From 043e1a18a904798a8a92ccc82173f6239dfd0332 Mon Sep 17 00:00:00 2001
From: Ross Blair <rosswilsonblair@gmail.com>
Date: Wed, 29 Jun 2022 12:50:02 -0500
Subject: [PATCH 01/13] broken initial stab at summary object.

---
 bids-validator/src/main.ts                    |  1 +
 bids-validator/src/summary.ts                 | 72 +++++++++++++++++++
 bids-validator/src/types/validation-result.ts | 29 +++++++-
 bids-validator/src/validators/bids.ts         |  4 +-
 4 files changed, 103 insertions(+), 3 deletions(-)
 create mode 100644 bids-validator/src/summary.ts

diff --git a/bids-validator/src/main.ts b/bids-validator/src/main.ts
index 6e7748884..981ac0462 100644
--- a/bids-validator/src/main.ts
+++ b/bids-validator/src/main.ts
@@ -3,6 +3,7 @@ import { readFileTree } from './files/deno.ts'
 import { resolve } from './deps/path.ts'
 import { fullTestAdapter } from './compat/fulltest.ts'
 import { validate } from './validators/bids.ts'
+import { summary } from './summary.ts'
 
 function inspect(obj: any) {
   console.log(
diff --git a/bids-validator/src/summary.ts b/bids-validator/src/summary.ts
new file mode 100644
index 000000000..388d23149
--- /dev/null
+++ b/bids-validator/src/summary.ts
@@ -0,0 +1,72 @@
+// import { Summary } from '../types/summary.ts'
+
+export const summary = {
+  dataProcessed: false,
+  totalFiles: -1,
+  size: 0,
+  sessions: new Set(),
+  subjects: new Set(),
+  subjectMetadata: {},
+  tasks: new Set(),
+  modalities: {
+    mri: 0,
+    pet: 0,
+    meg: 0,
+    eeg: 0,
+    ieeg: 0,
+    microscopy: 0,
+  },
+  secondaryModalities: {
+    MRI_Diffusion: 0,
+    MRI_Structural: 0,
+    MRI_Functional: 0,
+    MRI_Perfusion: 0,
+    PET_Static: 0,
+    PET_Dynamic: 0,
+    iEEG_ECoG: 0,
+    iEEG_SEEG: 0,
+  },
+  pet: null,
+}
+
+const modalityLookup = {}
+
+const secondaryLookup = {
+  dwi: 'MRI_Diffusion',
+  anat: 'MRI_Structural',
+  bold: 'MRI_Functional',
+  perf: 'MRI_Perfusion',
+}
+
+export function updateSummary(context: Context): void {
+  if (context.file.path.startsWith('/derivatives')) {
+    return
+  }
+
+  summary.totalFiles++
+  summary.size += context.file.size
+
+  if ('sub' in context.entities) {
+    summary.subjects.add(context.entities.sub)
+  }
+  if ('ses' in context.entities) {
+    summary.sesssions.add(context.entities.ses)
+  }
+  if ('task' in context.entities) {
+    summary.tasks.add(context.entities.task)
+  }
+  if (context.modality) {
+    summary.modalities[context.modality]++
+  }
+
+  if (context.datatype in secondaryLookup) {
+    const key = secondaryLookup[context.datatype]
+    secondary[key]++
+  } else if (context.datatype === 'pet' && 'rec' in context.entities) {
+    if (['acstat', 'nacstat'].includes(context.entities.rec)) {
+      secondaty.PET_Static++
+    } else if (['acdyn', 'nacdyn'].includes(context.entities.rec)) {
+      secondaty.PET_Dynamic++
+    }
+  }
+}
diff --git a/bids-validator/src/types/validation-result.ts b/bids-validator/src/types/validation-result.ts
index 82f0f44d7..4c5d8a2a0 100644
--- a/bids-validator/src/types/validation-result.ts
+++ b/bids-validator/src/types/validation-result.ts
@@ -1,9 +1,36 @@
 import { DatasetIssues } from '../issues/datasetIssues.ts'
 
+interface SubjectMetadata {
+  PARTICIPANT_ID: string
+  age: string
+  sex: string
+  group: string
+}
+/*
+    BodyPart: {},
+    ScannerManufacturer: {},
+    ScannerManufacturersModelName: {},
+    TracerName: {},
+    TracerRadionuclide: {},
+*/
+
+export interface Summary {
+  sessions: string[]
+  subjects: string[]
+  subjectMetadata: SubjectMetaData[]
+  tasks: string[]
+  modalities: string[]
+  secondaryModalities: string[]
+  totalFiles: number
+  size: number
+  dataProcessed: boolean
+  pet: Record<string, any>
+}
+
 /**
  * The output of a validation run
  */
 export interface ValidationResult {
   issues: DatasetIssues
-  summary: Record<string, any>
+  summary: Summary
 }
diff --git a/bids-validator/src/validators/bids.ts b/bids-validator/src/validators/bids.ts
index ad1510cf2..194680d88 100644
--- a/bids-validator/src/validators/bids.ts
+++ b/bids-validator/src/validators/bids.ts
@@ -11,6 +11,7 @@ import {
 } from './filenames.ts'
 import { DatasetIssues } from '../issues/datasetIssues.ts'
 import { ValidationResult } from '../types/validation-result.ts'
+import { updateSummary } from '../summary.ts'
 
 /**
  * Full BIDS schema validation entrypoint
@@ -18,7 +19,6 @@ import { ValidationResult } from '../types/validation-result.ts'
 export async function validate(fileTree: FileTree): Promise<ValidationResult> {
   const issues = new DatasetIssues()
   // TODO - summary should be implemented in pure schema mode
-  const summary = {}
   const schema = await loadSchema()
   for await (const context of walkFileTree(fileTree, issues)) {
     // TODO - Skip ignored files for now (some tests may reference ignored files)
@@ -33,9 +33,9 @@ export async function validate(fileTree: FileTree): Promise<ValidationResult> {
       checkLabelFormat(schema, context)
     }
     applyRules(schema, context)
+    updateSummary(context)
   }
   return {
     issues,
-    summary,
   }
 }

From 3c60642464d1676159118cf4afab10c513f00462 Mon Sep 17 00:00:00 2001
From: Ross Blair <rosswilsonblair@gmail.com>
Date: Wed, 29 Jun 2022 15:23:07 -0500
Subject: [PATCH 02/13] move over collectSubjectMetadata, get typescript to
 play well with new summary code.

