Issue 44126: CommandTasks fail on remote pipeline servers

api/src/org/labkey/api/assay/DefaultDataTransformer.java

@@ -202,7 +202,7 @@ public TransformResult transformAndValidate(AssayRunUploadContext<ProviderType>
         return result;
     }
 
-    public static void addStandardParameters(@Nullable HttpServletRequest request, Container container, @Nullable File scriptFile, String apiKey, @NotNull Map<String, String> paramMap)
+    public static void addStandardParameters(@Nullable HttpServletRequest request, @Nullable Container container, @Nullable File scriptFile, @Nullable String apiKey, @NotNull Map<String, String> paramMap)
     {
         if (scriptFile != null)
         {
@@ -216,7 +216,7 @@ public static void addStandardParameters(@Nullable HttpServletRequest request, C
         paramMap.put(SecurityManager.API_KEY, apiKey);
         paramMap.put(BASE_SERVER_URL_REPLACEMENT, AppProps.getInstance().getBaseServerUrl()
                                                     + AppProps.getInstance().getContextPath());
-        paramMap.put(CONTAINER_PATH, container.getPath());
+        paramMap.put(CONTAINER_PATH, container == null ? null : container.getPath());
     }
 
     @Deprecated

api/src/org/labkey/api/pipeline/PipelineJob.java

@@ -1651,23 +1651,33 @@ public String getContainerId()
 
     /**
      * Gets the <code>User</code> instance from the <code>ViewBackgroundInfo</code>.
-     * WARNING: Not supported if job is not running in the LabKey Server.
+     * WARNING: Not supported if job is not running in the LabKey web server.
      *
      * @return the user who started the job
+     * @throws IllegalStateException if invoked on a remote pipeline server
      */
     public User getUser()
     {
+        if (!PipelineJobService.get().isWebServer())
+        {
+            throw new IllegalStateException("User lookup not available on remote pipeline servers");
+        }
         return getInfo().getUser();
     }
 
     /**
      * Gets the <code>Container</code> instance from the <code>ViewBackgroundInfo</code>.
-     * WARNING: Not supported if job is not running in the LabKey Server.
+     * WARNING: Not supported if job is not running in the LabKey web server.
      *
      * @return the container in which the job was started
+     * @throws IllegalStateException if invoked on a remote pipeline server
      */
     public Container getContainer()
     {
+        if (!PipelineJobService.get().isWebServer())
+        {
+            throw new IllegalStateException("User lookup not available on remote pipeline servers");
+        }
         return getInfo().getContainer();
     }
 

api/src/org/labkey/api/pipeline/PipelineJobService.java

@@ -175,5 +175,10 @@ enum LocationType
         RemoteExecutionEngine
     }
 
-    public FormSchema getFormSchema(Container container);
+    FormSchema getFormSchema(Container container);
+
+    /** @return true if the current instance is the web server, which has access to more resources including the
+     * primary database, or false if we're on a remote server
+     */
+    boolean isWebServer();
 }

api/src/org/labkey/api/security/SecurityManager.java

@@ -646,6 +646,9 @@ public String getApiKey()
         {
             return _apikey;
         }
+
+        @Override
+        public abstract void close();
     }
 
     private static final class HttpSessionTransformSession extends TransformSession
@@ -657,7 +660,7 @@ private HttpSessionTransformSession(@NotNull HttpServletRequest req, @NotNull Ht
         }
 
         @Override
-        public void close() throws IOException
+        public void close()
         {
             SessionApiKeyManager.get().invalidateKey(getApiKey());
         }
@@ -672,7 +675,7 @@ private DatabaseTransformSession(@NotNull User user)
         }
 
         @Override
-        public void close() throws IOException
+        public void close()
         {
             ApiKeyManager.get().deleteKey(getApiKey());
         }

pipeline/src/org/labkey/pipeline/analysis/CommandTaskImpl.java

@@ -24,13 +24,15 @@
 import org.junit.Test;
 import org.labkey.api.assay.DefaultDataTransformer;
 import org.labkey.api.collections.RowMapFactory;
+import org.labkey.api.data.Container;
 import org.labkey.api.data.TSVMapWriter;
 import org.labkey.api.exp.PropertyType;
 import org.labkey.api.module.Module;
 import org.labkey.api.pipeline.AbstractTaskFactory;
 import org.labkey.api.pipeline.PipeRoot;
 import org.labkey.api.pipeline.PipelineJob;
 import org.labkey.api.pipeline.PipelineJobException;
+import org.labkey.api.pipeline.PipelineJobService;
 import org.labkey.api.pipeline.RecordedAction;
 import org.labkey.api.pipeline.RecordedActionSet;
 import org.labkey.api.pipeline.TaskId;
@@ -586,7 +588,7 @@ protected void writeTaskInfo(File file, RecordedAction action) throws IOExceptio
      * to replace tokens the script or the command line before executing it.
      * The replaced paths will be resolved to paths in the work directory.
      */
-    protected Map<String, String> createReplacements(@Nullable File scriptFile, String apiKey) throws IOException
+    protected Map<String, String> createReplacements(@Nullable File scriptFile, @Nullable String apiKey, @Nullable Container container) throws IOException
     {
         Map<String, String> replacements = new HashMap<>();
 
@@ -660,7 +662,7 @@ else if (outputPaths.length == 1)
             replacements.put(PipelineJob.PIPELINE_TASK_OUTPUT_PARAMS_PARAM, taskOutputParamsRelativePath);
         }
 
