Add ItemPersistence to denote persistence behavior

Introduces the ItemPersistence enum (YES, NO, DEFAULT). YES and NO
overwrite additional checks (i.e. precedence of an initializer, value
is default value). In case of DEFAULT, the value is persisted only if
it is not the default value and no initializer is set.

src/main/java/org/scijava/ItemPersistence.java

@@ -0,0 +1,60 @@
+/*
+ * #%L
+ * SciJava Common shared library for SciJava software.
+ * %%
+ * Copyright (C) 2009 - 2016 Board of Regents of the University of
+ * Wisconsin-Madison, Broad Institute of MIT and Harvard, and Max Planck
+ * Institute of Molecular Cell Biology and Genetics.
+ * %%
+ * Redistribution and use in source and binary forms, with or without
+ * modification, are permitted provided that the following conditions are met:
+ * 
+ * 1. Redistributions of source code must retain the above copyright notice,
+ *    this list of conditions and the following disclaimer.
+ * 2. Redistributions in binary form must reproduce the above copyright notice,
+ *    this list of conditions and the following disclaimer in the documentation
+ *    and/or other materials provided with the distribution.
+ * 
+ * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+ * AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+ * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+ * ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDERS OR CONTRIBUTORS BE
+ * LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
+ * CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
+ * SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
+ * INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
+ * CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
+ * ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
+ * POSSIBILITY OF SUCH DAMAGE.
+ * #L%
+ */
+
+package org.scijava;
+
+import org.scijava.plugin.Parameter;
+
+/**
+ * Defines the persistence setting of a parameter.
+ * 
+ * @author Stefan Helfrich
+ */
+public enum ItemPersistence {
+
+	/**
+	 * Item is persisted in any case.
+	 */
+	YES,
+
+	/**
+	 * Item is never persisted.
+	 */
+	NO,
+
+	/**
+	 * Item is persisted unless an additional {@link Parameter#initializer()
+	 * initializer()} method is defined or the value to persist is the defined
+	 * default value.
+	 */
+	DEFAULT
+
+}

src/main/java/org/scijava/command/CommandModuleItem.java

@@ -37,6 +37,7 @@
 import java.util.List;
 
 import org.scijava.ItemIO;
+import org.scijava.ItemPersistence;
 import org.scijava.ItemVisibility;
 import org.scijava.Optional;
 import org.scijava.module.AbstractModuleItem;
@@ -109,7 +110,7 @@ public boolean isRequired() {
 	}
 
 	@Override
-	public boolean isPersisted() {
+	public ItemPersistence getPersistence() {
 		return getParameter().persist();
 	}
 

src/main/java/org/scijava/module/AbstractModuleItem.java

@@ -37,6 +37,7 @@
 
 import org.scijava.AbstractBasicDetails;
 import org.scijava.ItemIO;
+import org.scijava.ItemPersistence;
 import org.scijava.ItemVisibility;
 import org.scijava.util.ClassUtils;
 import org.scijava.util.ConversionUtils;
@@ -71,7 +72,7 @@ public String toString() {
 		sm.append("description", getDescription());
 		sm.append("visibility", getVisibility(), ItemVisibility.NORMAL);
 		sm.append("required", isRequired());
-		sm.append("persisted", isPersisted());
+		sm.append("persisted", getPersistence());
 		sm.append("persistKey", getPersistKey());
 		sm.append("callback", getCallback());
 		sm.append("widgetStyle", getWidgetStyle());
@@ -131,8 +132,8 @@ public boolean isRequired() {
 	}
 
 	@Override
-	public boolean isPersisted() {
-		return true;
+	public ItemPersistence getPersistence() {
+		return ItemPersistence.DEFAULT;
 	}
 
 	@Override
@@ -149,7 +150,7 @@ public String getPersistKey() {
 	@Deprecated
 	public T loadValue() {
 		// if there is nothing to load from persistence return nothing
-		if (!isPersisted()) return null;
+		if (getPersistence() == ItemPersistence.NO) return null;
 
 		final String sValue;
 		final String persistKey = getPersistKey();
@@ -169,7 +170,7 @@ public T loadValue() {
 	@Override
 	@Deprecated
 	public void saveValue(final T value) {
-		if (!isPersisted()) return;
+		if (getPersistence() == ItemPersistence.NO) return;
 
 		final String sValue = value == null ? "" : value.toString();
 

src/main/java/org/scijava/module/DefaultModuleService.java

@@ -42,6 +42,7 @@
 import java.util.concurrent.Future;
 
 import org.scijava.Identifiable;
+import org.scijava.ItemPersistence;
 import org.scijava.MenuPath;
 import org.scijava.Priority;
 import org.scijava.convert.ConvertService;
@@ -289,12 +290,16 @@ public ModuleItem<?> getSingleOutput(Module module, Collection<Class<?>> types)
 
 	@Override
 	public <T> void save(final ModuleItem<T> item, final T value) {
-		if (!item.isPersisted()) return;
+		ItemPersistence persistence = item.getPersistence();
+
+		if (persistence == ItemPersistence.NO) return;
 
