From 9a5d7e7b012aa7e39aa91abbdc88a24a8e8ea28f Mon Sep 17 00:00:00 2001
From: Piotr Gawron <piotr.gawron@uni.lu>
Date: Tue, 6 Jun 2017 15:07:08 +0200
Subject: [PATCH] new api call format for removing overlay
---
.../17296/DELETE_token=MOCK_TOKEN_ID&} | 0
pom.xml | 3 +
rest-api/.classpath | 66 +++++++++++--------
.../org.eclipse.core.resources.prefs | 2 +
.../org.eclipse.wst.common.component | 1 -
rest-api/pom.xml | 12 ++++
.../lcsb/mapviewer/api/BaseController.java | 3 +
.../java/lcsb/mapviewer/api/BaseRestImpl.java | 1 -
.../api/ObjectNotFoundException.java | 13 ++++
.../projects/overlays/OverlayController.java | 66 +++++++++++--------
.../projects/overlays/OverlayRestImpl.java | 7 +-
.../api/projects/AllProjectTests.java | 2 +
.../projects/overlays/AllOverlaysTests.java | 11 ++++
.../overlays/OverlayControllerTest.java | 43 ++++++++++++
14 files changed, 168 insertions(+), 62 deletions(-)
rename frontend-js/testFiles/apiCalls/{overlay/removeOverlay/POST_overlayId=17296&projectId=sample&token=MOCK_TOKEN_ID& => projects/sample/overlays/17296/DELETE_token=MOCK_TOKEN_ID&} (100%)
create mode 100644 rest-api/src/main/java/lcsb/mapviewer/api/ObjectNotFoundException.java
create mode 100644 rest-api/src/test/java/lcsb/mapviewer/api/projects/overlays/AllOverlaysTests.java
create mode 100644 rest-api/src/test/java/lcsb/mapviewer/api/projects/overlays/OverlayControllerTest.java
diff --git a/frontend-js/testFiles/apiCalls/overlay/removeOverlay/POST_overlayId=17296&projectId=sample&token=MOCK_TOKEN_ID& b/frontend-js/testFiles/apiCalls/projects/sample/overlays/17296/DELETE_token=MOCK_TOKEN_ID&
similarity index 100%
rename from frontend-js/testFiles/apiCalls/overlay/removeOverlay/POST_overlayId=17296&projectId=sample&token=MOCK_TOKEN_ID&
rename to frontend-js/testFiles/apiCalls/projects/sample/overlays/17296/DELETE_token=MOCK_TOKEN_ID&
diff --git a/pom.xml b/pom.xml
index 7e0e056d56..c4ae7d49e1 100644
--- a/pom.xml
+++ b/pom.xml
@@ -35,6 +35,9 @@
<jersey.version>1.18.1</jersey.version>
<rs-jax.version>1.1.1</rs-jax.version>
+ <jackson.version>2.8.8</jackson.version>
+
+
<log4j.version>1.2.17</log4j.version>
<apache.commons-lang3.version>3.1</apache.commons-lang3.version>
diff --git a/rest-api/.classpath b/rest-api/.classpath
index f2b9c43c7c..3783d3d93c 100644
--- a/rest-api/.classpath
+++ b/rest-api/.classpath
@@ -1,29 +1,37 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<classpath>
- <classpathentry kind="src" output="target/classes" path="src/main/java">
- <attributes>
- <attribute name="optional" value="true"/>
- <attribute name="maven.pomderived" value="true"/>
- </attributes>
- </classpathentry>
- <classpathentry kind="src" output="target/test-classes" path="src/test/java">
- <attributes>
- <attribute name="optional" value="true"/>
- <attribute name="maven.pomderived" value="true"/>
- </attributes>
- </classpathentry>
- <classpathentry kind="src" path="src/main/resources"/>
- <classpathentry kind="src" path="src/test/resources"/>
- <classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-1.8">
- <attributes>
- <attribute name="maven.pomderived" value="true"/>
- </attributes>
- </classpathentry>
- <classpathentry kind="con" path="org.eclipse.m2e.MAVEN2_CLASSPATH_CONTAINER">
- <attributes>
- <attribute name="maven.pomderived" value="true"/>
- <attribute name="org.eclipse.jst.component.nondependency" value=""/>
- </attributes>
- </classpathentry>
- <classpathentry kind="output" path="target/classes"/>
-</classpath>
+<?xml version="1.0" encoding="UTF-8"?>
+<classpath>
