Delete MS2 GWT code. Switch to simple job launcher

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

@@ -182,14 +182,6 @@ else if (!TaskStatus.splitWaiting.matches(statusText) && statusText.toLowerCase(
             @Override
             public boolean isActive() { return false; }
         },
-        waitingForFiles
-        {
-            @Override
-            public boolean isActive() { return false; }
-
-            @Override
-            public String toString() { return "WAITING FOR FILES"; }
-        },
         splitWaiting
         {
             @Override

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

@@ -19,6 +19,7 @@
 import org.apache.logging.log4j.Logger;
 import org.apache.xmlbeans.XmlOptions;
 import org.fhcrc.cpas.pipeline.protocol.xml.PipelineProtocolPropsDocument;
+import org.labkey.api.data.Container;
 import org.labkey.api.util.FileUtil;
 import org.labkey.api.util.NetworkDrive;
 
@@ -63,20 +64,10 @@ public static File locateProtocolRootDir(File rootDir, File systemDir)
 
     public T load(PipeRoot root, String name, boolean archived) throws IOException
     {
-        return load(getProtocolFile(root, name, archived));
+        return load(getProtocolFile(root, name, archived), root.getContainer());
     }
 
-    public T loadInstance(File file) throws IOException
-    {
-        return load(file);
-    }
-
-    protected T load(File file) throws IOException
-    {
-        return load(file.toPath());
-    }
-
-    protected T load(Path file) throws IOException
+    protected T load(Path file, Container container) throws IOException
     {
         try
         {
@@ -100,7 +91,7 @@ protected T load(Path file) throws IOException
                 type = type.replace("org.labkey.ms2.protocol.", "org.labkey.ms2.pipeline.");
             }
 
-            PipelineProtocol protocol = (PipelineProtocol) Class.forName(type).newInstance();
+            PipelineProtocol protocol = (PipelineProtocol) Class.forName(type).getDeclaredConstructor().newInstance();
             PipelineProtocolPropsDocument.PipelineProtocolProps.Property[] props =
                     ppp.getPropertyArray();
             if (ppp.isSetTemplate())
@@ -118,7 +109,7 @@ protected T load(Path file) throws IOException
         }
         catch (Exception e)
         {
-            throw (IOException)new IOException("Failed to load protocol document " + file.toAbsolutePath() + ".").initCause(e);
+            throw new IOException("Failed to load protocol document " + file.toAbsolutePath() + ".", e);
         }
     }
 

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

@@ -17,6 +17,7 @@
 package org.labkey.api.pipeline;
 
 import org.apache.logging.log4j.Logger;
+import org.jetbrains.annotations.NotNull;
 import org.jetbrains.annotations.Nullable;
 import org.labkey.api.data.Container;
 import org.labkey.api.module.Module;
@@ -94,7 +95,7 @@ public FileTypesEntryFilter(List<FileType> initialFileTypes)
             }
             else
             {
-                _initialFileTypes = initialFileTypes.toArray(new FileType[initialFileTypes.size()]);
+                _initialFileTypes = initialFileTypes.toArray(new FileType[0]);
             }
         }
 
@@ -180,30 +181,6 @@ public boolean accept(Path f, boolean checkSiblings)
         }
     }
 
-    /**
-     * Operations that can be performed on a job belonging to this provider from the job's status details page.
-     * Cancel and retry are examples.
-     */
-    public static class StatusAction
-    {
-        private final String _label;
-
-        public StatusAction(String label)
-        {
-            _label = label;
-        }
-
-        public String getLabel()
-        {
-            return _label;
-        }
-
-        public boolean isVisible(PipelineStatusFile statusFile)
-        {
-            return true;
-        }
-    }
-
     protected String _name;
     private final Module _owningModule;
 
@@ -258,7 +235,6 @@ public boolean isStatusViewableFile(Container container, String name, String bas
     /**
      * Override to do any extra work necessary before deleting a status entry.
      *
-     * @param user
      * @param sf the entry to delete
      */
     public void preDeleteStatusFile(User user, PipelineStatusFile sf)
@@ -279,7 +255,7 @@ public boolean supportsCloud()
      * @return Web part shown on the setup page.
      */
     @Nullable
-    public HttpView getSetupWebPart(Container container)
+    public HttpView<?> getSetupWebPart(Container container)
     {
         // No setup.
         return null;
@@ -317,12 +293,17 @@ public HandlerException(String message)
         }
     }
 
-    protected String createActionId(Class action, String description)
+    protected String createActionId(@NotNull Class<?> action, @Nullable String description)
+    {
+        return createActionId(action.getName(), description);
+    }
+
+    protected String createActionId(@NotNull String action, @Nullable String description)
     {
         if (description != null)
-            return action.getName() + ':' + description;
+            return action + ':' + description;
         else
-            return action.getName();
+            return action;
     }
 
