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Merge pull request #121 from scijava/scijava-ops-legacy/openv-utils
Add utilities for OpEnvironment injection
2 parents cac4104 + d0b1183 commit 234a190

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‎docs/ops/doc/ScriptingInImageJ2.md‎

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@@ -4,11 +4,10 @@ Using SciJava Ops and ImageJ Ops2 within scripts provide the most powerful aspec
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## Obtaining an OpEnvironment
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To run Ops, scripts must first create an `OpEnvironment`. The following line will create a new `OpEnvironment` containing all Ops available in the environment:
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To run Ops, scripts require an `OpEnvironment`. The easiest way to obtain an `OpEnvironment` with all available Ops is to declare an `OpEnvironment` as a script parameter:
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```text
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import org.scijava.ops.api.OpEnvironment
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ops = OpEnvironment.getEnvironment()
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#@ OpEnvironment ops
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```
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## Obtaining inputs
@@ -35,14 +34,11 @@ out = ops.op("filter.gauss").arity2().input(imgInput, new Double(3.0)).apply()
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The below script can be pasted into the Script Editor. **Ensure that the Script Editor is configured to run a Groovy script**.
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```text
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#@ OpEnvironment ops
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#@ ThreadService ts
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#@ Img imgInput
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#@output Img out
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// Obtain an OpEnvironment
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import org.scijava.ops.api.OpEnvironment
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ops = OpEnvironment.getEnvironment()
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// Call some Ops!
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out = ops.op("filter.gauss").arity2().input(imgInput, new Double(3.0)).apply()
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```

‎scijava-ops-legacy/pom.xml‎

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@@ -91,7 +91,36 @@
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<!-- NB: Deploy releases to the SciJava Maven repository. -->
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<releaseProfiles>sign,deploy-to-scijava</releaseProfiles>
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<scijava-common.version>2.98.0</scijava-common.version>
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</properties>
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<build>
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<plugins>
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<plugin>
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<artifactId>maven-compiler-plugin</artifactId>
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<configuration>
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<annotationProcessorPaths>
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<path>
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<groupId>org.scijava</groupId>
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<artifactId>scijava-ops-indexer</artifactId>
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<version>${project.version}</version>
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</path>
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<path>
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<groupId>org.scijava</groupId>
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<artifactId>scijava-common</artifactId>
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<version>${scijava-common.version}</version>
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</path>
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</annotationProcessorPaths>
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<fork>true</fork>
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<showWarnings>true</showWarnings>
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<compilerArgs>
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<arg>-Aparse.ops="${scijava.parse.ops}"</arg>
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<arg>-Aop.version="${project.version}"</arg>
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</compilerArgs>
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</configuration>
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</plugin>
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</plugins>
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</build>
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<repositories>
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<repository>
@@ -112,6 +141,10 @@
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<artifactId>scijava-collections</artifactId>
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<version>${project.version}</version>
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</dependency>
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<dependency>
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<groupId>org.scijava</groupId>
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<artifactId>scijava-common</artifactId>
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</dependency>
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<dependency>
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<groupId>org.scijava</groupId>
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<artifactId>scijava-priority</artifactId>
@@ -156,5 +189,23 @@
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<version>${project.version}</version>
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<scope>test</scope>
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</dependency>
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</dependencies>
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<dependency>
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<groupId>org.scijava</groupId>
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<artifactId>scijava-ops-api</artifactId>
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<version>${project.version}</version>
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<scope>compile</scope>
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</dependency>
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<dependency>
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<groupId>org.scijava</groupId>
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<artifactId>scijava-ops-engine</artifactId>
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<version>${project.version}</version>
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<scope>test</scope>
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</dependency>
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<dependency>
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<groupId>org.scijava</groupId>
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<artifactId>scijava-progress</artifactId>
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<version>0-SNAPSHOT</version>
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<scope>compile</scope>
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</dependency>
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</dependencies>
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</project>

