void setConfig(Configuration config) {
log.debug("config: " + config);
proxyHost = config.get(PARAM_PROXY_HOST);
proxyPort = config.getInt(PARAM_PROXY_PORT, DEFAULT_PROXY_PORT);
if (StringUtil.isNullString(proxyHost) || proxyPort <= 0) {
String http_proxy = System.getenv("http_proxy");
if (!StringUtil.isNullString(http_proxy)) {
try {
HostPortParser hpp = new HostPortParser(http_proxy);
proxyHost = hpp.getHost();
proxyPort = hpp.getPort();
} catch (HostPortParser.InvalidSpec e) {
log.warning("Can't parse http_proxy environment var, ignoring: " + http_proxy + ": " + e);
}
}
}
if (StringUtil.isNullString(proxyHost) || proxyPort <= 0) {
proxyHost = null;
} else {
log.info("Proxying through " + proxyHost + ":" + proxyPort);
}
userAgent = config.get(PARAM_USER_AGENT);
if (StringUtil.isNullString(userAgent)) {
userAgent = null;
} else {
log.debug("Setting User-Agent to " + userAgent);
}
}
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);
}
}
}
// If there is a <title> element on the start page, use that as our AU
// name.
String recomputeRegName() {
if (!isStarted()) {
// This can get invoked (seveeral times, mostly from logging) before
// enough mechanism has started to make it possible to resolve the CuUrl
// below.
return null;
}
try {
CachedUrl cu = makeCachedUrl(m_registryUrl);
if (cu == null) return null;
URL cuUrl = CuUrl.fromCu(cu);
Parser parser = new Parser(cuUrl.toString());
NodeList nodelst = parser.extractAllNodesThatMatch(new NodeClassFilter(TitleTag.class));
Node nodes[] = nodelst.toNodeArray();
recomputeRegName = false;
if (nodes.length < 1) return null;
// Get the first title found
TitleTag tag = (TitleTag) nodes[0];
if (tag == null) return null;
return tag.getTitle();
} catch (MalformedURLException e) {
log.warning("recomputeRegName", e);
return null;
} catch (ParserException e) {
if (e.getThrowable() instanceof FileNotFoundException) {
log.warning("recomputeRegName: " + e.getThrowable().toString());
} else {
log.warning("recomputeRegName", e);
}
return null;
}
}
/** Create LockssKeystores from config subtree below {@link #PARAM_KEYSTORE} */
void configureKeyStores(Configuration config) {
Configuration allKs = config.getConfigTree(PARAM_KEYSTORE);
for (Iterator iter = allKs.nodeIterator(); iter.hasNext(); ) {
String id = (String) iter.next();
Configuration oneKs = allKs.getConfigTree(id);
try {
LockssKeyStore lk = createLockssKeyStore(oneKs);
String name = lk.getName();
if (name == null) {
log.error("KeyStore definition missing name: " + oneKs);
continue;
}
LockssKeyStore old = keystoreMap.get(name);
if (old != null && !lk.equals(old)) {
log.warning(
"Keystore "
+ name
+ " redefined. "
+ "New definition may not take effect until daemon restart");
}
log.debug("Adding keystore " + name);
keystoreMap.put(name, lk);
} catch (Exception e) {
log.error("Couldn't create keystore: " + oneKs, e);
}
}
}
public void emitMetadata(ArticleFiles af, ArticleMetadata md) {
if (log.isDebug3()) log.debug3("emit(" + af + ", " + md + ")");
if (md != null) {
log.debug3("add " + md + " to amlist");
amlst.add(md);
}
;
}
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);
}
}
}
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);
}
/*
* When testing no-pdf-check basic XML parsing, you will get partial MD records
* depending on whether the info comes from dataset.xml or from main.xml
*/
private void validateDatasetMetadataRecord(ArticleMetadata am) {
log.debug3("valideDatasetMetadatRecord");
String doi_val = am.get(MetadataField.FIELD_DOI);
assertEquals(common_issn, am.get(MetadataField.FIELD_ISSN));
