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Commit 4880b4be authored by Matija Obreza's avatar Matija Obreza
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Merge branch 'drop-obsolete-code' into 'master' 

Drop obsolete code for /api/v0

See merge request !16
parents fe5db68a c20b7a71
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src/test/java/org/geneys2/client/oauth/AccessionApiTest.java deleted 100644 → 0
View file @ fe5db68a
/*
* 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
View file @ 4880b4be
...@@ -29,7 +29,7 @@ import org.junit.Test; ...@@ -29,7 +29,7 @@ import org.junit.Test;
public class AccessionImagesTest { public class AccessionImagesTest {
/** The mapper. */ /** The mapper. */
private static ObjectMapper objectMapper; private static final ObjectMapper objectMapper;
static { static {
objectMapper = new ObjectMapper(); objectMapper = new ObjectMapper();
......
src/test/java/org/geneys2/client/oauth/MockGenesysServer.java deleted 100644 → 0
View file @ fe5db68a
/*
* 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;
}
}
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