[phylr commit] r34 - Updated ORG to org completely

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Jun 25, 2009, 4:22:03 AM6/25/09

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Author: dazhi.jiao
Date: Wed Jun 24 19:53:15 2009
New Revision: 34

Added:
trunk/phylr-gsoc/README.txt
Modified:
trunk/phylr-gsoc/ (props changed)
trunk/phylr-gsoc/src/main/java/org/oclc/os/SRW/EmbeddedSRWDatabase.java

trunk/phylr-gsoc/src/main/java/org/oclc/os/SRW/Lucene/SRWLuceneDatabase.java
trunk/phylr-gsoc/src/main/java/org/oclc/os/SRW/SRWDatabase.java
trunk/phylr-gsoc/src/main/java/org/oclc/os/SRW/SRWJaxrDatabase.java.later

trunk/phylr-gsoc/src/main/java/org/oclc/os/SRW/SRWZ3950Database.java.later
trunk/phylr-gsoc/src/main/java/org/oclc/os/SRW/SortEntry.java
trunk/phylr-gsoc/src/main/resources/SRWServer.props
trunk/phylr-gsoc/src/main/resources/TreeIndex.props
trunk/phylr-gsoc/src/main/resources/log4j.properties
trunk/phylr-gsoc/src/main/webapp/WEB-INF/web.xml

Log:
Updated ORG to org completely

Added: trunk/phylr-gsoc/README.txt
==============================================================================
--- (empty file)
+++ trunk/phylr-gsoc/README.txt Wed Jun 24 19:53:15 2009
@@ -0,0 +1,12 @@
+To create a war file:
+
+# mvn package
+
+To compile
+
+# mvn compile
+
+Before deploy, don't forget to update the file
src/main/resources/SRWServer.props,
+basically you need to already created lucene index with
nexmlLuceneIndexer. Put the
+path to the lucene index directory in the props file.
+

Modified:
trunk/phylr-gsoc/src/main/java/org/oclc/os/SRW/EmbeddedSRWDatabase.java
==============================================================================
--- trunk/phylr-gsoc/src/main/java/org/oclc/os/SRW/EmbeddedSRWDatabase.java
(original)
+++ trunk/phylr-gsoc/src/main/java/org/oclc/os/SRW/EmbeddedSRWDatabase.java
Wed Jun 24 19:53:15 2009
@@ -59,9 +59,6 @@
import org.w3c.dom.Element;
import org.xml.sax.InputSource;

-//import ORG.oclc.ber.DataDir;
-//import ORG.oclc.RecordHandler.HandleSGML;
-
public class EmbeddedSRWDatabase {

public EmbeddedSRWDatabase() {
@@ -491,6 +488,6 @@
}

static void usage() {
- System.out.println("usage: java
ORG.oclc.os.SRW.EmbeddedSRWDatabase [-p<SRWServer.props>] -d<dbname>");
+ System.out.println("usage: java
org.oclc.os.SRW.EmbeddedSRWDatabase [-p<SRWServer.props>] -d<dbname>");
}
}

Modified:
trunk/phylr-gsoc/src/main/java/org/oclc/os/SRW/Lucene/SRWLuceneDatabase.java
==============================================================================
---
trunk/phylr-gsoc/src/main/java/org/oclc/os/SRW/Lucene/SRWLuceneDatabase.java
(original)
+++
trunk/phylr-gsoc/src/main/java/org/oclc/os/SRW/Lucene/SRWLuceneDatabase.java
Wed Jun 24 19:53:15 2009
@@ -281,7 +281,7 @@
}

String
translatorName=dbProperties.getProperty("SRWLuceneDatabase.CqlToLuceneQueryTranslator",
- "ORG.oclc.os.SRW.Lucene.BasicLuceneQueryTranslator");
+ "org.oclc.os.SRW.Lucene.BasicLuceneQueryTranslator");
try {
log.debug("creating translator "+translatorName);
Class translatorClass=Class.forName(translatorName);

