Use API v1 endpoints

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

 /*
- * Copyright 2016 Global Crop Diversity Trust
+ * Copyright 2018 Global Crop Diversity Trust
  *
  * Licensed under the Apache License, Version 2.0 (the "License");
  * you may not use this file except in compliance with the License.
@@ -32,16 +32,16 @@ public class AccessionJson {
 	private Long genesysId;
 
 	/** The puid. */
-	@JsonProperty(value = Accession.PUID)
-	private String puid;
+	@JsonProperty(value = Accession.DOI)
+	private String doi;
 	
 	/** The inst code. */
 	@JsonProperty(value = Accession.INSTCODE)
-	private String instCode;
+	private String instituteCode;
 
 	/** The acce numb. */
 	@JsonProperty(value = Accession.ACCENUMB)
-	private String acceNumb;
+	private String accessionNumber;
 
 	/** The new acce numb. */
 	@JsonProperty(value = Accession.ACCENUMB_NEW)
@@ -81,7 +81,7 @@ public class AccessionJson {
 
 	/** The acq date. */
 	@JsonProperty(value = Accession.ACQDATE)
-	private String acqDate;
+	private String acquisitionDate;
 
 	/** The mls stat. */
 	@JsonProperty(value = Accession.MLSSTAT)
@@ -109,7 +109,11 @@ public class AccessionJson {
 
 	/** The bred code. */
 	@JsonProperty(value = Accession.BREDCODE)
-	private String[] bredCode;
+	private String[] breederCode;
+
+	/** The bred code. */
+	@JsonProperty(value = Accession.BREDNAME)
+	private String[] breederName;
 
 	/** The ancest. */
 	@JsonProperty(value = Accession.ANCEST)
@@ -205,56 +209,49 @@ public class AccessionJson {
 	 * @return the puid
 	 */
 	public String getPuid() {
-		return puid;
-	}
-
-	/**
-	 * @param puid the puid to set
-	 */
-	public void setPuid(String puid) {
-		this.puid = puid;
+		return doi;
 	}
 
 	/**
-	 * Gets the inst code.
+	 * Gets the FAO WIEWS institute code.
 	 *
 	 * @return the inst code
 	 */
-	public String getInstCode() {
-		return instCode;
+	public String getInstituteCode() {
+		return instituteCode;
 	}
 
 	/**
 	 * Sets the inst code.
 	 *
-	 * @param instCode the new inst code
+	 * @param instituteCode the new inst code
 	 */
-	public void setInstCode(final String instCode) {
-		this.instCode = instCode;
+	public void setInstituteCode(final String instituteCode) {
+		this.instituteCode = instituteCode;
 	}
 
 	/**
-	 * Gets the acce numb.
+	 * Gets the accession number.
 	 *
-	 * @return the acce numb
+	 * @return the accession number
 	 */
-	public String getAcceNumb() {
-		return acceNumb;
+	public String getAccessionNumber() {
+		return accessionNumber;
 	}
-
+	
 	/**
-	 * Sets the acce numb.
+	 * Sets the accession number.
 	 *
-	 * @param acceNumb the new acce numb
+	 * @param accessionNumber the new accession number
 	 */
-	public void setAcceNumb(final String acceNumb) {
-		this.acceNumb = acceNumb;
+	public void setAccessionNumber(String accessionNumber) {
+		this.accessionNumber = accessionNumber;
 	}
-
+	
 	/**
-	 * Gets the new acce numb.
+	 * Gets the new accession number.
 	 *
-	 * @return the new acce numb
+	 * @return the new accession number
 	 */
 	public String getNewAcceNumb() {
 		return newAcceNumb;
@@ -414,21 +411,21 @@ public class AccessionJson {
 	}
 
 	/**
-	 * Gets the acq date.
+	 * Gets the acquisition date.
 	 *
-	 * @return the acq date
+	 * @return the acquisition date
 	 */
-	public String getAcqDate() {
-		return acqDate;
+	public String getAcquisitionDate() {
+		return acquisitionDate;
 	}
-
+	
 	/**
-	 * Sets the acq date.
+	 * Sets the acquisition date.
 	 *
-	 * @param acqDate the new acq date
+	 * @param acquisitionDate the new acquisition date
 	 */
-	public void setAcqDate(final String acqDate) {
-		this.acqDate = acqDate;
+	public void setAcquisitionDate(String acquisitionDate) {
+		this.acquisitionDate = acquisitionDate;
 	}
 