     @Deprecated //Prefer List<Path> version
@@ -343,15 +324,13 @@ protected void addAction(String actionId, Class<? extends Controller> action, St
             return;
         ActionURL actionURL = directory.cloneHref();
         actionURL.setAction(action);
-//        Uncomment to debug GWT app - can't just edit the URL and reload because it's a POST
-//        actionURL.addParameter("gwt.codesvr", "127.0.0.1:9997");
         directory.addAction(new PipelineAction(actionId, description, actionURL, files, allowMultiSelect, allowEmptySelect));
       }
 
     protected void addAction(String actionId, URLHelper actionURL, String description, PipelineDirectory entry, List<Path> files,
                              boolean allowMultiSelect, boolean allowEmptySelect, boolean includeAll)
     {
-        if (!includeAll && (files == null || files.size() == 0))
+        if (!includeAll && (files == null || files.isEmpty()))
             return;
 
         entry.addAction(new PipelineAction(actionId, description, actionURL, files, allowMultiSelect, allowEmptySelect));
@@ -360,7 +339,7 @@ protected void addAction(String actionId, URLHelper actionURL, String descriptio
     protected void addAction(String actionId, Class<? extends Controller> action, String description, PipelineDirectory directory, List<Path> files,
                              boolean allowMultiSelect, boolean allowEmptySelect, boolean includeAll)
     {
-        if (!includeAll && (files == null || files.size() == 0))
+        if (!includeAll && (files == null || files.isEmpty()))
             return;
         ActionURL actionURL = directory.cloneHref();
         actionURL.setAction(action);

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

@@ -184,22 +184,11 @@ enum PipelineButtonOption { Minimal, Assay, Standard }
     boolean savePipelineSetup(ViewContext context, SetupForm form, BindException errors) throws Exception;
 
     // TODO: This should be on PipelineProtocolFactory
-    String getLastProtocolSetting(PipelineProtocolFactory factory, Container container, User user);
+    String getLastProtocolSetting(PipelineProtocolFactory<?> factory, Container container, User user);
 
     // TODO: This should be on PipelineProtocolFactory
-    void rememberLastProtocolSetting(PipelineProtocolFactory factory, Container container,
+    void rememberLastProtocolSetting(PipelineProtocolFactory<?> factory, Container container,
                                      User user, String protocolName);
-
-    String getLastSequenceDbSetting(PipelineProtocolFactory factory, Container container, User user);
-
-    void rememberLastSequenceDbSetting(PipelineProtocolFactory factory, Container container, User user,
-                                       String sequenceDbPath, String sequenceDb);
-
-    List<String> getLastSequenceDbPathsSetting(PipelineProtocolFactory factory, Container container, User user);
-
-    void rememberLastSequenceDbPathsSetting(PipelineProtocolFactory factory, Container container,
-                                            User user, List<String> sequenceDbPaths);
-
     boolean hasSiteDefaultRoot(Container container);
 
     TableInfo getJobsTable(User user, Container container);
@@ -236,9 +225,9 @@ class PathAnalysisProperties
     {
         private final PipeRoot _pipeRoot;
         private final Path _dirData;
-        private final AbstractFileAnalysisProtocolFactory _factory;
+        private final AbstractFileAnalysisProtocolFactory<?> _factory;
 
-        public PathAnalysisProperties(PipeRoot pipeRoot, Path dirData, AbstractFileAnalysisProtocolFactory factory)
+        public PathAnalysisProperties(PipeRoot pipeRoot, Path dirData, AbstractFileAnalysisProtocolFactory<?> factory)
         {
             _pipeRoot = pipeRoot;
             _dirData = dirData;
@@ -256,7 +245,7 @@ public Path getDirData()
             return _dirData;
         }
 
-        public AbstractFileAnalysisProtocolFactory getFactory()
+        public AbstractFileAnalysisProtocolFactory<?> getFactory()
         {
             return _factory;
         }

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

@@ -45,8 +45,6 @@ interface StatusReader
         List<? extends PipelineStatusFile> getQueuedStatusFiles() throws SQLException;
 
         List<? extends PipelineStatusFile> getQueuedStatusFiles(Container c) throws SQLException;
-
-        List<? extends PipelineStatusFile> getJobsWaitingForFiles(Container c);
     }
 
     interface StatusWriter

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

@@ -69,4 +69,6 @@ public interface TaskPipeline<SettingsType extends TaskPipelineSettings>
 
     /**@return When true, the module providing this task must be enabled in the current container */
     boolean isActiveModuleRequired();
+
+    String getPipelineProviderName();
 }

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

@@ -29,7 +29,7 @@
  */
 public class TaskPipelineSettings
 {
-    private TaskId _id;
+    private final TaskId _id;
     private Object[] _taskProgressionSpec = new Object[0];
 
     /**
@@ -53,6 +53,8 @@ public class TaskPipelineSettings
 
     private boolean _activeModuleRequired = true;
 
