Merge branch 'drop-obsolete-code' into 'master'

Drop obsolete code for /api/v0

See merge request !16

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

-/*
- * Copyright 2019 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.
- * You may obtain a copy of the License at
- *
- *   http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package org.geneys2.client.oauth;
-
-import static org.hamcrest.CoreMatchers.*;
-import static org.hamcrest.MatcherAssert.assertThat;
-import static org.mockito.Matchers.*;
-import static org.mockito.Mockito.when;
-
-import java.io.IOException;
-import java.util.ArrayList;
-import java.util.List;
-
-import org.genesys2.client.oauth.GenesysApiException;
-import org.genesys2.client.oauth.GenesysClient;
-import org.genesys2.client.oauth.OAuthAuthenticationException;
-import org.genesys2.client.oauth.PleaseRetryException;
-import org.genesys2.client.oauth.api.accession.AccessionJson;
-import org.hamcrest.CoreMatchers;
-import org.junit.Before;
-import org.junit.Test;
-import org.junit.runner.RunWith;
-import org.mockito.Matchers;
-import org.mockito.Mock;
-import org.mockito.runners.MockitoJUnitRunner;
-
-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;
-
-/**
- * Accession API v1 test
- */
-@RunWith(MockitoJUnitRunner.class)
-public class AccessionApiTest {
-
-	/** The object mapper. */
-	private static final ObjectMapper objectMapper;
-
-	/** The genesys client. */
-	@Mock
-	protected GenesysClient genesysClient;
-
-	/** The inst code. */
-	private final String instituteCode = "INS000";
-
-	/** The mock server. */
-	private final MockGenesysServer mockServer = new MockGenesysServer();
-
-	static {
-		objectMapper = new ObjectMapper();
-		objectMapper.configure(SerializationFeature.WRITE_ENUMS_USING_TO_STRING, true);
-		objectMapper.setSerializationInclusion(Include.NON_EMPTY);
-		objectMapper.setSerializationInclusion(Include.NON_NULL);
-	}
-
-	/**
-	 * Inits the mocks.
-	 *
-	 * @throws OAuthAuthenticationException the o auth authentication exception
-	 * @throws PleaseRetryException the please retry exception
-	 * @throws GenesysApiException the genesys api exception
-	 * @throws InterruptedException the interrupted exception
-	 * @throws JsonProcessingException the json processing exception
-	 */
-	@Before
-	public void initMocks() throws OAuthAuthenticationException, PleaseRetryException, GenesysApiException, InterruptedException, JsonProcessingException {
-		System.err.println("Initializing mocks");
-		when(genesysClient.listAccessions(anyString(), anyInt(), Matchers.isNull(String.class))).then(mockServer.listAccessions());
-		when(genesysClient.updateAccessions(anyString(), anyCollectionOf(AccessionJson.class))).then(mockServer.updateAccessions());
-	}
-
-	/**
-	 * Test accessions0.
-	 *
-	 * @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 testAccessions0() throws OAuthAuthenticationException, PleaseRetryException, GenesysApiException, JsonProcessingException, IOException {
-
-		final List<AccessionJson> results = objectMapper.readValue(genesysClient.listAccessions(instituteCode, 1, null), new TypeReference<List<AccessionJson>>() {
-		});
-
-		assertThat("Expected empty list", results.size(), is(0));
-	}
-
-	/**
-	 * Test accessions1.
-	 *
-	 * @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 testAccessions1() throws OAuthAuthenticationException, PleaseRetryException, GenesysApiException, JsonProcessingException, IOException {
-
-		when(genesysClient.listAccessions(instituteCode, 1, null)).thenReturn("[{\"instituteCode\":\"INS000\",\"accessionNumber\":\"ACC-1\"}]");
-
-		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.getInstituteCode(), is(instituteCode));
-
-		acc1.setHistoric(true);
-
-	}
-
-	/**
-	 * Test upsert accessions1.
-	 *
-	 * @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.
-	 * @throws InterruptedException the interrupted exception
-	 */
-	@Test
-	public void testUpsertAccessions1() throws OAuthAuthenticationException, PleaseRetryException, GenesysApiException, JsonProcessingException, IOException, InterruptedException {
-
-		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>>() {
-		});
-
-		assertThat("Expected empty list", results.size(), is(0));
-
-		final List<AccessionJson> ajList = new ArrayList<AccessionJson>();
-
-		for (int i = 0; i < 4; i++) {
-			final AccessionJson aj = new AccessionJson();
-			aj.setInstituteCode(instituteCode);
-			aj.setAccessionNumber("ACC-" + (i + 1));
-			aj.getTaxonomy().setGenus("Genus");
-			ajList.add(aj);
-		}
-
-		result = genesysClient.updateAccessions(instituteCode, ajList);
-		System.err.println(result);
-
-		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.getInstituteCode(), is(instituteCode));
-			assertThat("Expected ACCENUMB starting with", aj1.getAccessionNumber(), CoreMatchers.startsWith("ACC-"));
-			assertThat("Expected GENUS=Genus", aj1.getTaxonomy().getGenus(), is("Genus"));
-			assertThat("Expected SPECIES=null", aj1.getTaxonomy().getSpecies(), nullValue());
-		}
-
-	}
-
-}

