Refactor scijava integration

Author: dietzc

org.knime.scijava.commands/.classpath

@@ -3,5 +3,6 @@
 	<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-1.8"/>
 	<classpathentry kind="con" path="org.eclipse.pde.core.requiredPlugins"/>
 	<classpathentry excluding="org/knime/knip/scijava/commands/adapter/basic/ImgInputAdapter.java|org/knime/knip/scijava/commands/adapter/basic/ImgOutputAdapter.java|org/knime/knip/scijava/commands/adapter/basic/ImgPlusInputAdapter.java|org/knime/knip/scijava/commands/adapter/basic/ImgPlusOutputAdapter.java" kind="src" path="src"/>
+	<classpathentry exported="true" kind="lib" path="lib/tools.jar"/>
 	<classpathentry kind="output" path="bin"/>
 </classpath>

org.knime.scijava.commands/META-INF/MANIFEST.MF

@@ -16,10 +16,16 @@ Require-Bundle: org.eclipse.core.runtime;bundle-version="3.11.0",
  scijava-plugins-text-plain;bundle-version="0.1.2",
  scijava-ui-awt;bundle-version="0.1.4",
  scijava-ui-swing;bundle-version="0.8.0",
- org.knime.scijava.core;bundle-version="0.2.1"
+ org.knime.scijava.core;bundle-version="0.2.1",
+ com.google.guava;bundle-version="19.0.0",
+ scripting-jython;bundle-version="0.3.0",
+ jython-shaded;bundle-version="2.5.3",
+ scripting-java;bundle-version="0.4.0",
+ scripting-clojure;bundle-version="0.1.4"
 Bundle-RequiredExecutionEnvironment: JavaSE-1.8
 Bundle-ActivationPolicy: lazy
-Bundle-ClassPath: scijava_commands.jar
+Bundle-ClassPath: scijava_commands.jar,
+ lib/tools.jar
 Export-Package: org.knime.scijava.commands,
  org.knime.scijava.commands.adapter,
  org.knime.scijava.commands.adapter.basic,

org.knime.scijava.commands/build.properties

@@ -6,7 +6,8 @@ bin.includes = plugin.xml,\
                lib/,\
                icons/,\
                lib/mvn/scijava-common-2.1.0.jar,\
-               scijava_commands.jar
+               scijava_commands.jar,\
+               lib/tools.jar
 output.knipknime.jar = bin/
 src.includes = lib/src/,\
                src/

org.knime.scijava.commands/lib/tools.jar

@@ -1,4 +1,16 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <?eclipse version="3.0"?>
 <plugin>
+   <extension
+         point="org.knime.workbench.repository.nodes">
+   </extension>
+   <extension
+         point="org.knime.workbench.repository.nodesets">
+      <nodeset
+            default-category-icon="org.knime.scijava.commands.nodes.SciJavaNodeSetFactory"
+            deprecated="false"
+            factory-class="org.knime.scijava.commands.nodes.SciJavaNodeSetFactory"
+            id="SciJavaNodeSet (TMP)">
+      </nodeset>
+   </extension>
 </plugin>

org.knime.scijava.commands/plugin.xml

@@ -0,0 +1,6 @@
+# @double value
+# @OUTPUT double greeting
+
+greeting = value
+
+print greeting

org.knime.scijava.commands/scripts/myjython.py

@@ -0,0 +1,4 @@
+; @Integer(label="My integer",description="Input integer.",value=17) test-int
+; @OUTPUT Integer output-int
+
+(def output-int test-int)

org.knime.scijava.commands/scripts/test.clj

@@ -0,0 +1,7 @@
+package org.knime.scijava.commands;
+
+import org.knime.core.data.DataCell;
+
+public interface CellOutput {
+    void push(final DataCell[] cells);
+}

org.knime.scijava.commands/src/org/knime/scijava/commands/CellOutput.java

@@ -0,0 +1,5 @@
+package org.knime.scijava.commands;
+
+public interface MultiOutputListener {
+    public void notifyListener();
+}

org.knime.scijava.commands/src/org/knime/scijava/commands/DefaultKnimeExecutionService.java

@@ -4,13 +4,9 @@
 import java.util.List;
 
 import org.knime.scijava.commands.converter.ConverterCacheService;
-import org.knime.scijava.commands.io.InputDataRowService;
-import org.knime.scijava.commands.io.OutputDataRowService;
-import org.knime.scijava.commands.settings.NodeModelSettingsService;
+import org.knime.scijava.commands.module.NodeModuleService;
 import org.knime.scijava.commands.settings.NodeSettingsService;
 import org.knime.scijava.commands.settings.SettingsModelTypeService;
-import org.knime.scijava.commands.simplemapping.SimpleColumnMappingService;
-import org.knime.scijava.commands.widget.KNIMEWidgetService;
 import org.knime.scijava.core.ResourceAwareClassLoader;
 import org.knime.scijava.core.SubContext;
 import org.knime.scijava.core.pluginindex.ReusablePluginIndex;
@@ -22,6 +18,7 @@
 import org.scijava.plugin.PluginIndex;
 import org.scijava.plugin.PluginService;
 import org.scijava.prefs.PrefService;
+import org.scijava.script.ScriptService;
 import org.scijava.service.Service;
 import org.scijava.ui.UIService;
 import org.scijava.widget.WidgetService;
@@ -50,15 +47,11 @@ public class SciJavaGateway {
 
