Skip to content

Keep the ECOD read lock balanced when loading fails #1150

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Merged
josemduarte merged 1 commit into from
Sep 1, 2026
+18 −6
Merged

Keep the ECOD read lock balanced when loading fails #1150

Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
24 changes: 18 additions & 6 deletions biojava-structure/src/main/java/org/biojava/nbio/structure/ecod/EcodInstallation.java
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -137,9 +137,15 @@ public List<EcodDomain> getDomainsForPdb(String id) throws IOException {
// unlock to allow ensureDomainsFileInstalled to get the write lock
logger.trace("UNLOCK readlock");
domainsFileLock.readLock().unlock();
indexDomains();
domainsFileLock.readLock().lock();
logger.trace("LOCK readlock");
try {
indexDomains();
} finally {
// re-acquire even if indexing failed, so the outer finally has a
// lock to release; otherwise IllegalMonitorStateException replaces
// the real cause and the failure becomes unreadable
domainsFileLock.readLock().lock();
logger.trace("LOCK readlock");
}
}

PdbId pdbId = null;
Expand Down Expand Up @@ -244,9 +250,15 @@ public List<EcodDomain> getAllDomains() throws IOException {
// unlock to allow ensureDomainsFileInstalled to get the write lock
logger.trace("UNLOCK readlock");
domainsFileLock.readLock().unlock();
ensureDomainsFileInstalled();
domainsFileLock.readLock().lock();
logger.trace("LOCK readlock");
try {
ensureDomainsFileInstalled();
} finally {
// re-acquire even if the download failed, so the outer finally has a
// lock to release; otherwise IllegalMonitorStateException replaces
// the real cause and the failure becomes unreadable
domainsFileLock.readLock().lock();
logger.trace("LOCK readlock");
}
}
return allDomains;
} finally {
Expand Down
Loading