Modified: trunk/phylr-gsoc/src/main/java/org/oclc/os/SRW/SRWDatabase.java
==============================================================================
--- trunk/phylr-gsoc/src/main/java/org/oclc/os/SRW/SRWDatabase.java
(original)
+++ trunk/phylr-gsoc/src/main/java/org/oclc/os/SRW/SRWDatabase.java Wed Jun
24 19:53:15 2009
@@ -966,40 +966,40 @@
dbn+".class entry in properties file");
dbn="db.default";
}
- if(className.equals("ORG.oclc.os.SRW.SRWPearsDatabase")) {
- log.info("** Warning ** the class
ORG.oclc.os.SRW.SRWPearsDatabase has been replaced with
ORG.oclc.os.SRW.Pears.SRWPearsDatabase");
+ if(className.equals("org.oclc.os.SRW.SRWPearsDatabase")) {
+ log.info("** Warning ** the class
org.oclc.os.SRW.SRWPearsDatabase has been replaced with
org.oclc.os.SRW.Pears.SRWPearsDatabase");
log.info(" Please correct the server's properties
file");
- className="ORG.oclc.os.SRW.Pears.SRWPearsDatabase";
+ className="org.oclc.os.SRW.Pears.SRWPearsDatabase";
log.debug("new className="+className);
}
- else if(className.equals("ORG.oclc.os.SRW.SRWRemoteDatabase")) {
- log.info("** Warning ** the class
ORG.oclc.os.SRW.SRWRemoteDatabase has been replaced with
ORG.oclc.os.SRW.ParallelSearching.SRWRemoteDatabase");
+ else if(className.equals("org.oclc.os.SRW.SRWRemoteDatabase")) {
+ log.info("** Warning ** the class
org.oclc.os.SRW.SRWRemoteDatabase has been replaced with
org.oclc.os.SRW.ParallelSearching.SRWRemoteDatabase");
log.info(" Please correct the server's properties
file");
-
className="ORG.oclc.os.SRW.ParallelSearching.SRWRemoteDatabase";
+
className="org.oclc.os.SRW.ParallelSearching.SRWRemoteDatabase";
log.debug("new className="+className);
}
- else
if(className.equals("ORG.oclc.os.SRW.Pears.SRWRemoteDatabase")) {
- log.info("** Warning ** the class
ORG.oclc.os.SRW.Pears.SRWRemoteDatabase has been replaced with
ORG.oclc.os.SRW.ParallelSearching.SRWRemoteDatabase");
+ else
if(className.equals("org.oclc.os.SRW.Pears.SRWRemoteDatabase")) {
+ log.info("** Warning ** the class
org.oclc.os.SRW.Pears.SRWRemoteDatabase has been replaced with
org.oclc.os.SRW.ParallelSearching.SRWRemoteDatabase");
log.info(" Please correct the server's properties
file");
-
className="ORG.oclc.os.SRW.ParallelSearching.SRWRemoteDatabase";
+
className="org.oclc.os.SRW.ParallelSearching.SRWRemoteDatabase";
log.debug("new className="+className);
}
- else if(className.equals("ORG.oclc.os.SRW.SRWMergeDatabase")) {
- log.info("** Warning ** the class
ORG.oclc.os.SRW.SRWMergeDatabase has been replaced with
ORG.oclc.os.SRW.ParallelSearching.SRWMergeDatabase");
+ else if(className.equals("org.oclc.os.SRW.SRWMergeDatabase")) {
+ log.info("** Warning ** the class
org.oclc.os.SRW.SRWMergeDatabase has been replaced with
org.oclc.os.SRW.ParallelSearching.SRWMergeDatabase");
log.info(" Please correct the server's properties
file");
- className="ORG.oclc.os.SRW.ParallelSearching.SRWMergeDatabase";
+ className="org.oclc.os.SRW.ParallelSearching.SRWMergeDatabase";
log.debug("new className="+className);
}
- else
if(className.equals("ORG.oclc.os.SRW.Pears.SRWMergeDatabase")) {
- log.info("** Warning ** the class
ORG.oclc.os.SRW.Pears.SRWMergeDatabase has been replaced with
ORG.oclc.os.SRW.ParallelSearching.SRWMergeDatabase");
+ else
if(className.equals("org.oclc.os.SRW.Pears.SRWMergeDatabase")) {
+ log.info("** Warning ** the class
org.oclc.os.SRW.Pears.SRWMergeDatabase has been replaced with
org.oclc.os.SRW.ParallelSearching.SRWMergeDatabase");
log.info(" Please correct the server's properties
file");
- className="ORG.oclc.os.SRW.ParallelSearching.SRWMergeDatabase";
+ className="org.oclc.os.SRW.ParallelSearching.SRWMergeDatabase";
log.debug("new className="+className);
}
- else if(className.equals("ORG.oclc.os.SRW.SRWDLuceneDatabase")) {
- log.info("** Warning ** the class
ORG.oclc.os.SRW.SRWLuceneDatabase has been replaced with
ORG.oclc.os.SRW.DSpaceLucene.SRWLuceneDatabase");
+ else if(className.equals("org.oclc.os.SRW.SRWDLuceneDatabase")) {
+ log.info("** Warning ** the class
org.oclc.os.SRW.SRWLuceneDatabase has been replaced with
org.oclc.os.SRW.DSpaceLucene.SRWLuceneDatabase");
log.info(" Please correct the server's properties
file");
- className="ORG.oclc.os.SRW.DSpaceLucene.SRWLuceneDatabase";
+ className="org.oclc.os.SRW.DSpaceLucene.SRWLuceneDatabase";
log.debug("new className="+className);
}
SRWDatabase db=null;