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

@@ -29,7 +29,7 @@ import org.junit.Test;
 public class AccessionImagesTest {
 
 	/** The mapper. */
-	private static ObjectMapper objectMapper;
+	private static final ObjectMapper objectMapper;
 
 	static {
 		objectMapper = new ObjectMapper();

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

-/*
- * Copyright 2019 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.
- * You may obtain a copy of the License at
- *
- *   http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package org.geneys2.client.oauth;
-
-import java.io.IOException;
-import java.util.ArrayList;
-import java.util.HashMap;
-import java.util.List;
-import java.util.Map;
-
-import com.fasterxml.jackson.annotation.JsonInclude.Include;
-import com.fasterxml.jackson.core.JsonParseException;
-import com.fasterxml.jackson.databind.JsonMappingException;
-import com.fasterxml.jackson.databind.ObjectMapper;
-import com.fasterxml.jackson.databind.SerializationFeature;
-
-import org.genesys2.client.oauth.GenesysApiException;
-import org.genesys2.client.oauth.api.accession.AccessionJson;
-import org.mockito.invocation.InvocationOnMock;
-import org.mockito.stubbing.Answer;
-
-// TODO: Auto-generated Javadoc
-/**
- * Mock Genesys server.
- *
- * @author mobreza
- */
-public class MockGenesysServer {
-
-	/** The Constant BLANK_LIST. */
-	private static final ArrayList<AccessionJson> BLANK_LIST = new ArrayList<AccessionJson>();
-
-	/** The inst acc. */
-	private final Map<String, List<AccessionJson>> instAcc = new HashMap<String, List<AccessionJson>>();
-
-	/** The object mapper. */
-	private static final ObjectMapper objectMapper;
-
-	static {
-		objectMapper = new ObjectMapper();
-		objectMapper.configure(SerializationFeature.WRITE_ENUMS_USING_TO_STRING, true);
-		objectMapper.setSerializationInclusion(Include.NON_EMPTY);
-		objectMapper.setSerializationInclusion(Include.NON_NULL);
-	}
-
-	/**
-	 * List accessions.
-	 *
-	 * @return the answer
-	 */
-	public Answer<String> listAccessions() {
-		return new Answer<String>() {
-			@Override
-			public String answer(final InvocationOnMock invocation) throws Throwable {
-				final Object[] args = invocation.getArguments();
-				if (args[2] != null) {
-					throw new MockGenesysException("Querying is not supported.");
-				}
-				final String instituteCode = (String) args[0];
-				final int page = (Integer) args[1];
-
-				System.err.println("Listing accessions instituteCode=" + instituteCode + " page=" + page);
-
-				return objectMapper.writeValueAsString(getAccessionsPage(instituteCode, page));
-			}
-		};
-	}
-
-	/**
-	 * Update accessions.
-	 *
-	 * @return the answer
-	 */
-	public Answer<String> updateAccessions() {
-		return new Answer<String>() {
-			@Override
-			public String answer(final InvocationOnMock invocation) throws Throwable {
-				final Object[] args = invocation.getArguments();
-				final String instituteCode = (String) args[0];
-				final List<?> arrayNode = (List<?>) args[1];
-
-				final String res = objectMapper.writeValueAsString(upsertAccessions(instituteCode, arrayNode));
-				System.err.println("Result: " + res);
-				return res;
-			}
-		};
-	}
-
-	/**
-	 * Upsert accessions.
-	 *
-	 * @param instituteCode the inst code
-	 * @param nodeList the node list
-	 * @return the string
-	 * @throws JsonParseException the json parse exception
-	 * @throws JsonMappingException the json mapping exception
-	 * @throws IOException Signals that an I/O exception has occurred.
-	 * @throws GenesysApiException the genesys api exception
-	 */
-	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(instituteCode, accList = new ArrayList<AccessionJson>());
-		}
