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Revision 7824

Added by ben leinfelder over 11 years ago

do not use tmp file to return an inputstream on read() operations - just read from the file we already have. https://projects.ecoinformatics.org/ecoinfo/issues/6009

     import java.io.ByteArrayInputStream;
     import java.io.ByteArrayOutputStream;
     import java.io.File;
     import java.io.FileInputStream;
     import java.io.FileOutputStream;
     import java.io.IOException;
     import java.io.InputStream;
-...
     	 *            matter withinInlineData's value, the document will
+    	 *
     	 */
     	public void toXml(OutputStream out, String user, String[] groups, boolean withInLineData)
     	public InputStream toXml(OutputStream out, String user, String[] groups, boolean withInLineData)
     			throws McdbException {
     		String documentDir = null;
     		String documentPath = null;
-...
     			throw new McdbException("Attempting to read a zero length document from disk: " + documentPath);
+    		}
     		readFromFileSystem(out, user, groups, documentPath);
     		return readFromFileSystem(out, user, groups, documentPath);
+    	}
         /**
-...
     	 *            the location of the document on disk
+    	 *
     	 */
         public void readFromFileSystem(
         public InputStream readFromFileSystem(
         		OutputStream out, String user, String[] groups, String documentPath) throws McdbException {
     		String xmlFileContents = "";
     		String xmlFileContents = null;
     		String encoding = null;
     		try {
     			// detect and use correct encoding
                 xmlFileContents = FileUtil.readFileToString(documentPath);
                 // guess the encoding from default bytes
     			XmlStreamReader xsr = new XmlStreamReader(new ByteArrayInputStream(xmlFileContents.getBytes()));
     			String encoding = xsr.getEncoding();
     			// reread the contents using the correct encoding
     			if (encoding != null) {
     				xmlFileContents = FileUtil.readFileToString(documentPath, encoding);
+    			}
     			// get a list of inline data sections that are not readable
     			// by this user
-...
                 // If this is for each unreadable section, strip the inline data
     			// from the doc
     			if (unReadableInlineDataList.size() > 0 && doctype != null) {
     				// detect and use correct encoding
     	            xmlFileContents = FileUtil.readFileToString(documentPath);
     	            // guess the encoding from default bytes
     				XmlStreamReader xsr = new XmlStreamReader(new ByteArrayInputStream(xmlFileContents.getBytes()));
     				encoding = xsr.getEncoding();
     				xsr.close();
     				// reread the contents using the correct encoding
     				if (encoding != null) {
     					xmlFileContents = FileUtil.readFileToString(documentPath, encoding);
+    				}
     				Set<String> inlineKeySet = unReadableInlineDataList.keySet();
     				boolean pre210Doc = doctype.equals(EML2_0_0NAMESPACE)
     						|| doctype.equals(EML2_0_1NAMESPACE);
-...
     						// on whether this is a 2.0.1 or earlier doc or 2.1.0 and later.  This
     						// is because of eml schema changes for inline access.
     						if (pre210Doc) {
     							xmlFileContents = stripInline20XData(xmlFileContents,
     									inlineKey);
     							xmlFileContents = stripInline20XData(xmlFileContents, inlineKey);
     						} else {
     							xmlFileContents = stripInline21XData(xmlFileContents, inlineKey);
+    						}
-...
+    				}
+    			}
     			// write with the detected encoding
     			Writer pw = new OutputStreamWriter(out, encoding);
                 // write the doc
     			pw.write(xmlFileContents);
     			pw.close();
     			// will get input either from string content or file on disk
     			InputStream is = null;
     			// get the input stream
     			if (xmlFileContents != null) {
     				is = IOUtils.toInputStream(xmlFileContents, encoding);
     			} else {
     				is = new FileInputStream(documentPath);
+    			}
     			// send it to out
     			if (out != null) {
     				IOUtils.copyLarge(is, out);
+    			}
     			// return the stream
     			return is;
     	     } catch (UtilException e) {
                  throw new McdbException(e.getMessage());
              } catch (IOException e) {
                  throw new McdbException(e.getMessage());
+            }
+        }
         /**