Modified:
trunk/phylr-gsoc/src/main/java/org/oclc/os/SRW/SRWJaxrDatabase.java.later
==============================================================================
---
trunk/phylr-gsoc/src/main/java/org/oclc/os/SRW/SRWJaxrDatabase.java.later
(original)
+++
trunk/phylr-gsoc/src/main/java/org/oclc/os/SRW/SRWJaxrDatabase.java.later
Wed Jun 24 19:53:15 2009
@@ -19,7 +19,7 @@
* Created on August 5, 2003, 4:17 PM
*/

-package ORG.oclc.os.SRW;
+package org.oclc.os.SRW;

import gov.loc.www.zing.srw.v1_0.*;
import gov.loc.www.zing.srw.v1_0.diagnostic.DiagnosticType;
@@ -152,7 +152,7 @@
try {
byteRecord=null; // get record from JAXR
log.info("XML version as provided by
HandleSGML:");
-
log.info("\n"+ORG.oclc.util.Util.byteArrayToString(byteRecord));
+
log.info("\n"+org.oclc.util.Util.byteArrayToString(byteRecord));
try {
stringRecord=new
String(byteRecord, "UTF8");
}
@@ -173,7 +173,7 @@
record.setRecordPosition(new
RecordType_recordPosition(Integer.toString(startPoint)));

//log.info("transformed record:");
-
//log.info(ORG.oclc.util.Util.byteArrayToString(stringRecord.getBytes()));
+
//log.info(org.oclc.util.Util.byteArrayToString(stringRecord.getBytes()));
records.setRecord(i, record);
} catch (NoSuchElementException e) {
log.error("Read beyond the end of list!!");

Modified:
trunk/phylr-gsoc/src/main/java/org/oclc/os/SRW/SRWZ3950Database.java.later
==============================================================================
---
trunk/phylr-gsoc/src/main/java/org/oclc/os/SRW/SRWZ3950Database.java.later
(original)
+++
trunk/phylr-gsoc/src/main/java/org/oclc/os/SRW/SRWZ3950Database.java.later
Wed Jun 24 19:53:15 2009
@@ -19,7 +19,7 @@
* Created on February 9, 2004, 10:04 AM
*/

-package ORG.oclc.os.SRW;
+package org.oclc.os.SRW;

import java.util.Stack;
import gov.loc.www.zing.srw.ScanRequestType;
@@ -29,10 +29,10 @@
import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory;
import ORG.oclc.ber.BerString;
-import ORG.oclc.ber.DataDir;
-import ORG.oclc.z39.Diagnostic1;
-import ORG.oclc.z39.Z39presentApi;
-import ORG.oclc.z39.Z39session;
+import org.oclc.ber.DataDir;
+import org.oclc.z39.Diagnostic1;
+import org.oclc.z39.Z39presentApi;
+import org.oclc.z39.Z39session;
import org.z3950.zing.cql.CQLNode;

/**
@@ -115,7 +115,7 @@
null, "f", Z39presentApi.OCLC_BER_SYNTAX, null, 101,
null,
attributesPlusTerm, true);
}
- catch(ORG.oclc.z39.AccessControl e) {
+ catch(org.oclc.z39.AccessControl e) {
diagnostic(SRWDiagnostics.GeneralSystemError,
e.getMessage(),
response);
log.error(e, e);

Modified: trunk/phylr-gsoc/src/main/java/org/oclc/os/SRW/SortEntry.java
==============================================================================
--- trunk/phylr-gsoc/src/main/java/org/oclc/os/SRW/SortEntry.java (original)
+++ trunk/phylr-gsoc/src/main/java/org/oclc/os/SRW/SortEntry.java Wed Jun
24 19:53:15 2009
@@ -77,7 +77,7 @@
}

public String toString() {
- StringBuffer sb=new StringBuffer("ORG.oclc.os.SRW.SortEntry:
key=").append(key);
+ StringBuffer sb=new StringBuffer("org.oclc.os.SRW.SortEntry:
key=").append(key);
if(number!=-1)
sb.append(", number=").append(number);
if(entry!=null)

