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[Treebase-guts] SF.net SVN: treebase:[280] trunk
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From: <rv...@us...> - 2009-11-18 12:41:44
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Revision: 280
http://treebase.svn.sourceforge.net/treebase/?rev=280&view=rev
Author: rvos
Date: 2009-11-18 12:41:37 +0000 (Wed, 18 Nov 2009)
Log Message:
-----------
Changed nexus file contents type from Clob (which we used under DB2) to Text (which we use under postgres), which is mapped onto a string by hibernate.
Modified Paths:
--------------
trunk/treebase-core/src/main/java/org/cipres/treebase/TreebaseUtil.java
trunk/treebase-core/src/main/java/org/cipres/treebase/domain/study/Study.java
trunk/treebase-core/src/main/java/org/cipres/treebase/service/study/StudyServiceImpl.java
trunk/treebase-core/src/main/java/org/cipres/treebase/util/RawNexusImporter.java
trunk/treebase-core/src/main/java/org/cipres/treebase/util/RebuildNexusFiletable.java
trunk/treebase-core/src/main/java/org/cipres/treebase/util/RepatriateData.java
trunk/treebase-core/src/test/java/org/cipres/treebase/dao/study/StudyDAOTest.java
trunk/treebase-core/src/test/java/org/cipres/treebase/service/study/StudyServiceImplTest.java
trunk/treebase-core/src/test/java/org/cipres/treebase/service/study/SubmissionServiceImplTest.java
trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/DownloadANexusFileController.java
trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/NexusFilesController.java
Modified: trunk/treebase-core/src/main/java/org/cipres/treebase/TreebaseUtil.java
===================================================================
--- trunk/treebase-core/src/main/java/org/cipres/treebase/TreebaseUtil.java 2009-11-18 12:25:46 UTC (rev 279)
+++ trunk/treebase-core/src/main/java/org/cipres/treebase/TreebaseUtil.java 2009-11-18 12:41:37 UTC (rev 280)
@@ -1,6 +1,10 @@
package org.cipres.treebase;
+import java.io.BufferedReader;
+import java.io.File;
+import java.io.FileReader;
+import java.io.IOException;
import java.text.ParseException;
import java.text.SimpleDateFormat;
import java.util.Arrays;
@@ -136,7 +140,42 @@
return buf.toString();
}
+
+ /**
+ * Reads the contents of a file into a string
+ * @param file
+ * @return file contents as string
+ */
+ public static String readFileToString(File file) {
+ StringBuilder contents = new StringBuilder();
+ try {
+ //use buffering, reading one line at a time
+ //FileReader always assumes default encoding is OK!
+ BufferedReader input = new BufferedReader(new FileReader(file));
+ try {
+ String line = null; //not declared within while loop
+ /*
+ * readLine is a bit quirky :
+ * it returns the content of a line MINUS the newline.
+ * it returns null only for the END of the stream.
+ * it returns an empty String if two newlines appear in a row.
+ */
+ while (( line = input.readLine()) != null){
+ contents.append(line);
+ contents.append(System.getProperty("line.separator"));
+ }
+ }
+ finally {
+ input.close();
+ }
+ }
+ catch (IOException ex){
+ ex.printStackTrace();
+ }
+ return contents.toString();
+ }
+
/**
* For Testing use. Output the content of the array to a string. If the all element parameter is
* false, output only the first 10 elements.
Modified: trunk/treebase-core/src/main/java/org/cipres/treebase/domain/study/Study.java
===================================================================
--- trunk/treebase-core/src/main/java/org/cipres/treebase/domain/study/Study.java 2009-11-18 12:25:46 UTC (rev 279)
+++ trunk/treebase-core/src/main/java/org/cipres/treebase/domain/study/Study.java 2009-11-18 12:41:37 UTC (rev 280)
@@ -1,6 +1,5 @@
package org.cipres.treebase.domain.study;
-import java.sql.Clob;
import java.util.ArrayList;
import java.util.Collection;
import java.util.Collections;
@@ -72,7 +71,7 @@
private List<Analysis> mAnalyses = new ArrayList<Analysis>();
private Set<TaxonLabelSet> mTaxonLabelSets = new HashSet<TaxonLabelSet>();
- private Map<String, Clob> mNexusFiles = new HashMap<String, Clob>();
+ private Map<String, String> mNexusFiles = new HashMap<String, String>();
// transient fields
private String mTransientDescription;
@@ -318,14 +317,14 @@
// @Cascade(org.hibernate.annotations.CascadeType.DELETE_ORPHAN)
// @Cache(usage = CacheConcurrencyStrategy.READ_WRITE, region = "studyCache")
// @Transient
- public Map<String, Clob> getNexusFiles() {
+ public Map<String, String> getNexusFiles() {
return mNexusFiles;
}
/**
* Set the NexusFiles field.
