org.icgc.dcc.metadata.client.core.MetadataClient.java Source code

Introduction

Here is the source code for org.icgc.dcc.metadata.client.core.MetadataClient.java

Source

/*
 * Copyright (c) 2015 The Ontario Institute for Cancer Research. All rights reserved.                             
 *                                                                                                               
 * This program and the accompanying materials are made available under the terms of the GNU Public License v3.0.
 * You should have received a copy of the GNU General Public License along with                                  
 * this program. If not, see <http://www.gnu.org/licenses/>.                                                     
 *                                                                                                               
 * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY                           
 * EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES                          
 * OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT                           
 * SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT,                                
 * INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED                          
 * TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;                               
 * OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER                              
 * IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN                         
 * ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 */
package org.icgc.dcc.metadata.client.core;

import static org.icgc.dcc.common.core.util.FormatUtils.formatCount;

import java.io.File;
import java.io.IOException;
import java.util.Arrays;
import java.util.List;

import lombok.SneakyThrows;
import lombok.val;
import lombok.extern.slf4j.Slf4j;

import org.icgc.dcc.metadata.client.core.GNOSFileDirectoryReader.GNOSFile;
import org.icgc.dcc.metadata.client.model.Entity;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.beans.factory.annotation.Value;
import org.springframework.stereotype.Component;
import org.springframework.web.client.HttpClientErrorException;
import org.springframework.web.client.RestTemplate;

import com.google.common.collect.ImmutableList;

@Slf4j
@Component
public class MetadataClient {

    @Value("${server.baseUrl}")
    private String baseUrl;
    @Autowired
    private RestTemplate restTemplate;

    @SneakyThrows
    public void register(File inputDir, File outputDir, String manifestFileName) {
        log.info("Regisitering: inputDir: {}, outputDir: {}, manifestFileName: {}", inputDir.getCanonicalPath(),
                outputDir.getCanonicalPath(), manifestFileName);

        log.info("Reading '{}' for files...", inputDir.getCanonicalPath());
        val files = readFiles(inputDir);
        log.info("Read {} files", formatCount(files));

        val entities = register(files);

        val manifestWriter = new ManifestWriter(inputDir, outputDir);
        manifestWriter.writeManifest(manifestFileName, entities);
    }

    private List<Entity> register(List<GNOSFile> files) {
        val registeredEntities = ImmutableList.<Entity>builder();

        for (val file : files) {
            val entities = getEntities(file.getGnosId(), file.getFileName());

            if (!entities.isEmpty()) {
                log.info("Entity {} already registered. Returning...", entities);

                registeredEntities.addAll(entities);
                continue;
            } else {
                val entity = createEntity(file.getGnosId(), file.getFileName());

                registeredEntities.add(entity);
            }
        }

        return registeredEntities.build();
    }

    private List<Entity> getEntities(String gnosId, String fileName) {
        val url = baseUrl + "/" + "entities?gnosId=" + gnosId + "&" + "fileName=" + fileName;

        try {
            val entities = Arrays.asList(restTemplate.getForObject(url, Entity[].class));
            log.info("Entities: {}", entities);

            return entities;
        } catch (HttpClientErrorException e) {
            log.error("Unexpected response code {} requesting entity with gnosId = {}, fileName = {}",
                    e.getStatusCode(), gnosId, fileName);

            throw e;
        }
    }

    private Entity createEntity(String gnosId, String fileName) {
        val url = baseUrl + "/" + "entities";
        val entity = new Entity().setGnosId(gnosId).setFileName(fileName);

        try {
            log.info("Posting: {}", entity);
            val response = restTemplate.postForEntity(url, entity, Entity.class);
            log.info("Entity: {}", response);

            return response.getBody();
        } catch (HttpClientErrorException e) {
            log.error("Unexpected response code {} creating entity {}", e.getStatusCode(), entity);

            throw e;
        }
    }

    private List<GNOSFile> readFiles(File gnosDir) throws IOException {
        return new GNOSFileDirectoryReader().readFiles(gnosDir);
    }

}