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Made changes based on the viewer's suggestion.
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@taojing2002
taojing2002 committed Aug 14, 2024
1 parent 3af3f88 commit 9bc801c
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Showing 3 changed files with 41 additions and 45 deletions.
9 changes: 9 additions & 0 deletions helm/config/dataone-indexer.properties
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Original file line number Diff line number Diff line change
Expand Up @@ -40,3 +40,12 @@ index.resourcemap.waitingComponent.time={{ default 800 .Values.idxworker.resourc
index.resourcemap.waitingComponent.max.attempts={{ default 25 .Values.idxworker.resourcemapMaxTries }}
index.solr.versionConflict.waiting.time={{ default 1000 .Values.idxworker.solrVerConflictWaitMs }}
index.solr.versionConflict.max.attempts={{ default 50 .Values.idxworker.solrVerConflictMaxTries }}

# Storage properties
storage.className={{ default "org.dataone.hashstore.filehashstore.FileHashStore" .Values.idxworker.storage.hashStoreClassName }}
storage.hashstore.rootDirectory={{ default "./target/hashstore" .Values.idxworker.storage.hashStoreRootDir }}
storage.hashstore.defaultNamespace={{ default "https://ns.dataone.org/service/types/v2.0#SystemMetadata" .Values.idxworker.storage.hashStoreDefaultNamespace }}
# The following three properties must NOT be modified after the hash store is initialized
storage.hashstore.fileNameAlgorithm={{ default "SHA-256" .Values.idxworker.storage.hashStoreAlgorithm }}
storage.hashstore.directory.width={{ default 2 .Values.idxworker.storage.hashStoreDirWidth }}
storage.hashstore.directory.depth={{ default 3 .Values.idxworker.storage.hashStoreDirDepth }}
71 changes: 29 additions & 42 deletions src/main/java/org/dataone/cn/indexer/object/ObjectManager.java
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Original file line number Diff line number Diff line change
Expand Up @@ -50,41 +50,26 @@ public class ObjectManager {

static {
try {
manager = new ObjectManager();
} catch (ServiceFailure | IOException e) {
logger.error("Metacat cannot initialize the ObjectManager class since " + e.getMessage());
refreshD1Node();
} catch (ServiceFailure e) {
logger.warn("Metacat cannot initialize the d1Node since " + e.getMessage());
}
storage = Storage.getInstance();
manager = new ObjectManager();
}


/**
* Private constructor
* @throws ServiceFailure
* @throws IOException
* @throws IllegalArgumentException
*/
private ObjectManager() throws ServiceFailure, IllegalArgumentException, IOException {
if (storage == null) {
storage = Storage.getInstance();
}
if (d1Node == null) {
refreshD1Node();
} else {
logger.info("ObjectManager ---NOT going to create the d1node with the url " + nodeBaseURL
+ " since the ObjectManager already was assigned a d1node with the url "
+ d1Node.getNodeBaseServiceUrl());
}
private ObjectManager() {
}

/**
* Get an ObjectManager instance through the singleton pattern.
* @return the instance of ObjectManager
* @throws ServiceFailure
* @throws IOException
* @throws IllegalArgumentException
*/
public static ObjectManager getInstance() throws ServiceFailure,
IllegalArgumentException, IOException {
public static ObjectManager getInstance() {
return manager;
}

