private void checkSubstance(ArchivalUnit au) {
SubstanceChecker subChecker = new SubstanceChecker(au);
if (!subChecker.isEnabled()) {
errMsg = "No substance patterns defined for plugin.";
return;
}
AuState auState = AuUtil.getAuState(au);
SubstanceChecker.State oldState = auState.getSubstanceState();
SubstanceChecker.State newState = subChecker.findSubstance();
String chtxt = (newState == oldState ? "(unchanged)" : "(was " + oldState.toString() + ")");
switch (newState) {
case Unknown:
log.error("Shouldn't happen: SubstanceChecker returned Unknown");
errMsg = "Error in SubstanceChecker; see log.";
break;
case Yes:
statusMsg = "AU has substance " + chtxt + ": " + au.getName();
auState.setSubstanceState(SubstanceChecker.State.Yes);
break;
case No:
statusMsg = "AU has no substance " + chtxt + ": " + au.getName();
auState.setSubstanceState(SubstanceChecker.State.No);
break;
}
}
private void deleteBlock(CachedUrl cu) throws IOException {
log.info("deleting " + cu.getUrl());
CachedUrlSetSpec cuss = new SingleNodeCachedUrlSetSpec(cu.getUrl());
ArchivalUnit au = cu.getArchivalUnit();
CachedUrlSet cus = au.makeCachedUrlSet(cuss);
NodeManager nm = au.getPlugin().getDaemon().getNodeManager(au);
nm.deleteNode(cus);
}
public void testFunctionalFromTarHierarchy() throws Exception {
log.debug3("in testFromTarHierarchy");
// load the tarballs
InputStream file_input = null;
try {
file_input = getResourceAsStream(realTARFile_A);
// UrlCacher uc = au.makeUrlCacher(TAR_A_BASE);
// uc.storeContent(file_input, tarHeader);
UrlCacher uc = tarAu.makeUrlCacher(new UrlData(file_input, tarHeader, TAR_A_BASE));
uc.storeContent();
IOUtil.safeClose(file_input);
file_input = getResourceAsStream(realTARFile_B);
// uc = au.makeUrlCacher(TAR_B_BASE);
// uc.storeContent(file_input, tarHeader);
uc = tarAu.makeUrlCacher(new UrlData(file_input, tarHeader, TAR_B_BASE));
uc.storeContent();
IOUtil.safeClose(file_input);
} catch (IOException e) {
// TODO Auto-generated catch block
e.printStackTrace();
} finally {
IOUtil.safeClose(file_input);
}
CachedUrlSet cus = tarAu.getAuCachedUrlSet();
for (CachedUrl cu : cus.getCuIterable()) {
log.debug3("AU - cu is: " + cu.getUrl());
cu.release();
}
// We need to start from the level of the ArticleMetadataExtractor
MyListEmitter emitter = new MyListEmitter();
ArticleMetadataExtractor amEx =
new ElsevierDeferredArticleMetadataExtractor(ArticleFiles.ROLE_ARTICLE_METADATA);
Iterator<ArticleFiles> it = tarAu.getArticleIterator(MetadataTarget.Any());
while (it.hasNext()) {
ArticleFiles af = it.next();
log.debug3("Metadata test - articlefiles " + af.toString());
// CachedUrl cu = af.getFullTextCu();
CachedUrl cu = af.getRoleCu(ArticleFiles.ROLE_ARTICLE_METADATA);
log.debug3("metadata cu is " + cu.getUrl());
// List<ArticleMetadata> mdlist = mle.extract(MetadataTarget.Any(), cu);
amEx.extract(MetadataTarget.Any(), af, emitter);
List<ArticleMetadata> returnList = emitter.getAmList();
assertNotNull(returnList);
log.debug3("size of returnList is " + returnList.size());
Iterator<ArticleMetadata> mdIt = returnList.iterator();
ArticleMetadata mdRecord = null;
while (mdIt.hasNext()) {
mdRecord = (ArticleMetadata) mdIt.next();
validateCompleteMetadataRecord(mdRecord);
}
}
}
private boolean startReindexingMetadata(ArchivalUnit au, boolean force) {
if (metadataMgr == null) {
errMsg = "Metadata processing is not enabled.";
return false;
}
if (!force) {
if (!AuUtil.hasCrawled(au)) {
errMsg = "Au has never crawled. Click again to reindex metadata";
showForceReindexMetadata = true;
return false;
}
AuState auState = AuUtil.getAuState(au);
switch (auState.getSubstanceState()) {
case No:
errMsg = "Au has no substance. Click again to reindex metadata";
showForceReindexMetadata = true;
return false;
case Unknown:
errMsg = "Unknown substance for Au. Click again to reindex metadata.";
showForceReindexMetadata = true;
return false;
case Yes:
// fall through
}
}
// Fully reindex metadata with the highest priority.
