Merge pull request #1190 from jadh4v/fix-runPipelineNode-unmounting-o…

…verlapping-paths

fix(runPipelineNode): unmounting overlapping paths

packages/core/typescript/itk-wasm/src/pipeline/run-pipeline-node.ts

@@ -50,17 +50,26 @@ async function runPipelineNode (
     pipelinePath
   )) as PipelineEmscriptenModule
   const mountedDirs: Set<string> = new Set()
+  const unmountable: Set<string> = new Set()
   if (typeof mountDirs !== 'undefined') {
     mountDirs.forEach((dir) => {
       mountedDirs.add(Module.mountDir(dir))
     })
+    /**
+     * Identify mountable dirs. Some paths may be parent to others.
+     * Only keep the parent paths, to avoid error when unmounting.
+     */
+    Array.from(mountedDirs)
+      .filter((x, _, a) => a.every((y) => x === y || !x.includes(y)))
+      .forEach((dir) => unmountable.add(dir)
+    )
   }
   if (typeof mountDirs !== 'undefined') {
     args = replaceArgumentsWithEmscriptenPaths(args, mountDirs)
   }
   const result = runPipelineEmscripten(Module, args, outputs, inputs)
   if (typeof mountDirs !== 'undefined') {
-    mountedDirs.forEach((dir) => {
+    unmountable.forEach((dir) => {
       Module.unmountDir(dir)
     })
   }

packages/core/typescript/itk-wasm/test/node/pipeline/run-pipeline-node-test.js

@@ -170,6 +170,84 @@ test('runPipelineNode uses input and output text and binary data via memory io',
   )
 })
 
+test('runPipelineNode uses input and output text and binary files', (t) => {
+  const pipelinePath = path.resolve(
+    'test',
+    'pipelines',
+    'emscripten-build',
+    'input-output-files-pipeline',
+    'input-output-files-test'
+  )
+  const testInputTextFile = path.resolve(
+    'test',
+    'data',
+    'cow.iwm',
+    'index.json'
+  )
+  const testInputBinFile = path.resolve(
+    'test',
+    'data',
+    'cow.iwm',
+    'data',
+    'cells.raw'
+  )
+  const testOutputTextFile = path.resolve(
+    'test',
+    'data',
+    'cow.iwm',
+    'data',
+    'output.txt'
+  )
+  const testOutputBinFile = path.resolve(
+    'test',
+    'data',
+    'cow.iwm',
+    'data',
+    'output.bin'
+  )
+
+  const args = [
+    '--memory-io',
+    '--input-text-stream',
+    '0',
+    '--input-binary-stream',
+    '1',
+    '0',
+    '1',
+    testOutputTextFile,
+    testOutputBinFile,
+    '-f',
+    '--input-text-file',
+    testInputTextFile,
+    '--input-binary-file',
+    testInputBinFile,
+  ]
+  const desiredOutputs = [
+    { type: InterfaceTypes.TextStream },
+    { type: InterfaceTypes.BinaryStream }
+  ]
+  const inputs = [
+    { type: InterfaceTypes.TextStream, data: { data: 'The answer is 42.' } },
+    {
+      type: InterfaceTypes.BinaryStream,
+      data: { data: new Uint8Array([222, 173, 190, 239]) }
+    }
+  ]
+
+  const mountDirs = new Set()
+  mountDirs.add(path.dirname(testInputTextFile))
+  mountDirs.add(path.dirname(testInputBinFile))
+  mountDirs.add(path.dirname(testOutputTextFile))
+  mountDirs.add(path.dirname(testOutputBinFile))
+
+  return runPipelineNode(pipelinePath, args, desiredOutputs, inputs, mountDirs).then(
+    function ({ stdout, stderr, outputs }) {
+      t.is(outputs[0].type, InterfaceTypes.TextStream)
+      t.is(outputs[1].type, InterfaceTypes.BinaryStream)
+    }
+  )
+})
+
 test('runPipelineNode uses input and output json data via memory io', (t) => {
   const pipelinePath = path.resolve(
     'test',