From bc7c6b545d858f698f4e60f782b354e59430dddb Mon Sep 17 00:00:00 2001
From: Mateusz Warowny <mmzwarowny@dundee.ac.uk>
Date: Fri, 1 Oct 2021 17:35:55 +0200
Subject: [PATCH] JAL-3878 Fix workers done condition to account for broken
 jobs.

---
 src/jalview/ws2/WebServiceExecutor.java            |    5 +++--
 src/jalview/ws2/WebServiceWorkerI.java             |    2 +-
 src/jalview/ws2/operations/AlignmentOperation.java |    7 ++++---
 3 files changed, 8 insertions(+), 6 deletions(-)

diff --git a/src/jalview/ws2/WebServiceExecutor.java b/src/jalview/ws2/WebServiceExecutor.java
index 4b41464..86016d2 100644
--- a/src/jalview/ws2/WebServiceExecutor.java
+++ b/src/jalview/ws2/WebServiceExecutor.java
@@ -35,9 +35,10 @@ public class WebServiceExecutor
 
   private void pollJobs(WebServiceWorkerI worker)
   {
+    boolean done;
     try
     {
-      worker.pollJobs();
+      done = worker.pollJobs();
     } catch (Exception e)
     {
       Cache.log.error("Failed to poll web service jobs.", e);
@@ -48,7 +49,7 @@ public class WebServiceExecutor
       wsThreadSupport.pollFailed(worker, e);
       return;
     }
-    if (!worker.isDone())
+    if (!done)
     {
       executor.schedule(() -> pollJobs(worker), 1, TimeUnit.SECONDS);
     }
diff --git a/src/jalview/ws2/WebServiceWorkerI.java b/src/jalview/ws2/WebServiceWorkerI.java
index be719c1..f1864fc 100644
--- a/src/jalview/ws2/WebServiceWorkerI.java
+++ b/src/jalview/ws2/WebServiceWorkerI.java
@@ -25,7 +25,7 @@ public interface WebServiceWorkerI
       return false;
     for (WSJob job : getJobs())
     {
-      if (!job.getStatus().isDone())
+      if (!job.getStatus().isDone() && !job.getStatus().isFailed())
         return false;
     }
     return true;
diff --git a/src/jalview/ws2/operations/AlignmentOperation.java b/src/jalview/ws2/operations/AlignmentOperation.java
index f72978a..f836c91 100644
--- a/src/jalview/ws2/operations/AlignmentOperation.java
+++ b/src/jalview/ws2/operations/AlignmentOperation.java
@@ -366,6 +366,7 @@ public class AlignmentOperation implements Operation
     @Override
     public void startJobs() throws IOException
     {
+      Cache.log.info(format("Starting new %s job.", service.getName()));
       String outputHeader = String.format("%s of %s%nJob details%n",
               submitGaps ? "Re-alignment" : "Alignment", alnTitle);
       SequenceI[][] conmsa = msa.getVisibleContigs('-');
@@ -382,7 +383,7 @@ public class AlignmentOperation implements Operation
         WSJob job = new WSJob(service.getProviderName(), service.getName(),
                 service.getHostName());
         job.setJobNum(wsInfo.addJobPane());
-        if (conmsa.length > 0)
+        if (conmsa.length > 1)
         {
           wsInfo.setProgressName(String.format("region %d", i),
                   job.getJobNum());
@@ -448,7 +449,7 @@ public class AlignmentOperation implements Operation
       boolean done = true;
       for (WSJob job : getJobs())
       {
-        if (!job.getStatus().isDone())
+        if (!job.getStatus().isDone() && !job.getStatus().isFailed())
         {
           Cache.log.debug(format("Polling job %s.", job));
           try
@@ -479,7 +480,7 @@ public class AlignmentOperation implements Operation
           Cache.log.debug(
                   format("Job %s status is %s", job, job.getStatus()));
         }
-        done &= job.getStatus().isDone();
+        done &= job.getStatus().isDone() || job.getStatus().isFailed();
       }
       updateWSInfoGlobalStatus();
       return done;
-- 
1.7.10.2