+ <classpathentry kind="src" output="target/classes" path="src/main/java">
+ <attributes>
+ <attribute name="optional" value="true"/>
+ <attribute name="maven.pomderived" value="true"/>
+ </attributes>
+ </classpathentry>
+ <classpathentry kind="src" output="target/test-classes" path="src/test/java">
+ <attributes>
+ <attribute name="optional" value="true"/>
+ <attribute name="maven.pomderived" value="true"/>
+ </attributes>
+ </classpathentry>
+ <classpathentry excluding="**" kind="src" output="target/classes" path="src/main/resources">
+ <attributes>
+ <attribute name="maven.pomderived" value="true"/>
+ </attributes>
+ </classpathentry>
+ <classpathentry excluding="**" kind="src" output="target/test-classes" path="src/test/resources">
+ <attributes>
+ <attribute name="maven.pomderived" value="true"/>
+ </attributes>
+ </classpathentry>
+ <classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-1.8">
+ <attributes>
+ <attribute name="maven.pomderived" value="true"/>
+ </attributes>
+ </classpathentry>
+ <classpathentry kind="con" path="org.eclipse.m2e.MAVEN2_CLASSPATH_CONTAINER">
+ <attributes>
+ <attribute name="maven.pomderived" value="true"/>
+ <attribute name="org.eclipse.jst.component.nondependency" value=""/>
+ </attributes>
+ </classpathentry>
+ <classpathentry kind="output" path="target/classes"/>
+</classpath>
diff --git a/rest-api/.settings/org.eclipse.core.resources.prefs b/rest-api/.settings/org.eclipse.core.resources.prefs
index 4c28b1a898..04cfa2c1a8 100644
--- a/rest-api/.settings/org.eclipse.core.resources.prefs
+++ b/rest-api/.settings/org.eclipse.core.resources.prefs
@@ -1,4 +1,6 @@
eclipse.preferences.version=1
encoding//src/main/java=UTF-8
+encoding//src/main/resources=UTF-8
encoding//src/test/java=UTF-8
+encoding//src/test/resources=UTF-8
encoding/<project>=UTF-8
diff --git a/rest-api/.settings/org.eclipse.wst.common.component b/rest-api/.settings/org.eclipse.wst.common.component
index e049d3a484..30ef6cd5dc 100644
--- a/rest-api/.settings/org.eclipse.wst.common.component
+++ b/rest-api/.settings/org.eclipse.wst.common.component
@@ -2,6 +2,5 @@
<wb-module deploy-name="MapViewer-rest-api">
<wb-resource deploy-path="/" source-path="/src/main/java"/>
<wb-resource deploy-path="/" source-path="/src/main/resources"/>
- <wb-resource deploy-path="/" source-path="/src/test/resources"/>
</wb-module>
</project-modules>
diff --git a/rest-api/pom.xml b/rest-api/pom.xml
index cb185247b6..6898343897 100644
--- a/rest-api/pom.xml
+++ b/rest-api/pom.xml
@@ -48,6 +48,18 @@
<artifactId>spring-faces</artifactId>
<version>${springframework.webflow.version}</version>
</dependency>
+
+ <dependency>
+ <groupId>com.fasterxml.jackson.core</groupId>
+ <artifactId>jackson-core</artifactId>
+ <version>${jackson.version}</version>
+ </dependency>
+
+ <dependency>
+ <groupId>com.fasterxml.jackson.core</groupId>
+ <artifactId>jackson-databind</artifactId>
+ <version>${jackson.version}</version>
+ </dependency>
<dependency>
<groupId>org.mockito</groupId>
diff --git a/rest-api/src/main/java/lcsb/mapviewer/api/BaseController.java b/rest-api/src/main/java/lcsb/mapviewer/api/BaseController.java
index d7f6e3c8fe..6d7382eb32 100644
--- a/rest-api/src/main/java/lcsb/mapviewer/api/BaseController.java
+++ b/rest-api/src/main/java/lcsb/mapviewer/api/BaseController.java
@@ -18,6 +18,9 @@ public abstract class BaseController {
logger.error(e, e);
if (e instanceof SecurityException) {
return new ResponseEntity<Object>("{\"error\" : \"Access denied.\",\"reason\":\"" + e.getMessage() + "\"}", new HttpHeaders(), HttpStatus.FORBIDDEN);
