WIP: start migrating Pipeline class

Author: ctrueden

packages/core/java/src/main/java/org/itk/wasm/Pipeline.java

@@ -0,0 +1,90 @@
+package org.itk.wasm;
+
+import com.google.gson.Gson;
+import com.google.gson.JsonObject;
+
+import java.io.FileInputStream;
+import java.io.IOException;
+import java.nio.ByteBuffer;
+import java.nio.charset.StandardCharsets;
+import java.nio.file.Path;
+import java.util.ArrayList;
+import java.util.List;
+
+public class Pipeline {
+    private Config config;
+    private Engine engine;
+    private Store store;
+    private Linker linker;
+    private Module module;
+    private Memory memory;
+    private Function inputArrayAlloc;
+    private Function inputJsonAlloc;
+    private Function outputArrayAddress;
+    private Function outputArraySize;
+    private Function outputJsonAddress;
+    private Function outputJsonSize;
+
+    public Pipeline(Path pipeline) throws IOException {
+        config = new Config();
+        config.wasmBulkMemory(true);
+        config.wasmSimd(true);
+        config.wasmMemory64(true);
+        engine = new Engine(config);
+        store = new Store(engine);
+        linker = new Linker(engine);
+        linker.allowShadowing(true);
+
+        byte[] wasmBytes = new byte[(int) pipeline.toFile().length()];
+        try (FileInputStream fis = new FileInputStream(pipeline.toFile())) {
+            fis.read(wasmBytes);
+        }
+
+        module = Module.create(engine, wasmBytes);
+        store.setWasi(WasiConfig.inheritStdin().inheritStdout().inheritStderr().build());
+
+        linker.defineWasi();
+        Instance instance = linker.instantiate(store, module);
+
+        memory = instance.exports(store).getMemory("memory");
+        inputArrayAlloc = instance.exports(store).getFunction("itk_wasm_input_array_alloc");
+        inputJsonAlloc = instance.exports(store).getFunction("itk_wasm_input_json_alloc");
+        outputArrayAddress = instance.exports(store).getFunction("itk_wasm_output_array_address");
+        outputArraySize = instance.exports(store).getFunction("itk_wasm_output_array_size");
+        outputJsonAddress = instance.exports(store).getFunction("itk_wasm_output_json_address");
+        outputJsonSize = instance.exports(store).getFunction("itk_wasm_output_json_size");
+
+        Function initialize = instance.exports(store).getFunction("_initialize");
+        initialize.call(store);
+    }
+
+    public List<PipelineOutput> run(List<String> args, List<PipelineOutput> outputs, List<PipelineInput> inputs) {
+        WasiConfig wasiConfig = WasiConfig.inheritEnv()
+                .inheritStdin()
+                .inheritStdout()
+                .inheritStderr()
+                .args(args)
+                .build();
+
+        List<String> preopenDirectories = new ArrayList<>();
+        for (int index = 0; index < inputs.size(); index++) {
+            PipelineInput input = inputs.get(index);
+            if (input.getType() == InterfaceTypes.TextFile || input.getType() == InterfaceTypes.BinaryFile) {
+                Path parentPath = input.getData().getPath().getParent();
+                if (parentPath != null) {
+                    preopenDirectories.add(parentPath.toString());
+                }
+            }
+        }
+        for (int index = 0; index < outputs.size(); index++) {
+            PipelineOutput output = outputs.get(index);
+            if (output.getType() == InterfaceTypes.TextFile || output.getType() == InterfaceTypes.BinaryFile) {
+                Path parentPath = output.getData().getPath().getParent();
+                if (parentPath != null) {
+                    preopenDirectories.add(parentPath.toString());
+                }
+            }
+        }
+        String[] preopenDirectoriesArray = preopenDirectories.toArray(new String[0]);
+        wasiConfig.setPreopenDirectories(preopenDirectoriesArray);
+        store.set