Connection conn = null;
PreparedStatement insertPendingAuBatchStatement = null;
try {
conn = dbMgr.getConnection();
insertPendingAuBatchStatement = metadataMgr.getPrioritizedInsertPendingAuBatchStatement(conn);
if (metadataMgr.enableAndAddAuToReindex(
au, conn, insertPendingAuBatchStatement, false, true)) {
statusMsg = "Reindexing metadata for " + au.getName();
return true;
}
} catch (DbException dbe) {
log.error("Cannot reindex metadata for " + au.getName(), dbe);
} finally {
DbManager.safeCloseStatement(insertPendingAuBatchStatement);
DbManager.safeRollbackAndClose(conn);
}
if (force) {
errMsg = "Still cannot reindex metadata for " + au.getName();
} else {
errMsg = "Cannot reindex metadata for " + au.getName();
}
return false;
}
public void testArticleCountAndType() throws Exception {
int expCount = 28;
PluginTestUtil.crawlSimAu(sau);
String pat1 = "branch(\\d+)/(\\d+file\\.html)";
String rep1 = "aps/journal/v123/n$1/full/$2";
PluginTestUtil.copyAu(sau, nau, ".*[^.][^p][^d][^f]$", pat1, rep1);
String pat2 = "branch(\\d+)/(\\d+file\\.pdf)";
String rep2 = "aps/journal/v123/n$1/pdf/$2";
PluginTestUtil.copyAu(sau, nau, ".*\\.pdf$", pat2, rep2);
// Remove some URLs
int deleted = 0;
for (Iterator it = nau.getAuCachedUrlSet().contentHashIterator(); it.hasNext(); ) {
CachedUrlSetNode cusn = (CachedUrlSetNode) it.next();
if (cusn instanceof CachedUrl) {
CachedUrl cu = (CachedUrl) cusn;
String url = cu.getUrl();
if (url.contains("/journal/")
&& (url.endsWith("1file.html") || url.endsWith("2file.pdf"))) {
deleteBlock(cu);
++deleted;
}
}
}
assertEquals(8, deleted);
Iterator<ArticleFiles> it = nau.getArticleIterator();
int count = 0;
int countHtmlOnly = 0;
int countPdfOnly = 0;
while (it.hasNext()) {
ArticleFiles af = it.next();
log.info(af.toString());
CachedUrl cu = af.getFullTextCu();
String url = cu.getUrl();
assertNotNull(cu);
String contentType = cu.getContentType();
log.debug("count " + count + " url " + url + " " + contentType);
count++;
if (af.getRoleUrl(ArticleFiles.ROLE_FULL_TEXT_PDF) == null) {
++countHtmlOnly;
}
if (af.getRoleUrl(ArticleFiles.ROLE_FULL_TEXT_PDF) == url) {
++countPdfOnly;
}
}
log.debug("Article count is " + count);
assertEquals(expCount, count);
assertEquals(4, countHtmlOnly);
assertEquals(4, countPdfOnly);
}
private boolean disableMetadataIndexing(ArchivalUnit au, boolean force) {
if (metadataMgr == null) {
errMsg = "Metadata processing is not enabled.";
return false;
}
try {
metadataMgr.disableAuIndexing(au);
statusMsg = "Disabled metadata indexing for " + au.getName();
return true;
} catch (Exception e) {
errMsg = "Cannot reindex metadata for " + au.getName() + ": " + e.getMessage();
return false;
}
}
private void crawlPluginRegistries() {
StringBuilder sb = new StringBuilder();
for (ArchivalUnit au : pluginMgr.getAllRegistryAus()) {
sb.append(au.getName());
sb.append(": ");
try {
startCrawl(au, true, false);
sb.append("Queued.");
} catch (CrawlManagerImpl.NotEligibleException e) {
sb.append("Failed: ");
sb.append(e.getMessage());
}
sb.append("\n");
}
statusMsg = sb.toString();
}