Modified: trunk/phylr-gsoc/src/main/resources/SRWServer.props
==============================================================================
--- trunk/phylr-gsoc/src/main/resources/SRWServer.props (original)
+++ trunk/phylr-gsoc/src/main/resources/SRWServer.props Wed Jun 24 19:53:15
2009
@@ -49,13 +49,13 @@
#

# parameters for the test database
-db.test.class=ORG.oclc.os.SRW.SRWTestDatabase
+db.test.class=org.oclc.os.SRW.SRWTestDatabase

-db.treebase.class=ORG.oclc.os.SRW.Lucene.SRWLuceneDatabase
+db.treebase.class=org.oclc.os.SRW.Lucene.SRWLuceneDatabase
db.treebase.home=/home/djiao/workspace/phylr-gsoc/data/phylr-index
db.treebase.configuration=TreeIndex.props

-db.lucene.class=ORG.oclc.os.SRW.Lucene.SRWLuceneDatabase
+db.lucene.class=org.oclc.os.SRW.Lucene.SRWLuceneDatabase
db.lucene.home=/Users/ryan/phylr-data/dryadSearch
db.lucene.configuration=Test.props

Modified: trunk/phylr-gsoc/src/main/resources/TreeIndex.props
==============================================================================
--- trunk/phylr-gsoc/src/main/resources/TreeIndex.props (original)
+++ trunk/phylr-gsoc/src/main/resources/TreeIndex.props Wed Jun 24 19:53:15
2009
@@ -5,13 +5,15 @@

configInfo.maximumRecords=50

-
# Mapping between the CQL indexes (query fields) and searchable fields
# within the Lucene index.
-qualifier.dc.identifier=treeid
-qualifier.dc.creator=author
-qualifier.dc.description=abstract
-qualifier.dc.subject=keywords
+qualifier.dc.identifier=dc.identifier
+qualifier.dc.creator=dc.creator
+qualifier.dc.contributor=dc.contributor
+qualifier.dc.description=dc.description
+qualifier.dc.title=dc.title
+qualifier.dc.subject=dc.subject
+qualifier.phylo.treeid=phylo.treeid
qualifier.phylo.scientificName=otu
qualifier.phylo.datatype=datatype
qualifier.phylo.treesize=treesize

Modified: trunk/phylr-gsoc/src/main/resources/log4j.properties
==============================================================================
--- trunk/phylr-gsoc/src/main/resources/log4j.properties (original)
+++ trunk/phylr-gsoc/src/main/resources/log4j.properties Wed Jun 24
19:53:15 2009
@@ -3,12 +3,12 @@
#log4j.rootLogger=INFO, A1
#log4j.rootLogger=DEBUG, A1

-#log4j.logger.ORG.oclc.os.SRW.Pears.SRWPearsDatabase=DEBUG
-#log4j.logger.ORG.oclc.os.SRW.Lucene.SRWLuceneDatabase=DEBUG
-#log4j.logger.ORG.oclc.os.SRW.DSpaceLucene.SRWLuceneDatabase=DEBUG
-#log4j.logger.ORG.oclc.os.SRW.SRWDatabaseImpl=INFO
-#log4j.logger.ORG.oclc.os.SRW.SRWDatabase=INFO
-log4j.logger.ORG.oclc.os.SRW=DEBUG
+#log4j.logger.org.oclc.os.SRW.Pears.SRWPearsDatabase=DEBUG
+#log4j.logger.org.oclc.os.SRW.Lucene.SRWLuceneDatabase=DEBUG
+#log4j.logger.org.oclc.os.SRW.DSpaceLucene.SRWLuceneDatabase=DEBUG
+#log4j.logger.org.oclc.os.SRW.SRWDatabaseImpl=INFO
+#log4j.logger.org.oclc.os.SRW.SRWDatabase=INFO
+log4j.logger.org.oclc.os.SRW=DEBUG

# A1 is set to be a ConsoleAppender.
log4j.appender.A1=org.apache.log4j.ConsoleAppender

Modified: trunk/phylr-gsoc/src/main/webapp/WEB-INF/web.xml
==============================================================================
--- trunk/phylr-gsoc/src/main/webapp/WEB-INF/web.xml (original)
+++ trunk/phylr-gsoc/src/main/webapp/WEB-INF/web.xml Wed Jun 24 19:53:15
2009
@@ -9,7 +9,7 @@
<servlet-name>SRWServlet</servlet-name>

<servlet-class>
- ORG.oclc.os.SRW.SRWServlet
+ org.oclc.os.SRW.SRWServlet
</servlet-class>

- <servlet-class>ORG.oclc.os.SRW.SRUServerTesterServlet</servlet-class>
+ <servlet-class>org.oclc.os.SRW.SRUServerTesterServlet</servlet-class>
</servlet>