Fix for postgres instance process closing #12927

UdayHE · 2025-04-13T05:13:53Z

Summary

Added logic to detect and clean up stale embedded PostgreSQL instances left behind by previous JabRef sessions.
Introduced PostgreProcessCleaner to safely shut down any orphaned PostgreSQL processes using port-based detection and Java PID tracking.
Registered a shutdown hook in Launcher to ensure embedded PostgreSQL is properly terminated during normal or abrupt shutdowns (excluding SIGKILL).

Mandatory checks

I own the copyright of the code submitted and I license it under the MIT license.
Change in CHANGELOG.md described in a way that is understandable for the average user (if change is visible to the user)
Tests created for changes (if applicable)
Manually tested changed features in running JabRef (always required)
Screenshots added in PR description (if change is visible to the user)
Checked developer's documentation: Is the information available and up to date? If not, I outlined it in this pull request.
Checked documentation: Is the information available and up to date? If not, I created an issue at https://github.com/JabRef/user-documentation/issues or, even better, I submitted a pull request to the documentation repository.

macOS Sequoia 15.4.
https://www.loom.com/share/9ed0da7815714797b4f0568c33f6df03?sid=34114b6c-ca32-43ff-9896-bfae39b36c81

Windows
https://github.com/user-attachments/assets/aa7a7da4-661e-464e-a08f-f6befba66363

…ination (Fix JabRef#12844) * Added logic to detect and clean up stale embedded PostgreSQL instances left behind by previous JabRef sessions. * Introduced PostgresProcessCleaner to safely shut down any orphaned PostgreSQL processes using PID-based detection. * Registered a shutdown hook in Launcher to ensure embedded PostgreSQL is properly terminated during normal or abrupt shutdown.

…ination (Fix JabRef#12844) * Added logic to detect and clean up stale embedded PostgreSQL instances left behind by previous JabRef sessions. * Introduced PostgresProcessCleaner to safely shut down any orphaned PostgreSQL processes using PID-based detection. * Registered a shutdown hook in Launcher to ensure embedded PostgreSQL is properly terminated during normal or abrupt shutdown. * Updated CHANGELOG.md

…ination (Fix JabRef#12844) * Added logic to detect and clean up stale embedded PostgreSQL instances left behind by previous JabRef sessions. * Introduced PostgresProcessCleaner to safely shut down any orphaned PostgreSQL processes using PID-based detection. * Registered a shutdown hook in Launcher to ensure embedded PostgreSQL is properly terminated during normal or abrupt shutdown.

…ination (Fix JabRef#12844) * Added logic to detect and clean up stale embedded PostgreSQL instances left behind by previous JabRef sessions. * Introduced PostgresProcessCleaner to safely shut down any orphaned PostgreSQL processes using PID-based detection. * Registered a shutdown hook in Launcher to ensure embedded PostgreSQL is properly terminated during normal or abrupt shutdown. * Updated CHANGELOG.md

…ssue-12844

…ination (Fix JabRef#12844) * Added logic to detect and clean up stale embedded PostgreSQL instances left behind by previous JabRef sessions. * Introduced PostgresProcessCleaner to safely shut down any orphaned PostgreSQL processes using PID-based detection. * Registered a shutdown hook in Launcher to ensure embedded PostgreSQL is properly terminated during normal or abrupt shutdown. * Updated CHANGELOG.md

…ination (Fix JabRef#12844) * style changes in PostgreProcessCleaner, Launcher

koppor · 2025-04-13T06:58:02Z

src/main/java/org/jabref/logic/search/PostgreProcessCleaner.java

+
+    private void destroyPreviousJavaProcess(Map<String, Object> meta) throws InterruptedException {
+        long javaPid = ((Number) meta.get("javaPid")).longValue();
+        destroyProcessByPID(javaPid, 1000);


How does one know whether this stores JabRef data? Shouldn't a connection attempt be made?

In writeMetadataToFile method, I am using ProcessHandle.current().pid(), so that the current running process id will be stored in the json file.

koppor · 2025-04-13T07:01:43Z

This is AI generated, isn't it?

subhramit · 2025-04-13T07:05:04Z

Have you tested this by observing the processes? If so, on which OS?
I tried on Windows. Doesn't work.

