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Add the code to handle more types of input stream for the non-xml met…
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…adata objects.
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@taojing2002
taojing2002 committed Apr 28, 2021
1 parent 9d9baef commit 5959671
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Showing 3 changed files with 268 additions and 26 deletions.
4 changes: 4 additions & 0 deletions src/edu/ucsb/nceas/metacat/object/handler/JsonLDHandler.java
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Expand Up @@ -25,16 +25,20 @@
import java.io.IOException;
import java.io.InputStream;

import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory;
import org.dataone.service.exceptions.InvalidRequest;

import com.github.jsonldjava.utils.JsonUtils;


/**
* The handler of JSON-LD objects to save bites into disk
* @author tao
*
*/
public class JsonLDHandler extends NonXMLMetadataHandler {
private static Log logMetacat = LogFactory.getLog(JsonLDHandler.class);

/**
* Default constructor
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146 changes: 125 additions & 21 deletions src/edu/ucsb/nceas/metacat/object/handler/NonXMLMetadataHandler.java
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Expand Up @@ -25,8 +25,11 @@
import java.io.File;
import java.io.FileInputStream;
import java.io.FileNotFoundException;
import java.io.FileOutputStream;
import java.io.IOException;
import java.io.InputStream;

import org.apache.commons.io.IOUtils;
import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory;
import org.dataone.service.exceptions.InvalidRequest;
Expand All @@ -38,8 +41,6 @@
import org.dataone.service.types.v1.Identifier;
import org.dataone.service.types.v1.Session;

import edu.ucsb.nceas.metacat.IdentifierManager;
import edu.ucsb.nceas.metacat.dataone.CNodeService;
import edu.ucsb.nceas.metacat.dataone.D1NodeService;
import edu.ucsb.nceas.metacat.properties.PropertyService;
import edu.ucsb.nceas.metacat.restservice.multipart.DetailedFileInputStream;
Expand All @@ -52,7 +53,7 @@
*
*/
public abstract class NonXMLMetadataHandler {
private static Log logMetacat = LogFactory.getLog(CNodeService.class);
private static Log logMetacat = LogFactory.getLog(NonXMLMetadataHandler.class);
private static String metadataStoragePath = null;
static {
try {
Expand All @@ -67,7 +68,7 @@ public abstract class NonXMLMetadataHandler {
* @param source the input stream contains the content of the meta data object
* @param docType the doc type of this object in the xml_document table. Usually it is the format id.
* @param pid the identifier associated with the input stream
* @param expectedChecksum the expected checksum for the saved file
* @param expectedChecksum the expected checksum for the saved file. The value usually comes from the system meta data
* @param session the user's session who makes this call
* @param ipAddress the ip address of the client who makes the call (for the log information)
* @param userAgent the user agent of the client who makes the call (for the log information)
Expand All @@ -90,7 +91,7 @@ public String save(InputStream source, String docType, Identifier pid, Checksum
* @param source the input stream contains the content of the meta data object
* @param docType the doc type of this object in the xml_document table. Usually it is the format id.
* @param pid the identifier associated with the input stream
* @param expectedChecksum the expected checksum for the saved file
* @param expectedChecksum the expected checksum for the saved file. The value usually comes from the system meta data
* @param replicationNtofication server the server name notifying the replication (only for the replication process)
* @param session the user's session who makes this call
* @param ipAddress the ip address of the client who makes the call (for the log information)
Expand All @@ -108,33 +109,106 @@ public String save(InputStream source, String docType, Identifier pid, Checksum
if (pid == null || pid.getValue() == null || pid.getValue().trim().equals("")) {
throw new InvalidRequest("1102", "NonXMLMetadataHandler.save - the pid parameter should not be blank.");
}
if (!(source instanceof DetailedFileInputStream)) {
throw new UnsupportedType("1140", "NonXMLMetadataHandler.save - Metacat only supports the DetailedFileInputStream object for saving "
+ pid.getValue() +" into disk");
File tmpFile = null;
boolean canReset = false;
InputStream forValidationStream = null;
if (source instanceof DetailedFileInputStream) {
logMetacat.debug("NonXMLMetadataHandler.save - in the DetailedFileInputStream route for pid " + pid.getValue());
DetailedFileInputStream input = (DetailedFileInputStream) source;
File sourceFile = input.getFile();
try {
forValidationStream = new FileInputStream(sourceFile);
} catch (FileNotFoundException e) {
throw new ServiceFailure("1190", "NonXMLMetadataHandler.save - cannot valid the meta data object " +
" because cannot find the file associated with the detailed file input stream " +
" for the object " + pid.getValue() + " since " + e.getMessage());
}
} else if ( source.markSupported()) {
logMetacat.debug("NonXMLMetadataHandler.save - in the resetable input stream route for pid " + pid.getValue());
forValidationStream = source;
canReset = true;
} else {
logMetacat.debug("NonXMLMetadataHandler.save - in the another type of the input stream route for pid " + pid.getValue());
FileOutputStream out = null;
try {
tmpFile = generateTempFile("NonXML");
out = new FileOutputStream(tmpFile);
IOUtils.copyLarge(source, out);
forValidationStream = new FileInputStream(tmpFile);
source = new FileInputStream(tmpFile);
} catch (IOException e) {
if (tmpFile != null) {
tmpFile.delete();
}
throw new ServiceFailure("1190", "NonXMLMetadataHandler.save - cannot save the meta data object " +
pid.getValue() + " into a temporary file since " + e.getMessage());
} finally {
try {
IOUtils.close(out);
} catch (IOException e) {
logMetacat.warn("NonXMLMetadataHandler.save - cannot close the out put stream after saving the object for pid "
+ pid.getValue() + "into a temporary file");
}
}

