org.opencb.cellbase.lib.managers.DataReleaseManager Maven / Gradle / Ivy
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/*
* 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.cellbase.lib.managers;
import com.fasterxml.jackson.core.JsonProcessingException;
import com.fasterxml.jackson.databind.ObjectMapper;
import com.fasterxml.jackson.databind.ObjectReader;
import org.apache.commons.collections4.CollectionUtils;
import org.apache.commons.collections4.MapUtils;
import org.apache.commons.lang3.StringUtils;
import org.opencb.cellbase.core.common.GitRepositoryState;
import org.opencb.cellbase.core.config.CellBaseConfiguration;
import org.opencb.cellbase.core.exception.CellBaseException;
import org.opencb.cellbase.core.models.DataRelease;
import org.opencb.cellbase.core.models.DataReleaseSource;
import org.opencb.cellbase.core.result.CellBaseDataResult;
import org.opencb.cellbase.lib.impl.core.CellBaseDBAdaptor;
import org.opencb.cellbase.lib.impl.core.ReleaseMongoDBAdaptor;
import java.io.IOException;
import java.nio.file.Path;
import java.text.SimpleDateFormat;
import java.util.*;
import java.util.stream.Collectors;
public class DataReleaseManager extends AbstractManager {
private ReleaseMongoDBAdaptor releaseDBAdaptor;
public DataReleaseManager(String databaseName, CellBaseConfiguration configuration) throws CellBaseException {
super(databaseName, configuration);
init();
}
public DataReleaseManager(String species, String assembly, CellBaseConfiguration configuration) throws CellBaseException {
super(species, assembly, configuration);
init();
}
private void init() {
releaseDBAdaptor = dbAdaptorFactory.getReleaseDBAdaptor();
}
public CellBaseDataResult getReleases() {
return releaseDBAdaptor.getAll();
}
public DataRelease createRelease() throws JsonProcessingException {
SimpleDateFormat sdf = new SimpleDateFormat("yyyyMMddHHmmss");
// If collection release does not exist, it has to be created from zero (release 1), otherwise the biggest release
// will be used to increment the release number and then create the new document release with the current date
DataRelease lastRelease = null;
CellBaseDataResult releaseResult = getReleases();
if (CollectionUtils.isNotEmpty(releaseResult.getResults())) {
for (DataRelease dataRelease : releaseResult.getResults()) {
if (lastRelease == null || dataRelease.getRelease() > lastRelease.getRelease()) {
lastRelease = dataRelease;
}
}
}
// Is it the first release?
if (lastRelease == null) {
// Create the first release, collections and sources are empty
lastRelease = new DataRelease()
.setRelease(1)
.setDate(sdf.format(new Date()));
releaseDBAdaptor.insert(lastRelease);
} else {
// Check if collections are empty, a new data release will be created only if collections is not empty
if (MapUtils.isNotEmpty(lastRelease.getCollections())) {
// Increment the release number, only if the previous release has collections
lastRelease.setRelease(lastRelease.getRelease() + 1)
.setActiveByDefaultIn(new ArrayList<>())
.setDate(sdf.format(new Date()));
// Write it to the database
releaseDBAdaptor.insert(lastRelease);
} else {
lastRelease = null;
}
}
return lastRelease;
}
public DataRelease get(int release) throws CellBaseException {
CellBaseDataResult result = releaseDBAdaptor.getAll();
if (CollectionUtils.isNotEmpty(result.getResults())) {
for (DataRelease dataRelease : result.getResults()) {
if (dataRelease.getRelease() == release) {
return dataRelease;
}
}
}
throw new CellBaseException("Data release '" + release + "' does not exist for species = " + species + ", assembly = " + assembly);
}
public DataRelease getDefault(String cellBaseVersion) throws CellBaseException {
CellBaseDataResult result = releaseDBAdaptor.getAll();
if (CollectionUtils.isNotEmpty(result.getResults())) {
for (DataRelease dataRelease : result.getResults()) {
if (dataRelease.getActiveByDefaultIn().contains(cellBaseVersion)) {
return dataRelease;
}
}
}
throw new CellBaseException("No data release found for CellBase " + cellBaseVersion + " (species = " + species + ", assembly = "
