Port Develop to Master

CHANGELOG.md

@@ -5,6 +5,13 @@ All notable changes to this project will be documented in this file.
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## [3.0.2] - 2026-09-04
+
+### Fixed
+
+- **A successful CX2 network update was reported as a failure.** `updateCX2Network` treated only `204 No Content` as success, but `PUT /v3/networks/{networkid}` answers `200` with an `NdexObjectUpdateStatus` body. A successful v3 update therefore took the error path, where its own success body failed to parse as an `NDExError` and surfaced as `Unrecognized field "uuid"` — on an update the server had already applied, making it a false failure a caller would retry. Any 2xx is now treated as success, so both the v2 (`204`) and v3 (`200`) contracts are honoured.
+- **Update errors are read from the error stream.** The same method read the response body with `getInputStream()`, which throws for a 4xx or 5xx, so a genuine server error surfaced as an `IOException` rather than the `NdexException` the body describes. It now reads `getErrorStream()`, matching every other method in the client.
+
 ## [3.0.1] - 2026-09-03
 
 ### Added

pom.xml

@@ -4,7 +4,7 @@
 	<modelVersion>4.0.0</modelVersion>
 	<groupId>org.ndexbio.client</groupId>
 	<artifactId>ndex-java-client</artifactId>
-	<version>3.0.1</version>
+	<version>3.0.2</version>
 	<name>NDEx Java REST Client</name>
 	<description>REST Client for in applications that access NDEx</description>
 	<inceptionYear>2013</inceptionYear>

src/main/java/org/ndexbio/rest/client/NdexRestClientModelAccessLayer.java

@@ -889,8 +889,16 @@ private void updateNetwork(UUID networkUUID, InputStream input, final String rou
 			HttpURLConnection con = ndexRestClient.createReturningConnection(route + "/" + networkUUID.toString() + query,
 					input, "PUT",
 					jsonAcceptContentRequestProperties);
-			if (con.getResponseCode() != HttpURLConnection.HTTP_NO_CONTENT){
-				ndexRestClient.processNdexSpecificException(con.getInputStream(), con.getResponseCode(), new ObjectMapper());
+			final int status = con.getResponseCode();
+			// Any 2xx is a success. The v2 endpoint answers 204 No Content, but v3 answers 200 with an
+			// NdexObjectUpdateStatus body -- so checking only for 204 sent a successful v3 update down the
+			// error path, where the success body failed to parse as an NDExError and surfaced as
+			// 'Unrecognized field "uuid"' on an update that had in fact already been applied.
+			if (status < HttpURLConnection.HTTP_OK || status >= HttpURLConnection.HTTP_MULT_CHOICE) {
+				// Error bodies arrive on the error stream; getInputStream() throws for 4xx and 5xx.
+				try (InputStream errorBody = con.getErrorStream()) {
+					ndexRestClient.processNdexSpecificException(errorBody, status, new ObjectMapper());
+				}
 			}
 	   }
 

src/test/java/org/ndexbio/rest/client/NdexRestClientModelAccessLayerV3Test.java

@@ -8,6 +8,7 @@
 import static org.easymock.EasyMock.replay;
 import static org.easymock.EasyMock.verify;
 import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.fail;
 import static org.junit.Assert.assertNull;
 import static org.junit.Assert.assertSame;
 import static org.junit.Assert.assertTrue;
@@ -254,6 +255,53 @@ private String captureUpdateRoute(VisibilityType visibility) throws Exception {
 		return route.getValue();
 	}
 