*/
- public void setNexusFiles(Map<String, Clob> pNewNexusFiles) {
+ public void setNexusFiles(Map<String, String> pNewNexusFiles) {
mNexusFiles = pNewNexusFiles;
}
@@ -415,9 +414,9 @@
* Creation date: Feb 22, 2006 12:06:25 PM
*
* @param pFileName
- * @param pNexusFile Clob
+ * @param pNexusFile
*/
- public void addNexusFile(String pFileName, Clob pNexusFile) {
+ public void addNexusFile(String pFileName, String pNexusFile) {
if (TreebaseUtil.isEmpty(pFileName)) {
if (pNexusFile == null) {
return;
Modified: trunk/treebase-core/src/main/java/org/cipres/treebase/service/study/StudyServiceImpl.java
===================================================================
--- trunk/treebase-core/src/main/java/org/cipres/treebase/service/study/StudyServiceImpl.java 2009-11-18 12:25:46 UTC (rev 279)
+++ trunk/treebase-core/src/main/java/org/cipres/treebase/service/study/StudyServiceImpl.java 2009-11-18 12:41:37 UTC (rev 280)
@@ -1,9 +1,11 @@
package org.cipres.treebase.service.study;
+import java.io.BufferedReader;
import java.io.File;
import java.io.FileNotFoundException;
import java.io.FileReader;
+import java.io.IOException;
import java.sql.Clob;
import java.util.Collection;
import java.util.Iterator;
@@ -353,23 +355,11 @@
Study s = update(pStudy);
Iterator<File> fileIter = pNexusFiles.iterator();
- try {
- while (fileIter.hasNext()) {
- File element = (File) fileIter.next();
-
- String fileName = element.getName();
- FileReader reader;
- reader = new FileReader(element);
-
- int fileLength = (int) (element.length());
- Clob nexus = Hibernate.createClob(reader, fileLength);
- s.addNexusFile(fileName, nexus);
-
- }
- } catch (FileNotFoundException ex) {
- LOGGER.error(ex.getMessage());
+ while (fileIter.hasNext()) {
+ File element = (File) fileIter.next();
+ String fileName = element.getName();
+ s.addNexusFile(fileName, TreebaseUtil.readFileToString(element));
}
-
}
/**
Modified: trunk/treebase-core/src/main/java/org/cipres/treebase/util/RawNexusImporter.java
===================================================================
--- trunk/treebase-core/src/main/java/org/cipres/treebase/util/RawNexusImporter.java 2009-11-18 12:25:46 UTC (rev 279)
+++ trunk/treebase-core/src/main/java/org/cipres/treebase/util/RawNexusImporter.java 2009-11-18 12:41:37 UTC (rev 280)
@@ -15,6 +15,7 @@
import java.util.Set;
import org.cipres.treebase.ContextManager;
+import org.cipres.treebase.TreebaseUtil;
import org.cipres.treebase.domain.matrix.Matrix;
import org.cipres.treebase.domain.matrix.MatrixHome;
import org.cipres.treebase.domain.study.Study;
@@ -121,20 +122,8 @@
return false;
}
- Clob clob;
- try {
- clob = buildClob(file);
- } catch (FileNotFoundException e) {
- err.println(fileName + ": file not found");
- return false;
- } catch (UnsupportedEncodingException e) {
- throw e;
- } catch (IOException e) {
- err.println(fileName + ": I/O error; skipping");
- return false;
- }
-
- if (clob == null) return false;
+ String fileContents = TreebaseUtil.readFileToString(file);
+ if (fileContents == null) return false;
Set<Study> studies = new HashSet<Study> ();
studies.addAll(handleMatricesInFile(file));
@@ -142,7 +131,7 @@
for (Study s : studies) {
if (liveMode())
- s.getNexusFiles().put(fileName, clob);
+ s.getNexusFiles().put(fileName, fileContents);
verbose("Study S" + s.getId() + " now linked to nexus file " + fileName);
