/**
* Copyright (C) 2012-2013 Selventa, Inc.
*
* This file is part of the OpenBEL Framework.
*
* This program is free software; you can redistribute it and/or modify it
* under the terms of the GNU Lesser General Public License as published by
* the Free Software Foundation, either version 3 of the License, or
* (at your option) any later version.
*
* The OpenBEL Framework is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY
* or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public
* License for more details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with the OpenBEL Framework. If not, see <http://www.gnu.org/licenses/>.
*
* Additional Terms under LGPL v3:
*
* This license does not authorize you and you are prohibited from using the
* name, trademarks, service marks, logos or similar indicia of Selventa, Inc.,
* or, in the discretion of other licensors or authors of the program, the
* name, trademarks, service marks, logos or similar indicia of such authors or
* licensors, in any marketing or advertising materials relating to your
* distribution of the program or any covered product. This restriction does
* not waive or limit your obligation to keep intact all copyright notices set
* forth in the program as delivered to you.
*
* If you distribute the program in whole or in part, or any modified version
* of the program, and you assume contractual liability to the recipient with
* respect to the program or modified version, then you will indemnify the
* authors and licensors of the program for any liabilities that these
* contractual assumptions directly impose on those licensors and authors.
*/
package org.openbel.framework.core.cache;
import static org.apache.commons.io.FileUtils.deleteDirectory;
import static org.openbel.framework.common.BELUtilities.hasItems;
import static org.openbel.framework.common.cfg.SystemConfiguration.getSystemConfiguration;
import static org.openbel.framework.core.df.cache.CacheUtil.downloadResource;
import static org.openbel.framework.core.df.cache.ResourceType.fromLocation;
import java.io.File;
import java.io.IOException;
import org.openbel.framework.common.Reportable;
import org.openbel.framework.common.index.Index;
import org.openbel.framework.common.index.ResourceLocation;
import org.openbel.framework.core.df.cache.CacheLookupService;
import org.openbel.framework.core.df.cache.CachedResource;
import org.openbel.framework.core.df.cache.ResourceType;
import org.openbel.framework.core.indexer.IndexingFailure;
import org.openbel.framework.core.namespace.NamespaceService;
import org.openbel.framework.core.protocol.ResourceDownloadError;
/**
* DefaultCacheManagerService implements a service to manage the framework
* cache by loading, updating and purging cached resources.
*
* @author Anthony Bargnesi {@code <abargnesi@selventa.com>}
*/
public class DefaultCacheManagerService implements CacheManagerService {
private final CacheLookupService lookupService;
private final NamespaceService nsService;
private final Reportable reportable;
public DefaultCacheManagerService(CacheLookupService lookupService,
NamespaceService nsService, Reportable reportable) {
this.lookupService = lookupService;
this.nsService = nsService;
this.reportable = reportable;
}
/**
* {@inheritDoc}
*/
@Override
public void purgeResources() throws IOException {
File cacheDirectory = getSystemConfiguration().getCacheDirectory();
for (File cacheFile : cacheDirectory.listFiles()) {
if (cacheFile.isDirectory()) {
ResourceType rt = ResourceType.fromFolder(cacheFile.getName());
if (rt != null) {
// we own it, so delete it.
