/*
* 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);
}
}