Expand Down Expand Up @@ -113,23 +98,25 @@ public InputStream getSystemMetadataStream(String id) throws InvalidToken, NotAu
logger.info("Finish getting the system metadata via the file system for the pid " + id
+ " and it took " + (end - start) + "milliseconds");
} catch (FileNotFoundException exception ) {
// Metacat can't find the system metadata from the storage system.
// So try to get it from the dataone api
SystemMetadata sysmeta = null;
Identifier identifier = new Identifier();
identifier.setValue(id);
sysmeta = d1Node.getSystemMetadata(session, identifier);
logger.debug("Finish getting the system metadata via the DataONE API call for the pid "
+ id);
if (sysmeta != null) {
ByteArrayOutputStream systemMetadataOutputStream = new ByteArrayOutputStream();
TypeMarshaller.marshalTypeToOutputStream(sysmeta, systemMetadataOutputStream);
sysmetaInputStream =
new ByteArrayInputStream(systemMetadataOutputStream.toByteArray());
if (d1Node != null) {
// Metacat can't find the system metadata from the storage system.
// So try to get it from the dataone api
SystemMetadata sysmeta = null;
Identifier identifier = new Identifier();
identifier.setValue(id);
sysmeta = d1Node.getSystemMetadata(session, identifier);
logger.debug("Finish getting the system metadata via the DataONE API call for the pid "
+ id);
if (sysmeta != null) {
ByteArrayOutputStream systemMetadataOutputStream = new ByteArrayOutputStream();
TypeMarshaller.marshalTypeToOutputStream(sysmeta, systemMetadataOutputStream);
sysmetaInputStream =
new ByteArrayInputStream(systemMetadataOutputStream.toByteArray());
}
long end = System.currentTimeMillis();
logger.info("Finish getting the system metadata via DataONE API for the pid " + id
+ " and it took " + (end - start) + "milliseconds");
}
long end = System.currentTimeMillis();
logger.info("Finish getting the system metadata via DataONE API for the pid " + id
+ " and it took " + (end - start) + "milliseconds");
}
return sysmetaInputStream;
}
Expand Down Expand Up @@ -201,7 +188,7 @@ public static void setD1Node(MultipartD1Node node) {
* In case the token expired, the method will retrieve the token and create a new d1 node
* @throws ServiceFailure
*/
private void refreshD1Node() throws ServiceFailure {
private static void refreshD1Node() throws ServiceFailure {
//get the token
DataONEauthToken = System.getenv(TOKEN_VARIABLE_NAME);
if (DataONEauthToken == null || DataONEauthToken.trim().equals("")) {
Expand Down Expand Up @@ -244,7 +231,7 @@ private void refreshD1Node() throws ServiceFailure {
* @param authToken the authentication token
* @return the DataONE session
*/
private Session createSession(String authToken) {
private static Session createSession(String authToken) {
Session session = null;
if (authToken == null || authToken.trim().equals("")) {
logger.info("ObjectManager.createSession - Creating the public session");
Expand All @@ -265,7 +252,7 @@ private Session createSession(String authToken) {
* @throws ClientSideException
* @throws IOException
*/
private MultipartD1Node getMultipartD1Node(Session session, String serviceUrl) throws IOException, ClientSideException {
private static MultipartD1Node getMultipartD1Node(Session session, String serviceUrl) throws IOException, ClientSideException {
MultipartRestClient mrc = null;
MultipartD1Node d1Node = null;
// First create a default HTTP client
Expand All @@ -288,7 +275,7 @@ private MultipartD1Node getMultipartD1Node(Session session, String serviceUrl) t
* @param nodeStr either a DataONE node serviceURL (e.g. https://knb.ecoinformatics.org/knb/d1/mn)
* or a DataONE node identifier (e.g. urn:node:CN)
*/
private Boolean isCN(String nodeStr) {
private static Boolean isCN(String nodeStr) {
Boolean isCN = false;
// match node urn, e.g. "https://cn.dataone.org/cn"
if (nodeStr.matches("^\\s*urn:node:.*")) {
Expand Down
6 changes: 3 additions & 3 deletions src/main/java/org/dataone/indexer/storage/Storage.java
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Original file line number Diff line number Diff line change
Expand Up @@ -26,7 +26,8 @@ public class Storage {
instance = new Storage();
} catch (IOException e) {
log.error(
"Dataone-indexer cannot initialize the Storage class since " + e.getMessage());
"Dataone-indexer cannot initialize the Storage class since " + e.getMessage(), e);
System.exit(1);
}
}

Expand Down Expand Up @@ -63,9 +64,8 @@ private Storage() throws HashStoreFactoryException, IOException {
/**
* Get the instance of the class through the singleton pattern
* @return the instance of the class
* @throws IOException
*/
public static Storage getInstance() throws IOException {
public static Storage getInstance() {
return instance;
}

Expand Down

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