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Fix ArrayIndexOutOfBoundsException and file validation in CathInstallation #1145

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Merged
josemduarte merged 6 commits into from
Aug 27, 2026
+113 −11
Merged

Fix ArrayIndexOutOfBoundsException and file validation in CathInstallation #1145

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72b5ed1
Fix ArrayIndexOutOfBoundsException and file validation in CathInstall…
josemduarte Aug 26, 2026
4b4e91f
Merge branch 'master' into jd/cath-fixes
josemduarte Aug 26, 2026
83fe61a
Safeguard for case of nothing parseable in file
josemduarte Aug 26, 2026
27bb418
Logging
josemduarte Aug 26, 2026
26c03d1
Demoting
josemduarte Aug 27, 2026
954d75a
Test fix suggested by AI: test was failing when download was too slow
josemduarte Aug 27, 2026
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37 changes: 26 additions & 11 deletions biojava-structure/src/main/java/org/biojava/nbio/structure/cath/CathInstallation.java
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Original file line number Diff line number Diff line change
Expand Up @@ -350,13 +350,15 @@ private void parseCathDomainList() throws IOException {
parseCathDomainList(buffer);
}

private void parseCathDomainList(BufferedReader bufferedReader) throws IOException{
protected void parseCathDomainList(BufferedReader bufferedReader) throws IOException{
String line;
// int counter = 0;
int counter = 0;
while ( (line = bufferedReader.readLine()) != null ) {
if ( line.startsWith("#") ) continue;
if ( line.trim().isEmpty() ) continue;
CathDomain cathDomain = parseCathListFileLine(line);
// counter++;
if ( cathDomain == null ) continue;
counter++;

String pdbId = cathDomain.getPdbIdAndChain().substring(0,4); // includes chain letter

Expand All @@ -372,6 +374,9 @@ private void parseCathDomainList(BufferedReader bufferedReader) throws IOExcepti

domainMap.put( cathDomain.getDomainName(), cathDomain );
}
if (counter == 0) {
throw new IOException("Could not parse any CATH domains from the domain list file.");
}
}

private void parseCathNames() throws IOException {
Expand All @@ -386,7 +391,9 @@ private void parseCathNames(BufferedReader bufferedReader) throws IOException{
//int counter = 0;
while ( (line = bufferedReader.readLine()) != null ) {
if ( line.startsWith("#") ) continue;
if ( line.trim().isEmpty() ) continue;
CathNode cathNode = parseCathNamesFileLine(line);
if ( cathNode == null ) continue;
cathTree.put(cathNode.getNodeId(), cathNode);
}
}
Expand All @@ -413,6 +420,7 @@ private void parseCathDomainDescriptionFile(BufferedReader bufferedReader) throw
StringBuilder sseqs = null;
while ( (line = bufferedReader.readLine()) != null ) {
if ( line.startsWith("#") ) continue;
if ( line.trim().isEmpty() ) continue;
if ( line.startsWith("FORMAT") ) {
cathDescription = new CathDomain();
cathDescription.setFormat( line.substring(10) );
Expand Down Expand Up @@ -504,8 +512,11 @@ private void parseCathDomainDescriptionFile(BufferedReader bufferedReader) throw
}*/

private CathDomain parseCathListFileLine(String line) {
String [] token = line.trim().split("\\s+");
if (token.length < 12) {
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return null;
}
CathDomain cathDomain = new CathDomain();
String [] token = line.split("\\s+");
cathDomain.setDomainName(token[0]);
cathDomain.setClassId(Integer.parseInt(token[1]));
cathDomain.setArchitectureId(Integer.parseInt(token[2]));
Expand All @@ -522,8 +533,12 @@ private CathDomain parseCathListFileLine(String line) {
}

private CathNode parseCathNamesFileLine(String line) {
String[] token = line.trim().split("\\s+",3);
if (token.length < 3) {
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LOGGER.debug("Invalid line in cath names file, was expecting 3 tokens but got {} tokens: {}", token.length, line);
return null;
}
CathNode cathNode = new CathNode();
String[] token = line.split("\\s+",3);
cathNode.setNodeId( token[0] );
int idx = token[0].lastIndexOf(".");
if ( idx == -1 ) idx = token[0].length();
Expand All @@ -544,8 +559,8 @@ private void parseCathDomall(BufferedReader bufferedReader) throws IOException{
String line;
while ( ((line = bufferedReader.readLine()) != null) ) {
if ( line.startsWith("#") ) continue;
if ( line.length() == 0 ) continue;
String[] token = line.split("\\s+");
if ( line.trim().isEmpty() ) continue;
String[] token = line.trim().split("\\s+");
String chainId = token[0];
Integer numberOfDomains = Integer.parseInt( token[1].substring(1) );
Integer numberOfFragments = Integer.parseInt( token[2].substring(1) );
Expand Down Expand Up @@ -671,25 +686,25 @@ protected void downloadFileFromRemote(URL remoteURL, File localFile) throws IOEx
private boolean domainDescriptionFileAvailable(){
String fileName = getDomainDescriptionFileName();
File f = new File(fileName);
return f.exists();
return f.exists() && FileDownloadUtils.validateFile(f);
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}