‎scijava-ops-legacy/src/main/java/module-info.java‎

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@@ -26,11 +26,13 @@
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* POSSIBILITY OF SUCH DAMAGE.
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* #L%
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*/
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module org.scijava.legacy {
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open module org.scijava.legacy {
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requires net.imagej;
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requires org.scijava;
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requires org.scijava.types;
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requires org.scijava.priority;
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requires org.scijava.ops.api;
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provides org.scijava.types.TypeExtractor with org.scijava.legacy.types.DatasetTypeExtractor;
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}

‎scijava-ops-legacy/src/main/java/org/scijava/legacy/module/process/OpEnvironmentPreprocessorPlugin.java‎

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@@ -0,0 +1,43 @@
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package org.scijava.legacy.module.process;
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import org.scijava.Priority;
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import org.scijava.legacy.service.OpEnvironmentService;
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import org.scijava.module.Module;
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import org.scijava.module.ModuleItem;
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import org.scijava.module.process.AbstractPreprocessorPlugin;
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import org.scijava.module.process.PreprocessorPlugin;
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import org.scijava.ops.api.OpEnvironment;
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import org.scijava.plugin.Parameter;
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import org.scijava.plugin.Plugin;
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/**
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* A {@link PreprocessorPlugin} used to inject an {@link OpEnvironment}, created
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* by the {@link OpEnvironmentService}, into {@link Module}s.
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*
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* @author Gabriel Selzer
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*/
20+
@Plugin(type = PreprocessorPlugin.class, priority = Priority.HIGH)
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public class OpEnvironmentPreprocessorPlugin extends
22+
AbstractPreprocessorPlugin
23+
{
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@Parameter
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private OpEnvironmentService opEnvironmentService;
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@Override
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public void process(Module module) {
30+
for (final ModuleItem<?> input : module.getInfo().inputs()) {
31+
if (!input.isAutoFill()) continue;
32+
if (module.isInputResolved(input.getName())) continue;
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final Class<?> type = input.getType();
34+
if (OpEnvironment.class.equals(type)) {
35+
@SuppressWarnings("unchecked")
36+
final ModuleItem<OpEnvironment> envInput =
37+
(ModuleItem<OpEnvironment>) input;
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envInput.setValue(module, opEnvironmentService.env());
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module.resolveInput(input.getName());
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}
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}
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}
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}

‎scijava-ops-legacy/src/main/java/org/scijava/legacy/service/DefaultOpEnvironmentService.java‎

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package org.scijava.legacy.service;
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import org.scijava.ops.api.OpEnvironment;
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import org.scijava.plugin.Attr;
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import org.scijava.plugin.Parameter;
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import org.scijava.plugin.Plugin;
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import org.scijava.script.ScriptService;
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import org.scijava.service.AbstractService;
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import org.scijava.service.Service;
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/**
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* Default implementation of {@link OpEnvironmentService}
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*
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* @author Gabriel Selzer
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*/
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@Plugin(type = Service.class, attrs = { @Attr(name = "noAlias") })
18+
public class DefaultOpEnvironmentService extends AbstractService implements
19+
OpEnvironmentService
20+
{
21+
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@Parameter(required = false)
23+
private ScriptService scriptService;
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25+
private OpEnvironment env;
26+
27+
@Override
28+
public void initialize() {
29+
// Build the Op Environment
30+
env = OpEnvironment.build();
31+
32+
// Set up alias, if ScriptService available
33+
if (scriptService != null) {
34+
scriptService.addAlias(OpEnvironment.class);
35+
}
36+
}
37+
38+
@Override
39+
public OpEnvironment env() {
40+
return env;
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}
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}

‎scijava-ops-legacy/src/main/java/org/scijava/legacy/service/OpEnvironmentService.java‎

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@@ -0,0 +1,25 @@
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package org.scijava.legacy.service;
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import org.scijava.ops.api.OpEnvironment;
5+
import org.scijava.service.SciJavaService;
6+
import org.scijava.service.Service;
7+
8+
/**
9+
* A SciJava {@link Service} that instantiates a single {@link OpEnvironment}.
10+
* The primary use case is in SciJava scripting, but within scripts this service
11+
* should not be used - instead, users should declare an {@link OpEnvironment}
12+
* parameter, which will be filled using a preprocessor plugin.
13+
*
14+
* @author Gabriel Selzer
15+
*/
16+
public interface OpEnvironmentService extends SciJavaService {
17+
18+
/**
19+
* Returns this Service's {@link OpEnvironment}.
20+
*
21+
* @return an {@link OpEnvironment}
22+
*/
23+
OpEnvironment env();
24+
25+
}

