Merge pull request #850 from thewtex/run-pipeline-node-pass-mounts

runPipelineNode pass mounts

Author: thewtex

docs/api/browser_pipelines.md

@@ -12,7 +12,7 @@ These functions return the [`WebWorker`](https://developer.mozilla.org/en-US/doc
 ## `runPipeline`
 
 ```ts
-runPipelineNode(webWorker: Worker | null | boolean,
+runPipeline(webWorker: Worker | null | boolean,
   pipelinePath: string | URL,
   args: string[],
   outputs: PipelineOutput[] | null,

docs/api/node_pipelines.md

@@ -12,7 +12,8 @@ Similar to the [web browser API](./browser_pipelines.html), most of these functi
 runPipelineNode(pipelinePath: string,
   args: string[],
   outputs: PipelineOutput[],
-  inputs: PipelineInput[] | null):
+  inputs: PipelineInput[] | null,
+  mountContainingDirs?: Set<string>):
   Promise<{
     returnValue: number,
     stdout: string,
@@ -49,6 +50,10 @@ A JavaScript Array of [`PipelineInput`](https://github.com/InsightSoftwareConsor
 - `data` contains the corresponding data for the interface type.
 - `path` is the optional file path on the filesystem to read after execution has completed.
 
+### `mountContainingDirs`
+
+Filepaths on the local filesystem whose dirname will be mounted to provide the wasm module direct access to the file.
+
 ### Result
 
 Promise resolving a JavaScript object with the properties:

package.json

@@ -26,7 +26,7 @@
     "commit": "git cz",
     "bindgen": "node ./src/itk-wasm-cli.js bindgen ./dist/dicom/src ./dist/dicom/public/pipelines/*.wasm",
     "build": "npm run build:testData && npm run build:emscripten && npm run build:tsc && npm run build:tscWorkersModuleLoader && npm run build:tscWebWorkers && npm run build:workerBundles && npm run build:workerMinBundles && npm run build:webpack && node ./src/io/internal/packages/package-json-gen.cjs && npm run build:emscripten:packages",
-    "build:testData": "dam download packages/dicom/test/data packages/dicom/test/data.tar.gz bafybeic2ckitzhl5b476fgfewt7ilel3mkzi5x66o6gga5s7n34g2t36xm https://w3s.link/ipfs/bafkreibxuanogkwccski66azxafdpjjj3sbua6g3pqdvwwwe72h3d6agoi",
+    "build:testData": "dam download packages/dicom/test/data packages/dicom/test/data.tar.gz bafybeic2ckitzhl5b476fgfewt7ilel3mkzi5x66o6gga5s7n34g2t36xm https://github.com/InsightSoftwareConsortium/itk-wasm/releases/download/itk-wasm-v1.0.0-b.113/test-data.tar.gz https://w3s.link/ipfs/bafkreibxuanogkwccski66azxafdpjjj3sbua6g3pqdvwwwe72h3d6agoi",
     "build:debug": "npm run build:emscripten -- --debug && npm run build:tsc && npm run build:tscWorkersModuleLoader && npm run build:tscWebWorkers && npm run build:workerBundles && npm run build:workerMinBundles && npm run build:webpack -- --mode development",
     "build:tsc": "tsc --pretty",
     "build:tscWorkersModuleLoader": "tsc --types --lib es2017,webworker --rootDir ./src/ --outDir ./dist/ --moduleResolution node --target es2017 --module es2020 --strict --forceConsistentCasingInFileNames --declaration ./src/core/internal/loadEmscriptenModuleWebWorker.ts",

packages/dicom/typescript/package.json

@@ -64,4 +64,4 @@
     "type": "git",
     "url": "https://github.com/InsightSoftwareConsortium/itk-wasm"
   }
-}
+}

src/emscripten-module/itkJSPost.js

@@ -1,16 +1,15 @@
 /** Given an absolute path to a file, mount its containing directory in the
  * Emscripten virtual filesystem. Only relevant when within the Node.js
- * environment. If the containing directory already exists with the
- * Emscripten filesystem, it will not be mounted. */
+ * environment. */
 Module.mountContainingDir = function (filePath) {
   if (!ENVIRONMENT_IS_NODE) {
     return
   }
   var path = require('path')
   var containingDir = path.dirname(filePath)
-  // If the directory already exists, abort
-  if (FS.isDir(containingDir) || containingDir === '/') {
-    return
+  // If the root, abort
+  if (containingDir === '/') {
+    throw new Error('Cannot mount root directory')
   }
 
   var currentDir = '/'

src/io/readImageLocalFile.ts

@@ -12,6 +12,7 @@ import loadEmscriptenModule from '../core/internal/loadEmscriptenModuleNode.js'
 import runPipelineEmscripten from '../pipeline/internal/runPipelineEmscripten.js'
 import PipelineEmscriptenModule from '../pipeline/PipelineEmscriptenModule.js'
 import findLocalImageIOPath from './internal/findLocalImageIOPath.js'
+import runPipelineNode from '../pipeline/runPipelineNode.js'
 import InterfaceTypes from '../core/InterfaceTypes.js'
 import PipelineInput from '../pipeline/PipelineInput.js'
 import CastImageOptions from '../core/CastImageOptions.js'
@@ -57,10 +58,9 @@ async function readImageLocalFile (filePath: string, options?: CastImageOptions)
   }
 
   const modulePath = path.join(imageIOsPath, io as string + '-read-image.js')
-  const readImageModule = await loadEmscriptenModule(modulePath) as PipelineEmscriptenModule
-  const mountedFilePath = readImageModule.mountContainingDir(absoluteFilePath)
-  const { outputs } = runPipelineEmscripten(readImageModule, args, desiredOutputs, inputs)
-  readImageModule.unmountContainingDir(mountedFilePath)
+  const mountContainingDirs = new Set([absoluteFilePath])
+  const { outputs } = await runPipelineNode(modulePath, args, desiredOutputs, inputs, mountContainingDirs)
+
   let result = outputs[0].data as Image
 
   if (typeof options !== 'undefined') {

src/itk-wasm-cli.js

@@ -13,7 +13,7 @@ import pythonBindgen from './bindgen/python.js'
 const program = new Command()
 
 // Array of types that will require an import from itk-wasm
-const defaultImageTag = '20230526-f226ba4e'
+const defaultImageTag = '20230605-8a333e7c'
 
 function processCommonOptions(wasiDefault=false) {
   const options = program.opts()

src/pipeline/runPipelineNode.ts

@@ -10,12 +10,24 @@ async function runPipelineNode (
   pipelinePath: string,
   args: string[],
   outputs: PipelineOutput[],
-  inputs: PipelineInput[] | null
+  inputs: PipelineInput[] | null,
+  mountContainingDirs?: Set<string>
 ): Promise<RunPipelineResult> {
   const Module = (await loadEmscriptenModuleNode(
     pipelinePath
   )) as PipelineEmscriptenModule
+  const mountedDirs: Set<string> = new Set()
+  if (typeof mountContainingDirs !== 'undefined') {
+    mountContainingDirs.forEach((filePath) => {
+      mountedDirs.add(Module.mountContainingDir(filePath))
+    })
+  }
   const result = runPipelineEmscripten(Module, args, outputs, inputs)
+  if (typeof mountContainingDirs !== 'undefined') {
+    mountedDirs.forEach((filePath) => {
+      Module.unmountContainingDir(filePath)
+    })
+  }
   return result
 }