log.debug3("doi val is: " + doi_val);
// The dataset doesn't set this value, it'll fail over the main.xml value
if (doi_val.equals("10.1016/S0140-1111(14)61865-1")) {
assertEquals(null, am.get(MetadataField.FIELD_DATE));
} else {
assertEquals(dateMap.get(doi_val), am.get(MetadataField.FIELD_DATE));
}
assertEquals(pubTitleMap.get(doi_val), am.get(MetadataField.FIELD_PUBLICATION_TITLE));
}
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;
}
}
/** Create LockssKeystore from a config subtree */
LockssKeyStore createLockssKeyStore(Configuration config) {
log.debug2("Creating LockssKeyStore from config: " + config);
String name = config.get(KEYSTORE_PARAM_NAME);
LockssKeyStore lk = new LockssKeyStore(name);
String file = config.get(KEYSTORE_PARAM_FILE);
String resource = config.get(KEYSTORE_PARAM_RESOURCE);
String url = config.get(KEYSTORE_PARAM_URL);
if (!StringUtil.isNullString(file)) {
lk.setLocation(file, LocationType.File);
} else if (!StringUtil.isNullString(resource)) {
lk.setLocation(resource, LocationType.Resource);
} else if (!StringUtil.isNullString(url)) {
lk.setLocation(url, LocationType.Url);
}
lk.setType(config.get(KEYSTORE_PARAM_TYPE, defaultKeyStoreType));
lk.setProvider(config.get(KEYSTORE_PARAM_PROVIDER, defaultKeyStoreProvider));
lk.setPassword(config.get(KEYSTORE_PARAM_PASSWORD));
lk.setKeyPassword(config.get(KEYSTORE_PARAM_KEY_PASSWORD));
lk.setKeyPasswordFile(config.get(KEYSTORE_PARAM_KEY_PASSWORD_FILE));
lk.setMayCreate(config.getBoolean(KEYSTORE_PARAM_CREATE, DEFAULT_CREATE));
return lk;
}
protected void checkLeaf(SimulatedArchivalUnit sau) {
log.debug("checkLeaf()");
String parent = sau.getUrlRoot() + "/branch1";
CachedUrlSetSpec spec = new RangeCachedUrlSetSpec(parent);
CachedUrlSet set = sau.makeCachedUrlSet(spec);
Iterator setIt = set.contentHashIterator();
ArrayList childL = new ArrayList(16);
while (setIt.hasNext()) {
childL.add(((CachedUrlSetNode) setIt.next()).getUrl());
}
String[] expectedA =
new String[] {
parent,
parent + "/001file.html",
parent + "/001file.txt",
parent + "/002file.html",
parent + "/002file.txt",
parent + "/branch1",
parent + "/branch1/001file.html",
parent + "/branch1/001file.txt",
parent + "/branch1/002file.html",
parent + "/branch1/002file.txt",
parent + "/branch1/index.html",
parent + "/branch2",
parent + "/branch2/001file.html",
parent + "/branch2/001file.txt",
parent + "/branch2/002file.html",
parent + "/branch2/002file.txt",
parent + "/branch2/index.html",
parent + "/index.html",
};
assertIsomorphic(expectedA, childL);
}
protected void checkRoot(SimulatedArchivalUnit sau) {
log.debug("checkRoot()");
CachedUrlSet set = sau.getAuCachedUrlSet();
Iterator setIt = set.flatSetIterator();
ArrayList childL = new ArrayList(1);
CachedUrlSet cus = null;
while (setIt.hasNext()) {
cus = (CachedUrlSet) setIt.next();
childL.add(cus.getUrl());
}
String urlRoot = sau.getUrlRoot();
String[] expectedA = new String[1];
expectedA[0] = urlRoot;
assertIsomorphic(expectedA, childL);
setIt = cus.flatSetIterator();
childL = new ArrayList(7);
while (setIt.hasNext()) {
childL.add(((CachedUrlSetNode) setIt.next()).getUrl());
}
expectedA =
new String[] {
urlRoot + "/001file.html",
urlRoot + "/001file.txt",
urlRoot + "/002file.html",
urlRoot + "/002file.txt",
urlRoot + "/branch1",
urlRoot + "/branch2",
urlRoot + "/index.html"
};
assertIsomorphic(expectedA, childL);
}
/**
* Method that creates a simulated Cached URL from the source code provided by the goodContent
* String. It then asserts that the metadata extracted, by using the
* MetaPressRisMetadataExtractorFactory, match the metadata in the source code.