+ } else if (e instanceof ObjectNotFoundException) {
+ return new ResponseEntity<Object>(
+ "{\"error\" : \"Object not found.\",\"reason\":\"" + e.getMessage() + "\"}", new HttpHeaders(), HttpStatus.NOT_FOUND);
} else if (e instanceof QueryException) {
return new ResponseEntity<Object>(
"{\"error\" : \"Query server error.\",\"reason\":\"" + e.getMessage() + "\"}", new HttpHeaders(), HttpStatus.BAD_REQUEST);
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 8cfea323f1..272e3998a2 100644
--- a/rest-api/src/main/java/lcsb/mapviewer/api/BaseRestImpl.java
+++ b/rest-api/src/main/java/lcsb/mapviewer/api/BaseRestImpl.java
@@ -26,7 +26,6 @@ public abstract class BaseRestImpl {
protected Map<String, Object> okStatus() {
Map<String, Object> result = new HashMap<>();
- result.put("status", "OK");
return result;
}
diff --git a/rest-api/src/main/java/lcsb/mapviewer/api/ObjectNotFoundException.java b/rest-api/src/main/java/lcsb/mapviewer/api/ObjectNotFoundException.java
new file mode 100644
index 0000000000..907d839df8
--- /dev/null
+++ b/rest-api/src/main/java/lcsb/mapviewer/api/ObjectNotFoundException.java
@@ -0,0 +1,13 @@
+package lcsb.mapviewer.api;
+
+public class ObjectNotFoundException extends QueryException {
+
+ public ObjectNotFoundException(String message) {
+ super(message);
+ }
+
+ public ObjectNotFoundException(String message, Exception reason) {
+ super(message, reason);
+ }
+
+}
diff --git a/rest-api/src/main/java/lcsb/mapviewer/api/projects/overlays/OverlayController.java b/rest-api/src/main/java/lcsb/mapviewer/api/projects/overlays/OverlayController.java
index fec3dc8f94..0b74eab909 100644
--- a/rest-api/src/main/java/lcsb/mapviewer/api/projects/overlays/OverlayController.java
+++ b/rest-api/src/main/java/lcsb/mapviewer/api/projects/overlays/OverlayController.java
@@ -4,17 +4,20 @@ import java.io.IOException;
import java.util.List;
import java.util.Map;
-import javax.ws.rs.PathParam;
-
+import org.apache.log4j.Logger;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.http.MediaType;
import org.springframework.http.ResponseEntity;
import org.springframework.web.bind.annotation.PathVariable;
+import org.springframework.web.bind.annotation.RequestBody;
import org.springframework.web.bind.annotation.RequestMapping;
import org.springframework.web.bind.annotation.RequestMethod;
import org.springframework.web.bind.annotation.RequestParam;
import org.springframework.web.bind.annotation.RestController;
+import com.fasterxml.jackson.databind.ObjectMapper;
+import com.fasterxml.jackson.databind.node.ObjectNode;
+
import lcsb.mapviewer.api.BaseController;
import lcsb.mapviewer.api.QueryException;
import lcsb.mapviewer.model.cache.FileEntry;
@@ -24,15 +27,19 @@ import lcsb.mapviewer.services.view.LayoutView;
@RestController
public class OverlayController extends BaseController {
+ private Logger logger = Logger.getLogger(OverlayController.class);
+
@Autowired
- private OverlayRestImpl overlayController;
+ private OverlayRestImpl overlayRestImp;
+
+ private ObjectMapper mapper = new ObjectMapper();
@RequestMapping(value = "/projects/{projectId}/overlays/", method = { RequestMethod.GET }, produces = { MediaType.APPLICATION_JSON_VALUE })
public List<LayoutView> getOverlayList(//
@RequestParam(value = "token") String token, //
@PathVariable(value = "projectId") String projectId //
) throws SecurityException, QueryException {
- return overlayController.getOverlayList(token, projectId);
+ return overlayRestImp.getOverlayList(token, projectId);
}