 	/**
@@ -545,7 +542,7 @@ public class AccessionJson {
 	 * @return the bred code
 	 */
 	public String[] getBredCode() {
-		return bredCode;
+		return breederCode;
 	}
 
 	/**
@@ -554,7 +551,7 @@ public class AccessionJson {
 	 * @param bredCode the new bred code
 	 */
 	public void setBredCode(final String[] bredCode) {
-		this.bredCode = bredCode;
+		this.breederCode = bredCode;
 	}
 
 	/**

src/main/java/org/genesys2/client/oauth/api/accession/Api1Constants.java

@@ -40,12 +40,12 @@ public interface Api1Constants {
 		/**
 		 * WIEWS code of accession holding institute.
 		 */
-		public static final String INSTCODE = "instCode";
+		public static final String INSTCODE = "instituteCode";
 
 		/**
 		 * Accession number.
 		 */
-		public static final String ACCENUMB = "acceNumb";
+		public static final String ACCENUMB = "accessionNumber";
 
 		/** Used to assign new ACCENUMB. */
 		public static final String ACCENUMB_NEW = "newAcceNumb";
@@ -84,13 +84,13 @@ public interface Api1Constants {
 		/**
 		 * ISO3 country code of country of origin.
 		 */
-		public static final String ORIGCTY = "orgCty";
+		public static final String ORIGCTY = "origCty";
 
 		/**
 		 * Date on which the accession entered the collection as YYYYMMDD. Missing data (MM or DD)
 		 * should be indicated with hyphens. Leading zeros are required.
 		 */
-		public static final String ACQDATE = "acqDate";
+		public static final String ACQDATE = "acquisitionDate";
 
 		/**
 		 * The status of an accession with regards to the Multilateral System (MLS) of the
@@ -123,7 +123,12 @@ public interface Api1Constants {
 		/**
 		 * Corresponds to BREDCODE.
 		 */
-		public static final String BREDCODE = "bredCode";
+		public static final String BREDCODE = "breederCode";
+
+		/**
+		 * Corresponds to BREDNAME.
+		 */
+		public static final String BREDNAME = "breederName";
 
 		/**
 		 * Corresponds to ANCEST.

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

@@ -17,20 +17,14 @@
 package org.geneys2.client.oauth;
 
 import static org.hamcrest.CoreMatchers.*;
-import static org.hamcrest.MatcherAssert.*;
+import static org.hamcrest.MatcherAssert.assertThat;
 import static org.mockito.Matchers.*;
-import static org.mockito.Mockito.*;
+import static org.mockito.Mockito.when;
 
 import java.io.IOException;
 import java.util.ArrayList;
 import java.util.List;
 
-import com.fasterxml.jackson.annotation.JsonInclude.Include;
-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 org.genesys2.client.oauth.GenesysApiException;
 import org.genesys2.client.oauth.GenesysClient;
 import org.genesys2.client.oauth.OAuthAuthenticationException;
@@ -44,9 +38,14 @@ import org.mockito.Matchers;
 import org.mockito.Mock;
 import org.mockito.runners.MockitoJUnitRunner;
 
-// TODO: Auto-generated Javadoc
+import com.fasterxml.jackson.annotation.JsonInclude.Include;
+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;
+
 /**
- * The Class AccessionApiTest.
+ * Accession API v1 test
  */
 @RunWith(MockitoJUnitRunner.class)
 public class AccessionApiTest {
@@ -59,7 +58,7 @@ public class AccessionApiTest {
 	protected GenesysClient genesysClient;
 
 	/** The inst code. */
-	private final String instCode = "INS000";
+	private final String instituteCode = "INS000";
 
 	/** The mock server. */
 	private final MockGenesysServer mockServer = new MockGenesysServer();
@@ -99,7 +98,7 @@ public class AccessionApiTest {
 	@Test
 	public void testAccessions0() throws OAuthAuthenticationException, PleaseRetryException, GenesysApiException, JsonProcessingException, IOException {
 
-		final List<AccessionJson> results = objectMapper.readValue(genesysClient.listAccessions(instCode, 1, null), new TypeReference<List<AccessionJson>>() {
+		final List<AccessionJson> results = objectMapper.readValue(genesysClient.listAccessions(instituteCode, 1, null), new TypeReference<List<AccessionJson>>() {
 		});
 
 		assertThat("Expected empty list", results.size(), is(0));
@@ -117,14 +116,14 @@ public class AccessionApiTest {
 	@Test
 	public void testAccessions1() throws OAuthAuthenticationException, PleaseRetryException, GenesysApiException, JsonProcessingException, IOException {
 
