From c28403cb2652fa2f79384292d1e864f5154fc859 Mon Sep 17 00:00:00 2001
From: worku005 <dirk-jan.vanworkum@wur.nl>
Date: Mon, 2 Dec 2024 13:30:32 +0100
Subject: [PATCH] introducing small class to handle stderr for mcl to fix
hanging issue
---
.../construction/grouping/Grouping.java | 33 ++++++------
.../java/nl/wur/bif/pantools/utils/Utils.java | 51 +++++++++++++++----
2 files changed, 57 insertions(+), 27 deletions(-)
diff --git a/src/main/java/nl/wur/bif/pantools/construction/grouping/Grouping.java b/src/main/java/nl/wur/bif/pantools/construction/grouping/Grouping.java
index 28c709209..fc338b509 100644
--- a/src/main/java/nl/wur/bif/pantools/construction/grouping/Grouping.java
+++ b/src/main/java/nl/wur/bif/pantools/construction/grouping/Grouping.java
@@ -717,8 +717,7 @@ public class Grouping {
* @param pangenome_path The path to the current graph database
*/
void break_component(LinkedList<Node> component, String pangenome_path) throws InterruptedException {
- int group_size, wating_time, time;
- double infl;
+ int group_size;
LinkedList<Node> homology_group, singletons_group = new LinkedList();
String graph_path, clusters_path, line, command;
BufferedReader clusters_file;
@@ -726,25 +725,23 @@ public class Grouping {
group_size = component.size();
graph_path = pangenome_path + "/" + component.getFirst().getId() + ".graph";
clusters_path = pangenome_path + "/" + component.getFirst().getId() + ".clusters";
- // Prepare the input file for MCL
+
+ // Prepare the input file for MCL
write_similaity_matrix(component, graph_path);
- // Estimate the run-time of MCL
- time = wating_time = 1 + (int) Math.round(group_size / 100000000.0 * group_size);
- for( infl = MCL_INFLATION; infl < 30; infl += 0.5) {
- command = "mcl " + graph_path + " --abc -I " + infl + " -o " + clusters_path + " -overlap keep";
- //Pantools.logger.info(command);
- if(executeCommand_for(command, wating_time))
- break;
- if((tmp_file = new File(clusters_path)).exists())
- tmp_file.delete();
- wating_time += time;
- }
- if (infl >= 30) {
+
+ // Run MCL
+ command = "mcl " + graph_path + " --abc -I " + MCL_INFLATION + " -o " + clusters_path + " -overlap keep -V all";
+ Pantools.logger.debug(command);
+ if (!executeCommand_for(command, 5)) {
Pantools.logger.info("Failed to split group ID = {}", component.getFirst().getId());
homology_groups_list.put(component);
+ if ((tmp_file = new File(clusters_path)).exists()) {
+ tmp_file.delete();
+ }
} else {
+ // Read the output of MCL and create homology groups
try (Transaction tx = GRAPH_DB.beginTx()) {
- try{
+ try {
clusters_file = new BufferedReader(new FileReader(clusters_path));
final List<Set<Long>> cluster = new ArrayList<>();
// For each line of the MCL output
@@ -772,7 +769,7 @@ public class Grouping {
clusters_file.close();
new File(clusters_path).delete();
new File(graph_path).delete();
- }catch (IOException ex) {
+ } catch (IOException ex) {
Pantools.logger.info(ex.getMessage());
}
tx.success();
@@ -2994,4 +2991,4 @@ public class Grouping {
tx.success();
}
}
-}
\ No newline at end of file
+}
diff --git a/src/main/java/nl/wur/bif/pantools/utils/Utils.java b/src/main/java/nl/wur/bif/pantools/utils/Utils.java
index 084d7e770..0af62a900 100644
--- a/src/main/java/nl/wur/bif/pantools/utils/Utils.java
+++ b/src/main/java/nl/wur/bif/pantools/utils/Utils.java
@@ -571,19 +571,52 @@ public final class Utils {
* Executes a shell command in a limited number of seconds.
*
* @param command The command
- * @param seconds The number of seconds
+ * @param timeout The number of seconds before the command is killed
* @return The output of the bash command
*/
- public static boolean executeCommand_for(String command, int seconds) {
- Process p;
- boolean success = false;
+ public static boolean executeCommand_for(String command, int timeout) {
+ Process process = null;
try {
- p = Runtime.getRuntime().exec(command);
- success = p.waitFor(seconds, TimeUnit.SECONDS);
- } catch (Exception e) {
- e.printStackTrace();
+ process = Runtime.getRuntime().exec(command);
+ StreamGobbler outputGobbler = new StreamGobbler(process.getInputStream()); //to make sure the process does not hang
+ StreamGobbler errorGobbler = new StreamGobbler(process.getErrorStream()); //to make sure the process does not hang
+
+ outputGobbler.start();
+ errorGobbler.start();
+
+ boolean finished = process.waitFor(timeout, TimeUnit.SECONDS);
+ outputGobbler.join();
+ errorGobbler.join();
+
+ return finished && process.exitValue() == 0;
+ } catch (IOException | InterruptedException e) {
+ Pantools.logger.error("Error executing command: {}", command, e);
+ return false;
+ } finally {
+ if (process != null) {
+ process.destroy();
+ }
+ }
+ }
+
+ private static class StreamGobbler extends Thread {
+ private final InputStream inputStream;
+
+ public StreamGobbler(InputStream inputStream) {
+ this.inputStream = inputStream;
+ }
+
+ @Override
+ public void run() {
+ try (BufferedReader reader = new BufferedReader(new InputStreamReader(inputStream))) {
+ String line;
+ while ((line = reader.readLine()) != null) {
+ Pantools.logger.trace("{}", line);
+ }
+ } catch (IOException e) {
+ e.printStackTrace();
+ }
}
- return success;
}
/**
--
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