@RequestMapping(value = "/projects/{projectId}/overlays/{overlayId}/", method = { RequestMethod.GET }, produces = { MediaType.APPLICATION_JSON_VALUE })
@@ -41,7 +48,7 @@ public class OverlayController extends BaseController {
@PathVariable(value = "projectId") String projectId, //
@PathVariable(value = "overlayId") String overlayId//
) throws SecurityException, QueryException {
- return overlayController.getOverlayById(token, projectId, overlayId);
+ return overlayRestImp.getOverlayById(token, projectId, overlayId);
}
@RequestMapping(value = "/projects/{projectId}/overlays/{overlayId}/models/{modelId}/bioEntities/", method = { RequestMethod.GET },
@@ -51,7 +58,7 @@ public class OverlayController extends BaseController {
@PathVariable(value = "projectId") String projectId, //
@PathVariable(value = "overlayId") String overlayId, @RequestParam(value = "columns", defaultValue = "") String columns)
throws SecurityException, QueryException {
- return overlayController.getOverlayElements(token, projectId, Integer.valueOf(overlayId), columns);
+ return overlayRestImp.getOverlayElements(token, projectId, Integer.valueOf(overlayId), columns);
}
@RequestMapping(value = "/projects/{projectId}/overlays/{overlayId}/models/{modelId}/bioEntities/reactions/{reactionId}/", method = { RequestMethod.GET },
@@ -64,7 +71,7 @@ public class OverlayController extends BaseController {
@PathVariable(value = "reactionId") String reactionId, //
@RequestParam(value = "columns", defaultValue = "") String columns //
) throws SecurityException, QueryException {
- return overlayController
+ return overlayRestImp
.getOverlayElement(token, projectId, Integer.valueOf(modelId), Integer.valueOf(overlayId), Integer.valueOf(reactionId), "REACTION", columns);
}
@@ -78,7 +85,7 @@ public class OverlayController extends BaseController {
@PathVariable(value = "elementId") String reactionId, //
@RequestParam(value = "columns", defaultValue = "") String columns //
) throws SecurityException, QueryException {
- return overlayController
+ return overlayRestImp
.getOverlayElement(token, projectId, Integer.valueOf(modelId), Integer.valueOf(overlayId), Integer.valueOf(reactionId), "ALIAS", columns);
}
@@ -92,12 +99,22 @@ public class OverlayController extends BaseController {
@RequestParam(value = "filename") String filename, //
@RequestParam(value = "type", defaultValue = "") String type //
) throws SecurityException, QueryException, IOException {
- return overlayController.addOverlay(token, projectId, name, description, content, filename, type);
+ return overlayRestImp.addOverlay(token, projectId, name, description, content, filename, type);
+ }
+
+ @RequestMapping(value = "/projects/{projectId}/overlays/{overlayId}", method = { RequestMethod.DELETE }, produces = { MediaType.APPLICATION_JSON_VALUE })
+ public Map<String, Object> removeOverlay( //
+ @RequestBody String body, //
+ @PathVariable(value = "projectId") String projectId, //
+ @PathVariable(value = "overlayId") String overlayId //
+ ) throws SecurityException, QueryException, IOException {
+ ObjectNode node = mapper.readValue(body, ObjectNode.class);
+ return overlayRestImp.removeOverlay(node.get("token").asText(), projectId, overlayId);
}
@RequestMapping(value = "/overlay/getOverlayTypes", method = { RequestMethod.GET }, produces = { MediaType.APPLICATION_JSON_VALUE })
public List<Map<String, Object>> getOverlayTypes(@RequestParam(value = "token") String token) throws SecurityException, QueryException {
- return overlayController.getOverlayTypes(token);