UdayHE · 2025-04-13T07:18:13Z

This is AI generated, isn't it?

nope.

koppor · 2025-04-13T07:48:13Z

src/main/java/org/jabref/logic/search/PostgreServer.java

 import static org.jabref.model.search.PostgreConstants.BIB_FIELDS_SCHEME;

 public class PostgreServer {
    private static final Logger LOGGER = LoggerFactory.getLogger(PostgreServer.class);
+    public static final Path POSTGRES_METADATA_FILE = Path.of("/tmp/jabref-postgres-info.json");


Will not work in Windows. Will not work if multiple JabRef instances run.

For the former, AppDirs can be used (can't it?) - for the latter, the whole flow needs to be thought through.

Got it, I need to check about AppDirs once & get back on this.

UdayHE · 2025-04-13T07:51:04Z

Have you tested this by observing the processes? If so, on which OS? I tried on Windows. Doesn't work.

yes, I have tested on macOS Sequoia 15.4.
https://www.loom.com/share/9ed0da7815714797b4f0568c33f6df03?sid=34114b6c-ca32-43ff-9896-bfae39b36c81

I will check on windows and update here.

subhramit · 2025-04-13T09:23:15Z

yes, I have tested on macOS Sequoia 15.4.
https://www.loom.com/share/9ed0da7815714797b4f0568c33f6df03?sid=34114b6c-ca32-43ff-9896-bfae39b36c81

Interesting - this seems to be going in a positive direction, if we can fix it for Windows.
Let me know if you want me to test and give feedback after a certain round of changes.

…ination (Fix JabRef#12844) * style changes in PostgreServer imports

…ination (Fix JabRef#12844) * Updated CHANGELOG.md

…ination (Fix JabRef#12844) * Modified PostgreProcessCleaner logic to fix windows os issue.

src/main/java/org/jabref/Launcher.java

UdayHE · 2025-04-15T08:55:10Z

Have you tested this by observing the processes? If so, on which OS? I tried on Windows. Doesn't work.

checked on windows as well, can you please check from your end as well?

screen-capture-windows.mp4

…ination (Fix JabRef#12844) * Used Path.of() instead of Paths.get() in PostgreProcessCleaner.

src/main/java/org/jabref/logic/search/PostgreProcessCleaner.java

UdayHE · 2025-04-15T09:15:44Z

Embedded Postgres Cleanup Flow
1.Start the Application
When a new JabRef instance starts, it initiates the embedded Postgres server.

2.Write Metadata File
During startup, the application writes a JSON file to the temporary directory (java.io.tmpdir).
File naming convention: jabref-postgres-info-.json (e.g., jabref-postgres-info-1234.json).
This file contains:
javaPid: The PID of the current Java process.
postgresPort: The port used by the embedded Postgres instance.
etc..

3.Check for Metadata Files on Startup
On startup, the application scans the temp directory for any matching metadata files (jabref-postgres-info-*.json).
This supports scenarios where multiple instances may have left behind multiple metadata files.
Read Stored Process Details.
For each metadata file found:
It reads the javaPid and postgresPort from the JSON.

4.Verify Java Process Liveness
For each javaPid, the application checks whether the corresponding Java process is still alive.

5.Handle Stale Java Processes
If any Java process is no longer running:
It indicates that a previous JabRef instance was terminated (e.g., via kill -9 or SIGKILL).

6.Lookup Postgres Processes
For each stale entry:
The application performs a port-based lookup to check if any process is still listening on the postgresPort.

7.Kill Stale Postgres
If a Postgres process is found on that port:
It is considered stale and is safely terminated.

8.Delete Metadata Files
After handling each stale process:
The corresponding metadata file (jabref-postgres-info-.json) is deleted.
Metadata files for live Java processes are retained, to avoid interfering with other active instances.

9.Proceed with Fresh Initialization
The current instance proceeds to launch a new embedded Postgres server.
A new metadata file is created specific to this instance.

10. Multiple Instance Safety
Each JabRef instance maintains its own metadata file, isolated by Java PID.
Stale cleanup only affects processes no longer alive, ensuring that active instances are never disrupted.