*
* @throws Exception
*/
public void testExtractGoodRisContent() throws Exception {
String goodContent = createGoodRisContent();
log.debug3(goodContent);
List<ArticleMetadata> mdlist = setupContentForAU(bau1, RIS_URL, goodContent, false);
assertNotEmpty(mdlist);
ArticleMetadata md = mdlist.get(0);
assertNotNull(md);
assertEquals(goodVolume, md.get(MetadataField.FIELD_VOLUME));
assertEquals(goodIssue, md.get(MetadataField.FIELD_ISSUE));
assertEquals(goodStartPage, md.get(MetadataField.FIELD_START_PAGE));
assertEquals(goodEndPage, md.get(MetadataField.FIELD_END_PAGE));
assertEquals(goodIssn, md.get(MetadataField.FIELD_ISSN));
Iterator<String> actAuthIter = md.getList(MetadataField.FIELD_AUTHOR).iterator();
for (String expAuth : goodAuthors) {
assertEquals(expAuth, actAuthIter.next());
}
assertEquals(goodTitle, md.get(MetadataField.FIELD_ARTICLE_TITLE));
assertEquals(goodJournal, md.get(MetadataField.FIELD_PUBLICATION_TITLE));
assertEquals(goodDate, md.get(MetadataField.FIELD_DATE));
assertEquals(goodPublisher, md.get(MetadataField.FIELD_PUBLISHER));
assertEquals(goodDOI, md.get(MetadataField.FIELD_DOI));
// This shouldn't get set. It will default later to fuill_text_cu
assertNotEquals(doiURL, md.get(MetadataField.FIELD_ACCESS_URL));
}
protected void checkContent(SimulatedArchivalUnit sau) throws IOException {
log.debug("checkContent()");
checkRoot(sau);
checkLeaf(sau);
checkStoredContent(sau);
checkDepth(sau);
}
/*
* You will have to tell it the DOI and the schema because those normally come from dataset
*/
private void validateSingleMainMetadataRecord(ArticleMetadata am, String doi_val, String schema) {
log.debug3("valideSingleMainMetadatRecord");
if ("simple-article".equals(schema)) {
assertEquals(common_simple_article_title, am.get(MetadataField.FIELD_ARTICLE_TITLE));
} else {
assertEquals(common_article_title, am.get(MetadataField.FIELD_ARTICLE_TITLE));
}
log.debug3("doi val is: " + doi_val);
assertEquals(authorMap.get(doi_val), am.getList(MetadataField.FIELD_AUTHOR));
assertEquals(volMap.get(doi_val), am.get(MetadataField.FIELD_VOLUME));
assertEquals(issueMap.get(doi_val), am.get(MetadataField.FIELD_ISSUE));
assertEquals("Comment", am.getRaw(ElsevierMainDTD5XmlSchemaHelper.common_dochead));
assertEquals(doi_val, am.getRaw(ElsevierMainDTD5XmlSchemaHelper.common_doi));
assertEquals("2014", am.getRaw(ElsevierMainDTD5XmlSchemaHelper.common_copyright));
}
/**
* Returns the base url of the provided CachedUrl, checking to see if it's the result of a
* redirect.
*/
public static String getBaseUrl(CachedUrl cu) {
// See the comments in LockssResourceHandler.handleLockssRedirect();
// this is the same logic.
CIProperties props = cu.getProperties();
if (props != null) {
String redir = props.getProperty(CachedUrl.PROPERTY_CONTENT_URL);
if (redir != null) {
return redir;
} else {
String url = cu.getUrl();
String nodeUrl = props.getProperty(CachedUrl.PROPERTY_NODE_URL);
if (nodeUrl != null && !nodeUrl.equals(url)) {
log.debug("getBaseUrl(" + url + "), nodeUrl: " + nodeUrl);
if (dirNodeCheckSlash) {
URI uri = new URI(url);
if (!uri.getPath().endsWith("/")) {
URI nodeUri = new URI(nodeUrl);
if (nodeUri.getPath().endsWith("/")) {
return nodeUrl;
}
}
} else {
return nodeUrl;
}
}
}
}
return cu.getUrl();
}
void stopThread() {
if (sizeCalcThread != null) {
log.debug2("Stopping thread");
sizeCalcThread.stopSizeCalc();
sizeCalcThread = null;
}
}
protected void logParams() {
Enumeration en = req.getParameterNames();
while (en.hasMoreElements()) {
String name = (String) en.nextElement();
String vals[];
String dispval;
if (StringUtil.indexOfIgnoreCase(name, "passw") >= 0) {
dispval = req.getParameter(name).length() == 0 ? "" : "********";
} else if (log.isDebug2() && (vals = req.getParameterValues(name)).length > 1) {