+ return overlayRestImp.getOverlayTypes(token);
}
@RequestMapping(value = "/overlay/updateOverlay", method = { RequestMethod.GET, RequestMethod.PUT, RequestMethod.POST },
@@ -105,21 +122,14 @@ public class OverlayController extends BaseController {
public Map<String, Object> updateOverlay(@RequestParam(value = "token") String token, @RequestParam(value = "projectId") String projectId,
@RequestParam(value = "overlayId") String overlayId, @RequestParam(value = "name") String name, @RequestParam(value = "description") String description)
throws SecurityException, QueryException {
- return overlayController.updateOverlay(token, projectId, overlayId, name, description);
- }
-
- @RequestMapping(value = "/overlay/removeOverlay", method = { RequestMethod.GET, RequestMethod.DELETE, RequestMethod.POST },
- produces = { MediaType.APPLICATION_JSON_VALUE })
- public Map<String, Object> removeOverlay(@RequestParam(value = "token") String token, @RequestParam(value = "projectId") String projectId,
- @RequestParam(value = "overlayId") String overlayId) throws SecurityException, QueryException, IOException {
- return overlayController.removeOverlay(token, projectId, overlayId);
+ return overlayRestImp.updateOverlay(token, projectId, overlayId, name, description);
}
@RequestMapping(value = "/overlay/getOverlaySource", method = { RequestMethod.GET }, produces = { MediaType.APPLICATION_JSON_VALUE })
public ResponseEntity<byte[]> getOverlaySource(@RequestParam(value = "token") String token, @RequestParam(value = "projectId") String projectId,
@RequestParam(value = "overlayId") String overlayId) throws SecurityException, QueryException {
- FileEntry file = overlayController.getOverlaySource(token, projectId, overlayId);
+ FileEntry file = overlayRestImp.getOverlaySource(token, projectId, overlayId);
MediaType type = MediaType.TEXT_PLAIN;
if (file.getOriginalFileName().endsWith("xml")) {
type = MediaType.APPLICATION_XML;
@@ -130,20 +140,20 @@ public class OverlayController extends BaseController {
}
/**
- * @return the overlayController
- * @see #overlayController
+ * @return the overlayRestImp
+ * @see #overlayRestImp
*/
- public OverlayRestImpl getOverlayController() {
- return overlayController;
+ public OverlayRestImpl getOverlayRestImp() {
+ return overlayRestImp;
}
/**
- * @param overlayController
- * the overlayController to set
- * @see #overlayController
+ * @param overlayRestImp
+ * the overlayRestImp to set
+ * @see #overlayRestImp
*/
- public void setOverlayController(OverlayRestImpl overlayController) {
- this.overlayController = overlayController;
+ public void setOverlayRestImp(OverlayRestImpl overlayRestImp) {
+ this.overlayRestImp = overlayRestImp;
}
}
\ No newline at end of file
diff --git a/rest-api/src/main/java/lcsb/mapviewer/api/projects/overlays/OverlayRestImpl.java b/rest-api/src/main/java/lcsb/mapviewer/api/projects/overlays/OverlayRestImpl.java
index aef38648ff..72c881ef10 100644
--- a/rest-api/src/main/java/lcsb/mapviewer/api/projects/overlays/OverlayRestImpl.java
+++ b/rest-api/src/main/java/lcsb/mapviewer/api/projects/overlays/OverlayRestImpl.java
@@ -14,6 +14,7 @@ import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.transaction.annotation.Transactional;
import lcsb.mapviewer.api.BaseRestImpl;
+import lcsb.mapviewer.api.ObjectNotFoundException;
import lcsb.mapviewer.api.QueryException;
import lcsb.mapviewer.common.Configuration;
import lcsb.mapviewer.model.cache.FileEntry;
@@ -194,17 +195,17 @@ public class OverlayRestImpl extends BaseRestImpl {
AuthenticationToken authenticationToken = userService.getToken(token);