+ assembly + ")");
}
public DataRelease update(int release, List versions) throws CellBaseException {
return releaseDBAdaptor.update(release, versions).first();
}
public DataRelease update(int release, String collection, String data, List dataSourcePaths)
throws CellBaseException {
DataRelease currDataRelease = get(release);
if (currDataRelease != null) {
// Update collections
currDataRelease.getCollections().put(collection, CellBaseDBAdaptor.buildCollectionName(collection, release));
// Check sources
if (StringUtils.isNotEmpty(data) && CollectionUtils.isNotEmpty(dataSourcePaths)) {
List newSources = new ArrayList<>();
// First, add new data sources
Set sourceSet = new HashSet<>();
ObjectMapper jsonObjectMapper = new ObjectMapper();
ObjectReader jsonObjectReader = jsonObjectMapper.readerFor(DataReleaseSource.class);
for (Path dataSourcePath : dataSourcePaths) {
if (dataSourcePath.toFile().exists()) {
try {
DataReleaseSource dataReleaseSource = jsonObjectReader.readValue(dataSourcePath.toFile());
newSources.add(dataReleaseSource);
sourceSet.add(dataReleaseSource.getData() + "__" + dataReleaseSource.getName());
} catch (IOException e) {
logger.warn("Something wrong happened when reading data release source " + dataSourcePath + ". "
+ e.getMessage());
}
}
}
// Second, add previous data sources if necessary (to avoid duplicated sources)
for (DataReleaseSource source : currDataRelease.getSources()) {
String key = source.getData() + "__" + source.getName();
if (!sourceSet.contains(key)) {
newSources.add(source);
}
}
if (CollectionUtils.isNotEmpty(newSources)) {
currDataRelease.setSources(newSources);
}
}
// Update data release in the database
update(currDataRelease);
return currDataRelease;
}
throw new CellBaseException("Data release '" + release + "' does not exist for species = " + species + ", assembly = " + assembly);
}
public void update(DataRelease dataRelase) {
if (MapUtils.isNotEmpty(dataRelase.getCollections())) {
releaseDBAdaptor.update(dataRelase.getRelease(), "collections", dataRelase.getCollections());
}
if (CollectionUtils.isNotEmpty(dataRelase.getSources())) {
// TODO: use native functions
List> tmp = new ArrayList<>();
for (DataReleaseSource source : dataRelase.getSources()) {
Map map = new HashMap<>();
if (StringUtils.isNotEmpty(source.getData())) {
map.put("data", source.getData());
}
if (StringUtils.isNotEmpty(source.getName())) {
map.put("name", source.getName());
}
if (StringUtils.isNotEmpty(source.getVersion())) {
map.put("version", source.getVersion());
}
if (CollectionUtils.isNotEmpty(source.getUrl())) {
map.put("url", source.getUrl());
}
if (StringUtils.isNotEmpty(source.getDate())) {
map.put("date", source.getDate());
}
tmp.add(map);
}
releaseDBAdaptor.update(dataRelase.getRelease(), "sources", tmp);
}
}
public String getMaintenanceFlagFile() {
return configuration.getMaintenanceFlagFile();
}
public String getMaintainerContact() {
return configuration.getMaintainerContact();
}
public DataRelease checkDataRelease(int inRelease) throws CellBaseException {
DataRelease outRelease;
if (inRelease < 0) {
throw new CellBaseException("Invalid data release " + inRelease + ". Data release must be greater or equal to 0");
}
if (inRelease == 0) {
String[] split = GitRepositoryState.get().getBuildVersion().split("[.-]");
String version = "v" + split[0] + "." + split[1];
outRelease = getDefault(version);
logger.info("Using data release 0: it means to take default data release '" + outRelease.getRelease()
+ "' for CellBase version '" + version + "'");
return outRelease;
}
List dataReleases = getReleases().getResults();
for (DataRelease dataRelease : dataReleases) {
if (inRelease == dataRelease.getRelease()) {
return dataRelease;
}
}
throw new CellBaseException("Invalid data release " + inRelease + " for species = " + species + ", assembly = " + assembly
+ ". Valid data releases are: " + StringUtils.join(dataReleases.stream().map(dr -> dr.getRelease())
.collect(Collectors.toList()), ","));
}
}
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