+    private String _pipelineProviderName;
+
     public TaskPipelineSettings(TaskId id)
     {
         _id = id;
@@ -63,7 +65,7 @@ public TaskPipelineSettings(TaskId id)
      *
      * @param namespaceClass namespace class for TaskId
      */
-    public TaskPipelineSettings(Class namespaceClass)
+    public TaskPipelineSettings(Class<?> namespaceClass)
     {
         this(namespaceClass, null);
     }
@@ -74,7 +76,7 @@ public TaskPipelineSettings(Class namespaceClass)
      * @param namespaceClass namespace class for TaskId
      * @param name name for TaskId
      */
-    public TaskPipelineSettings(Class namespaceClass, String name)
+    public TaskPipelineSettings(Class<?> namespaceClass, String name)
     {
         this(new TaskId(namespaceClass, name));
     }
@@ -198,6 +200,16 @@ public void setActiveModuleRequired(boolean activeModuleRequired)
         _activeModuleRequired = activeModuleRequired;
     }
 
+    public String getPipelineProviderName()
+    {
+        return _pipelineProviderName;
+    }
+
+    public void setPipelineProviderName(String pipelineProviderName)
+    {
+        _pipelineProviderName = pipelineProviderName;
+    }
+
     protected void parseWorkflowProcessKey()
     {
         // This is an optional setting that will either be of the form "processKey" or "moduleName:processKey"

api/src/org/labkey/api/pipeline/file/AbstractFileAnalysisProtocol.java

@@ -18,6 +18,7 @@
 import org.apache.commons.io.input.ReaderInputStream;
 import org.apache.logging.log4j.LogManager;
 import org.apache.logging.log4j.Logger;
+import org.jetbrains.annotations.NotNull;
 import org.jetbrains.annotations.Nullable;
 import org.labkey.api.action.ApiUsageException;
 import org.labkey.api.data.Container;
@@ -50,15 +51,14 @@
 import java.util.HashMap;
 import java.util.List;
 import java.util.Map;
-import java.util.stream.Collectors;
 
 /**
  * <code>AbstractFileAnalysisProtocol</code>
  */
 public abstract class AbstractFileAnalysisProtocol<JOB extends AbstractFileAnalysisJob>
         extends PipelineProtocol
 {
-    private static Logger _log = LogManager.getLogger(AbstractFileAnalysisProtocol.class);
+    private static final Logger _log = LogManager.getLogger(AbstractFileAnalysisProtocol.class);
 
     public static final String LEGACY_JOINED_BASENAME = "all";
 
@@ -189,23 +189,17 @@ public void saveInstance(Path file, Container c) throws IOException
         save(file, null, addParams);
     }
 
-    @Deprecated //Prefer the Path based version
-    protected void save(File file, Map<String, String> addParams, Map<String, String> instanceParams) throws IOException
-    {
-        save(file.toPath(), addParams, instanceParams);
-    }
-
     protected void save(Path file, Map<String, String> addParams, Map<String, String> instanceParams) throws IOException
     {
-        if (xml == null || xml.length() == 0)
+        if (xml == null || xml.isEmpty())
         {
-            xml = "<?xml version=\"1.0\"?>\n" +
-                    "<bioml>\n" +
-                    "</bioml>";
+            xml = """
+                    <?xml version="1.0"?>
+                    <bioml>
+                    </bioml>""";
         }
 
-        ParamParser parser = getFactory().createParamParser();
-        parser.parse(new ReaderInputStream(new StringReader(xml), Charset.defaultCharset()));
+        ParamParser parser = parse();
         if (parser.getErrors() != null)
         {
             ParamParser.Error err = parser.getErrors()[0];
@@ -256,6 +250,14 @@ protected void save(Path file, Map<String, String> addParams, Map<String, String
         }
     }
 
+    @NotNull
+    protected ParamParser parse()
+    {
+        ParamParser parser = getFactory().createParamParser();
+        parser.parse(new ReaderInputStream(new StringReader(xml), Charset.defaultCharset()));
+        return parser;
+    }
+
     @Deprecated  //Prefer the Path version
     public FileType findInputType(File file)
     {
@@ -277,18 +279,9 @@ public FileType findInputType(Path file)
     @Override
     public abstract AbstractFileAnalysisProtocolFactory getFactory();
 
-    @Deprecated //Prefer Path version
     public abstract JOB createPipelineJob(ViewBackgroundInfo info,
-                                          PipeRoot root, List<File> filesInput,
-                                          File fileParameters, @Nullable Map<String, String> variableMap) throws IOException;
-
-    //TODO convert existing File based versions to Path, then make this abstract
-    public JOB createPipelineJob(ViewBackgroundInfo info,
                                           PipeRoot root, List<Path> filesInput,
-                                          Path fileParameters, @Nullable Map<String, String> variableMap) throws IOException
-    {
-        return createPipelineJob(info, root, filesInput.stream().map(Path::toFile).collect(Collectors.toList()), fileParameters.toFile(), variableMap);
-    }
+                                          Path fileParameters, @Nullable Map<String, String> variableMap) throws IOException;
 
     public boolean timestampLog()
     {