     /** a list of services which need to be present in newly created contexts */
     protected static List<Class<? extends Service>> requiredServices = Arrays
-            .<Class<? extends Service>> asList(InputDataRowService.class,
-                    OutputDataRowService.class, PrefService.class,
-                    KNIMEExecutionService.class, NodeSettingsService.class,
-                    ObjectService.class, WidgetService.class,
-                    KNIMEWidgetService.class, UIService.class,
+            .<Class<? extends Service>> asList(PrefService.class,
+                    ObjectService.class, WidgetService.class, UIService.class,
                     ConverterCacheService.class, CommandService.class,
-                    NodeModelSettingsService.class,
-                    SettingsModelTypeService.class,
-                    SimpleColumnMappingService.class);
+                    NodeModuleService.class, SettingsModelTypeService.class,
+                    NodeSettingsService.class, ScriptService.class);
 
     /**
      * Constructor. Only to be called from {@link #get()}.
@@ -101,7 +94,7 @@ public Context createSubContext() {
         return context;
     }
 
-    private Context getGlobalContext() {
+    public Context getGlobalContext() {
         if (m_globalContext == null) {
             m_globalContext = new Context(m_pluginIndex);
 

org.knime.scijava.commands/src/org/knime/scijava/commands/KNIMEExecutionService.java

@@ -0,0 +1,33 @@
+
+package org.knime.scijava.commands;
+
+import org.scijava.ItemIO;
+import org.scijava.command.Command;
+import org.scijava.plugin.Parameter;
+import org.scijava.plugin.Plugin;
+
+@Plugin(type = Command.class, headless = true, label = "Test Command")
+public class SciJavaTestCommand implements Command {
+
+    @Parameter
+    private MultiOutputListener rowOutput;
+
+    @Parameter(label = "From Text", style = StyleHook.COLUMNSELECTION)
+    private String fromText;
+
+    @Parameter(label = "From Int")
+    private int fromInt;
+
+    @Parameter(type = ItemIO.OUTPUT, label = "Output Int")
+    private int outInt;
+
+    @Override
+    public void run() {
+        for (int i = 0; i < fromInt; i++) {
+            outInt = i;
+            rowOutput.notifyListener();
+        }
+    }
+
+
+}

org.knime.scijava.commands/src/org/knime/scijava/commands/KNIMESciJavaConstants.java

@@ -0,0 +1,5 @@
+package org.knime.scijava.commands;
+
+public interface StyleHook {
+    public final static String COLUMNSELECTION = "colSel";
+}

org.knime.scijava.commands/src/org/knime/scijava/commands/MultiOutputListener.java

@@ -1,12 +1,19 @@
 package org.knime.scijava.commands.converter;
 
+import java.util.Collection;
 import java.util.Optional;
 
 import org.knime.core.data.DataCell;
 import org.knime.core.data.DataType;
 import org.knime.core.data.DataValue;
+import org.knime.core.data.convert.datacell.JavaToDataCellConverterFactory;
+import org.knime.core.data.convert.java.DataCellToJavaConverterFactory;
+import org.knime.core.node.ExecutionContext;
 import org.scijava.service.Service;
 
+// FIXME NAMING (KNIPConverterCache?!)
+// FIXME CACHING (isn't implemented everywhere, yet)
+// FIXME can we always delegate to Jonathans implementations?
 public interface ConverterCacheService extends Service {
 
     /**
@@ -35,7 +42,8 @@ public interface ConverterCacheService extends Service {
      * @throws Exception
      *             When the conversion fails
      */
-    DataCell convertToKnime(Object in, Class<?> inType) throws Exception;
+    DataCell convertToKnime(Object in, Class<?> inType, DataType type,
+            ExecutionContext es) throws Exception;
 
     /**
      * Flush all caches.
@@ -67,7 +75,22 @@ public interface ConverterCacheService extends Service {
      *            the preferred value class
      * @return the matching java type
      */
-    Optional<Class<?>> getMatchingJavaType(
-            DataType dataType);
+    Optional<Class<?>> getMatchingJavaType(DataType dataType);
+
+    /**
+     * @FIXME
+     *
+     * @return
+     */
+    Collection<DataCellToJavaConverterFactory<?, ?>> getMatchingJavaTypes(
+            ClassLoader loader, DataType dataType);
+
+    /**
+     * FIXME
+     *
+     * @return
+     */
+    Collection<JavaToDataCellConverterFactory<?>> getMatchingFactories(
+            Class<?> javaType);
 
 }