Merge 25.1 to develop

Author: labkey-teamcity

nextflow/src/org/labkey/nextflow/pipeline/NextFlowPipelineJob.java

@@ -2,17 +2,23 @@
 
 import lombok.Getter;
 import org.apache.commons.lang3.StringUtils;
+import org.apache.logging.log4j.Logger;
 import org.jetbrains.annotations.NotNull;
+import org.json.JSONObject;
 import org.labkey.api.data.Container;
 import org.labkey.api.files.FileContentService;
 import org.labkey.api.pipeline.ParamParser;
 import org.labkey.api.pipeline.PipeRoot;
 import org.labkey.api.pipeline.PipelineJobService;
+import org.labkey.api.pipeline.PipelineService;
+import org.labkey.api.pipeline.PipelineStatusFile;
 import org.labkey.api.pipeline.TaskId;
 import org.labkey.api.pipeline.TaskPipeline;
 import org.labkey.api.pipeline.file.AbstractFileAnalysisJob;
 import org.labkey.api.util.FileUtil;
 import org.labkey.api.util.PageFlowUtil;
+import org.labkey.api.util.StringUtilsLabKey;
+import org.labkey.api.util.logging.LogHelper;
 import org.labkey.api.view.ViewBackgroundInfo;
 
 import java.io.BufferedWriter;
@@ -26,6 +32,8 @@
 @Getter
 public class NextFlowPipelineJob extends AbstractFileAnalysisJob
 {
+    protected static final Logger LOG = LogHelper.getLogger(NextFlowPipelineJob.class, "NextFlow jobs");
+
     private Path config;
 
     @SuppressWarnings("unused") // For serialization
@@ -51,6 +59,24 @@ public NextFlowPipelineJob(ViewBackgroundInfo info, @NotNull PipeRoot root, Path
         super(new NextFlowProtocol(), NextFlowPipelineProvider.NAME, info, root, config.getFileName().toString(), config, inputFiles, false, false);
         this.config = config;
         setLogFile(log);
+        LOG.info("NextFlow job queued: {}", getJsonJobInfo());
+    }
+
+    protected JSONObject getJsonJobInfo()
+    {
+        JSONObject result = new JSONObject();
+        result.put("user", getUser().getEmail());
+        result.put("container", getContainer().getPath());
+        result.put("filePath", getLogFilePath().getParent().toString());
+        result.put("runName", getNextFlowRunName());
+        result.put("configFile", getConfig().getFileName().toString());
+        return result;
+    }
+
+    protected String getNextFlowRunName()
+    {
+        PipelineStatusFile file = PipelineService.get().getStatusFile(getJobGUID());
+        return file == null ? "Unknown" : ("LabKeyJob" + file.getRowId());
     }
 
     @Override
@@ -87,7 +113,7 @@ private static Path createConfig(Path configTemplate, Path parentDir, Path jobDi
     @Override
     public String getDescription()
     {
-        return "NextFlow analysis using " + config.getFileName() + " of " + getInputFilePaths().size() + " files";
+        return "NextFlow analysis of " + StringUtilsLabKey.pluralize(getInputFilePaths().size(), "file") + " using config: " + config.getFileName();
     }
 
     @Override

nextflow/src/org/labkey/nextflow/pipeline/NextFlowRunTask.java

@@ -42,14 +42,14 @@ public NextFlowRunTask(Factory factory, PipelineJob job)
         super(factory, job);
     }
 
-
-
     @Override
     public @NotNull RecordedActionSet run() throws PipelineJobException
     {
         Logger log = getJob().getLogger();
+        NextFlowPipelineJob.LOG.info("Starting to execute NextFlow: {}", getJob().getJsonJobInfo());
 
         SecurityManager.TransformSession session = null;
+        boolean success = false;
 
         try
         {
@@ -69,13 +69,14 @@ public NextFlowRunTask(Factory factory, PipelineJob job)
 
             // Need to pass to the main process directly in the future to allow concurrent execution for different users
             ProcessBuilder secretsPB = new ProcessBuilder("nextflow", "secrets", "set", "PANORAMA_API_KEY", apiKey);
-            log.info("Job Started");
+            log.info("Setting secrets");
             File dir = getJob().getLogFile().getParentFile();
             getJob().runSubProcess(secretsPB, dir);
 
             ProcessBuilder executionPB = new ProcessBuilder(getArgs());
             getJob().runSubProcess(executionPB, dir);
             log.info("Job Finished");
+            NextFlowPipelineJob.LOG.info("Finished executing NextFlow: {}", getJob().getJsonJobInfo());
 
             RecordedAction action = new RecordedAction(ACTION_NAME);
             for (Path inputFile : getJob().getInputFilePaths())
@@ -84,6 +85,7 @@ public NextFlowRunTask(Factory factory, PipelineJob job)
             }
             addOutputs(action, getJob().getLogFilePath().getParent().resolve("reports"), log);
             addOutputs(action, getJob().getLogFilePath().getParent().resolve("results"), log);
+            success = true;
             return new RecordedActionSet(action);
         }
         catch (IOException e)
@@ -96,6 +98,10 @@ public NextFlowRunTask(Factory factory, PipelineJob job)
             {
                 session.close();
             }
+            if (!success)
+            {
+                NextFlowPipelineJob.LOG.info("Failed executing NextFlow: {}", getJob().getJsonJobInfo());
+            }
         }
     }
 
@@ -182,6 +188,8 @@ private boolean hasAwsSection(Path configFile) throws PipelineJobException
         }
         args.add("-c");
         args.add(configFile.toAbsolutePath().toString());
+        args.add("-name");
+        args.add(getJob().getNextFlowRunName());
         return args;
     }
 

nextflow/webapp/WEB-INF/nextflow/nextflowContext.xml

@@ -19,23 +19,10 @@
                             <bean id="nextFlowPipelineTask" class="org.labkey.api.pipeline.TaskId">
                                 <constructor-arg><value type="java.lang.Class">org.labkey.nextflow.pipeline.NextFlowRunTask</value></constructor-arg>
                             </bean>
-                            <ref bean="xarGeneratorNextFlow"/>
                         </list>
                     </property>
                 </bean>
             </list>
         </property>
     </bean>
-
-    <!-- Experiment derived tasks -->
-    <bean id="xarGeneratorNextFlow" class="org.labkey.api.exp.pipeline.XarGeneratorFactorySettings">
-        <constructor-arg value="xarGeneratorNextFlow"/>
-        <!-- Import in the same thread pool as other Skyline doc imports -->
-        <property name="location" value="webserver-high-priority" />
-    </bean>
-
-    <!-- Tasks registered in experiment module -->
-    <bean id="xarGeneratorId" class="org.labkey.api.pipeline.TaskId">
-        <constructor-arg><value type="java.lang.Class">org.labkey.api.exp.pipeline.XarGeneratorId</value></constructor-arg>
-    </bean>
 </beans>