org.opencb.opencga.client.rest.OpenCGAClient Maven / Gradle / Ivy
/*
* Copyright 2015-2020 OpenCB
*
* 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.opencb.opencga.client.rest;
import io.jsonwebtoken.Claims;
import io.jsonwebtoken.Jwts;
import org.apache.commons.lang3.StringUtils;
import org.opencb.commons.datastore.core.Event;
import org.opencb.opencga.client.config.ClientConfiguration;
import org.opencb.opencga.client.exceptions.ClientException;
import org.opencb.opencga.client.rest.clients.*;
import org.opencb.opencga.core.models.user.AuthenticationResponse;
import org.opencb.opencga.core.models.user.LoginParams;
import org.opencb.opencga.core.response.RestResponse;
import java.util.HashMap;
import java.util.Map;
import java.util.Objects;
import java.util.concurrent.TimeUnit;
import java.util.function.Supplier;
/**
* Created by imedina on 04/05/16.
*/
public class OpenCGAClient {
protected String userId;
protected String token;
protected String refreshToken;
protected ClientConfiguration clientConfiguration;
protected Map clients;
protected boolean throwExceptionOnError;
public OpenCGAClient(ClientConfiguration clientConfiguration) {
this.init(null, clientConfiguration);
}
public OpenCGAClient(String organizationId, String user, String password, ClientConfiguration clientConfiguration)
throws ClientException {
AuthenticationResponse login = login(organizationId, user, password);
this.init(login, clientConfiguration);
}
public OpenCGAClient(AuthenticationResponse authenticationTokens, ClientConfiguration clientConfiguration) {
this.init(authenticationTokens, clientConfiguration);
}
protected static String getUserFromToken(String token) {
// https://github.com/jwtk/jjwt/issues/280
// https://github.com/jwtk/jjwt/issues/86
// https://stackoverflow.com/questions/34998859/android-jwt-parsing-payload-claims-when-signed
String withoutSignature = token.substring(0, token.lastIndexOf('.') + 1);
Claims claims = (Claims) Jwts.parser()
.setAllowedClockSkewSeconds(TimeUnit.DAYS.toSeconds(3650))
.parse(withoutSignature)
.getBody();
return claims.getSubject();
}
private void init(AuthenticationResponse tokens, ClientConfiguration clientConfiguration) {
this.clients = new HashMap<>(25);
if (tokens != null) {
setToken(tokens.getToken());
setRefreshToken(tokens.getRefreshToken());
this.userId = getUserFromToken(tokens.getToken());
}
this.clientConfiguration = clientConfiguration;
}
public OrganizationClient getOrganizationClient() {
return getClient(OrganizationClient.class, () -> new OrganizationClient(token, clientConfiguration));
}
public UserClient getUserClient() {
return getClient(UserClient.class, () -> new UserClient(token, clientConfiguration));
}
public ProjectClient getProjectClient() {
return getClient(ProjectClient.class, () -> new ProjectClient(token, clientConfiguration));
}
public StudyClient getStudyClient() {
return getClient(StudyClient.class, () -> new StudyClient(token, clientConfiguration));
}
public FileClient getFileClient() {
return getClient(FileClient.class, () -> new FileClient(token, clientConfiguration));
}
public JobClient getJobClient() {
return getClient(JobClient.class, () -> new JobClient(token, clientConfiguration));
}
public IndividualClient getIndividualClient() {
return getClient(IndividualClient.class, () -> new IndividualClient(token, clientConfiguration));
}
public SampleClient getSampleClient() {
return getClient(SampleClient.class, () -> new SampleClient(token, clientConfiguration));
}
public AdminClient getAdminClient() {
return getClient(AdminClient.class, () -> new AdminClient(token, clientConfiguration));
}
public CohortClient getCohortClient() {
return getClient(CohortClient.class, () -> new CohortClient(token, clientConfiguration));
}
public ClinicalAnalysisClient getClinicalAnalysisClient() {
return getClient(ClinicalAnalysisClient.class, () -> new ClinicalAnalysisClient(token, clientConfiguration));
}
public DiseasePanelClient getDiseasePanelClient() {
return getClient(DiseasePanelClient.class, () -> new DiseasePanelClient(token, clientConfiguration));
}
public FamilyClient getFamilyClient() {
return getClient(FamilyClient.class, () -> new FamilyClient(token, clientConfiguration));
}
public AlignmentClient getAlignmentClient() {
return getClient(AlignmentClient.class, () -> new AlignmentClient(token, clientConfiguration));
}
public VariantClient getVariantClient() {
return getClient(VariantClient.class, () -> new VariantClient(token, clientConfiguration));
}
public VariantOperationClient getVariantOperationClient() {
return getClient(VariantOperationClient.class, () -> new VariantOperationClient(token, clientConfiguration));
}
public MetaClient getMetaClient() {
return getClient(MetaClient.class, () -> new MetaClient(token, clientConfiguration));
}
@SuppressWarnings("unchecked")
protected T getClient(Class clazz, Supplier constructor) {
return (T) clients.computeIfAbsent(clazz.getName(), (k) -> {
T t = constructor.get();
t.setThrowExceptionOnError(throwExceptionOnError);
return t;
});
}
/**
* Refresh the user token.