 		// NB: Do not persist values which are computed via an initializer.
-		if (item.getInitializer() != null && !item.getInitializer().isEmpty()) return;
+		if (item.getInitializer() != null && !item.getInitializer().isEmpty() &&
+			persistence == ItemPersistence.DEFAULT) return;
 
-		if (MiscUtils.equal(item.getDefaultValue(), value)) {
+		if (MiscUtils.equal(item.getDefaultValue(), value) &&
+			persistence == ItemPersistence.DEFAULT) {
 			// NB: Do not persist the value if it is the default.
 			// This is nice if the default value might change later,
 			// such as when iteratively developing a script.
@@ -318,7 +323,7 @@ public <T> void save(final ModuleItem<T> item, final T value) {
 	@Override
 	public <T> T load(final ModuleItem<T> item) {
 		// if there is nothing to load from persistence return nothing
-		if (!item.isPersisted()) return null;
+		if (item.getPersistence() == ItemPersistence.NO) return null;
 
 		final String sValue;
 		final String persistKey = item.getPersistKey();

src/main/java/org/scijava/module/DefaultMutableModuleItem.java

@@ -37,6 +37,7 @@
 import java.util.List;
 
 import org.scijava.ItemIO;
+import org.scijava.ItemPersistence;
 import org.scijava.ItemVisibility;
 
 /**
@@ -54,7 +55,7 @@ public class DefaultMutableModuleItem<T> extends AbstractModuleItem<T>
 	private ItemIO ioType;
 	private ItemVisibility visibility;
 	private boolean required;
-	private boolean persisted;
+	private ItemPersistence persistence;
 	private String persistKey;
 	private String initializer;
 	private String callback;
@@ -87,7 +88,7 @@ public DefaultMutableModuleItem(final ModuleInfo info, final String name,
 		ioType = super.getIOType();
 		visibility = super.getVisibility();
 		required = super.isRequired();
-		persisted = super.isPersisted();
+		persistence = super.getPersistence();
 		persistKey = super.getPersistKey();
 		initializer = super.getInitializer();
 		callback = super.getCallback();
@@ -113,7 +114,7 @@ public DefaultMutableModuleItem(final ModuleInfo info,
 		ioType = item.getIOType();
 		visibility = item.getVisibility();
 		required = item.isRequired();
-		persisted = item.isPersisted();
+		persistence = item.getPersistence();
 		persistKey = item.getPersistKey();
 		initializer = item.getInitializer();
 		callback = item.getCallback();
@@ -148,8 +149,8 @@ public void setRequired(final boolean required) {
 	}
 
 	@Override
-	public void setPersisted(final boolean persisted) {
-		this.persisted = persisted;
+	public void setPersistence(final ItemPersistence persistence) {
+		this.persistence = persistence;
 	}
 
 	@Override
@@ -241,8 +242,8 @@ public boolean isRequired() {
 	}
 
 	@Override
-	public boolean isPersisted() {
-		return persisted;
+	public ItemPersistence getPersistence() {
+		return persistence;
 	}
 
 	@Override

src/main/java/org/scijava/module/ModuleItem.java

@@ -37,6 +37,7 @@
 
 import org.scijava.BasicDetails;
 import org.scijava.ItemIO;
+import org.scijava.ItemPersistence;
 import org.scijava.ItemVisibility;
 
 /**
@@ -84,7 +85,7 @@ public interface ModuleItem<T> extends BasicDetails {
 	boolean isRequired();
 
 	/** Gets whether to remember the most recent value of the parameter. */
-	boolean isPersisted();
+	ItemPersistence getPersistence();
 
 	/** Gets the key to use for saving the value persistently. */
 	String getPersistKey();

src/main/java/org/scijava/module/MutableModuleItem.java

@@ -34,6 +34,7 @@
 import java.util.List;
 
 import org.scijava.ItemIO;
+import org.scijava.ItemPersistence;
 import org.scijava.ItemVisibility;
 
 /**
@@ -50,7 +51,7 @@ public interface MutableModuleItem<T> extends ModuleItem<T> {
 
 	void setRequired(boolean required);
 
-	void setPersisted(boolean persisted);
+	void setPersistence(ItemPersistence persistence);
 
 	void setPersistKey(String persistKey);
 

src/main/java/org/scijava/plugin/Parameter.java

@@ -37,6 +37,7 @@
 import java.lang.annotation.Target;
 
 import org.scijava.ItemIO;
+import org.scijava.ItemPersistence;
 import org.scijava.ItemVisibility;
 
 /**
@@ -111,15 +112,16 @@
 	boolean required() default true;
 
 	/** Defines whether to remember the most recent value of the parameter. */
-	boolean persist() default true;
+	ItemPersistence persist() default ItemPersistence.DEFAULT;
 
 	/** Defines a key to use for saving the value persistently. */
 	String persistKey() default "";
 
