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Add Op dependency information to OpInfo
And implement Op dependency parsing for OpClassInfo.
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8 files changed

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‎src/main/java/org/scijava/ops/AnnotatedOpDependencyMember.java‎

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/*
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* #%L
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* ImageJ software for multidimensional image processing and analysis.
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* %%
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* Copyright (C) 2014 - 2016 Board of Regents of the University of
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* Wisconsin-Madison and University of Konstanz.
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* %%
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* Redistribution and use in source and binary forms, with or without
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* modification, are permitted provided that the following conditions are met:
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*
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* 1. Redistributions of source code must retain the above copyright notice,
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* this list of conditions and the following disclaimer.
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* 2. Redistributions in binary form must reproduce the above copyright notice,
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* this list of conditions and the following disclaimer in the documentation
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* and/or other materials provided with the distribution.
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*
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* THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
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* AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
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* IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
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* ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDERS OR CONTRIBUTORS BE
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* LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
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* CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
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* SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
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* INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
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* CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
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* ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
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* POSSIBILITY OF SUCH DAMAGE.
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* #L%
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*/
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package org.scijava.ops;
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import java.lang.reflect.Type;
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/**
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* @author Marcel Wiedenmann
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*/
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public abstract class AnnotatedOpDependencyMember<T> implements
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OpDependencyMember<T>
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{
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private String key;
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private Type type;
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private final OpDependency annotation;
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public AnnotatedOpDependencyMember(String key, Type type,
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final OpDependency annotation)
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{
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this.key = key;
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this.type = type;
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this.annotation = annotation;
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}
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public OpDependency getAnnotation() {
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return annotation;
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}
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// -- OpDependencyMember methods --
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@Override
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public String getDependencyName() {
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return annotation.name();
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}
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// -- Member methods --
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@Override
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public String getKey() {
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return key;
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}
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@Override
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public Type getType() {
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return type;
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}
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}

‎src/main/java/org/scijava/ops/FieldOpDependencyMember.java‎

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/*
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* #%L
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* ImageJ software for multidimensional image processing and analysis.
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* %%
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* Copyright (C) 2014 - 2016 Board of Regents of the University of
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* Wisconsin-Madison and University of Konstanz.
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* %%
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* Redistribution and use in source and binary forms, with or without
9+
* modification, are permitted provided that the following conditions are met:
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*
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* 1. Redistributions of source code must retain the above copyright notice,
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* this list of conditions and the following disclaimer.
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* 2. Redistributions in binary form must reproduce the above copyright notice,
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* this list of conditions and the following disclaimer in the documentation
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* and/or other materials provided with the distribution.
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*
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* THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
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* AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
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* IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
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* ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDERS OR CONTRIBUTORS BE
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* LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
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* CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
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* SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
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* INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
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* CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
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* ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
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* POSSIBILITY OF SUCH DAMAGE.
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* #L%
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*/
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package org.scijava.ops;
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import java.lang.reflect.Field;
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import org.scijava.struct.MemberInstance;
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import org.scijava.struct.ValueAccessible;
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import org.scijava.struct.ValueAccessibleMemberInstance;
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import org.scijava.util.Types;
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/**
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* @author Marcel Wiedenmann
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*/
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public class FieldOpDependencyMember<T> extends AnnotatedOpDependencyMember<T>
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implements ValueAccessible<T>
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{
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private final Field field;
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public FieldOpDependencyMember(final Field field, final Class<?> structType) {
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super(field.getName(), Types.fieldType(field, structType), field
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.getAnnotation(OpDependency.class));
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this.field = field;
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}
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// -- ValueAccessible methods --
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@Override
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public T get(Object o) {
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field.setAccessible(true);
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try {
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@SuppressWarnings("unchecked")
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final T value = (T) field.get(o);
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return value;
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}
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catch (final IllegalAccessException exc) {
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// FIXME
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throw new RuntimeException(exc);
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}
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}
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@Override
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public void set(T value, Object o) {
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field.setAccessible(true);
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try {
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field.set(o, value);
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}
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catch (final IllegalAccessException exc) {
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// FIXME
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throw new RuntimeException(exc);
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}
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}
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// -- Member methods --
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@Override
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public MemberInstance<T> createInstance(final Object o) {
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return new ValueAccessibleMemberInstance<>(this, o);
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}
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}