…ination (Fix JabRef#12844) * Fix for trag-bot comments.

src/main/java/org/jabref/logic/search/PostgreProcessCleaner.java

…ination (Fix JabRef#12844) * Fix for trag-bot comments.

src/main/java/org/jabref/logic/search/PostgreProcessCleaner.java

* Fix for trag-bot comments.

* Fix for trag-bot comments. * Created separate class PostgresMetadataWriter to follow SRP.

src/main/java/org/jabref/logic/search/PostgreServer.java

* Fix for trag-bot comments.

src/main/java/org/jabref/logic/search/PostgresMetadataWriter.java

trag-bot · 2025-04-16T02:07:18Z

src/main/java/org/jabref/logic/search/PostgresMetadataWriter.java

+        Map<String, Object> meta = new HashMap<>();
+        meta.put("javaPid", ProcessHandle.current().pid());
+        meta.put("postgresPort", port);
+        meta.put("startedBy", "jabref");


The string 'jabref' is a magic string and should be defined as a constant to improve maintainability and readability.

In some sense, trag-bot is right.

Is it possible to, maybe, make a serializable class?

trag-bot · 2025-04-16T08:54:09Z

@trag-bot didn't find any issues in the code! ✅✨

ungerts · 2025-04-16T09:00:07Z

src/main/java/org/jabref/logic/search/PostgreProcessCleaner.java

+            Map<String, Object> metadata = new HashMap<>(OBJECT_MAPPER.readValue(Files.readAllBytes(metadataPath), HashMap.class));
+            long javaPid = ((Number) metadata.get("javaPid")).longValue();
+            if (isJavaProcessAlive(javaPid)) {
+                return;


If the database is still running, is it necessary to clean up the data to ensure it's in the same state as a freshly started database?

ungerts · 2025-04-16T09:02:04Z

src/main/java/org/jabref/logic/search/PostgreProcessCleaner.java

+            }
+            int postgresPort = ((Number) metadata.get("postgresPort")).intValue();
+            destroyPostgresProcess(postgresPort);
+            Files.deleteIfExists(metadataPath);


Interesting question—what happens if you're running multiple JabRef instances? How can you distinguish between them?

Normally JabRef has only a single instance open, it is a setting in the preferences

Yeah, the question was for the other case.

Maybe, we should just start to disallow multiple instances?

ungerts · 2025-04-16T09:09:58Z

src/main/java/org/jabref/logic/search/PostgreProcessCleaner.java

+                    .redirectErrorStream(true).start();
+        } else if (OS.WINDOWS) {
+            return executeWindowsCommand(port);
+        }


Minor question: Is lsof included by default on macOS and Linux? For example, if someone is running Ubuntu with a standard configuration—without adding any extra packages—the solution should ideally work out of the box.

Additionally, there could be security or access rights issues. For instance, on Windows, a domain admin might block users from executing cmd.exe.

At the very least, the documentation should specify the conditions under which the solution is expected to run successfully.

ungerts · 2025-04-16T09:19:40Z

src/main/java/org/jabref/logic/search/PostgresMetadataWriter.java

+    }
+
+    public static Path getMetadataFilePath() {
+        return Path.of(System.getProperty("java.io.tmpdir"),


I think the org.jabref.logic.util.Directories class should be used here to obtain the directory in a standardized way.

InAnYan · 2025-04-16T14:04:45Z

src/main/java/org/jabref/logic/search/PostgreProcessCleaner.java

+    private Process executeWindowsCommand(int port) throws IOException {
+        String systemRoot = System.getenv("SystemRoot");
+        if (systemRoot != null && !systemRoot.isBlank()) {
+            String netStatPath = systemRoot + "\\System32\\netstat.exe";


Is it possible to use Java paths?