/* private support methods */
private List<ArticleMetadata> setupContentForAU(
ArchivalUnit au, String url, String content, boolean isHtmlExtractor)
throws IOException, PluginException {
FileMetadataExtractor me;
InputStream input = null;
CIProperties props = null;
if (isHtmlExtractor) {
input = IOUtils.toInputStream(content, "utf-8");
props = getContentHtmlProperties();
me =
new BaseAtyponHtmlMetadataExtractorFactory()
.createFileMetadataExtractor(MetadataTarget.Any(), "text/html");
} else {
input = IOUtils.toInputStream(content, "utf-8");
props = getContentRisProperties();
me =
new BaseAtyponRisMetadataExtractorFactory()
.createFileMetadataExtractor(MetadataTarget.Any(), "text/plain");
}
UrlData ud = new UrlData(input, props, url);
UrlCacher uc = au.makeUrlCacher(ud);
uc.storeContent();
CachedUrl cu = uc.getCachedUrl();
FileMetadataListExtractor mle = new FileMetadataListExtractor(me);
return mle.extract(MetadataTarget.Any(), cu);
}
public void export() {
log.debug("export(" + au.getName() + ")");
log.debug(
"dir: "
+ dir
+ ", pref: "
+ prefix
+ ", size: "
+ maxSize
+ ", ver: "
+ maxVersions
+ (compress ? ", (C)" : ""));
checkArgs();
try {
start();
} catch (IOException e) {
recordError("Error opening file", e);
return;
}
writeFiles();
try {
finish();
} catch (IOException e) {
if (!isDiskFull) {
// If we already knew (and reported) disk full, also reporting it
// as a close error is misleading.
recordError("Error closing file", e);
}
}
}
public static String getRepositorySpec(ArchivalUnit au) {
Configuration auConfig = au.getConfiguration();
if (auConfig != null) { // can be null in unit tests
String repoSpec = auConfig.get(PluginManager.AU_PARAM_REPOSITORY);
if (repoSpec != null && repoSpec.startsWith("local:")) {
return repoSpec;
}
}
return "local:" + CurrentConfig.getParam(PARAM_CACHE_LOCATION);
}
List<String> auUrls(ArchivalUnit au) {
List<String> res = new ArrayList<String>();
for (Iterator iter = au.getAuCachedUrlSet().contentHashIterator(); iter.hasNext(); ) {
CachedUrlSetNode cusn = (CachedUrlSetNode) iter.next();
if (cusn.hasContent()) {
res.add(cusn.getUrl());
}
}
return res;
}
public BePressArticleIterator(
ArchivalUnit au, SubTreeArticleIterator.Spec spec, boolean isSection) {
super(au, spec);
String volumeAsString = au.getConfiguration().get(ConfigParamDescr.VOLUME_NUMBER.getKey());
String journalAbbr = au.getConfiguration().get(ConfigParamDescr.JOURNAL_ABBR.getKey());
if (isSection) {
journalAbbr = journalAbbr + "/" + au.getConfiguration().get("journal_section");
}
// pick up issue level and lower (make (art)?[0-9]+ optional because a few au's have article
// at issue level
this.pattern =
Pattern.compile(
String.format(
"/%s/((([^0-9]+/)?(vol)?%s/(iss)?[0-9]+(/(art)?[0-9]+)?)|(vol%s/(?-i:[A-Z])[0-9]+))$",
journalAbbr, volumeAsString, volumeAsString),
Pattern.CASE_INSENSITIVE);
this.TOC_pattern =
Pattern.compile(
String.format("/%s/([^0-9]+/)?(vol)?%s/(iss)?[0-9]+$", journalAbbr, volumeAsString),
Pattern.CASE_INSENSITIVE);
}
/**
* Factory method to create new LockssRepository instances.
