feat(cli): Add --max-rows flag

Author: effigies

src/schema/associations.ts

@@ -36,8 +36,8 @@ const associationLookup = {
     suffix: 'events',
     extensions: ['.tsv'],
     inherit: true,
-    load: async (file: BIDSFile): Promise<Events> => {
-      const columns = await loadTSV(file)
+    load: async (file: BIDSFile, options: { maxRows: number }): Promise<Events> => {
+      const columns = await loadTSV(file, options.maxRows)
         .catch((e) => {
           return new Map()
         })
@@ -53,8 +53,9 @@ const associationLookup = {
     inherit: true,
     load: async (
       file: BIDSFile,
+      options: { maxRows: number },
     ): Promise<Aslcontext> => {
-      const columns = await loadTSV(file)
+      const columns = await loadTSV(file, options.maxRows)
         .catch((e) => {
           return new Map()
         })
@@ -69,31 +70,31 @@ const associationLookup = {
     suffix: 'm0scan',
     extensions: ['.nii', '.nii.gz'],
     inherit: false,
-    load: (file: BIDSFile): Promise<M0Scan> => {
+    load: (file: BIDSFile, options: any): Promise<M0Scan> => {
       return Promise.resolve({ path: file.path })
     },
   },
   magnitude: {
     suffix: 'magnitude',
     extensions: ['.nii', '.nii.gz'],
     inherit: false,
-    load: (file: BIDSFile): Promise<Magnitude> => {
+    load: (file: BIDSFile, options: any): Promise<Magnitude> => {
       return Promise.resolve({ path: file.path })
     },
   },
   magnitude1: {
     suffix: 'magnitude1',
     extensions: ['.nii', '.nii.gz'],
     inherit: false,
-    load: (file: BIDSFile): Promise<Magnitude1> => {
+    load: (file: BIDSFile, options: any): Promise<Magnitude1> => {
       return Promise.resolve({ path: file.path })
     },
   },
   bval: {
     suffix: 'dwi',
     extensions: ['.bval'],
     inherit: true,
-    load: async (file: BIDSFile): Promise<Bval> => {
+    load: async (file: BIDSFile, options: any): Promise<Bval> => {
       const contents = await file.text()
       const rows = parseBvalBvec(contents)
       return {
@@ -109,7 +110,7 @@ const associationLookup = {
     suffix: 'dwi',
     extensions: ['.bvec'],
     inherit: true,
-    load: async (file: BIDSFile): Promise<Bvec> => {
+    load: async (file: BIDSFile, options: any): Promise<Bvec> => {
       const contents = await file.text()
       const rows = parseBvalBvec(contents)
 
@@ -128,8 +129,8 @@ const associationLookup = {
     suffix: 'channels',
     extensions: ['.tsv'],
     inherit: true,
-    load: async (file: BIDSFile): Promise<Channels> => {
-      const columns = await loadTSV(file)
+    load: async (file: BIDSFile, options: { maxRows: number }): Promise<Channels> => {
+      const columns = await loadTSV(file, options.maxRows)
         .catch((e) => {
           return new Map()
         })
@@ -145,7 +146,7 @@ const associationLookup = {
     suffix: 'coordsystem',
     extensions: ['.json'],
     inherit: true,
-    load: (file: BIDSFile): Promise<Coordsystem> => {
+    load: (file: BIDSFile, options: any): Promise<Coordsystem> => {
       return Promise.resolve({ path: file.path })
     },
   },
@@ -154,6 +155,7 @@ const associationLookup = {
 export async function buildAssociations(
   source: BIDSFile,
   issues: DatasetIssues,
+  maxRows: number = -1,
 ): Promise<Associations> {
   const associations: Associations = {}
 
@@ -177,7 +179,7 @@ export async function buildAssociations(
 
     if (file) {
       // @ts-expect-error Matching load return value to key is hard
-      associations[key] = await load(file).catch((error) => {
+      associations[key] = await load(file, { maxRows }).catch((error) => {
         if (error.key) {
           issues.add({ code: error.key, location: file.path })
         }

src/schema/context.ts

@@ -232,7 +232,7 @@ export class BIDSContext implements Context {
       return
     }
 
-    this.columns = await loadTSV(this.file)
+    this.columns = await loadTSV(this.file, this.dataset.options?.maxRows)
       .catch((error) => {
         if (error.key) {
           this.dataset.issues.add({ code: error.key, location: this.file.path })
@@ -247,7 +247,11 @@ export class BIDSContext implements Context {
   }
 
   async loadAssociations(): Promise<void> {
-    this.associations = await buildAssociations(this.file, this.dataset.issues)
+    this.associations = await buildAssociations(
+      this.file,
+      this.dataset.issues,
+      this.dataset.options?.maxRows,
+    )
     return
   }
 

src/setup/options.test.ts

@@ -10,6 +10,7 @@ Deno.test('options parsing', async (t) => {
       json: true,
       color: false,
       blacklistModalities: [],
+      maxRows: 1000,
     })
   })
 })

src/setup/options.ts

@@ -30,6 +30,7 @@ export type ValidatorOptions = {
   outfile?: string
   blacklistModalities: string[]
   prune?: boolean
+  maxRows?: number
 }
 
 const modalityType = new EnumType<string>(
@@ -50,6 +51,11 @@ export const validateCommand: Command<void, void, any, string[], void> = new Com
     'Specify a schema version to use for validation',
   )
   .option('-c, --config <file:string>', 'Path to a JSON configuration file')
+  .option(
+    '--max-rows <nrows:number>',
+    'Maximum number of rows to validate in TSVs. Use 0 to validate headers only. Use -1 to validate all.',
+    { default: 1000 },
+  )
   .option('-v, --verbose', 'Log more extensive information about issues')
   .option('--ignoreWarnings', 'Disregard non-critical issues')
   .option(