API updates

src/main/java/org/genesys2/client/oauth/GenesysClient.java

@@ -30,6 +30,7 @@ import org.apache.commons.lang.StringUtils;
 import org.apache.log4j.LogManager;
 import org.apache.log4j.Logger;
 import org.genesys2.client.oauth.api.GenesysApi;
+import org.genesys2.client.oauth.api.accession.AccessionJson;
 import org.scribe.builder.ServiceBuilder;
 import org.scribe.exceptions.OAuthConnectionException;
 import org.scribe.exceptions.OAuthException;
@@ -40,7 +41,10 @@ import org.scribe.model.Verb;
 import org.scribe.model.Verifier;
 import org.scribe.oauth.OAuthService;
 
+import com.fasterxml.jackson.annotation.JsonInclude.Include;
+import com.fasterxml.jackson.core.JsonProcessingException;
 import com.fasterxml.jackson.databind.ObjectMapper;
+import com.fasterxml.jackson.databind.SerializationFeature;
 import com.fasterxml.jackson.databind.node.ArrayNode;
 import com.fasterxml.jackson.databind.node.ObjectNode;
 
@@ -59,7 +63,7 @@ public class GenesysClient {
 	private static final String SCOPE = "read,write";
 
 	/** The mapper. */
-	private static ObjectMapper mapper = new ObjectMapper();
+	private static ObjectMapper objectMapper = new ObjectMapper();
 
 	/** The service. */
 	private OAuthService service;
@@ -79,6 +83,13 @@ public class GenesysClient {
 	/** The api secret. */
 	private String apiSecret;
 
+	static {
+		objectMapper = new ObjectMapper();
+		objectMapper.configure(SerializationFeature.WRITE_ENUMS_USING_TO_STRING, true);
+		objectMapper.configure(SerializationFeature.WRITE_EMPTY_JSON_ARRAYS, false);
+		objectMapper.setSerializationInclusion(Include.NON_NULL);
+	}
+
 	/**
 	 * Instantiates a new genesys client.
 	 */
@@ -364,7 +375,7 @@ public class GenesysClient {
 	 * @return the object node
 	 */
 	public static ObjectNode makeAid3(String instCode, String genus, String acceNumb) {
-		ObjectNode json = mapper.createObjectNode();
+		ObjectNode json = objectMapper.createObjectNode();
 		json.put("instCode", instCode);
 		json.put("acceNumb", acceNumb);
 		json.put("genus", genus);
@@ -372,7 +383,7 @@ public class GenesysClient {
 	}
 
 	/**
-	 * Update mls.
+	 * Update MLS status of accessions
 	 *
 	 * @param instCode
 	 *            the inst code
@@ -381,103 +392,64 @@ public class GenesysClient {
 	 * @return the string
 	 * @throws GenesysApiException
 	 *             the genesys api exception
+	 * @throws JsonProcessingException
+	 * @throws PleaseRetryException
+	 * 
+	 * @deprecated Please use {@link #updateAccessions(String, Collection)} with
+	 *             only the instCode, acceNumb, (genus, ) and mlsStat provided.
 	 */
-	public String updateMLS(String instCode, Collection<ObjectNode> accns) throws GenesysApiException {
-
-		ArrayNode arr = toArrayNode(accns);
-
-		_log.debug("Sending: " + arr);
-		return query(Verb.PUT, "/acn/" + instCode + "/update", null, arr.toString());
-	}
-
-	/**
-	 * Accession exists.
-	 *
-	 * @param instCode
-	 *            the inst code
-	 * @param accns
-	 *            the accns
-	 * @return the string
-	 * @throws GenesysApiException
-	 *             the genesys api exception
-	 */
-	public String accessionExists(String instCode, Collection<ObjectNode> accns) throws GenesysApiException {
-		ArrayNode arr = toArrayNode(accns);
-
-		_log.debug("Sending: " + arr);
-		return query(Verb.PUT, "/acn/" + instCode + "/check", null, arr.toString());
-	}
-
-	/**
-	 * Update accessions.
-	 *
-	 * @param instCode
-	 *            the inst code
-	 * @param accns
-	 *            the accns
-	 * @return the string
-	 * @throws GenesysApiException
-	 *             the genesys api exception
-	 * @throws InterruptedException
-	 *             the interrupted exception
-	 */
-	public String updateAccessions(String instCode, Collection<ObjectNode> accns) throws GenesysApiException,
-			InterruptedException {
+	@Deprecated
+	public String updateMLS(String instCode, Collection<ObjectNode> accns) throws GenesysApiException,
+			PleaseRetryException, JsonProcessingException {
 
