bids-validator-deno 2.0.5__tar.gz → 2.0.7__tar.gz

{bids_validator_deno-2.0.5 → bids_validator_deno-2.0.7}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: bids-validator-deno
-Version: 2.0.5
+Version: 2.0.7
 Summary: Typescript implementation of the BIDS validator
 Keywords: BIDS,BIDS validator
 Author: bids-standard developers

{bids_validator_deno-2.0.5 → bids_validator_deno-2.0.7}/deno.json

@@ -1,6 +1,6 @@
 {
   "name": "@bids/validator",
-  "version": "2.0.5",
+  "version": "2.0.7",
   "exports": {
     ".": "./src/bids-validator.ts",
     "./main": "./src/main.ts",

{bids_validator_deno-2.0.5 → bids_validator_deno-2.0.7}/pdm_build.py

@@ -27,6 +27,9 @@ def pdm_build_initialize(context):
             "compile",
             "-ERNW",
             "--allow-run",
+            # Types are checked elsewhere. Type checking at wheel build
+            # is painful if some platforms have newer typescript than others.
+            "--no-check",
             "-o",
             str(target),
             "src/bids-validator.ts",

{bids_validator_deno-2.0.5 → bids_validator_deno-2.0.7}/pyproject.toml

@@ -18,7 +18,7 @@ keywords = [
     "BIDS validator",
 ]
 dynamic = []
-version = "2.0.5"
+version = "2.0.7"
 
 [project.license]
 text = "MIT"
@@ -55,8 +55,8 @@ scripts = [
 build = "cp39-*"
 skip = "*musllinux* *_i686 *-win32"
 build-frontend = "build"
-manylinux-x86_64-image = "quay.io/pypa/manylinux_2_24_x86_64:latest"
-manylinux-aarch64-image = "quay.io/pypa/manylinux_2_24_aarch64:latest"
+manylinux-x86_64-image = "quay.io/pypa/manylinux_2_28_x86_64:latest"
+manylinux-aarch64-image = "quay.io/pypa/manylinux_2_28_aarch64:latest"
 before-build = "curl -fsSL https://deno.land/install.sh | DENO_INSTALL=/usr/local sh && deno --version"
 test-command = "bids-validator-deno --version"
 overrides = [

{bids_validator_deno-2.0.5 → bids_validator_deno-2.0.7}/src/bids-validator.ts

@@ -4,5 +4,5 @@ const result = await main()
 
 const errors = result.issues.get({ severity: 'error' })
 if (errors.length) {
-  Deno.exit(1)
+  Deno.exit(16)
 }

{bids_validator_deno-2.0.5 → bids_validator_deno-2.0.7}/src/schema/applyRules.ts

@@ -181,7 +181,9 @@ function evalJsonCheck(
   const sidecarRule = schemaPath.match(/rules\.sidecar/)
   // Sidecar rules apply specifically to data files, as JSON files cannot have sidecars
   // Count on other JSON rules to use selectors to match the correct files
-  if (context.extension === '.json' && sidecarRule) return
+  // Text files at the root do not have sidecars. We might want a cleaner
+  // or more schematic way to identify them in the future.
+  if (sidecarRule && (['.json', '', '.md', '.txt', '.rst', '.cff'].includes(context.extension))) return
 
   const json: Record<string, any> = sidecarRule ? context.sidecar : context.json
   for (const [key, requirement] of Object.entries(rule.fields)) {