*
* @param au the {@link ArchivalUnit}
* @return the new LockssRepository instance
*/
public static LockssRepository createNewLockssRepository(ArchivalUnit au) {
String root = getRepositoryRoot(au);
if (root == null || root.equals("null")) {
logger.error("No repository dir set in config");
throw new LockssRepository.RepositoryStateException("No repository dir set in config");
}
String auDir = LockssRepositoryImpl.mapAuToFileLocation(root, au);
if (logger.isDebug2()) {
logger.debug2("repo: " + auDir + ", au: " + au.getName());
}
staticCacheLocation = extendCacheLocation(root);
LockssRepositoryImpl repo = new LockssRepositoryImpl(auDir);
Plugin plugin = au.getPlugin();
if (plugin != null) {
LockssDaemon daemon = plugin.getDaemon();
if (daemon != null) {
RepositoryManager mgr = daemon.getRepositoryManager();
if (mgr != null) {
mgr.setRepositoryForPath(auDir, repo);
}
}
}
return repo;
}
private boolean startCrawl(ArchivalUnit au, boolean force, boolean deep)
throws CrawlManagerImpl.NotEligibleException {
CrawlManagerImpl cmi = (CrawlManagerImpl) crawlMgr;
if (force) {
RateLimiter limit = cmi.getNewContentRateLimiter(au);
if (!limit.isEventOk()) {
limit.unevent();
}
}
cmi.checkEligibleToQueueNewContentCrawl(au);
String delayMsg = "";
String deepMsg = "";
try {
cmi.checkEligibleForNewContentCrawl(au);
} catch (CrawlManagerImpl.NotEligibleException e) {
delayMsg = ", Start delayed due to: " + e.getMessage();
}
Configuration config = ConfigManager.getCurrentConfig();
int pri = config.getInt(PARAM_CRAWL_PRIORITY, DEFAULT_CRAWL_PRIORITY);
CrawlReq req;
try {
req = new CrawlReq(au);
req.setPriority(pri);
if (deep) {
int d = Integer.parseInt(formDepth);
if (d < 0) {
errMsg = "Illegal refetch depth: " + d;
return false;
}
req.setRefetchDepth(d);
deepMsg = "Deep (" + req.getRefetchDepth() + ") ";
}
} catch (NumberFormatException e) {
errMsg = "Illegal refetch depth: " + formDepth;
return false;
} catch (RuntimeException e) {
log.error("Couldn't create CrawlReq: " + au, e);
errMsg = "Couldn't create CrawlReq: " + e.toString();
return false;
}
cmi.startNewContentCrawl(req, null);
statusMsg = deepMsg + "Crawl requested for " + au.getName() + delayMsg;
return true;
}
public void setUp() throws Exception {
super.setUp();
setUpDiskSpace(); // you need this to have startService work properly...
theDaemon = getMockLockssDaemon();
theDaemon.getAlertManager();
theDaemon.getPluginManager().setLoadablePluginsReady(true);
theDaemon.setDaemonInited(true);
theDaemon.getPluginManager().startService();
theDaemon.getCrawlManager();
// in this directory this is file "test_baseatypon.tdb" but it becomes xml
ConfigurationUtil.addFromUrl(getResource("test_baseatypon.xml"));
Tdb tdb = ConfigManager.getCurrentConfig().getTdb();
TdbAu tdbau1 = tdb.getTdbAusLikeName(goodJournal + " Volume " + goodVolume).get(0);
assertNotNull("Didn't find named TdbAu", tdbau1);
bau1 = PluginTestUtil.createAndStartAu(tdbau1);
assertNotNull(bau1);
TypedEntryMap auConfig = bau1.getProperties();
assertEquals(BASE_URL, auConfig.getString(BASE_URL_KEY));
}
/**
* Finds the directory for this AU. If none found in the map, designates a new dir for it.