-		when(genesysClient.listAccessions(instCode, 1, null)).thenReturn("[{\"instCode\":\"INS000\",\"acceNumb\":\"ACC-1\"}]");
+		when(genesysClient.listAccessions(instituteCode, 1, null)).thenReturn("[{\"instituteCode\":\"INS000\",\"accessionNumber\":\"ACC-1\"}]");
 
-		final List<AccessionJson> results = objectMapper.readValue(genesysClient.listAccessions(instCode, 1, null), new TypeReference<List<AccessionJson>>() {
+		final List<AccessionJson> results = objectMapper.readValue(genesysClient.listAccessions(instituteCode, 1, null), new TypeReference<List<AccessionJson>>() {
 		});
 
 		assertThat("Expected empty list", results.size(), is(1));
 		final AccessionJson acc1 = results.get(0);
-		assertThat("INSTCODE doesn't match", acc1.getInstCode(), is(instCode));
+		assertThat("INSTCODE doesn't match", acc1.getInstituteCode(), is(instituteCode));
 
 		acc1.setHistoric(true);
 
@@ -143,7 +142,7 @@ public class AccessionApiTest {
 	@Test
 	public void testUpsertAccessions1() throws OAuthAuthenticationException, PleaseRetryException, GenesysApiException, JsonProcessingException, IOException, InterruptedException {
 
-		String result = genesysClient.listAccessions(instCode, 1, null);
+		String result = genesysClient.listAccessions(instituteCode, 1, null);
 		assertThat("Non-null result expected from genesysClient", result, notNullValue());
 		List<AccessionJson> results = objectMapper.readValue(result, new TypeReference<List<AccessionJson>>() {
 		});
@@ -154,23 +153,23 @@ public class AccessionApiTest {
 
 		for (int i = 0; i < 4; i++) {
 			final AccessionJson aj = new AccessionJson();
-			aj.setInstCode(instCode);
-			aj.setAcceNumb("ACC-" + (i + 1));
+			aj.setInstituteCode(instituteCode);
+			aj.setAccessionNumber("ACC-" + (i + 1));
 			aj.setGenus("Genus");
 			ajList.add(aj);
 		}
 
-		result = genesysClient.updateAccessions(instCode, ajList);
+		result = genesysClient.updateAccessions(instituteCode, ajList);
 		System.err.println(result);
 
-		results = objectMapper.readValue(genesysClient.listAccessions(instCode, 1, null), new TypeReference<List<AccessionJson>>() {
+		results = objectMapper.readValue(genesysClient.listAccessions(instituteCode, 1, null), new TypeReference<List<AccessionJson>>() {
 		});
 
 		assertThat("Expected list with 4 entries", results.size(), is(4));
 
 		for (final AccessionJson aj1 : results) {
-			assertThat("Expected matching INSTCODE", aj1.getInstCode(), is(instCode));
-			assertThat("Expected ACCENUMB starting with", aj1.getAcceNumb(), CoreMatchers.startsWith("ACC-"));
+			assertThat("Expected matching INSTCODE", aj1.getInstituteCode(), is(instituteCode));
+			assertThat("Expected ACCENUMB starting with", aj1.getAccessionNumber(), CoreMatchers.startsWith("ACC-"));
 			assertThat("Expected GENUS=Genus", aj1.getGenus(), is("Genus"));
 			assertThat("Expected SPECIES=null", aj1.getSpecies(), nullValue());
 		}

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

@@ -51,7 +51,6 @@ import org.mockito.invocation.InvocationOnMock;
 import org.mockito.runners.MockitoJUnitRunner;
 import org.mockito.stubbing.Answer;
 
