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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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Fix ArrayIndexOutOfBoundsException and file validation in CathInstall… 
…ation
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@josemduarte
josemduarte committed Aug 26, 2026
commit 72b5ed10566b87a0d11b7bd81d05b0af34f95997
27 changes: 19 additions & 8 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 @@ -355,7 +355,9 @@ private void parseCathDomainList(BufferedReader bufferedReader) throws IOExcepti
// int counter = 0;
while ( (line = bufferedReader.readLine()) != null ) {
if ( line.startsWith("#") ) continue;
if ( line.trim().isEmpty() ) continue;
CathDomain cathDomain = parseCathListFileLine(line);
if ( cathDomain == null ) continue;
// counter++;

String pdbId = cathDomain.getPdbIdAndChain().substring(0,4); // includes chain letter
Expand Down Expand Up @@ -386,7 +388,9 @@ 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 +417,7 @@ 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 +509,11 @@ 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 +530,11 @@ 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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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 +555,8 @@ 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 +682,25 @@ 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
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