-        DefaultDataTransformer.addStandardParameters(null, getJob().getContainer(), scriptFile, apiKey, replacements);
+        DefaultDataTransformer.addStandardParameters(null, container, scriptFile, apiKey, replacements);
 
         return replacements;
     }
@@ -675,7 +677,16 @@ protected String rewritePath(String path)
     @NotNull
     public RecordedActionSet run() throws PipelineJobException
     {
-        try (TransformSession session = SecurityManager.createTransformSession(getJob().getUser()))
+        TransformSession session = null;
+        Container container = null;
+        if (PipelineJobService.get().isWebServer())
+        {
+            // We're inside of the web server so we have access to the DB and can set up a transform session, among
+            // other resources
+            session = SecurityManager.createTransformSession(getJob().getUser());
+            container = getJob().getContainer();
+        }
+        try
         {
             RecordedAction action = new RecordedAction(_factory.getProtocolActionName());
 
@@ -702,7 +713,7 @@ public RecordedActionSet run() throws PipelineJobException
             if (getJobSupport().getParametersFile() != null)
                 _wd.inputFile(getJobSupport().getParametersFile(), true);
 
-            if (!runCommand(action, session.getApiKey()))
+            if (!runCommand(action, session == null ? null : session.getApiKey(), container))
                 return new RecordedActionSet();
 
             // Read output parameters file, record output parameters, and discard it.
@@ -733,6 +744,10 @@ public RecordedActionSet run() throws PipelineJobException
         finally
         {
             _wd = null;
+            if (session != null)
+            {
+                session.close();
+            }
         }
     }
 
@@ -741,13 +756,11 @@ public RecordedActionSet run() throws PipelineJobException
      * @param action The recorded action.
      * @param apiKey API key to use for the duration of the command execution
      * @return true if the task was run, false otherwise.
-     * @throws IOException
-     * @throws PipelineJobException
      */
     // TODO: Add task and job version information to the recorded action.
-    protected boolean runCommand(RecordedAction action, String apiKey) throws IOException, PipelineJobException
+    protected boolean runCommand(RecordedAction action, @Nullable String apiKey, @Nullable Container container) throws IOException, PipelineJobException
     {
-        Map<String, String> replacements = createReplacements(null, apiKey);
+        Map<String, String> replacements = container == null ? Collections.emptyMap() : createReplacements(null, apiKey, container);
 
         ProcessBuilder pb = new ProcessBuilder(_factory.toArgs(this, replacements));
         applyEnvironment(pb);

pipeline/src/org/labkey/pipeline/analysis/ConvertTaskFactory.java

@@ -113,25 +113,34 @@ private TaskFactory findCommandFactory(PipelineJob job)
         // If this job is not actually running a conversion, then no
         // converter command can be determined.
         List<File> files = job.getJobSupport(FileAnalysisJobSupport.class).getInputFiles();
+        LOG.debug("Checking " + files + " for possible converters");
         if (files == null || files.size() != 1)
             return null;
 
         // Otherwise, find the appropriate converter.
         File fileInput = getInputFile(job);
+        LOG.debug("Checking " + fileInput + " against up to " + _commands.length + " possible converters");
         for (TaskId tid : _commands)
         {
+            LOG.debug("Checking " + fileInput + " against " + tid);
             TaskFactory<? extends TaskFactorySettings> factory = PipelineJobService.get().getTaskFactory(tid);
             for (FileType ft : factory.getInputTypes())
             {
+                LOG.debug("Checking " + fileInput + " against " + tid + ": " + ft);
                 try
                 {
                     // If we have a match based on the file type and the factory says that it's a participant based
                     // on the search protocol parameters, use it
                     if (ft.isType(fileInput) && factory.isParticipant(job))
+                    {
+                        LOG.debug("Matched");
                         return factory;
+                    }
+                    LOG.debug("No match");
                 }
-                catch (IOException ignored)
+                catch (IOException e)
                 {
+                    LOG.debug("Exception when checking " + fileInput + ", reporting that " + tid + " is not available", e);
                     // Consider this command out of the running, caller will report an error if there are no other options
                 }
             }

pipeline/src/org/labkey/pipeline/api/PipelineJobServiceImpl.java

@@ -589,6 +589,12 @@ public FormSchema getFormSchema(Container container)
         return new FormSchema(fields);
     }
 
+    @Override
+    public boolean isWebServer()
+    {
+        return ModuleLoader.getServletContext() != null;
+    }
+
     public void setJobStore(PipelineStatusFile.JobStore jobStore)
     {
         _jobStore = jobStore;

pipeline/src/org/labkey/pipeline/api/ScriptTaskImpl.java

@@ -82,7 +82,7 @@ private ScriptEngine getScriptEngine(Container c, LabKeyScriptEngineManager mgr,
     // TODO: Rhino engine.  A non-ExternalScriptEngine won't use the PARAM_REPLACEMENT_MAP binding.
     // CONSIDER: Use ScriptEngineReport to generate a script prolog
     @Override
-    protected boolean runCommand(RecordedAction action, String apiKey) throws IOException, PipelineJobException
+    protected boolean runCommand(RecordedAction action, @Nullable String apiKey, @Nullable Container container) throws IOException, PipelineJobException
     {
         // Get the script engine
         LabKeyScriptEngineManager mgr = LabKeyScriptEngineManager.get();
@@ -160,7 +160,7 @@ else if (factory._scriptPath != null)
             if (_factory.getTimeout() != null && _factory.getTimeout() > 0)
                 bindings.put(ExternalScriptEngine.TIMEOUT, _factory.getTimeout());
 
-            Map<String, String> replacements = createReplacements(scriptFile, apiKey);
+            Map<String, String> replacements = createReplacements(scriptFile, apiKey, container);
             bindings.put(ExternalScriptEngine.PARAM_REPLACEMENT_MAP, replacements);
 
             // Write task properties file into the work directory