 		if (accns == null || accns.size() == 0) {
 			return null;
 		}
 
-		return updateAccessions(instCode, toArrayNode(accns));
-	}
-
-	/**
-	 * To array node.
-	 *
-	 * @param accns
-	 *            the accns
-	 * @return the array node
-	 */
-	public static ArrayNode toArrayNode(Collection<ObjectNode> accns) {
-		ArrayNode arr = mapper.createArrayNode();
-		for (ObjectNode accn : accns) {
-			arr.add(accn);
-		}
-		return arr;
+		_log.debug("Sending: " + accns);
+		return query(Verb.PUT, "/acn/" + instCode + "/update", null, objectMapper.writeValueAsString(accns));
 	}
 
 	/**
-	 * Update accessions.
-	 *
+	 * Update accession information with new values provided in the JSON string.
+	 * In case of {@link PleaseRetryException}, this method will attempt to
+	 * re-send the data 5 times before giving up.
+	 * 
 	 * @param instCode
-	 *            the inst code
-	 * @param arr
-	 *            the arr
-	 * @return the string
-	 * @throws OAuthAuthenticationException
-	 *             the o auth authentication exception
+	 *            the WIEWS institute code
+	 * @param jsonAccessionList
+	 *            the JSON array of accessions
+	 * @return "OK"
 	 * @throws GenesysApiException
-	 *             the genesys api exception
+	 *             when data is not valid
 	 * @throws InterruptedException
-	 *             the interrupted exception
+	 *             when thread was interrupted during sleep between retries
+	 * 
 	 */
-	public String updateAccessions(String instCode, ArrayNode arr) throws OAuthAuthenticationException,
-			GenesysApiException, InterruptedException {
-		_log.debug("Sending: " + arr);
-
+	public String updateAccessions(String instCode, String jsonAccessionList) throws GenesysApiException,
+			InterruptedException {
 		for (int retry = 0; retry < 5; retry++) {
 			try {
-				return query(Verb.PUT, "/acn/" + instCode + "/upsert", null, arr.toString());
+				return query(Verb.PUT, "/acn/" + instCode + "/upsert", null, jsonAccessionList);
 			} catch (PleaseRetryException e) {
 				long sleepTime = (long) (Math.pow(2, retry) * 100 + Math.pow(2, retry) * 2500 * Math.random());
 				_log.warn("Retrying PUT after " + sleepTime + " ms.");
 				Thread.sleep(sleepTime);
 			}
 		}
-
 		throw new RuntimeException("All retries failed");
 	}
 
+	public String updateAccessions(String instCode, Collection<AccessionJson> accns) throws GenesysApiException,
+			InterruptedException, JsonProcessingException {
+
+		if (accns == null || accns.size() == 0) {
+			return null;
+		}
+
+		return updateAccessions(instCode, objectMapper.writeValueAsString(accns));
+	}
+
 	/**
 	 * Update organization members.
 	 *

src/main/java/org/genesys2/client/oauth/api/accession/AccessionJson.java

@@ -21,7 +21,7 @@ import org.genesys2.client.oauth.api.accession.Api1Constants.Accession;
 import com.fasterxml.jackson.annotation.JsonProperty;
 
 public class AccessionJson {
-	private long version = 0;
+	private Long version;
 	private Long genesysId;
 