‎src/main/java/org/scijava/ops/OpDependencyMember.java‎

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@@ -0,0 +1,49 @@
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/*
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* #%L
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* ImageJ software for multidimensional image processing and analysis.
4+
* %%
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* Copyright (C) 2014 - 2016 Board of Regents of the University of
6+
* Wisconsin-Madison and University of Konstanz.
7+
* %%
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* Redistribution and use in source and binary forms, with or without
9+
* modification, are permitted provided that the following conditions are met:
10+
*
11+
* 1. Redistributions of source code must retain the above copyright notice,
12+
* this list of conditions and the following disclaimer.
13+
* 2. Redistributions in binary form must reproduce the above copyright notice,
14+
* this list of conditions and the following disclaimer in the documentation
15+
* and/or other materials provided with the distribution.
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*
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* THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
18+
* AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
19+
* IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
20+
* ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDERS OR CONTRIBUTORS BE
21+
* LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
22+
* CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
23+
* SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
24+
* INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
25+
* CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
26+
* ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
27+
* POSSIBILITY OF SUCH DAMAGE.
28+
* #L%
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*/
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package org.scijava.ops;
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import org.scijava.struct.ItemIO;
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import org.scijava.struct.Member;
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/**
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* @author Marcel Wiedenmann
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*/
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public interface OpDependencyMember<T> extends Member<T> {
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String getDependencyName();
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// -- Member methods --
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@Override
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default ItemIO getIOType() {
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return ItemIO.NONE;
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}
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}

‎src/main/java/org/scijava/ops/OpUtils.java‎

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@@ -173,6 +173,13 @@ public static void checkHasSingleOutput(Struct struct) throws ValidityException
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}
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}
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public static List<OpDependencyMember<?>> dependencies(Struct struct) {
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return struct.members().stream() //
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.filter(member -> member instanceof OpDependencyMember) //
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.map(member -> (OpDependencyMember<?>) member) //
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.collect(Collectors.toList());
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}
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public static Type[] types(OpCandidate candidate) {
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return getTypes(candidate.struct().members());
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}

‎src/main/java/org/scijava/ops/matcher/OpInfo.java‎

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import java.lang.reflect.Type;
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import java.util.List;
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import org.scijava.ops.OpDependencyMember;
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import org.scijava.ops.OpUtils;
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import org.scijava.param.ValidityException;
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import org.scijava.struct.Member;
@@ -34,6 +35,11 @@ default Member<?> output() {
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return OpUtils.outputs(struct()).get(0);
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}
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/** Gets the op's dependencies on other ops. */
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default List<OpDependencyMember<?>> dependencies() {
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return OpUtils.dependencies(struct());
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}
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/** The op's priority. */
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double priority();
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‎src/main/java/org/scijava/ops/util/Inject.java‎

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@@ -6,6 +6,7 @@
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import java.util.stream.Collectors;
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import org.scijava.command.Command;
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import org.scijava.ops.OpDependencyMember;
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import org.scijava.param.ParameterStructs;
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import org.scijava.param.ValidityException;
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import org.scijava.struct.ItemIO;
@@ -23,7 +24,10 @@ private Structs() {
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}
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public static boolean isInjectable(final StructInstance<?> instance) {
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return !getAccessibles(instance).isEmpty();
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// HACK: Exclude Op dependencies since they were already injected when
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// constructing the instance.
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return !filterAccessibles(getAccessibles(instance), mi -> !(mi
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.member() instanceof OpDependencyMember)).isEmpty();
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}
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public static void inputs(StructInstance<?> instance, Object... objs) {

‎src/main/java/org/scijava/param/ParameterStructs.java‎

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import java.util.Set;
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import java.util.stream.Collectors;
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import org.scijava.ops.FieldOpDependencyMember;
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import org.scijava.ops.OpDependency;
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import org.scijava.ops.OpDependencyMember;
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import org.scijava.struct.ItemIO;
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import org.scijava.struct.Member;
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import org.scijava.struct.Struct;
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// Parse field level @Parameter annotations.
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parseFieldParameters(items, names, problems, type);
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// Parse field level @OpDependency annotations.
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parseFieldOpDependencies(items, problems, type);
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// Fail if there were any problems.
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if (!problems.isEmpty()) throw new ValidityException(problems);
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@@ -200,6 +206,28 @@ private static void parseFunctionalParameters(final ArrayList<Member<?>> items,
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}
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}
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private static void parseFieldOpDependencies(final List<Member<?>> items,
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final List<ValidityProblem> problems, Class<?> annotatedClass)
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{
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final List<Field> fields = ClassUtils.getAnnotatedFields(annotatedClass,
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OpDependency.class);
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for (final Field f : fields) {
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f.setAccessible(true);
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final boolean isFinal = Modifier.isFinal(f.getModifiers());
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if (isFinal) {
218+
final String name = f.getName();
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// Final fields are bad because they cannot be modified.
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final String error = "Invalid final Op dependency field: " + name;
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problems.add(new ValidityProblem(error));
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// Skip invalid Op dependencies.
223+
continue;
224+
}
225+
final OpDependencyMember<?> item = new FieldOpDependencyMember<>(f,
226+
annotatedClass);
227+
items.add(item);
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}
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}
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private static boolean isImmutable(final Class<?> type) {
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// NB: All eight primitive types, as well as the boxed primitive
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// wrapper classes, as well as strings, are immutable objects.

‎src/main/java/org/scijava/struct/ItemIO.java‎

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* @author Curtis Rueden
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*/
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public enum ItemIO {
50-
INPUT, OUTPUT, BOTH, AUTO
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INPUT, OUTPUT, BOTH, AUTO, NONE
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}

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