*
* @param au the AU
* @param repoRoot root of the repository
* @return the dir {@link String}
*/
static String getAuDir(ArchivalUnit au, String repoRoot, boolean create) {
return getAuDir(au.getAuId(), repoRoot, create);
}
private void callV3ContentPoll(ArchivalUnit au) throws PollManager.NotEligibleException {
log.debug("Enqueuing a V3 Content Poll on " + au.getName());
PollSpec spec = new PollSpec(au.getAuCachedUrlSet(), Poll.V3_POLL);
pollManager.enqueueHighPriorityPoll(au, spec);
statusMsg = "Enqueued V3 poll for " + au.getName();
}
public static V1Poll createCompletedPoll(
LockssDaemon daemon,
ArchivalUnit au,
V1LcapMessage testmsg,
int numAgree,
int numDisagree,
PollManager pollmanager)
throws Exception {
log.debug(
"createCompletedPoll: au: "
+ au.toString()
+ " peer "
+ testmsg.getOriginatorId()
+ " votes "
+ numAgree
+ "/"
+ numDisagree);
CachedUrlSetSpec cusSpec = null;
if ((testmsg.getLwrBound() != null)
&& (testmsg.getLwrBound().equals(PollSpec.SINGLE_NODE_LWRBOUND))) {
cusSpec = new SingleNodeCachedUrlSetSpec(testmsg.getTargetUrl());
} else {
cusSpec =
new RangeCachedUrlSetSpec(
testmsg.getTargetUrl(), testmsg.getLwrBound(), testmsg.getUprBound());
}
CachedUrlSet cus = au.makeCachedUrlSet(cusSpec);
PollSpec spec = new PollSpec(cus, Poll.V1_CONTENT_POLL);
((MockCachedUrlSet) spec.getCachedUrlSet()).setHasContent(false);
V1Poll p = null;
if (testmsg.isContentPoll()) {
p =
new V1ContentPoll(
spec,
pollmanager,
testmsg.getOriginatorId(),
testmsg.getChallenge(),
testmsg.getDuration(),
testmsg.getHashAlgorithm());
} else if (testmsg.isNamePoll()) {
p =
new V1NamePoll(
spec,
pollmanager,
testmsg.getOriginatorId(),
testmsg.getChallenge(),
testmsg.getDuration(),
testmsg.getHashAlgorithm());
} else if (testmsg.isVerifyPoll()) {
p =
new V1VerifyPoll(
spec,
pollmanager,
testmsg.getOriginatorId(),
testmsg.getChallenge(),
testmsg.getDuration(),
testmsg.getHashAlgorithm(),
testmsg.getVerifier());
}
assertNotNull(p);
p.setMessage(testmsg);
p.m_tally.quorum = numAgree + numDisagree;
p.m_tally.numAgree = numAgree;
p.m_tally.numDisagree = numDisagree;
p.m_tally.wtAgree = 2000;
p.m_tally.wtDisagree = 200;
p.m_tally.localEntries = makeEntries(1, 3);
p.m_tally.votedEntries = makeEntries(1, 5);
p.m_tally.votedEntries.remove(1);
p.m_pollstate = V1Poll.PS_COMPLETE;
p.m_callerID = testmsg.getOriginatorId();
log.debug3("poll " + p.toString());
p.m_tally.tallyVotes();
return p;
}
/** Explode the archive into its constituent elements */
public void explode() throws CacheException {
CachedUrl cachedUrl = null;
int goodEntries = 0;
int badEntries = 0;
int ignoredEntries = 0;
int entriesBetweenSleep = 0;
ArchiveReader arcReader = null;
logger.info(
(storeArchive ? "Storing" : "Fetching") + " WARC file: " + origUrl + " will explode");
try {
if (storeArchive) {
UrlCacher uc = au.makeUrlCacher(new UrlData(arcStream, arcProps, fetchUrl));
BitSet bs = new BitSet();
bs.set(UrlCacher.DONT_CLOSE_INPUT_STREAM_FLAG);
uc.setFetchFlags(bs);
uc.storeContent();
archiveData.resetInputStream();
arcStream = archiveData.input;
}