+	@Test
+	public void updateSucceedsWhenV3AnswersTwoHundredWithABody() throws Exception {
+		// The bug this guards: only 204 was treated as success, so a successful v3 update took the error
+		// path and failed parsing its own success body as an NDExError.
+		NdexRestClient client = mock(NdexRestClient.class);
+		expect(client.createReturningConnection(anyObject(String.class), anyObject(InputStream.class), eq("PUT"),
+				anyObject())).andReturn(okWithBodyConnection());
+		replay(client);
+
+		new NdexRestClientModelAccessLayer(client).updateCX2Network(NETWORK_ID, cx2Stream(),
+				VisibilityType.PUBLIC);
+
+		verify(client);
+	}
+
+	@Test
+	public void updateStillSucceedsWhenV2AnswersNoContent() throws Exception {
+		NdexRestClient client = mock(NdexRestClient.class);
+		expect(client.createReturningConnection(anyObject(String.class), anyObject(InputStream.class), eq("PUT"),
+				anyObject())).andReturn(noContentConnection());
+		replay(client);
+
+		new NdexRestClientModelAccessLayer(client).updateCXNetwork(NETWORK_ID, cx2Stream());
+
+		verify(client);
+	}
+
+	@Test
+	public void updateReportsAServerErrorFromTheErrorStream() throws Exception {
+		// getInputStream() throws for a 4xx, so the error body has to come off getErrorStream()
+		NdexRestClient client = mock(NdexRestClient.class);
+		expect(client.createReturningConnection(anyObject(String.class), anyObject(InputStream.class), eq("PUT"),
+				anyObject())).andReturn(notFoundConnection());
+		client.processNdexSpecificException(anyObject(InputStream.class), eq(HttpURLConnection.HTTP_NOT_FOUND),
+				anyObject(com.fasterxml.jackson.databind.ObjectMapper.class));
+		expectLastCall().andThrow(new org.ndexbio.model.exceptions.ObjectNotFoundException("network", NETWORK_ID.toString()));
+		replay(client);
+
+		try {
+			new NdexRestClientModelAccessLayer(client).updateCX2Network(NETWORK_ID, cx2Stream(), null);
+			fail("expected the server error to surface");
+		} catch (org.ndexbio.model.exceptions.NdexException expected) {
+			// the point is that it is an NdexException, not a Jackson parse failure
+		}
+		verify(client);
+	}
+
 	// ---------- helpers ----------
 
 	private static InputStream cx2Stream() {
@@ -269,6 +317,29 @@ private static HttpURLConnection createdConnection(UUID newId) throws Exception
 		return con;
 	}
 
+	/** What v3 actually answers to PUT /v3/networks/{id}: 200 with an NdexObjectUpdateStatus body. */
+	private static HttpURLConnection okWithBodyConnection() throws Exception {
+		HttpURLConnection con = mock(HttpURLConnection.class);
+		expect(con.getResponseCode()).andReturn(HttpURLConnection.HTTP_OK).anyTimes();
+		expect(con.getInputStream()).andReturn(new ByteArrayInputStream(
+				("{\"uuid\":\"" + NETWORK_ID + "\",\"modificationTime\":\"2026-09-04T00:00:00Z\"}")
+						.getBytes(StandardCharsets.UTF_8))).anyTimes();
+		expect(con.getErrorStream()).andReturn(null).anyTimes();
+		replay(con);
+		return con;
+	}
+
+	/** A failing update: an NDExError body on the error stream. */
+	private static HttpURLConnection notFoundConnection() throws Exception {
+		HttpURLConnection con = mock(HttpURLConnection.class);
+		expect(con.getResponseCode()).andReturn(HttpURLConnection.HTTP_NOT_FOUND).anyTimes();
+		expect(con.getErrorStream()).andReturn(new ByteArrayInputStream(
+				"{\"errorCode\":\"NDEx_Object_Not_Found\",\"message\":\"no such network\"}"
+						.getBytes(StandardCharsets.UTF_8))).anyTimes();
+		replay(con);
+		return con;
+	}
+
 	private static HttpURLConnection noContentConnection() throws Exception {
 		HttpURLConnection con = mock(HttpURLConnection.class);
 		expect(con.getResponseCode()).andReturn(HttpURLConnection.HTTP_NO_CONTENT).anyTimes();