InAnYan · 2025-04-16T14:05:41Z

src/main/java/org/jabref/logic/search/PostgreProcessCleaner.java

+        if (systemRoot != null && !systemRoot.isBlank()) {
+            String netStatPath = systemRoot + "\\System32\\netstat.exe";
+            String findStrPath = systemRoot + "\\System32\\findstr.exe";
+            String command = netStatPath + " -ano | " + findStrPath + " :" + port;


Hmm.. is there an API, where you specify this for running a process:

Command name

List of strings that represent arguments

I think this is more stable than just passing a string

InAnYan · 2025-04-16T14:06:10Z

src/main/java/org/jabref/logic/search/PostgreProcessCleaner.java

+        if (systemRoot != null && !systemRoot.isBlank()) {
+            String netStatPath = systemRoot + "\\System32\\netstat.exe";
+            String findStrPath = systemRoot + "\\System32\\findstr.exe";
+            String command = netStatPath + " -ano | " + findStrPath + " :" + port;


What does | do here? It's like a pipe from Unix? Does it work on Windows, or it has other meaning?

findstr should be programmed in Java

Code reads like AI generated...

tasklist ist the proposal by "the internet" - https://www.rgagnon.com/javadetails/java-0593.html

With java 9 + we can use Process Handles https://stackoverflow.com/a/45068036

findstr should be programmed in Java

Code reads like AI generated...

tasklist ist the proposal by "the internet" - https://www.rgagnon.com/javadetails/java-0593.html

Not AI, I have referred these for executing commands:
https://coderanch.com/t/688902/java/Executing-netstat-command-process-builder
https://mkyong.com/java/java-processbuilder-examples/

Also I will check the commands we need to program using java, We can make use of command design pattern, so that if any other command needs to be implemented, we can easily extend that as well

InAnYan · 2025-04-16T14:07:47Z

src/main/java/org/jabref/logic/search/PostgreProcessCleaner.java

+        return null;
+    }
+
+    private long extractPidFromOutput(BufferedReader reader) throws IOException {


So you call some external command to get PID, right?

I wonder, is there a nicer package for Java? Or some alternative in packages that we have.. (If there is no such thing, then I think it's okay to use commands)

I tried google, did not find something immediatly.

UdayHE added 7 commits April 13, 2025 10:22

Merge branch 'issue-12844' of https://github.com/UdayHE/jabref into i…

e245d2b

…ssue-12844

fix: ensure embedded PostgreSQL is cleaned up on crash or forced term…

d7b7586

…ination (Fix JabRef#12844) * style changes in PostgreProcessCleaner, Launcher

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Siedlerchr changed the title ~~Fix for Issue 12844~~ Fix for postgres instance process closing Apr 13, 2025

UdayHE added 3 commits April 13, 2025 18:17

fix: ensure embedded PostgreSQL is cleaned up on crash or forced term…

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…ination (Fix JabRef#12844) * style changes in PostgreServer imports

fix: ensure embedded PostgreSQL is cleaned up on crash or forced term…

318f01d

…ination (Fix JabRef#12844) * Updated CHANGELOG.md

fix: ensure embedded PostgreSQL is cleaned up on crash or forced term…

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…ination (Fix JabRef#12844) * Modified PostgreProcessCleaner logic to fix windows os issue.

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fix: ensure embedded PostgreSQL is cleaned up on crash or forced term…

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…ination (Fix JabRef#12844) * Used Path.of() instead of Paths.get() in PostgreProcessCleaner.

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UdayHE requested a review from koppor April 15, 2025 09:19

UdayHE added 3 commits April 15, 2025 15:02

fix: ensure embedded PostgreSQL is cleaned up on crash or forced term…

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…ination (Fix JabRef#12844) * Fix for trag-bot comments.

fix: ensure embedded PostgreSQL is cleaned up on crash or forced term…

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UdayHE added 5 commits April 15, 2025 17:56

fix: ensure embedded PostgreSQL is cleaned up on crash or forced term…

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fix: ensure embedded PostgreSQL is cleaned up on crash or forced term…

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fixes JabRef#12844

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fixes JabRef#12844

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fixes JabRef#12844

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* Fix for trag-bot comments. * Created separate class PostgresMetadataWriter to follow SRP.

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Merge remote-tracking branch 'upstream/main' into issue-12844

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Fixes JabRef#12844

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Fix for postgres instance process closing #12927

Fix for postgres instance process closing #12927

UdayHE commented Apr 13, 2025 •

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Fix for postgres instance process closing #12927

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Fix for postgres instance process closing #12927

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UdayHE commented Apr 13, 2025 • edited Loading

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