// Wrap it in an ArchiveReader
logger.debug3("About to wrap stream");
arcReader = wrapStream(fetchUrl, arcStream);
logger.debug3("wrapStream() returns " + (arcReader == null ? "null" : "non-null"));
// Explode it
if (arcReader == null) {
throw new CacheException.ExploderException("no WarcReader for " + origUrl);
}
ArchivalUnit au = crawlFacade.getAu();
Set stemSet = new HashSet();
logger.debug("Exploding " + fetchUrl);
// Iterate through the elements in the WARC file, except the first
Iterator i = arcReader.iterator();
// Skip first record
for (i.next(); i.hasNext(); ) {
// XXX probably not necessary
helper.pokeWDog();
if ((++entriesBetweenSleep % sleepAfter) == 0) {
long pauseTime =
CurrentConfig.getTimeIntervalParam(PARAM_RETRY_PAUSE, DEFAULT_RETRY_PAUSE);
Deadline pause = Deadline.in(pauseTime);
logger.debug3("Sleeping for " + StringUtil.timeIntervalToString(pauseTime));
while (!pause.expired()) {
try {
pause.sleep();
} catch (InterruptedException ie) {
// no action
}
}
}
ArchiveRecord element = (ArchiveRecord) i.next();
// Each element is a URL to be cached in a suitable AU
ArchiveRecordHeader elementHeader = element.getHeader();
String elementUrl = elementHeader.getUrl();
String elementMimeType = elementHeader.getMimetype();
long elementLength = elementHeader.getLength();
logger.debug2("WARC url " + elementUrl + " mime " + elementMimeType);
if (elementUrl.startsWith("http:")) {
ArchiveEntry ae =
new ArchiveEntry(
elementUrl,
elementLength,
0, // XXX need to convert getDate string to long
element, // ArchiveRecord extends InputStream
this,
fetchUrl);
ae.setHeaderFields(makeCIProperties(elementHeader));
long bytesStored = elementLength;
logger.debug3("ArchiveEntry: " + ae.getName() + " bytes " + bytesStored);
try {
helper.process(ae);
} catch (PluginException ex) {
throw new CacheException.ExploderException("helper.process() threw", ex);
}
if (ae.getBaseUrl() != null) {
if (ae.getRestOfUrl() != null && ae.getHeaderFields() != null) {
storeEntry(ae);
handleAddText(ae);
goodEntries++;
crawlFacade.getCrawlerStatus().addContentBytesFetched(bytesStored);
} else {
ignoredEntries++;
}
} else {
badEntries++;
logger.debug2("Can't map " + elementUrl + " from " + archiveUrl);
}
}
}
} catch (IOException ex) {
throw new CacheException.ExploderException(ex);
} finally {
if (arcReader != null)
try {
arcReader.close();
arcReader = null;
} catch (IOException ex) {
throw new CacheException.ExploderException(ex);
}
if (cachedUrl != null) {
cachedUrl.release();
}
IOUtil.safeClose(arcStream);
}
if (badEntries == 0 && goodEntries > 0) {
// Make it look like a new crawl finished on each AU to which
// URLs were added.
for (Iterator it = touchedAus.iterator(); it.hasNext(); ) {
ArchivalUnit au = (ArchivalUnit) it.next();
logger.debug3(archiveUrl + " touching " + au.toString());
AuUtil.getDaemon(au).getNodeManager(au).newContentCrawlFinished();
}
} else {
ArchivalUnit au = crawlFacade.getAu();
String msg = archiveUrl + ": " + badEntries + "/" + goodEntries + " bad entries";
throw new CacheException.UnretryableException(msg);
}
}