Model model = modelService.getLastModelByProjectId(projectId, authenticationToken);
if (model == null) {
- throw new QueryException("Project with given id doesn't exist");
+ throw new ObjectNotFoundException("Project with given id doesn't exist");
}
try {
Integer id = Integer.valueOf(overlayId);
LayoutView layout = layoutService.getLayoutById(model, id, authenticationToken);
if (layout == null) {
- throw new QueryException("Invalid overlay id");
+ throw new ObjectNotFoundException("Overlay doesn't exist");
}
layoutService.removeLayout(layout, null);
} catch (NumberFormatException e) {
- throw new QueryException("Invalid overlay id");
+ throw new QueryException("Invalid overlay id: " + overlayId);
}
return okStatus();
}
diff --git a/rest-api/src/test/java/lcsb/mapviewer/api/projects/AllProjectTests.java b/rest-api/src/test/java/lcsb/mapviewer/api/projects/AllProjectTests.java
index 61b2ebdb62..708c0ebd98 100644
--- a/rest-api/src/test/java/lcsb/mapviewer/api/projects/AllProjectTests.java
+++ b/rest-api/src/test/java/lcsb/mapviewer/api/projects/AllProjectTests.java
@@ -5,9 +5,11 @@ import org.junit.runners.Suite;
import org.junit.runners.Suite.SuiteClasses;
import lcsb.mapviewer.api.projects.models.AllModelsTests;
+import lcsb.mapviewer.api.projects.overlays.AllOverlaysTests;
@RunWith(Suite.class)
@SuiteClasses({ AllModelsTests.class, //
+ AllOverlaysTests.class, //
ModelMetaDataTest.class, //
ProjectRestImplTest.class })
public class AllProjectTests {
diff --git a/rest-api/src/test/java/lcsb/mapviewer/api/projects/overlays/AllOverlaysTests.java b/rest-api/src/test/java/lcsb/mapviewer/api/projects/overlays/AllOverlaysTests.java
new file mode 100644
index 0000000000..7ab3216f8e
--- /dev/null
+++ b/rest-api/src/test/java/lcsb/mapviewer/api/projects/overlays/AllOverlaysTests.java
@@ -0,0 +1,11 @@
+package lcsb.mapviewer.api.projects.overlays;
+
+import org.junit.runner.RunWith;
+import org.junit.runners.Suite;
+import org.junit.runners.Suite.SuiteClasses;
+
+@RunWith(Suite.class)
+@SuiteClasses({ OverlayControllerTest.class })
+public class AllOverlaysTests {
+
+}
diff --git a/rest-api/src/test/java/lcsb/mapviewer/api/projects/overlays/OverlayControllerTest.java b/rest-api/src/test/java/lcsb/mapviewer/api/projects/overlays/OverlayControllerTest.java
new file mode 100644
index 0000000000..53d680c49f
--- /dev/null
+++ b/rest-api/src/test/java/lcsb/mapviewer/api/projects/overlays/OverlayControllerTest.java
@@ -0,0 +1,43 @@
+package lcsb.mapviewer.api.projects.overlays;
+
+import static org.junit.Assert.fail;
+
+import org.junit.After;
+import org.junit.AfterClass;
+import org.junit.Before;
+import org.junit.Test;
+import org.springframework.beans.factory.annotation.Autowired;
+
+import lcsb.mapviewer.api.RestTestFunctions;
+import lcsb.mapviewer.services.InvalidTokenException;
+
+public class OverlayControllerTest extends RestTestFunctions {
+ OverlayController controller = new OverlayController();
+
+ @Autowired
+ OverlayRestImpl overlayRestImp;
+
+ @AfterClass
+ public static void tearDownAfterClass() throws Exception {
+ }
+
+ @Before
+ public void setUp() throws Exception {
+ controller.setOverlayRestImp(overlayRestImp);
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testTokenParsing() throws Exception {
+ String body = "{\"token\":\"" + token + "\"}";
+ try {
+ controller.removeOverlay(body, "p_id", "-1");
+ fail("Exception expected");
+ } catch (InvalidTokenException e) {
+ }
+ }
+
+}
--
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