FileStudyConfigurationManager.java

/*
 * Copyright 2015-2016 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.storage.core.metadata;

import com.fasterxml.jackson.core.JsonFactory;
import com.fasterxml.jackson.databind.ObjectMapper;
import org.opencb.commons.datastore.core.ObjectMap;
import org.opencb.commons.datastore.core.QueryOptions;
import org.opencb.commons.datastore.core.QueryResult;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;

import java.io.IOException;
import java.nio.file.Path;
import java.nio.file.Paths;
import java.util.Collections;
import java.util.HashMap;
import java.util.Map;

/**
 * @author Jacobo Coll <jacobo167@gmail.com>
 */
public class FileStudyConfigurationManager extends StudyConfigurationManager {
    public static final String STUDY_CONFIGURATION_PATH = "studyConfigurationPath";
    protected static Logger logger = LoggerFactory.getLogger(FileStudyConfigurationManager.class);

    private static final Map<Integer, Path> FILE_PATHS = new HashMap<>();

    public FileStudyConfigurationManager(ObjectMap objectMap) {
        super(objectMap);
    }

    @Override
    protected QueryResult<StudyConfiguration> internalGetStudyConfiguration(String studyName, Long timeStamp, QueryOptions options) {
        Path path = getPath(studyName, options);
        QueryResult<StudyConfiguration> result = readStudyConfiguration(path);
        result.first().setStudyName(studyName);
        return result;
    }

    @Override
    public QueryResult<StudyConfiguration> internalGetStudyConfiguration(int studyId, Long timeStamp, QueryOptions options) {
        Path path = getPath(studyId, options);
        QueryResult<StudyConfiguration> result = readStudyConfiguration(path);
        result.first().setStudyId(studyId);
        return result;
    }

    public QueryResult<StudyConfiguration> readStudyConfiguration(Path path) {
        long startTime = System.currentTimeMillis();
        StudyConfiguration studyConfiguration;
        try {
            studyConfiguration = read(path);
        } catch (IOException e) {
            logger.error("Fail at reading StudyConfiguration from " + path, e);
            return new QueryResult<>(path.getFileName().toString(),
                    (int) (System.currentTimeMillis() - startTime), 0, 0, "", e.getMessage(), Collections.<StudyConfiguration>emptyList());
        }

        return new QueryResult<>(path.getFileName().toString(),
                (int) (System.currentTimeMillis() - startTime), 1, 1, "", "", Collections.singletonList(studyConfiguration));
    }

    @Override
    protected QueryResult internalUpdateStudyConfiguration(StudyConfiguration studyConfiguration, QueryOptions options) {
        long startTime = System.currentTimeMillis();

        Path path = getPath(studyConfiguration.getStudyId(), options);
        try {
            write(studyConfiguration, path);
        } catch (IOException e) {
            e.printStackTrace();
        }

        return new QueryResult();
    }

    @Override
    public Map<String, Integer> getStudies(QueryOptions options) {
        return Collections.emptyMap();
    }

    private Path getPath(int studyId, QueryOptions options) {
        Path path;
        if (FILE_PATHS.containsKey(studyId)) {
            path = FILE_PATHS.get(studyId);
        } else {
            Object o = options.get(STUDY_CONFIGURATION_PATH);
            if (o == null) {
                //TODO: Read path from a default folder?
                return Paths.get(studyId + ".json");
            } else if (o instanceof Path) {
                path = (Path) o;
            } else {
                path = Paths.get(o.toString());
            }
            FILE_PATHS.put(studyId, path);
        }
        return path;
    }

    private Path getPath(String studyName, QueryOptions options) {
        Path path;
        Object o = options.get(STUDY_CONFIGURATION_PATH);
        if (o == null) {
            //TODO: Read path from a default folder?
            return Paths.get(studyName + ".json");
        } else if (o instanceof Path) {
            path = (Path) o;
        } else {
            path = Paths.get(o.toString());
        }
        return path;
    }

    public static StudyConfiguration read(Path path) throws IOException {
        if (path == null || !path.toFile().exists()) {
            return new StudyConfiguration(1, "default");
        } else {
            return new ObjectMapper(new JsonFactory()).readValue(path.toFile(), StudyConfiguration.class);
        }
    }

    public static void write(StudyConfiguration studyConfiguration, Path path) throws IOException {
        new ObjectMapper(new JsonFactory()).writerWithDefaultPrettyPrinter().withoutAttribute("inverseFileIds").writeValue(path.toFile(),
                studyConfiguration);
    }

}