*
* @return the new AuthenticationResponse object.
* @throws ClientException when it is not possible refreshing.
*/
public AuthenticationResponse refresh() throws ClientException {
if (StringUtils.isEmpty(refreshToken)) {
throw new ClientException("Could not refresh token. 'refreshToken' not available.");
}
RestResponse refresh = getUserClient().login(new LoginParams(refreshToken), null);
updateTokenFromClients(refresh);
return refresh.firstResult();
}
/**
* Logs in the user.
*
* @param organizationId Organization id.
* @param user userId.
* @param password Password.
* @return AuthenticationResponse object.
* @throws ClientException when it is not possible logging in.
*/
public AuthenticationResponse login(String organizationId, String user, String password) throws ClientException {
RestResponse login = getUserClient().login(new LoginParams(organizationId, user, password), null);
updateTokenFromClients(login);
this.userId = user;
return login.firstResult();
}
/**
* Logs in the user.
*
* @param refreshToken userId.
* @return AuthenticationResponse object.
* @throws ClientException when it is not possible logging in.
*/
public AuthenticationResponse refresh(String refreshToken) throws ClientException {
RestResponse login = getUserClient().login(new LoginParams(refreshToken), null);
updateTokenFromClients(login);
return login.firstResult();
}
public void updateTokenFromClients(RestResponse loginResponse) throws ClientException {
if (loginResponse.allResultsSize() == 1) {
setToken(loginResponse.firstResult().getToken());
setRefreshToken(loginResponse.firstResult().getRefreshToken());
} else {
for (Event event : loginResponse.getEvents()) {
if (event.getType() == Event.Type.ERROR) {
throw new ClientException(event.getMessage());
}
}
}
}
public void logout() {
if (this.token != null) {
// Remove token and userId for all clients
setToken(null);
setUserId(null);
}
}
@Override
public String toString() {
final StringBuilder sb = new StringBuilder("OpenCGAClient{");
sb.append("userId='").append(userId).append('\'');
sb.append(", token='").append(token).append('\'');
sb.append(", refreshToken='").append(refreshToken).append('\'');
sb.append(", clientConfiguration=").append(clientConfiguration);
sb.append('}');
return sb.toString();
}
public String getUserId() {
return userId;
}
public void setUserId(String userId) {
this.userId = userId;
}
public String getToken() {
return token;
}
public void setToken(String token) {
this.token = token;
// Update token for all clients
clients.values().stream()
.filter(Objects::nonNull)
.forEach(abstractParentClient -> {
abstractParentClient.setToken(this.token);
});
}
public String getRefreshToken() {
return refreshToken;
}
public OpenCGAClient setRefreshToken(String refreshToken) {
this.refreshToken = refreshToken;
return this;
}
public ClientConfiguration getClientConfiguration() {
return clientConfiguration;
}
public OpenCGAClient setClientConfiguration(ClientConfiguration clientConfiguration) {
this.clientConfiguration = clientConfiguration;
return this;
}
public boolean isThrowExceptionOnError() {
return throwExceptionOnError;
}
public OpenCGAClient setThrowExceptionOnError(boolean throwExceptionOnError) {
this.throwExceptionOnError = throwExceptionOnError;
// We have to set the value to all existing clients
clients.values().stream()
.filter(Objects::nonNull)
.forEach(abstractParentClient -> {
abstractParentClient.setThrowExceptionOnError(this.throwExceptionOnError);
});
return this;
}
}
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