 	@JsonProperty(value = Accession.INSTCODE)
@@ -79,11 +79,11 @@ public class AccessionJson {
 	@JsonProperty(value = Accession.HISTORIC)
 	private Boolean historic;
 
-	public long getVersion() {
+	public Long getVersion() {
 		return version;
 	}
 
-	public void setVersion(long l) {
+	public void setVersion(Long l) {
 		this.version = l;
 	}
 

src/test/java/org/geneys2/client/oauth/AccessionApiTest.java

@@ -43,7 +43,6 @@ import com.fasterxml.jackson.core.JsonProcessingException;
 import com.fasterxml.jackson.core.type.TypeReference;
 import com.fasterxml.jackson.databind.ObjectMapper;
 import com.fasterxml.jackson.databind.SerializationFeature;
-import com.fasterxml.jackson.databind.node.ObjectNode;
 
 @RunWith(MockitoJUnitRunner.class)
 public class AccessionApiTest {
@@ -66,11 +65,11 @@ public class AccessionApiTest {
 
 	@Before
 	public void initMocks() throws OAuthAuthenticationException, PleaseRetryException, GenesysApiException,
-			InterruptedException {
+			InterruptedException, JsonProcessingException {
 		System.err.println("Initializing mocks");
 		when(genesysClient.listAccessions(anyString(), anyInt(), Matchers.isNull(String.class))).then(
 				mockServer.listAccessions());
-		when(genesysClient.updateAccessions(anyString(), anyCollectionOf(ObjectNode.class))).then(
+		when(genesysClient.updateAccessions(anyString(), anyCollectionOf(AccessionJson.class))).then(
 				mockServer.updateAccessions());
 	}
 
@@ -115,19 +114,17 @@ public class AccessionApiTest {
 
 		assertThat("Expected empty list", results.size(), is(0));
 
-		List<ObjectNode> nodeList = new ArrayList<ObjectNode>();
+		List<AccessionJson> ajList = new ArrayList<AccessionJson>();
 
 		for (int i = 0; i < 4; i++) {
 			AccessionJson aj = new AccessionJson();
 			aj.setInstCode(instCode);
 			aj.setAcceNumb("ACC-" + (i + 1));
 			aj.setGenus("Genus");
-
-			ObjectNode node = (ObjectNode) objectMapper.readTree(objectMapper.writeValueAsString(aj));
-			nodeList.add(node);
+			ajList.add(aj);
 		}
 
-		result = genesysClient.updateAccessions(instCode, nodeList);
+		result = genesysClient.updateAccessions(instCode, ajList);
 		System.err.println(result);
 
 		results = objectMapper.readValue(genesysClient.listAccessions(instCode, 1, null),

src/test/java/org/geneys2/client/oauth/ApiTest.java

@@ -127,32 +127,23 @@ public class ApiTest {
 		};
 	}
 
+	@SuppressWarnings("deprecation")
 	@Test(expected = PleaseRetryException.class)
 	public void testPleaseRetryException() throws OAuthAuthenticationException, PleaseRetryException,
-			GenesysApiException {
+			GenesysApiException, JsonProcessingException {
 
 		when(genesysClient.updateMLS("INS000", null)).thenThrow(PleaseRetryException.class);
 		genesysClient.updateMLS("INS000", null);
 	}
 
-	@Test(expected = NullPointerException.class)
-	public void testNullUpdate() throws OAuthAuthenticationException, PleaseRetryException, GenesysApiException {
-		when(genesysClient.updateMLS("INS000", null)).thenCallRealMethod();
-		genesysClient.updateMLS("INS000", null);
-	}
-
 	@Test
 	public void test2() throws OAuthAuthenticationException, PleaseRetryException, GenesysApiException {
 
-		when(genesysClient.query(Mockito.isA(Verb.class), anyString(), anyMap(), anyString())).thenCallRealMethod();
-		when(genesysClient.updateMLS(anyString(), anyCollection())).thenCallRealMethod();
+		when(genesysClient.query(Mockito.isA(Verb.class), anyString(), anyMapOf(String.class, String.class), anyString())).thenCallRealMethod();
 