-// TODO: Auto-generated Javadoc
 /**
  * The Class ApiTest.
  */
@@ -105,95 +104,6 @@ public class ApiTest {
 		MockitoAnnotations.initMocks(this);
 		when(httpGetMock.getMethod()).thenReturn("GET");
 		when(httpPostMock.getMethod()).thenReturn("POST");
-
-		when(genesysClient.getCrop("banana")).thenReturn(bananaJson);
-	}
-
-	/**
-	 * Test mock get crop.
-	 *
-	 * @throws OAuthAuthenticationException the o auth authentication exception
-	 * @throws PleaseRetryException the please retry exception
-	 * @throws GenesysApiException the genesys api exception
-	 * @throws JsonProcessingException the json processing exception
-	 * @throws IOException Signals that an I/O exception has occurred.
-	 */
-	@Test
-	public void testMockGetCrop() throws OAuthAuthenticationException, PleaseRetryException, GenesysApiException, JsonProcessingException, IOException {
-
-		final String json = genesysClient.getCrop("banana");
-		assertThat("Returned banana JSON doesn't match", json, equalTo(bananaJson));
-
-		// Must be able to read the json
-		objectMapper.readTree(json);
-	}
-
-	/**
-	 * Test mock update crop.
-	 *
-	 * @throws OAuthAuthenticationException the o auth authentication exception
-	 * @throws PleaseRetryException the please retry exception
-	 * @throws GenesysApiException the genesys api exception
-	 * @throws JsonProcessingException the json processing exception
-	 * @throws IOException Signals that an I/O exception has occurred.
-	 */
-	@Test
-	public void testMockUpdateCrop() throws OAuthAuthenticationException, PleaseRetryException, GenesysApiException, JsonProcessingException, IOException {
-
-		final String json = genesysClient.getCrop("banana");
-		assertThat("Returned banana JSON doesn't match", json, equalTo(bananaJson));
-
-		// Must be able to read the json
-		objectMapper.readTree(json);
-	}
-
-	/**
-	 * Test organization members.
-	 *
-	 * @throws OAuthAuthenticationException the o auth authentication exception
-	 * @throws PleaseRetryException the please retry exception
-	 * @throws GenesysApiException the genesys api exception
-	 * @throws JsonProcessingException the json processing exception
-	 * @throws IOException Signals that an I/O exception has occurred.
-	 */
-	@Test
-	public void testOrganizationMembers() throws OAuthAuthenticationException, PleaseRetryException, GenesysApiException, JsonProcessingException, IOException {
-		final String orgSlug = "org";
-		when(genesysClient.getOrganizationMembers(orgSlug)).then(returnOrganizationMembers(orgSlug));
-		final String members = genesysClient.getOrganizationMembers(orgSlug);
-		objectMapper.readTree(members);
-		System.err.println(members);
-	}
-
-	/**
-	 * Return organization members.
-	 *
-	 * @param orgSlug the org slug
-	 * @return the answer
-	 */
-	private Answer<String> returnOrganizationMembers(final String orgSlug) {
-		return new Answer<String>() {
-			@Override
-			public String answer(final InvocationOnMock invocation) throws Throwable {
-				return "[\"ORG1\",\"ORG2\"]";
-			}
-		};
-	}
-
-	/**
-	 * Test please retry exception.
-	 *
-	 * @throws OAuthAuthenticationException the o auth authentication exception
-	 * @throws PleaseRetryException the please retry exception
-	 * @throws GenesysApiException the genesys api exception
-	 * @throws JsonProcessingException the json processing exception
-	 */
-	@SuppressWarnings("deprecation")
-	@Test(expected = PleaseRetryException.class)
-	public void testPleaseRetryException() throws OAuthAuthenticationException, PleaseRetryException, GenesysApiException, JsonProcessingException {
-
-		when(genesysClient.updateMLS("INS000", null)).thenThrow(PleaseRetryException.class);
-		genesysClient.updateMLS("INS000", null);
 	}
 
 	/**

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

@@ -70,12 +70,12 @@ public class MockGenesysServer {
 				if (args[2] != null) {
 					throw new MockGenesysException("Querying is not supported.");
 				}
-				final String instCode = (String) args[0];
+				final String instituteCode = (String) args[0];
 				final int page = (Integer) args[1];
 
-				System.err.println("Listing accessions instCode=" + instCode + " page=" + page);
+				System.err.println("Listing accessions instituteCode=" + instituteCode + " page=" + page);
 
-				return objectMapper.writeValueAsString(getAccessionsPage(instCode, page));
+				return objectMapper.writeValueAsString(getAccessionsPage(instituteCode, page));
 			}
 		};
 	}
@@ -90,10 +90,10 @@ public class MockGenesysServer {
 			@Override
 			public String answer(final InvocationOnMock invocation) throws Throwable {
 				final Object[] args = invocation.getArguments();
-				final String instCode = (String) args[0];
+				final String instituteCode = (String) args[0];
 				final List<?> arrayNode = (List<?>) args[1];
 