}
return true;
Modified: trunk/treebase-core/src/main/java/org/cipres/treebase/util/RebuildNexusFiletable.java
===================================================================
--- trunk/treebase-core/src/main/java/org/cipres/treebase/util/RebuildNexusFiletable.java 2009-11-18 12:25:46 UTC (rev 279)
+++ trunk/treebase-core/src/main/java/org/cipres/treebase/util/RebuildNexusFiletable.java 2009-11-18 12:41:37 UTC (rev 280)
@@ -23,7 +23,7 @@
for (TBPersistable obj : ContextManager.getStudyHome().findAll(Study.class)) {
Study s = (Study) obj;
- Map<String,Clob> studyNexusFile = s.getNexusFiles();
+ Map<String,String> studyNexusFile = s.getNexusFiles();
for (String fileName : studyNexusFile.keySet()) {
if (nexusFileStudy.containsKey(fileName)) {
nexusFileStudy.remove(fileName);
Modified: trunk/treebase-core/src/main/java/org/cipres/treebase/util/RepatriateData.java
===================================================================
--- trunk/treebase-core/src/main/java/org/cipres/treebase/util/RepatriateData.java 2009-11-18 12:25:46 UTC (rev 279)
+++ trunk/treebase-core/src/main/java/org/cipres/treebase/util/RepatriateData.java 2009-11-18 12:41:37 UTC (rev 280)
@@ -74,8 +74,8 @@
if (m.getStudy() != s) {
String nexusFileName = m.getNexusFileName();
- Map<String,Clob> nexusMap = m.getStudy().getNexusFiles();
- Clob nexusFile = nexusMap.remove(nexusFileName);
+ Map<String,String> nexusMap = m.getStudy().getNexusFiles();
+ String nexusFile = nexusMap.remove(nexusFileName);
s.getNexusFiles().put(nexusFileName, nexusFile);
m.setStudy(s);
}
@@ -93,8 +93,8 @@
+ " to study " + s.getId() + " submission " + sub.getId());
if (t.getStudy() != s) {
String nexusFileName = t.getNexusFileName();
- Map<String,Clob> nexusMap = t.getStudy().getNexusFiles();
- Clob nexusFile = nexusMap.remove(nexusFileName);
+ Map<String,String> nexusMap = t.getStudy().getNexusFiles();
+ String nexusFile = nexusMap.remove(nexusFileName);
s.getNexusFiles().put(nexusFileName, nexusFile);
t.setStudy(s);
}
Modified: trunk/treebase-core/src/test/java/org/cipres/treebase/dao/study/StudyDAOTest.java
===================================================================
--- trunk/treebase-core/src/test/java/org/cipres/treebase/dao/study/StudyDAOTest.java 2009-11-18 12:25:46 UTC (rev 279)
+++ trunk/treebase-core/src/test/java/org/cipres/treebase/dao/study/StudyDAOTest.java 2009-11-18 12:41:37 UTC (rev 280)
@@ -243,8 +243,10 @@
+ "f ctgactgctgaggagaaggctgccgtcaccgccttttggggcaaggtgaaagtggatgaagttggtggtgag gccctgggcaggctgctggttgtctacccctggactcagaggttctttgagtcctttggggacttgtccact gctgatgctgttatgaacaaccctaaggtgaaggcccatggcaagaaggtgctagattcctttagtaatggc atgaagcatctcgatgacctcaagggcacctttgctgcgctgagtgagctgcactgtgataagctgcatgtg gatcctgagaacttcaagctcctgggcaacgtgctagtggttgtgctggctcgcaattttggcaaggaattc accccggtgctgcaggctgactttcagaaggtggtggctggtgtggccaatgccctggcccacagatatcat\n"
+ "g ctgtccgatgcggtcaacgctgccgtcaccgccttttggggcaaggtgaaagtggatcaagttggtggtgag gccctgggcaggccgctggttgtctaccgctggactcagaggtgctatgagtcctttggagacttgtccact gctgatgctgttatgaacaaccctaaggtgaaggcccatggcaagaaggtgctagattcctttagtaatggc atgaagcatctcgatgacctcaagggcacctttgctgcgctgagtgagctgcactgtgataagctgcatgtg gatcctgagaacttcaagctcctgggcaacgtgctagtggttgtgctggctcgcaattttggcaaggaattc accccggtgctgcaggctgactttcagaaggtggtggctggtgtggccaatgccctggcccacagatatcat\n";
