestImpl.java b/rest-api/src/main/java/lcsb/mapviewer/api/projects/chemicals/ChemicalRestImpl.java
index 702cb56cb2..949e985122 100644
--- a/rest-api/src/main/java/lcsb/mapviewer/api/projects/chemicals/ChemicalRestImpl.java
+++ b/rest-api/src/main/java/lcsb/mapviewer/api/projects/chemicals/ChemicalRestImpl.java
@@ -120,7 +120,7 @@ public class ChemicalRestImpl extends BaseRestImpl {
this.modelService = modelService;
}
- private Map<String, Object> prepareChemical(Chemical chemical, Set<String> columnsSet, List<Model> models) {
+ protected Map<String, Object> prepareChemical(Chemical chemical, Set<String> columnsSet, List<Model> models) {
Map<String, Object> result = new HashMap<>();
String description = "Mesh term not available";
@@ -144,14 +144,18 @@ public class ChemicalRestImpl extends BaseRestImpl {
} else if (column.equals("references")) {
List<Map<String, Object>> references = new ArrayList<>();
references.add(createAnnotation(chemical.getChemicalId()));
- references.add(createAnnotation(chemical.getCasID()));
+ if (chemical.getCasID() != null) {
+ references.add(createAnnotation(chemical.getCasID()));
+ }
value = references;
} else if (column.equals("directevidencereferences")) {
value = createAnnotations(chemical.getDirectEvidencePublication());
} else if (column.equals("description")) {
value = description;
} else if (column.equals("directevidence")) {
- value = chemical.getDirectEvidence().getValue();
+ if (chemical.getDirectEvidence() != null) {
+ value = chemical.getDirectEvidence().getValue();
+ }
} else if (column.equals("synonyms")) {
value = synonyms;
} else if (column.equals("targets")) {
@@ -164,7 +168,7 @@ public class ChemicalRestImpl extends BaseRestImpl {
return result;
}
- private Set<String> createChemicalColumnSet(String columns) {
+ protected Set<String> createChemicalColumnSet(String columns) {
Set<String> columnsSet = new HashSet<>();
if (columns.equals("")) {
columnsSet.add("name");
diff --git a/rest-api/src/test/java/lcsb/mapviewer/api/projects/chemicals/ChemicalRestImplTest.java b/rest-api/src/test/java/lcsb/mapviewer/api/projects/chemicals/ChemicalRestImplTest.java
new file mode 100644
index 0000000000..86df7fbcaa
--- /dev/null
+++ b/rest-api/src/test/java/lcsb/mapviewer/api/projects/chemicals/ChemicalRestImplTest.java
@@ -0,0 +1,67 @@
+package lcsb.mapviewer.api.projects.chemicals;
+
+import static org.junit.Assert.assertNotNull;
+import static org.mockito.Matchers.any;
+import static org.mockito.Matchers.anyString;
+
+import java.util.ArrayList;
+import java.util.Map;
+
+import org.apache.log4j.Logger;
+import org.junit.After;
+import org.junit.AfterClass;
+import org.junit.Before;
+import org.junit.Test;
+import org.mockito.Mockito;
+import org.springframework.beans.factory.annotation.Autowired;
+
+import lcsb.mapviewer.annotation.data.Chemical;
+import lcsb.mapviewer.annotation.data.ChemicalDirectEvidence;
+import lcsb.mapviewer.annotation.data.ChemicalDirectEvidenceTest;
+import lcsb.mapviewer.api.RestTestFunctions;
+import lcsb.mapviewer.model.map.MiriamData;
+import lcsb.mapviewer.model.map.MiriamType;
+import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.services.interfaces.IModelService;
+
+public class ChemicalRestImplTest extends RestTestFunctions {
+ Logger logger = Logger.getLogger(ChemicalRestImplTest.class);
+
+ @Autowired
+
+ private ChemicalRestImpl _drugRestImpl;
+
+ @AfterClass
+ public static void tearDownAfterClass() throws Exception {
+ }
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testPrepareChemical() throws Exception {
+ try {
+ Chemical chemical = new Chemical();
+ chemical.setChemicalId(new MiriamData(MiriamType.MESH_2012, "D010300"));
+ Map<String, Object> result = _drugRestImpl.prepareChemical(chemical, _drugRestImpl.createChemicalColumnSet(""), new ArrayList<>());
+ assertNotNull(result);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ protected ChemicalRestImpl createMockChemicalRest(String string) throws Exception {
+ Model model = super.getModelForFile(string, true);
+ IModelService mockModelService = Mockito.mock(IModelService.class);
+ Mockito.when(mockModelService.getLastModelByProjectId(anyString(), any())).thenReturn(model);
+ _drugRestImpl.setModelService(mockModelService);
+ return _drugRestImpl;
+ }
+
+}
diff --git a/rest-api/src/test/java/lcsb/mapviewer/api/projects/drugs/DrugRestImplTest.java b/rest-api/src/test/java/lcsb/mapviewer/api/projects/drugs/DrugRestImplTest.java
index ecdad6a033..554b08329a 100644
--- a/rest-api/src/test/java/lcsb/mapviewer/api/projects/drugs/DrugRestImplTest.java
+++ b/rest-api/src/test/java/lcsb/mapviewer/api/projects/drugs/DrugRestImplTest.java
@@ -40,7 +40,7 @@ public class DrugRestImplTest extends RestTestFunctions {
@Test
@SuppressWarnings("unchecked")
- public void testGetModelAsImage() throws Exception {
+ public void testGetDrugsByQuery() throws Exception {
try {
DrugRestImpl drugRestImpl = createMockProjectRest("testFiles/model/sample.xml");
Map<String, Object> result = drugRestImpl.getDrugsByQuery(token.getId(), "sample", "", "nadh").get(0);
--
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