dispval = StringUtil.separatedString(vals, ", ");
} else {
dispval = req.getParameter(name);
}
log.debug(name + " = " + dispval);
}
}
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 testSimpleMainXML() throws Exception {
log.debug3("testSimpleMainXML");
String xml_url = TAR_A_BASE + SUBDIR + "01420615/v64sC/S0142061514004608/main.xml";
List<ArticleMetadata> mdList =
extractFromContent(xml_url, "text/xml", simpleMain, nocheck_mle, null);
assertEquals(1, mdList.size());
validateSingleMainMetadataRecord(mdList.get(0), "10.1016/j.jidx.2014.07.028", "article");
}
/** engqueue a size calculation for the node */
public void queueSizeCalc(RepositoryNode node) {
synchronized (sizeCalcQueue) {
if (sizeCalcQueue.add(node)) {
log.debug2("Queue size calc: " + node);
startOrKickThread();
}
}
}
protected String getHostIp() {
try {
IPAddr localHost = IPAddr.getLocalHost();
return localHost.getHostAddress();
} catch (UnknownHostException e) {
log.error("getHostIp()", e);
return "1.1.1.1";
}
}
void startOrKickThread() {
if (sizeCalcThread == null) {
log.debug2("Starting thread");
sizeCalcThread = new SizeCalcThread();
sizeCalcThread.start();
sizeCalcThread.waitRunning();
}
sizeCalcSem.give();
}
public PlatformUtil.DF getRepositoryDF(String repoName) {
String path = LockssRepositoryImpl.getLocalRepositoryPath(repoName);
log.debug("path: " + path);
// try {
return platInfo.getJavaDF(path);
// } catch (PlatformUtil.UnsupportedException e) {
// return null;
// }
}
/**
* Checks the consistency of the node, and continues with its children if it's consistent.
*
* @param node RepositoryNodeImpl the node to check
*/
private void recurseConsistencyCheck(RepositoryNodeImpl node) {
logger.debug2("Checking node '" + node.getNodeUrl() + "'...");
// check consistency at each node
// correct/deactivate as necessary
// 'checkNodeConsistency()' will repair if possible
if (node.checkNodeConsistency()) {
logger.debug3("Node consistent; recursing on children...");
List children = node.getNodeList(null, false);
Iterator iter = children.iterator();
while (iter.hasNext()) {
RepositoryNodeImpl child = (RepositoryNodeImpl) iter.next();
recurseConsistencyCheck(child);
}
} else {
logger.debug3("Node inconsistent; deactivating...");
deactivateInconsistentNode(node);
}
}
private void forceV3Poll() {
ArchivalUnit au = getAu();
if (au == null) return;
try {
callV3ContentPoll(au);
} catch (Exception e) {
log.error("Can't start poll", e);
errMsg = "Error: " + e.toString();
}
}
protected void checkDepth(SimulatedArchivalUnit sau) {
log.debug("checkDepth()");
String URL_ROOT = sau.getUrlRoot();
assertEquals(0, sau.getLinkDepth(URL_ROOT + "/index.html"));
assertEquals(0, sau.getLinkDepth(URL_ROOT + "/"));
assertEquals(1, sau.getLinkDepth(URL_ROOT + "/001file.html"));
assertEquals(1, sau.getLinkDepth(URL_ROOT + "/branch1/index.html"));
assertEquals(1, sau.getLinkDepth(URL_ROOT + "/branch1/"));
assertEquals(2, sau.getLinkDepth(URL_ROOT + "/branch1/001file.html"));
}
private void doDisableMetadataIndexing() {
ArchivalUnit au = getAu();
if (au == null) return;
try {
disableMetadataIndexing(au, false);
} catch (RuntimeException e) {
log.error("Can't disable metadata indexing", e);
errMsg = "Error: " + e.toString();
}
}
private void forceReindexMetadata() {
ArchivalUnit au = getAu();
if (au == null) return;
try {
startReindexingMetadata(au, true);
} catch (RuntimeException e) {
log.error("Can't reindex metadata", e);
errMsg = "Error: " + e.toString();
}
}
private void doCheckSubstance() {
ArchivalUnit au = getAu();
if (au == null) return;
try {
checkSubstance(au);
} catch (RuntimeException e) {
log.error("Error in SubstanceChecker", e);
errMsg = "Error in SubstanceChecker; see log.";
}
}