- Clob nexusC = Hibernate.createClob(nexus);
- s.addNexusFile(fileName, nexusC);
+ //XXX rav 18/11/09 - we no longer use Clobs, we use text for nexus strings
+ //Clob nexusC = Hibernate.createClob(nexus);
+ //s.addNexusFile(fileName, nexusC);
+ s.addNexusFile(fileName, nexus);
getFixture().store(s);
Modified: trunk/treebase-core/src/test/java/org/cipres/treebase/service/study/StudyServiceImplTest.java
===================================================================
--- trunk/treebase-core/src/test/java/org/cipres/treebase/service/study/StudyServiceImplTest.java 2009-11-18 12:25:46 UTC (rev 279)
+++ trunk/treebase-core/src/test/java/org/cipres/treebase/service/study/StudyServiceImplTest.java 2009-11-18 12:41:37 UTC (rev 280)
@@ -362,10 +362,10 @@
+ "f ctgactgctgaggagaaggctgccgtcaccgccttttggggcaaggtgaaagtggatgaagttggtggtgag gccctgggcaggctgctggttgtctacccctggactcagaggttctttgagtcctttggggacttgtccact gctgatgctgttatgaacaaccctaaggtgaaggcccatggcaagaaggtgctagattcctttagtaatggc atgaagcatctcgatgacctcaagggcacctttgctgcgctgagtgagctgcactgtgataagctgcatgtg gatcctgagaacttcaagctcctgggcaacgtgctagtggttgtgctggctcgcaattttggcaaggaattc accccggtgctgcaggctgactttcagaaggtggtggctggtgtggccaatgccctggcccacagatatcat\n"
+ "g ctgtccgatgcggtcaacgctgccgtcaccgccttttggggcaaggtgaaagtggatcaagttggtggtgag gccctgggcaggccgctggttgtctaccgctggactcagaggtgctatgagtcctttggagacttgtccact gctgatgctgttatgaacaaccctaaggtgaaggcccatggcaagaaggtgctagattcctttagtaatggc atgaagcatctcgatgacctcaagggcacctttgctgcgctgagtgagctgcactgtgataagctgcatgtg gatcctgagaacttcaagctcctgggcaacgtgctagtggttgtgctggctcgcaattttggcaaggaattc accccggtgctgcaggctgactttcagaaggtggtggctggtgtggccaatgccctggcccacagatatcat\n";
- Clob nexusC = Hibernate.createClob(nexus);
+ //Clob nexusC = Hibernate.createClob(nexus);
getStudyHome().refresh(s);
- s.addNexusFile(fileName, nexusC);
+ s.addNexusFile(fileName, nexus);
// force commit immeidately, important:
setComplete();
@@ -377,14 +377,14 @@
assertTrue(countNexus == 1);
startNewTransaction();
- Clob nexusClob = s.getNexusFiles().values().iterator().next();
- int clobLength = (int) nexusClob.length();
+ String nexusString = s.getNexusFiles().values().iterator().next();
+ int nexusLength = (int) nexusString.length();
// String clobStr = nexusClob.getSubString(0, 200);
- char[] clobchars = new char[clobLength];
- nexusClob.getCharacterStream().read(clobchars);
- logger.info("test clob: length=" + clobLength + "content = " + new String(clobchars));
- assertTrue(clobLength > 0);
+ //char[] clobchars = new char[clobLength];
+ //nexusClob.getCharacterStream().read(clobchars);
+ logger.info("test clob: length=" + nexusLength + "content = " + nexusString);
+ assertTrue(nexusLength > 0);
setComplete();
endTransaction();
Modified: trunk/treebase-core/src/test/java/org/cipres/treebase/service/study/SubmissionServiceImplTest.java
===================================================================
--- trunk/treebase-core/src/test/java/org/cipres/treebase/service/study/SubmissionServiceImplTest.java 2009-11-18 12:25:46 UTC (rev 279)
+++ trunk/treebase-core/src/test/java/org/cipres/treebase/service/study/SubmissionServiceImplTest.java 2009-11-18 12:41:37 UTC (rev 280)
@@ -472,13 +472,10 @@
Study study2 = (Study) hibernateTemplate.load(Study.class, sub.getStudy().getId());
// hibernateTemplate.refresh(sub);
- Clob nexusClob = study2.getNexusFiles().values().iterator().next();