-		for (int i = 0; i < nodeList.size(); i++) {
-			final AccessionJson aj = (AccessionJson) nodeList.get(i);
-			final AccessionJson existing = findMatch(accList, aj);
-			merge(accList, existing, aj);
-		}
-		return "OK";
-
-	}
-
-	/**
-	 * Merge.
-	 *
-	 * @param accList the acc list
-	 * @param existing the existing
-	 * @param aj the aj
-	 * @throws MockGenesysException the mock genesys exception
-	 */
-	private void merge(final List<AccessionJson> accList, final AccessionJson existing, final AccessionJson aj) throws MockGenesysException {
-		if (existing == null) {
-			accList.add(aj);
-		} else {
-			if (aj.getAvailable() != null) {
-				existing.setAvailable(aj.getAvailable());
-			}
-			if (aj.getHistoric() != null) {
-				existing.setHistoric(aj.getHistoric());
-			}
-			if (aj.getInTrust() != null) {
-				existing.setInTrust(aj.getInTrust());
-			}
-			if (aj.getMlsStat() != null) {
-				existing.setMlsStat(aj.getMlsStat());
-			}
-			if (aj.getAegis() != null) {
-				existing.setAegis(aj.getAegis());
-			}
-			if (aj.getAccessionNumber() != null) {
-				existing.setAccessionNumber(aj.getAccessionNumber());
-			}
-			if (aj.getAcquisitionDate() != null) {
-				existing.setAcquisitionDate(aj.getAcquisitionDate());
-			}
-			if (aj.getAncest() != null) {
-				existing.setAncest(aj.getAncest());
-			}
-			if (aj.getBredCode() != null) {
-				existing.setBredCode(aj.getBredCode());
-			}
-			if (aj.getColl() != null) {
-
-			}
-			if (aj.getDonorCode() != null) {
-				existing.setDonorCode(aj.getDonorCode());
-			}
-			if (aj.getDonorName() != null) {
-				existing.setDonorName(aj.getDonorName());
-			}
-			if (aj.getDonorNumb() != null) {
-				existing.setDonorNumb(aj.getDonorNumb());
-			}
-			if (aj.getDuplSite() != null) {
-				existing.setDuplSite(aj.getDuplSite());
-			}
-			if (aj.getGeo() != null) {
-
-			}
-			if (aj.getOrgCty() != null) {
-				existing.setOrgCty(aj.getOrgCty());
-			}
-			if (aj.getRemarks() != null) {
-				existing.setRemarks(aj.getRemarks());
-			}
-			if (aj.getSampStat() != null) {
-				existing.setSampStat(aj.getSampStat());
-			}
-			if (aj.getTaxonomy() != null) {
-
-			}
-			if (aj.getUuid() != null) {
-				if (existing.getUuid() == null) {
-					existing.setUuid(aj.getUuid());
-				} else if (!existing.getUuid().equals(aj.getUuid())) {
-					// Can this happen?
-					throw new MockGenesysException("UUID mismatch");
-				}
-			}
-			if (aj.getAvailable() != null) {
-				existing.setAvailable(aj.getAvailable());
-			}
-		}
-	}
-
-	/**
-	 * Find match.
-	 *
-	 * @param accList the acc list
-	 * @param aj the aj
-	 * @return the accession json
-	 */
-	private AccessionJson findMatch(final List<AccessionJson> accList, final AccessionJson aj) {
-		if (aj.getUuid() != null) {
-			return findMatch(accList, aj.getUuid());
-		} else {
-			for (final AccessionJson m : accList) {
-				if (m.getInstituteCode().equals(aj.getInstituteCode()) && m.getAccessionNumber().equals(aj.getAccessionNumber()) && m.getTaxonomy().getGenus().equals(aj.getTaxonomy().getGenus())) {
-					return m;
-				}
-			}
-		}
-		return null;
-	}
-
-	/**
-	 * Find match.
-	 *
-	 * @param accList the acc list
-	 * @param uuid the uuid
-	 * @return the accession json
-	 */
-	private AccessionJson findMatch(final List<AccessionJson> accList, final String uuid) {
-		for (final AccessionJson m : accList) {
-			if (m.getUuid().equals(uuid)) {
-				return m;
-			}
-		}
-		return null;
-	}
-
-	/**
-	 * Gets the accessions page.
-	 *
-	 * @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 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;
-		}
-		if (page != 1) {
-			throw new MockGenesysException("page argument is not suported");
-		}
-
-		return accList;
-	}
-
-}