fix issue where jobs could not run in headless mode

sirius-ms · Aug 9, 2024 · ccabc03 · ccabc03
1 parent 342eeba
commit ccabc03
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Showing 3 changed files with 24 additions and 18 deletions.
diff --git a/sirius_rest_service/src/main/java/de/unijena/bioinf/ms/backgroundruns/BackgroundRuns.java b/sirius_rest_service/src/main/java/de/unijena/bioinf/ms/backgroundruns/BackgroundRuns.java
@@ -22,6 +22,7 @@
 
 import com.googlecode.concurentlocks.ReadWriteUpdateLock;
 import com.googlecode.concurentlocks.ReentrantReadWriteUpdateLock;
+import de.unijena.bioinf.ChemistryBase.jobs.SiriusJobs;
 import de.unijena.bioinf.babelms.inputresource.InputResource;
 import de.unijena.bioinf.jjobs.*;
 import de.unijena.bioinf.ms.frontend.Run;
@@ -287,7 +288,10 @@ private BackgroundRunJob submitRunAndLockInstances(final BackgroundRunJob runToS
                 if (instances != null)
                     instances.forEach(i -> computingInstances.add(i.getId()));
                 log.info("...All instances locked!");
-                Jobs.submit(runToSubmit, runToSubmit::getName, psm::getName, runToSubmit::getDescription);
+                if (SiriusJobs.getGlobalJobManager() instanceof SwingJobManager) //todo hacky. get rid of this swing job dependency by solving job progress via api
+                    Jobs.submit(runToSubmit, runToSubmit::getName, psm::getName, runToSubmit::getDescription);
+                else
+                    SiriusJobs.getGlobalJobManager().submitJob(runToSubmit);
                 return runToSubmit;
             } catch (Exception e) {
                 // just in case something goes wrong during submission, then  we do not want to have locked instances

diff --git a/...src/main/java/de/unijena/bioinf/ms/frontend/subtools/middleware/MiddlewareAppOptions.java b/...src/main/java/de/unijena/bioinf/ms/frontend/subtools/middleware/MiddlewareAppOptions.java
@@ -171,10 +171,10 @@ public void run() {
                             splash.setVisible(false);
                             splash.dispose();
                         }
+                        Jobs.runEDTLater(() -> Thread.currentThread().setPriority(9));
                     } else {
                         log.info("No GUI service found. Skipping GUI startup, likely due to headless mode!");
                     }
-                    Jobs.runEDTLater(() -> Thread.currentThread().setPriority(9));
                 } catch (IOException e) {
                     throw new RuntimeException(e);
                 }

diff --git a/sirius_rest_service/src/main/java/de/unijena/bioinf/ms/middleware/SiriusContext.java b/sirius_rest_service/src/main/java/de/unijena/bioinf/ms/middleware/SiriusContext.java
@@ -21,10 +21,7 @@
 
 import de.unijena.bioinf.ChemistryBase.jobs.SiriusJobs;
 import de.unijena.bioinf.fingerid.fingerprints.cache.IFingerprinterCache;
-import de.unijena.bioinf.jjobs.JJob;
-import de.unijena.bioinf.jjobs.JobManager;
-import de.unijena.bioinf.jjobs.JobSubmitter;
-import de.unijena.bioinf.jjobs.ProgressJJob;
+import de.unijena.bioinf.jjobs.*;
 import de.unijena.bioinf.ms.frontend.core.ApplicationCore;
 import de.unijena.bioinf.ms.frontend.subtools.ToolChainJob;
 import de.unijena.bioinf.ms.frontend.workflow.InstanceBufferFactory;
@@ -104,18 +101,23 @@ public JobManager jobManager() {
     }
 
     @Bean
-    public InstanceBufferFactory<?> instanceBufferFactory() {
-        return (bufferSize, instances, tasks, dependJob, progressSupport) ->
-                new SimpleInstanceBuffer(bufferSize, instances, tasks, dependJob, progressSupport, new JobSubmitter() {
-                    @Override
-                    public <Job extends JJob<Result>, Result> Job submitJob(Job j) {
-                        if (j instanceof ToolChainJob<?> tj) {
-                            Jobs.submit((ProgressJJob<?>) j, j::identifier, tj::getProjectName, tj::getToolName);
-                            return j;
-                        } else {
-                            return Jobs.MANAGER().submitJob(j);
+    public InstanceBufferFactory<?> instanceBufferFactory(JobManager jobManager) {
+        //todo hacky. get rid of this swing job dependency by solving job progress via api
+        if (jobManager instanceof SwingJobManager) {
+            return (bufferSize, instances, tasks, dependJob, progressSupport) ->
+                    new SimpleInstanceBuffer(bufferSize, instances, tasks, dependJob, progressSupport, new JobSubmitter() {
+                        @Override
+                        public <Job extends JJob<Result>, Result> Job submitJob(Job j) {
+                            if (j instanceof ToolChainJob<?> tj) {
+                                Jobs.submit((ProgressJJob<?>) j, j::identifier, tj::getProjectName, tj::getToolName);
+                                return j;
+                            } else {
+                                return Jobs.MANAGER().submitJob(j);
+                            }
                         }
-                    }
-                });
+                    });
+        }else {
+           return new SimpleInstanceBuffer.Factory();
+        }
     }
 }