-				final String res = objectMapper.writeValueAsString(upsertAccessions(instCode, arrayNode));
+				final String res = objectMapper.writeValueAsString(upsertAccessions(instituteCode, arrayNode));
 				System.err.println("Result: " + res);
 				return res;
 			}
@@ -103,7 +103,7 @@ public class MockGenesysServer {
 	/**
 	 * Upsert accessions.
 	 *
-	 * @param instCode the inst code
+	 * @param instituteCode the inst code
 	 * @param nodeList the node list
 	 * @return the string
 	 * @throws JsonParseException the json parse exception
@@ -111,10 +111,10 @@ public class MockGenesysServer {
 	 * @throws IOException Signals that an I/O exception has occurred.
 	 * @throws GenesysApiException the genesys api exception
 	 */
-	protected String upsertAccessions(final String instCode, final List<?> nodeList) throws JsonParseException, JsonMappingException, IOException, GenesysApiException {
-		List<AccessionJson> accList = instAcc.get(instCode);
+	protected String upsertAccessions(final String instituteCode, final List<?> nodeList) throws JsonParseException, JsonMappingException, IOException, GenesysApiException {
+		List<AccessionJson> accList = instAcc.get(instituteCode);
 		if (accList == null) {
-			instAcc.put(instCode, accList = new ArrayList<AccessionJson>());
+			instAcc.put(instituteCode, accList = new ArrayList<AccessionJson>());
 		}
 		for (int i = 0; i < nodeList.size(); i++) {
 			final AccessionJson aj = (AccessionJson) nodeList.get(i);
@@ -149,11 +149,11 @@ public class MockGenesysServer {
 			if (aj.getMlsStat() != null) {
 				existing.setMlsStat(aj.getMlsStat());
 			}
-			if (aj.getAcceNumb() != null) {
-				existing.setAcceNumb(aj.getAcceNumb());
+			if (aj.getAccessionNumber() != null) {
+				existing.setAccessionNumber(aj.getAccessionNumber());
 			}
-			if (aj.getAcqDate() != null) {
-				existing.setAcqDate(aj.getAcqDate());
+			if (aj.getAcquisitionDate() != null) {
+				existing.setAcquisitionDate(aj.getAcquisitionDate());
 			}
 			if (aj.getAncest() != null) {
 				existing.setAncest(aj.getAncest());
@@ -226,7 +226,7 @@ public class MockGenesysServer {
 			return findMatch(accList, aj.getUuid());
 		} else {
 			for (final AccessionJson m : accList) {
-				if (m.getInstCode().equals(aj.getInstCode()) && m.getAcceNumb().equals(aj.getAcceNumb()) && m.getGenus().equals(aj.getGenus())) {
+				if (m.getInstituteCode().equals(aj.getInstituteCode()) && m.getAccessionNumber().equals(aj.getAccessionNumber()) && m.getGenus().equals(aj.getGenus())) {
 					return m;
 				}
 			}
@@ -253,13 +253,13 @@ public class MockGenesysServer {
 	/**
 	 * Gets the accessions page.
 	 *
-	 * @param instCode the inst code
+	 * @param instituteCode the inst code
 	 * @param page the page
 	 * @return the accessions page
 	 * @throws MockGenesysException the mock genesys exception
 	 */
-	protected List<AccessionJson> getAccessionsPage(final String instCode, final int page) throws MockGenesysException {
-		final List<AccessionJson> accList = instAcc.get(instCode);
+	protected List<AccessionJson> getAccessionsPage(final String instituteCode, final int page) throws MockGenesysException {
+		final List<AccessionJson> accList = instAcc.get(instituteCode);
 		if (accList == null || accList.isEmpty()) {
 			System.err.println("Returning blank list");
 			return BLANK_LIST;

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

@@ -57,8 +57,8 @@ public class ModelTests {
 	@Test
 	public void serializeCore() throws IOException {
 		final AccessionJson aj = new AccessionJson();
-		aj.setInstCode("INS000");
-		aj.setAcceNumb("ACC-1");
+		aj.setInstituteCode("INS000");
+		aj.setAccessionNumber("ACC-1");
 		aj.setGenus("Genus");
 
 		final JsonNode tree = getJsonTree(aj);