}

String localId = null;
DetailedFileInputStream input = (DetailedFileInputStream) source;
File sourceFile = input.getFile();
boolean valid = false;
try {
valid = validate(new FileInputStream(sourceFile));
} catch (FileNotFoundException e) {
throw new ServiceFailure("1190", "NonXMLMetadataHandler.save - cannot valid the meta data object " +
" because cannot find the file associated with the detailed file input stream " +
" for the object " + pid.getValue() + " since " + e.getMessage());
valid = validate(forValidationStream);
if (canReset) {
try {
source.reset();
} catch (IOException e) {
throw new ServiceFailure("1190", "NonXMLMetadataHandler.save - cannot save the object " +
" because Metacat cannot reset the input stream even though the inputstream " +
source.getClass().getCanonicalName() + " for the object " + pid.getValue() +
" claim sit is resetable since " + e.getMessage());
}

}
} catch (InvalidRequest e) {
throw new InvalidRequest("1102", "NonXMLMetadataHandler.save - the metadata object " + pid.getValue() + " is invalid: " + e.getMessage());
try {
if (forValidationStream != null) {
forValidationStream.close();
}
} catch (IOException ee) {
logMetacat.warn("NonXMLMetadataHandler.save - cannot close the invalidation stream since " + ee.getMessage());
}
throw new InvalidRequest("1102", "NonXMLMetadataHandler.save - the metadata object " + pid.getValue() +
" is invalid: " + e.getMessage());
}

if (!valid) {
throw new InvalidRequest("1102", "NonXMLMetadataHandler.save - the metadata object " + pid.getValue() + " is invalid.");
} else {
if (metadataStoragePath == null) {
throw new ServiceFailure("1190", "NonXMLMetadataHandler.save - cannot save the metadata object " + pid.getValue() +
" into disk since the property - application.documentfilepath is not found in the metacat.properties file ");
try {
if (metadataStoragePath == null) {
throw new ServiceFailure("1190", "NonXMLMetadataHandler.save - cannot save the metadata object " + pid.getValue() +
" into disk since the property - application.documentfilepath is not found in the metacat.properties file ");
}
//Save the meta data object to disk using "localId" as the name
localId = D1NodeService.insertObject(source, docType, pid, metadataStoragePath, session, expectedChecksum, ipAddress,
userAgent, replicationNotificationServer);
} finally {
if (tmpFile != null) {
tmpFile.delete();
}
try {
source.close();
if (forValidationStream != null) {
forValidationStream.close();
}
} catch (IOException ee) {
logMetacat.warn("NonXMLMetadataHandler.save - cannot close the invalidation stream since " + ee.getMessage());
}
try {
source.close();
} catch (IOException ee) {
logMetacat.warn("NonXMLMetadataHandler.save - cannot close the source stream since " + ee.getMessage());
}
}
//Save the meta data object to disk using "localId" as the name
localId = D1NodeService.insertObject(input, docType, pid, metadataStoragePath, session, expectedChecksum, ipAddress, userAgent, replicationNotificationServer);
}
return localId;
}
Expand All @@ -146,4 +220,34 @@ public String save(InputStream source, String docType, Identifier pid, Checksum
* @throws InvalidRequest when the content is not valid
*/
public abstract boolean validate(InputStream source) throws InvalidRequest;


/**
* Create a temporary file for the given prefix
* @param prefix the prefix of the temporary file
* @return the created file
* @throws IOException
*/
private static File generateTempFile(String prefix) throws IOException {
File tmpDir = null;
try {
tmpDir = new File(PropertyService.getProperty("application.tempDir"));
}
catch(PropertyNotFoundException pnfe) {
logMetacat.error("NonXMLMetadataHandler.generateTempFile: " +
"application.tmpDir not found. Using /tmp instead.");
tmpDir = new File("/tmp");
}
String newPrefix = prefix + "-" + System.currentTimeMillis();
String suffix = null;
File newFile = null;
try {
newFile = File.createTempFile(newPrefix, suffix, tmpDir);
} catch (Exception e) {
//try again if the first time fails
newFile = File.createTempFile(newPrefix, suffix, tmpDir);
}
logMetacat.debug("StreamingMultiplePartRequestResolver.generateTmepFile - the new file is " + newFile.getCanonicalPath());
return newFile;
}
}

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