deleteDirectory(cacheFile);
reportable.output("Deleted cache directory: "
+ cacheFile.getAbsolutePath());
}
}
}
}
/**
* {@inheritDoc}
*/
@Override
public void updateResourceInCache(ResourceType type, String location) {
try {
if (ResourceType.NAMESPACES.equals(type)) {
rebuildNamespace(location);
} else {
downloadResource(location, type);
}
reportable.output("Updated resource: " + location);
} catch (ResourceDownloadError e) {
reportable.error(e.getUserFacingMessage());
} catch (IndexingFailure e) {
reportable.error(e.getUserFacingMessage());
} catch (IOException e) {
logExceptionSimple(location, e);
}
}
/**
* {@inheritDoc}
*/
@Override
public void updateResourceIndexInCache(Index index) {
// update annotations in the index
if (hasItems(index.getAnnotationDefinitionResources())) {
for (ResourceLocation rloc : index
.getAnnotationDefinitionResources()) {
try {
downloadResource(rloc.getResourceLocation(),
ResourceType.ANNOTATIONS);
reportable.output("Updated annotation resource: "
+ rloc.getResourceLocation());
} catch (ResourceDownloadError e) {
reportable.error(e.getUserFacingMessage());
}
}
}
// update namespaces in the index
if (hasItems(index.getNamespaceResources())) {
for (ResourceLocation rloc : index.getNamespaceResources()) {
try {
rebuildNamespace(rloc.getResourceLocation());
reportable.output("Updated namespace resource: "
+ rloc.getResourceLocation());
} catch (ResourceDownloadError e) {
reportable.error(e.getUserFacingMessage());
} catch (IndexingFailure e) {
reportable.error(e.getUserFacingMessage());
} catch (IOException e) {
logExceptionSimple(rloc.getResourceLocation(), e);
}
}
}
// update equivalences in the index
if (hasItems(index.getEquivalenceResources())) {
for (ResourceLocation rloc : index.getEquivalenceResources()) {
try {
downloadResource(rloc.getResourceLocation(),
ResourceType.EQUIVALENCES);
reportable.output("Updated equivalence resource: "
+ rloc.getResourceLocation());
} catch (ResourceDownloadError e) {
reportable.error(e.getUserFacingMessage());
}
}
}
// update protein family
if (index.getProteinFamilyResource() != null) {
String pfamLocation =
index.getProteinFamilyResource().getResourceLocation();
try {
downloadResource(pfamLocation, fromLocation(pfamLocation));
reportable.output("Updated protein family resource: "
+ pfamLocation);
} catch (ResourceDownloadError e) {
reportable.error(e.getUserFacingMessage());
}
}
// update named complexes
if (index.getNamedComplexesResource() != null) {
String ncLocation =
index.getNamedComplexesResource().getResourceLocation();
try {
downloadResource(ncLocation, fromLocation(ncLocation));
reportable.output("Updated named complex resource: "
+ ncLocation);
} catch (ResourceDownloadError e) {
reportable.error(e.getUserFacingMessage());
}
}
// update gene scaffolding
if (index.getGeneScaffoldingResource() != null) {
String gsLocation =
index.getGeneScaffoldingResource().getResourceLocation();
try {
downloadResource(gsLocation, fromLocation(gsLocation));
reportable.output("Updated gene scaffolding resource: "
+ gsLocation);
} catch (ResourceDownloadError e) {
reportable.error(e.getUserFacingMessage());
}
}
}
private void rebuildNamespace(String resourceLocation)
throws IOException, ResourceDownloadError, IndexingFailure {
CachedResource cachedResource = lookupService.findInCache(
ResourceType.NAMESPACES, resourceLocation);
// if cached resource exists, remove cached namespace folder
// to force resolving and indexing of namespace
if (cachedResource != null) {
File resourceDirectory = cachedResource.getLocalFile()
.getParentFile();
deleteDirectory(resourceDirectory);
}
// compile namespace
nsService.compileNamespace(resourceLocation);
}
/**
* Reports an {@link Exception} as an error to the {@link Reportable}.
* The error output logged will use the <tt>location</tt> and the
* exception's message if it is not null.
*
* @param location {@link String}, the resource location behind the
* exception
* @param e {@link Exception}, the exception to output message from
*/
private void logExceptionSimple(String location, Exception e) {
StringBuilder bldr = new StringBuilder();
bldr.append("ERROR UPDATING CACHE");
if (location != null) {
bldr.append(" for ");
bldr.append(location);
}
bldr.append("\n\treason: ");
final String msg = e.getMessage();
if (msg != null)
bldr.append(msg);
else
bldr.append("Unknown");
bldr.append("\n");
reportable.error(bldr.toString());
}
}