‎scijava-ops-legacy/src/test/java/org/scijava/legacy/module/process/OpEnvironmentPreprocessorTest.java‎

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package org.scijava.legacy.module.process;
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import org.junit.jupiter.api.Test;
5+
import org.scijava.Context;
6+
import org.scijava.command.Command;
7+
import org.scijava.command.CommandService;
8+
import org.scijava.legacy.service.OpEnvironmentService;
9+
import org.scijava.ops.api.OpEnvironment;
10+
import org.scijava.plugin.Parameter;
11+
12+
import java.util.concurrent.ExecutionException;
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14+
/**
15+
* Tests the ability of {@link OpEnvironmentPreprocessorPlugin} to fill in
16+
* {@link OpEnvironment} module parameters.
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*
18+
* @author Gabriel Selzer
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*/
20+
public class OpEnvironmentPreprocessorTest {
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@Test
23+
public void testOpEnvironmentPreprocessor() throws ExecutionException,
24+
InterruptedException
25+
{
26+
var context = new Context(CommandService.class, OpEnvironmentService.class);
27+
var commandService = context.service(CommandService.class);
28+
commandService.run(CommandWithOpEnvironment.class, true).get();
29+
context.dispose();
30+
}
31+
32+
public static class CommandWithOpEnvironment implements Command {
33+
34+
@Parameter
35+
public OpEnvironment env;
36+
37+
@Override
38+
public void run() {
39+
// Fails the test if the OpEnvironment was not injected
40+
if (env == null) {
41+
throw new IllegalArgumentException(
42+
"OpEnvironment not properly injected!");
43+
}
44+
}
45+
}
46+
47+
}

‎scijava-ops-legacy/src/test/java/org/scijava/legacy/service/OpEnvironmentServiceTest.java‎

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@@ -0,0 +1,51 @@
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package org.scijava.legacy.service;
3+
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import org.junit.jupiter.api.Assertions;
5+
import org.junit.jupiter.api.Test;
6+
import org.scijava.Context;
7+
import org.scijava.ops.api.OpEnvironment;
8+
import org.scijava.script.ScriptService;
9+
10+
/**
11+
* Tests {@link OpEnvironmentService} API.
12+
*
13+
* @author Gabriel Selzer
14+
*/
15+
public class OpEnvironmentServiceTest {
16+
17+
/**
18+
* Tests that an {@link OpEnvironmentService} produces an
19+
* {@link OpEnvironment} with some Ops in it.
20+
*/
21+
@Test
22+
public void testOpEnvironmentService() {
23+
Context ctx = new Context(OpEnvironmentService.class);
24+
OpEnvironmentService ops = ctx.getService(OpEnvironmentService.class);
25+
Double result = ops.env().binary("math.add") //
26+
.input(2., 3.) //
27+
.outType(Double.class) //
28+
.apply();
29+
Assertions.assertEquals(5., result);
30+
ctx.dispose();
31+
}
32+
33+
/**
34+
* Test that when a {@link ScriptService} is present, the "OpEnvironment"
35+
* alias points to {@link OpEnvironment}.
36+
*/
37+
@Test
38+
public void testOpEnvironmentServiceAliases() {
39+
Context ctx = new Context(OpEnvironmentService.class, ScriptService.class);
40+
ScriptService script = ctx.getService(ScriptService.class);
41+
// Assert the correct alias for OpEnvironment
42+
Assertions.assertEquals( //
43+
OpEnvironment.class, //
44+
script.getAliases().get("OpEnvironment") //
45+
);
46+
// Assert no alias for OpEnvironmentService
47+
Assertions.assertNull(script.getAliases().get("OpEnvironmentService"));
48+
ctx.dispose();
49+
}
50+
51+
}

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