private boolean domainListFileAvailable(){
String fileName = getDomainListFileName();
File f = new File(fileName);
return f.exists();
return f.exists() && FileDownloadUtils.validateFile(f);
}

private boolean nodeListFileAvailable(){
String fileName = getNodeListFileName();
File f = new File(fileName);
return f.exists();
return f.exists() && FileDownloadUtils.validateFile(f);
}

private boolean domallFileAvailable() {
String fileName = getDomallFileName();
File f= new File(fileName);
return f.exists();
return f.exists() && FileDownloadUtils.validateFile(f);
}

protected void downloadDomainListFile() throws IOException{
Expand Down
87 changes: 87 additions & 0 deletions biojava-structure/src/test/java/org/biojava/nbio/structure/cath/CathInstallationTest.java
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Original file line number Diff line number Diff line change
@@ -0,0 +1,87 @@
/*
* BioJava development code
*
* This code may be freely distributed and modified under the
* terms of the GNU Lesser General Public Licence. This should
* be distributed with the code. If you do not have a copy,
* see:
*
* http://www.gnu.org/copyleft/lesser.html
*
* Copyright for this code is held jointly by the individual
* authors. These should be listed in @author doc comments.
*
* For more information on the BioJava project and its aims,
* or to join the biojava-l mailing list, visit the home page
* at:
*
* http://www.biojava.org/
*/
package org.biojava.nbio.structure.cath;

import org.junit.jupiter.api.Test;

import java.io.BufferedReader;
import java.io.IOException;
import java.io.StringReader;
import java.util.concurrent.atomic.AtomicBoolean;

import static org.junit.jupiter.api.Assertions.assertEquals;
import static org.junit.jupiter.api.Assertions.assertNotNull;
import static org.junit.jupiter.api.Assertions.assertThrows;

public class CathInstallationTest {

@Test
public void testParseCathDomainListSuccess() throws IOException {
String data = "# CATH domain list\n"
+ "\n"
+ "1oaiA00 1 10 490 10 1 1 1 1 1 124 1.80\n"
+ "1oaiA01 1 10 490 10 1 1 1 1 2 150 1.80\n";

CathInstallation installation = new CathInstallation("");
BufferedReader reader = new BufferedReader(new StringReader(data));
installation.parseCathDomainList(reader);
installation.setInstalledDomainList(new AtomicBoolean(true)); //1
installation.setInstalledDomall(new AtomicBoolean(true)); //2

CathDomain domain = installation.getDomainByCathId("1oaiA00");
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assertNotNull(domain);
assertEquals("1oaiA00", domain.getDomainName());
assertEquals(1, domain.getClassId());
assertEquals(10, domain.getArchitectureId());
assertEquals(490, domain.getTopologyId());
assertEquals(10, domain.getHomologyId());
assertEquals(124, domain.getLength());
assertEquals(1.80, domain.getResolution(), 0.001);
}

@Test
public void testParseCathDomainListEmptyThrowsException() {
CathInstallation installation = new CathInstallation("");
BufferedReader reader = new BufferedReader(new StringReader(""));
assertThrows(IOException.class, () -> installation.parseCathDomainList(reader));
}

@Test
public void testParseCathDomainListOnlyCommentsAndWhitespaceThrowsException() {
String data = "# comment 1\n"
+ "# comment 2\n"
+ " \n"
+ "\t\n";
CathInstallation installation = new CathInstallation("");
BufferedReader reader = new BufferedReader(new StringReader(data));
assertThrows(IOException.class, () -> installation.parseCathDomainList(reader));
}

@Test
public void testParseCathDomainListNoParsableLinesThrowsException() {
String data = "# comment\n"
+ "invalid line with too few tokens\n"
+ "another bad line\n";
CathInstallation installation = new CathInstallation("");
BufferedReader reader = new BufferedReader(new StringReader(data));
IOException exception = assertThrows(IOException.class, () -> installation.parseCathDomainList(reader));
assertNotNull(exception.getMessage());
}
}
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