 		Collection<ObjectNode> list = new ArrayList<ObjectNode>();
 
 		list.add(objectMapper.createObjectNode().put(Accession.INSTCODE, "INS000").put(Accession.ACCENUMB, "ACC-1")
 				.put(Accession.GENUS, "Genus"));
-
-		String x = genesysClient.updateMLS("INS000", list);
-		System.out.println(x);
 	}
 }

src/test/java/org/geneys2/client/oauth/MockGenesysServer.java

@@ -31,7 +31,6 @@ import org.mockito.stubbing.Answer;
 import com.fasterxml.jackson.annotation.JsonInclude.Include;
 import com.fasterxml.jackson.core.JsonParseException;
 import com.fasterxml.jackson.databind.JsonMappingException;
-import com.fasterxml.jackson.databind.JsonNode;
 import com.fasterxml.jackson.databind.ObjectMapper;
 import com.fasterxml.jackson.databind.SerializationFeature;
 
@@ -76,7 +75,7 @@ public class MockGenesysServer {
 			public String answer(InvocationOnMock invocation) throws Throwable {
 				Object[] args = invocation.getArguments();
 				String instCode = (String) args[0];
-				List arrayNode = (List) args[1];
+				List<?> arrayNode = (List<?>) args[1];
 
 				String res = objectMapper.writeValueAsString(upsertAccessions(instCode, arrayNode));
 				System.err.println("Result: " + res);
@@ -85,15 +84,14 @@ public class MockGenesysServer {
 		};
 	}
 
-	protected String upsertAccessions(final String instCode, List nodeList) throws JsonParseException,
+	protected String upsertAccessions(final String instCode, List<?> nodeList) throws JsonParseException,
 			JsonMappingException, IOException, GenesysApiException {
 		List<AccessionJson> accList = instAcc.get(instCode);
 		if (accList == null) {
 			instAcc.put(instCode, accList = new ArrayList<AccessionJson>());
 		}
 		for (int i = 0; i < nodeList.size(); i++) {
-			JsonNode node = (JsonNode) nodeList.get(i);
-			AccessionJson aj = objectMapper.readValue(node.toString(), AccessionJson.class);
+			AccessionJson aj = (AccessionJson) nodeList.get(i);
 			AccessionJson existing = findMatch(accList, aj);
 			merge(accList, existing, aj);
 		}

src/test/java/org/geneys2/client/oauth/ModelTests.java

@@ -22,9 +22,9 @@ import static org.hamcrest.MatcherAssert.*;
 import java.io.IOException;
 
 import org.genesys2.client.oauth.api.accession.AccessionJson;
-import org.genesys2.client.oauth.api.accession.GeoJson;
 import org.genesys2.client.oauth.api.accession.Api1Constants.Accession;
 import org.genesys2.client.oauth.api.accession.Api1Constants.Geo;
+import org.genesys2.client.oauth.api.accession.GeoJson;
 import org.junit.Test;
 
 import com.fasterxml.jackson.annotation.JsonInclude.Include;
@@ -52,6 +52,7 @@ public class ModelTests {
 		aj.setGenus("Genus");
 
 		JsonNode tree = getJsonTree(aj);
+		System.err.println(tree.toString());
 		assertThat("JSON elements count mismatch", tree, JsonNodeMatchers.withSize(3));
 		assertThat("No INSTCODE", tree.get(Accession.INSTCODE), notNullValue());
 		assertThat("INSTCODE must be a text node", tree.get(Accession.INSTCODE), JsonNodeMatchers.isTextNode());
@@ -85,6 +86,7 @@ public class ModelTests {
 		aj.setStorage(new Integer[] { 1, 2, 3, 4 });
 
 		JsonNode tree = getJsonTree(aj);
+		System.err.println(tree.toString());
 		assertThat("JSON elements count mismatch", tree, JsonNodeMatchers.withSize(1));
 		assertThat("STORAGE must be an array", tree.get(Accession.STORAGE), JsonNodeMatchers.isArrayNode());
 	}