- int clobLength = (int) nexusClob.length();
- char[] clobchars = new char[clobLength];
- nexusClob.getCharacterStream().read(clobchars);
- String clobStr = new String(clobchars);
- logger.info("test clob: length=" + clobLength + "content = " + clobStr);
- assertTrue(clobLength > 0);
+ String nexusString = study2.getNexusFiles().values().iterator().next();
+ int nexusStringLength = (int) nexusString.length();
+ logger.info("test clob: length=" + nexusStringLength + "content = " + nexusString);
+ assertTrue(nexusStringLength > 0);
// 4. delete: delete submission:
// after add Nexus files, sub is outdated:
@@ -569,13 +566,10 @@
// verify clob:
hibernateTemplate.refresh(sub);
- Clob nexusClob = sub.getStudy().getNexusFiles().values().iterator().next();
- int clobLength = (int) nexusClob.length();
- char[] clobchars = new char[clobLength];
- nexusClob.getCharacterStream().read(clobchars);
- String clobStr = new String(clobchars);
- logger.info("test clob: length=" + clobLength + "content = " + clobStr);
- assertTrue(clobLength > 0);
+ String nexusString = sub.getStudy().getNexusFiles().values().iterator().next();
+ int nexusStringLength = (int) nexusString.length();
+ logger.info("test clob: length=" + nexusStringLength + "content = " + nexusString);
+ assertTrue(nexusStringLength > 0);
// 4. delete: delete submission:
// after add Nexus files, sub is outdated:
Modified: trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/DownloadANexusFileController.java
===================================================================
--- trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/DownloadANexusFileController.java 2009-11-18 12:25:46 UTC (rev 279)
+++ trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/DownloadANexusFileController.java 2009-11-18 12:41:37 UTC (rev 280)
@@ -135,20 +135,11 @@
return null;
}
Study study = ControllerUtil.findStudy(req, mStudyService);
- Map<String, Clob> nexusMap = study.getNexusFiles();
- Clob clob = nexusMap.get(nexusFileName);
- String clobStr = "File Not Found. File Name is: " + nexusFileName;
- if (clob != null) {
- try {
- int clobLength = (int) clob.length();
- char[] clobchars = new char[clobLength];
- clob.getCharacterStream().read(clobchars);
- clobStr = new String(clobchars);
- } catch ( Exception e ) {
- e.printStackTrace();
- }
- }
- return clobStr;
+ Map<String, String> nexusMap = study.getNexusFiles();
+ String nexusString = nexusMap.get(nexusFileName);
+ return nexusString != null
+ ? nexusString
+ : "File Not Found. File Name is: " + nexusFileName;
}
}
Modified: trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/NexusFilesController.java
===================================================================
--- trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/NexusFilesController.java 2009-11-18 12:25:46 UTC (rev 279)
+++ trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/NexusFilesController.java 2009-11-18 12:41:37 UTC (rev 280)
@@ -51,7 +51,7 @@
throws Exception {
Study study = ControllerUtil.findStudy(pRequest, mStudyService);
- Map<String, Clob> nexusFilesMap = study.getNexusFiles();
+ Map<String, String> nexusFilesMap = study.getNexusFiles();
if (LOGGER.isDebugEnabled()) {
LOGGER.debug("MAP SIZE IS: " + nexusFilesMap.size());
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