     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 java.io.InputStreamReader;
-...
     import java.sql.Timestamp;
     import java.text.ParseException;
     import java.text.SimpleDateFormat;
     import java.util.Date;
     import java.util.Enumeration;
     import java.util.HashMap;
     import java.util.Hashtable;
-...
          * @throws ClassNotFoundException
          * @throws IOException
          */
         public static InputStream read(String docid)
             throws ParseLSIDException,
             PropertyNotFoundException, McdbException, SQLException,
             ClassNotFoundException, IOException
+        {
             logMetacat.debug("MetacatHandler.read() called.");
             InputStream fileInputStream = null;
             File tmpDir = null;
             // be sure we have a local ID from an LSID
             if (docid.startsWith("urn:")) {
               try {
                 docid = LSIDUtil.getDocId(docid, true);
               } catch ( ParseLSIDException ple ) {
                 logMetacat.debug("There was a problem parsing the LSID. The " +
                                  "error message was: " + ple.getMessage());
                 throw ple;
+              }
+            }
             // accomodate old clients that send docids without revision numbers
             docid = DocumentUtil.appendRev(docid);
             DocumentImpl doc = new DocumentImpl(docid, false);
             // deal with data or metadata cases
             if (doc.getRootNodeID() == 0) {
               // this is a data file
               // get the path to the file to read
               try {
                 String filepath = PropertyService.getProperty("application.datafilepath");
                 // ensure it is a directory path
                 if ( !(filepath.endsWith("/")) ) {
                     filepath += "/";
+                }
                 String filename = filepath + docid;
                 fileInputStream = (InputStream) readFromFilesystem(filename);
               } catch ( PropertyNotFoundException pnf ) {
                 logMetacat.debug("There was a problem finding the " +
                                  "application.datafilepath property. The error " +
                                  "message was: " + pnf.getMessage());
                 throw pnf;
               } // end try()
     	public static InputStream read(String docid) throws ParseLSIDException,
     			PropertyNotFoundException, McdbException, SQLException,
     			ClassNotFoundException, IOException {
     		logMetacat.debug("MetacatHandler.read() called.");
             } else {
               // this is an metadata document
               // get a temporary file handle to write to as an OutputStream
               try {
                 tmpDir = new File(PropertyService.getProperty("application.tempDir"));
     		InputStream inputStream = null;
               } catch ( PropertyNotFoundException pnfe ) {
                 logMetacat.debug("There was a problem getting the" +
                                  "application.tempDir property. Using /tmp " +
                                  "instead. The error was: " + pnfe.getMessage());
                 tmpDir = new File("/tmp");
     		// be sure we have a local ID from an LSID
     		if (docid.startsWith("urn:")) {
     			try {
     				docid = LSIDUtil.getDocId(docid, true);
     			} catch (ParseLSIDException ple) {
     				logMetacat.debug("There was a problem parsing the LSID. The "
     						+ "error message was: " + ple.getMessage());
     				throw ple;
+    			}
+    		}
               } //end try()
               final File outputFile = File.createTempFile("metacat.output", null, tmpDir);
               OutputStream out = new FileOutputStream(outputFile);
     		// accomodate old clients that send docids without revision numbers
     		docid = DocumentUtil.appendRev(docid);
     		DocumentImpl doc = new DocumentImpl(docid, false);
               // Try to get the metadata file from disk. If it isn't
               // found, create it from the db and write it to disk then.
               try {
                   doc.toXml(out, null, null, true);
               } catch (McdbException e) {
                   // any exceptions in reading the xml from disc, and we go back to the
                   // old way of creating the xml directly.
                   logMetacat.error("MetacatHandler.readFromMetacat() " +
                     "- could not read from document file " +
                     docid + ": " + e.getMessage());
                   e.printStackTrace(System.out);
                   doc.toXmlFromDb(out, null, null, true);
+              }
               // set the input stream
               fileInputStream = new FileInputStream(outputFile);
               outputFile.deleteOnExit();
+            }
             return fileInputStream;
+        }
     		// deal with data or metadata cases
     		if (doc.getRootNodeID() == 0) {
     			// this is a data file
     			// get the path to the file to read
     			try {
     				String filepath = PropertyService.getProperty("application.datafilepath");
     				// ensure it is a directory path
     				if (!(filepath.endsWith("/"))) {
     					filepath += "/";
+    				}
     				String filename = filepath + docid;
     				inputStream = readFromFilesystem(filename);
     			} catch (PropertyNotFoundException pnf) {
     				logMetacat.debug("There was a problem finding the "
     						+ "application.datafilepath property. The error "
     						+ "message was: " + pnf.getMessage());
     				throw pnf;
     			} // end try()
     		} else {
     			// this is an metadata document
     			// Get the xml (will try disk then DB)
     			try {
     				// force the InputStream to be returned
     				OutputStream nout = null;
     				inputStream = doc.toXml(nout, null, null, true);
     			} catch (McdbException e) {
     				// report the error
     				logMetacat.error(
     						"MetacatHandler.readFromMetacat() "
     								+ "- could not read document " + docid + ": "
     								+ e.getMessage(), e);
+    			}
+    		}
     		return inputStream;
+    	}
         /**
          * Read a file from Metacat's configured file system data directory.

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Revision 7824

Added by ben leinfelder over 11 years ago