bids_validator_deno-2.0.7/src/schema/associations.ts

@@ -0,0 +1,165 @@
+import type {
+  Aslcontext,
+  Associations,
+  Bval,
+  Bvec,
+  Channels,
+  Coordsystem,
+  Events,
+  M0Scan,
+  Magnitude,
+  Magnitude1,
+} from '@bids/schema/context'
+import type { Schema as MetaSchema } from '@bids/schema/metaschema'
+
+import type { BIDSFile, FileTree } from '../types/filetree.ts'
+import type { BIDSContext } from './context.ts'
+import type { DatasetIssues } from '../issues/datasetIssues.ts'
+import type { readEntities } from './entities.ts'
+import { loadTSV } from '../files/tsv.ts'
+import { parseBvalBvec } from '../files/dwi.ts'
+import { walkBack } from '../files/inheritance.ts'
+import { evalCheck } from './applyRules.ts'
+import { expressionFunctions } from './expressionLanguage.ts'
+
+// type AssociationsLookup = Record<keyof ContextAssociations, { extensions: string[], inherit: boolean, load: ... }
+
+/**
+ * This object describes associated files for data files in a bids dataset
+ * For any given datafile we iterate over every key/value in this object.
+ * For each entry we see if any files in the datafiles directory have:
+ *   - a suffix that matches the key
+ *   - an extension in the entry's extension array.
+ *   - that all the files entities and their values match those of the datafile
+ * If the entry allows for inheritance we recurse up the filetree looking for other applicable files.
+ * The load functions are incomplete, some associations need to read data from a file so they're
+ * returning promises for now.
+ */
+const associationLookup = {
+  events: async (file: BIDSFile, options: { maxRows: number }): Promise<Events> => {
+    const columns = await loadTSV(file, options.maxRows)
+      .catch((e) => {
+        return new Map()
+      })
+    return {
+      path: file.path,
+      onset: columns.get('onset') || [],
+    }
+  },
+  aslcontext: async (
+    file: BIDSFile,
+    options: { maxRows: number },
+  ): Promise<Aslcontext> => {
+    const columns = await loadTSV(file, options.maxRows)
+      .catch((e) => {
+        return new Map()
+      })
+    return {
+      path: file.path,
+      n_rows: columns.get('volume_type')?.length || 0,
+      volume_type: columns.get('volume_type') || [],
+    }
+  },
+  m0scan: (file: BIDSFile, options: any): Promise<M0Scan> => {
+    return Promise.resolve({ path: file.path })
+  },
+  magnitude: (file: BIDSFile, options: any): Promise<Magnitude> => {
+    return Promise.resolve({ path: file.path })
+  },
+  magnitude1: (file: BIDSFile, options: any): Promise<Magnitude1> => {
+    return Promise.resolve({ path: file.path })
+  },
+  bval: async (file: BIDSFile, options: any): Promise<Bval> => {
+    const contents = await file.text()
+    const rows = parseBvalBvec(contents)
+    return {
+      path: file.path,
+      n_cols: rows ? rows[0].length : 0,
+      n_rows: rows ? rows.length : 0,
+      // @ts-expect-error values is expected to be a number[], coerce lazily
+      values: rows[0],
+    }
+  },
+  bvec: async (file: BIDSFile, options: any): Promise<Bvec> => {
+    const contents = await file.text()
+    const rows = parseBvalBvec(contents)
+
+    if (rows.some((row) => row.length !== rows[0].length)) {
+      throw { key: 'BVEC_ROW_LENGTH' }
+    }
+
+    return {
+      path: file.path,
+      n_cols: rows ? rows[0].length : 0,
+      n_rows: rows ? rows.length : 0,
+    }
+  },
+  channels: async (file: BIDSFile, options: { maxRows: number }): Promise<Channels> => {
+    const columns = await loadTSV(file, options.maxRows)
+      .catch((e) => {
+        return new Map()
+      })
+    return {
+      path: file.path,
+      type: columns.get('type'),
+      short_channel: columns.get('short_channel'),
+      sampling_frequency: columns.get('sampling_frequency'),
+    }
+  },
+  coordsystem: (file: BIDSFile, options: any): Promise<Coordsystem> => {
+    return Promise.resolve({ path: file.path })
+  },
+}
+
+export async function buildAssociations(
+  context: BIDSContext,
+): Promise<Associations> {
+  const associations: Associations = {}
+
+  const schema: MetaSchema = context.dataset.schema as MetaSchema
+
+  Object.assign(context, expressionFunctions)
+  // @ts-expect-error
+  context.exists.bind(context)
+
+  for (const [key, rule] of Object.entries(schema.meta.associations)) {
+    if (!rule.selectors!.every((x) => evalCheck(x, context))) {
+      continue
+    }
+    let file
+    let extension: string[] = []
+    if (typeof rule.target.extension === 'string') {
+      extension = [rule.target.extension]
+    } else if (Array.isArray(rule.target.extension)) {
+      extension = rule.target.extension
+    }
+    try {
+      file = walkBack(context.file, rule.inherit, extension, rule.target.suffix).next().value
+    } catch (error) {
+      if (
+        error && typeof error === 'object' && 'code' in error &&
+        error.code === 'MULTIPLE_INHERITABLE_FILES'
+      ) {
+        // @ts-expect-error
+        context.dataset.issues.add(error)
+        break
+      } else {
+        throw error
+      }
+    }
+
+    if (file) {
+      // @ts-expect-error
+      const load = associationLookup[key]
+      // @ts-expect-error
+      associations[key] = await load(file, { maxRows: context.dataset.options?.maxRows }).catch(
+        (error: any) => {
+          if (key in error) {
+            context.dataset.issues.add({ code: error.key, location: file.path })
+          }
+        },
+      )
+    }
+  }
+  return Promise.resolve(associations)
+}