 	/**
 	 * Defines a function that is called to initialize the parameter. If an
 	 * initializer is defined, it takes precedence over {@link #persist()}, i.e.
-	 * the parameter is not persisted even if {@code persist=true} is set.
+	 * the parameter is not persisted even if {@link #persist()} returns
+	 * {@link ItemPersistence#YES}.
 	 */
 	String initializer() default "";
 

src/main/java/org/scijava/script/ScriptInfo.java

@@ -49,6 +49,7 @@
 import org.scijava.Context;
 import org.scijava.Contextual;
 import org.scijava.ItemIO;
+import org.scijava.ItemPersistence;
 import org.scijava.ItemVisibility;
 import org.scijava.NullContextException;
 import org.scijava.command.Command;
@@ -427,7 +428,7 @@ private <T> void assignAttribute(final DefaultMutableModuleItem<T> item,
 		else if (is(k, "max")) item.setMaximumValue(as(v, item.getType()));
 		else if (is(k, "min")) item.setMinimumValue(as(v, item.getType()));
 		else if (is(k, "name")) item.setName(as(v, String.class));
-		else if (is(k, "persist")) item.setPersisted(as(v, boolean.class));
+		else if (is(k, "persist")) item.setPersistence(as(v, ItemPersistence.class));
 		else if (is(k, "persistKey")) item.setPersistKey(as(v, String.class));
 		else if (is(k, "required")) item.setRequired(as(v, boolean.class));
 		else if (is(k, "softMax")) item.setSoftMaximum(as(v, item.getType()));

src/test/java/org/scijava/script/ScriptInfoTest.java

@@ -56,6 +56,7 @@
 import org.junit.Test;
 import org.scijava.Context;
 import org.scijava.ItemIO;
+import org.scijava.ItemPersistence;
 import org.scijava.log.LogService;
 import org.scijava.module.ModuleItem;
 import org.scijava.plugin.Plugin;
@@ -151,27 +152,32 @@ public void testParameters() {
 		final List<?> noChoices = Collections.emptyList();
 
 		final ModuleItem<?> log = info.getInput("log");
-		assertItem("log", LogService.class, null, ItemIO.INPUT, false, true, null,
-			null, null, null, null, null, null, null, noChoices, log);
+		assertItem("log", LogService.class, null, ItemIO.INPUT, false,
+			ItemPersistence.DEFAULT, null, null, null, null, null, null, null, null,
+			noChoices, log);
 
 		final ModuleItem<?> sliderValue = info.getInput("sliderValue");
 		assertItem("sliderValue", int.class, "Slider Value", ItemIO.INPUT, true,
-			true, null, "slider", 11, null, null, 5, 15, 3.0, noChoices, sliderValue);
+			ItemPersistence.DEFAULT, null, "slider", 11, null, null, 5, 15, 3.0,
+			noChoices, sliderValue);
 
 		final ModuleItem<?> animal = info.getInput("animal");
 		final List<String> animalChoices = //
 			Arrays.asList("quick brown fox", "lazy dog");
-		assertItem("animal", String.class, null, ItemIO.INPUT, true, false,
-			null, null, null, null, null, null, null, null, animalChoices, animal);
+		assertItem("animal", String.class, null, ItemIO.INPUT, true,
+			ItemPersistence.DEFAULT, null, null, null, null, null, null, null, null,
+			animalChoices, animal);
 		assertEquals(animal.get("family"), "Carnivora"); // test custom attribute
 
 		final ModuleItem<?> buffer = info.getOutput("buffer");
-		assertItem("buffer", StringBuilder.class, null, ItemIO.BOTH, true, true,
-			null, null, null, null, null, null, null, null, noChoices, buffer);
+		assertItem("buffer", StringBuilder.class, null, ItemIO.BOTH, true,
+			ItemPersistence.DEFAULT, null, null, null, null, null, null, null, null,
+			noChoices, buffer);
 
 		final ModuleItem<?> result = info.getOutput("result");
-		assertItem("result", Object.class, null, ItemIO.OUTPUT, true, true, null,
-			null, null, null, null, null, null, null, noChoices, result);
+		assertItem("result", Object.class, null, ItemIO.OUTPUT, true,
+			ItemPersistence.DEFAULT, null, null, null, null, null, null, null, null,
+			noChoices, result);
 
 		int inputCount = 0;
 		final ModuleItem<?>[] inputs = { log, sliderValue, animal, buffer };
@@ -188,7 +194,7 @@ public void testParameters() {
 
 	private void assertItem(final String name, final Class<?> type,
 		final String label, final ItemIO ioType, final boolean required,
-		final boolean persist, final String persistKey, final String style,
+		final ItemPersistence persist, final String persistKey, final String style,
 		final Object value, final Object min, final Object max,
 		final Object softMin, final Object softMax, final Number stepSize,
 		final List<?> choices, final ModuleItem<?> item)
@@ -198,7 +204,7 @@ private void assertItem(final String name, final Class<?> type,
 		assertEquals(label, item.getLabel());
 		assertSame(ioType, item.getIOType());
 		assertEquals(required, item.isRequired());
-		assertEquals(persist, item.isPersisted());
+		assertEquals(persist, item.getPersistence());
 		assertEquals(persistKey, item.getPersistKey());
 		assertEquals(style, item.getWidgetStyle());
 		assertEquals(value, item.getDefaultValue());