{bids_validator_deno-2.0.5 → bids_validator_deno-2.0.7}/src/schema/context.ts

@@ -261,9 +261,7 @@ export class BIDSContext implements Context {
 
   async loadAssociations(): Promise<void> {
     this.associations = await buildAssociations(
-      this.file,
-      this.dataset.issues,
-      this.dataset.options?.maxRows,
+      this,
     )
     return
   }

{bids_validator_deno-2.0.5 → bids_validator_deno-2.0.7}/src/schema/tables.ts

@@ -239,6 +239,11 @@ export function evalAdditionalColumns(
   if (context.extension !== '.tsv') return
   const headers = Object.keys(context?.columns)
   if (rule.columns) {
+    if (!rule.additional_columns || rule.additional_columns === 'n/a' ) {
+      // Old schemas might be missing the field, so be permissive.
+      // New schemas indicate it is not applicable with 'n/a'.
+      return
+    }
     const ruleHeadersNames = Object.keys(rule.columns).map(
       // @ts-expect-error
       (x) => schema.objects.columns[x].name,
@@ -250,11 +255,11 @@ export function evalAdditionalColumns(
     if (rule.additional_columns?.startsWith('allowed')) {
       extraCols = extraCols.filter((header) => !(header in context.sidecar))
     }
-    const code = rule.additional_columns === 'allowed'
-      ? 'TSV_ADDITIONAL_COLUMNS_UNDEFINED'
+    const code = rule.additional_columns === 'not_allowed'
+      ? 'TSV_ADDITIONAL_COLUMNS_NOT_ALLOWED'
       : rule.additional_columns === 'allowed_if_defined'
       ? 'TSV_ADDITIONAL_COLUMNS_MUST_DEFINE'
-      : 'TSV_ADDITIONAL_COLUMNS_NOT_ALLOWED'
+      : 'TSV_ADDITIONAL_COLUMNS_UNDEFINED'
     const issue = {
       code,
       location: context.path,

{bids_validator_deno-2.0.5 → bids_validator_deno-2.0.7}/src/summary/collectSubjectMetadata.ts

@@ -53,8 +53,14 @@ export const collectSubjectMetadata = (
           '',
         )
         // make age an integer
-        // @ts-expect-error
-        if (ageKey) data[ageKey.index] = parseInt(data[ageKey.index])
+        if (ageKey) {
+          if(data[ageKey.index] === "89+") {
+            data[ageKey.index] = "89+"
+          } else {
+            // @ts-expect-error
+            data[ageKey.index] = parseFloat(data[ageKey.index])
+          }
+        }
         return data
       })
       .map((data) =>

{bids_validator_deno-2.0.5 → bids_validator_deno-2.0.7}/src/types/validation-result.ts

@@ -2,8 +2,8 @@ import type { DatasetIssues } from '../issues/datasetIssues.ts'
 
 export interface SubjectMetadata {
   participantId: string
-  age: number
-  sex: string
+  age?: number | null | "89+"
+  sex?: string
 }
 /*
     BodyPart: {},

bids_validator_deno-2.0.5/src/schema/associations.ts

@@ -1,190 +0,0 @@
-import type {
-  Aslcontext,
-  Associations,
-  Bval,
-  Bvec,
-  Channels,
-  Coordsystem,
-  Events,
-  M0Scan,
-  Magnitude,
-  Magnitude1,
-} from '@bids/schema/context'
-import type { BIDSFile, FileTree } from '../types/filetree.ts'
-import type { BIDSContext } from './context.ts'
-import type { DatasetIssues } from '../issues/datasetIssues.ts'
-import type { readEntities } from './entities.ts'
-import { loadTSV } from '../files/tsv.ts'
-import { parseBvalBvec } from '../files/dwi.ts'
-import { walkBack } from '../files/inheritance.ts'
-
-// type AssociationsLookup = Record<keyof ContextAssociations, { extensions: string[], inherit: boolean, load: ... }
-
-/**
- * This object describes associated files for data files in a bids dataset
- * For any given datafile we iterate over every key/value in this object.
- * For each entry we see if any files in the datafiles directory have:
- *   - a suffix that matches the key
- *   - an extension in the entry's extension array.
- *   - that all the files entities and their values match those of the datafile
- * If the entry allows for inheritance we recurse up the filetree looking for other applicable files.
- * The load functions are incomplete, some associations need to read data from a file so they're
- * returning promises for now.
- */
-const associationLookup = {
-  events: {
-    suffix: 'events',
-    extensions: ['.tsv'],
-    inherit: true,
-    load: async (file: BIDSFile, options: { maxRows: number }): Promise<Events> => {
-      const columns = await loadTSV(file, options.maxRows)
-        .catch((e) => {
-          return new Map()
-        })
-      return {
-        path: file.path,
-        onset: columns.get('onset') || [],
-      }
-    },
-  },
-  aslcontext: {
-    suffix: 'aslcontext',
-    extensions: ['.tsv'],
-    inherit: true,
-    load: async (
-      file: BIDSFile,
-      options: { maxRows: number },
-    ): Promise<Aslcontext> => {
-      const columns = await loadTSV(file, options.maxRows)
-        .catch((e) => {
-          return new Map()
-        })
-      return {
-        path: file.path,
-        n_rows: columns.get('volume_type')?.length || 0,
-        volume_type: columns.get('volume_type') || [],
-      }
-    },
-  },
-  m0scan: {
-    suffix: 'm0scan',
-    extensions: ['.nii', '.nii.gz'],
-    inherit: false,
-    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, options: any): Promise<Magnitude> => {
-      return Promise.resolve({ path: file.path })
-    },
-  },
-  magnitude1: {
-    suffix: 'magnitude1',
-    extensions: ['.nii', '.nii.gz'],
-    inherit: false,
-    load: (file: BIDSFile, options: any): Promise<Magnitude1> => {
-      return Promise.resolve({ path: file.path })
-    },
-  },
-  bval: {
-    suffix: 'dwi',
-    extensions: ['.bval'],
-    inherit: true,
-    load: async (file: BIDSFile, options: any): Promise<Bval> => {
-      const contents = await file.text()
-      const rows = parseBvalBvec(contents)
-      return {
-        path: file.path,
-        n_cols: rows ? rows[0].length : 0,
-        n_rows: rows ? rows.length : 0,
-        // @ts-expect-error values is expected to be a number[], coerce lazily
-        values: rows[0],
-      }
-    },
-  },
-  bvec: {
-    suffix: 'dwi',
-    extensions: ['.bvec'],
-    inherit: true,
-    load: async (file: BIDSFile, options: any): Promise<Bvec> => {
-      const contents = await file.text()
-      const rows = parseBvalBvec(contents)
-
-      if (rows.some((row) => row.length !== rows[0].length)) {
-        throw { key: 'BVEC_ROW_LENGTH' }
-      }
-
-      return {
-        path: file.path,
-        n_cols: rows ? rows[0].length : 0,
-        n_rows: rows ? rows.length : 0,
-      }
-    },
-  },
-  channels: {
-    suffix: 'channels',
-    extensions: ['.tsv'],
-    inherit: true,
-    load: async (file: BIDSFile, options: { maxRows: number }): Promise<Channels> => {
-      const columns = await loadTSV(file, options.maxRows)
-        .catch((e) => {
-          return new Map()
-        })
-      return {
-        path: file.path,
-        type: columns.get('type'),
-        short_channel: columns.get('short_channel'),
-        sampling_frequency: columns.get('sampling_frequency'),
-      }
-    },
-  },
-  coordsystem: {
-    suffix: 'coordsystem',
-    extensions: ['.json'],
-    inherit: true,
-    load: (file: BIDSFile, options: any): Promise<Coordsystem> => {
-      return Promise.resolve({ path: file.path })
-    },
-  },
-}
-
-export async function buildAssociations(
-  source: BIDSFile,
-  issues: DatasetIssues,
-  maxRows: number = -1,
-): Promise<Associations> {
-  const associations: Associations = {}
-
-  for (const [key, value] of Object.entries(associationLookup)) {
-    const { suffix, extensions, inherit, load } = value
-    let file
-    try {
-      file = walkBack(source, inherit, extensions, suffix).next().value
-    } catch (error) {
-      if (
-        error && typeof error === 'object' && 'code' in error &&
-        error.code === 'MULTIPLE_INHERITABLE_FILES'
-      ) {
-        // @ts-expect-error
-        issues.add(error)
-        break
-      } else {
-        throw error
-      }
-    }
-
-    if (file) {
-      // @ts-expect-error Matching load return value to key is hard
-      associations[key] = await load(file, { maxRows }).catch((error) => {
-        if (error.key) {
-          issues.add({ code: error.key, location: file.path })
-        }
-      })
-    }
-  }
-  return Promise.resolve(associations)
-}