---
 bids-validator/src/main.ts                    |   1 -
 bids-validator/src/schema/context.ts          |   4 +-
 bids-validator/src/summary.ts                 |  72 ----------
 .../src/summary/collectSubjectMetadata.ts     |  71 ++++++++++
 bids-validator/src/summary/summary.ts         | 132 ++++++++++++++++++
 bids-validator/src/tests/local/common.ts      |   6 +-
 .../src/tests/local/valid_headers.test.ts     |   2 +-
 bids-validator/src/types/validation-result.ts |  12 +-
 bids-validator/src/validators/bids.ts         |   3 +-
 9 files changed, 219 insertions(+), 84 deletions(-)
 delete mode 100644 bids-validator/src/summary.ts
 create mode 100644 bids-validator/src/summary/collectSubjectMetadata.ts
 create mode 100644 bids-validator/src/summary/summary.ts

diff --git a/bids-validator/src/main.ts b/bids-validator/src/main.ts
index 981ac0462..6e7748884 100644
--- a/bids-validator/src/main.ts
+++ b/bids-validator/src/main.ts
@@ -3,7 +3,6 @@ import { readFileTree } from './files/deno.ts'
 import { resolve } from './deps/path.ts'
 import { fullTestAdapter } from './compat/fulltest.ts'
 import { validate } from './validators/bids.ts'
-import { summary } from './summary.ts'
 
 function inspect(obj: any) {
   console.log(
diff --git a/bids-validator/src/schema/context.ts b/bids-validator/src/schema/context.ts
index 7102af6a4..77ec8de22 100644
--- a/bids-validator/src/schema/context.ts
+++ b/bids-validator/src/schema/context.ts
@@ -17,7 +17,7 @@ export class BIDSContext implements Context {
   file: BIDSFile
   suffix: string
   extension: string
-  entities: object
+  entities: Record<string, string>
   dataset: ContextDataset
   subject: ContextSubject
   datatype: string
@@ -25,7 +25,7 @@ export class BIDSContext implements Context {
   sidecar: object
   associations: ContextAssociations
   columns: object
-  json: object
+  json: Record<string, any>
   nifti_header: ContextNiftiHeader
 
   constructor(fileTree: FileTree, file: BIDSFile, issues: DatasetIssues) {
diff --git a/bids-validator/src/summary.ts b/bids-validator/src/summary.ts
deleted file mode 100644
index 388d23149..000000000
--- a/bids-validator/src/summary.ts
+++ /dev/null
@@ -1,72 +0,0 @@
-// import { Summary } from '../types/summary.ts'
-
-export const summary = {
-  dataProcessed: false,
-  totalFiles: -1,
-  size: 0,
-  sessions: new Set(),
-  subjects: new Set(),
-  subjectMetadata: {},
-  tasks: new Set(),
-  modalities: {
-    mri: 0,
-    pet: 0,
-    meg: 0,
-    eeg: 0,
-    ieeg: 0,
-    microscopy: 0,
-  },
-  secondaryModalities: {
-    MRI_Diffusion: 0,
-    MRI_Structural: 0,
-    MRI_Functional: 0,
-    MRI_Perfusion: 0,
-    PET_Static: 0,
-    PET_Dynamic: 0,
-    iEEG_ECoG: 0,
-    iEEG_SEEG: 0,
-  },
-  pet: null,
-}
-
-const modalityLookup = {}
-
-const secondaryLookup = {
-  dwi: 'MRI_Diffusion',
-  anat: 'MRI_Structural',
-  bold: 'MRI_Functional',
-  perf: 'MRI_Perfusion',
-}
-
-export function updateSummary(context: Context): void {
-  if (context.file.path.startsWith('/derivatives')) {
-    return
-  }
-
-  summary.totalFiles++
-  summary.size += context.file.size
-
-  if ('sub' in context.entities) {
-    summary.subjects.add(context.entities.sub)
-  }
-  if ('ses' in context.entities) {
-    summary.sesssions.add(context.entities.ses)
-  }
-  if ('task' in context.entities) {
-    summary.tasks.add(context.entities.task)
-  }
-  if (context.modality) {
-    summary.modalities[context.modality]++
-  }
-
-  if (context.datatype in secondaryLookup) {
-    const key = secondaryLookup[context.datatype]
-    secondary[key]++
-  } else if (context.datatype === 'pet' && 'rec' in context.entities) {
-    if (['acstat', 'nacstat'].includes(context.entities.rec)) {
-      secondaty.PET_Static++
-    } else if (['acdyn', 'nacdyn'].includes(context.entities.rec)) {
-      secondaty.PET_Dynamic++
-    }
-  }
-}
diff --git a/bids-validator/src/summary/collectSubjectMetadata.ts b/bids-validator/src/summary/collectSubjectMetadata.ts
new file mode 100644
index 000000000..41e728200
--- /dev/null
+++ b/bids-validator/src/summary/collectSubjectMetadata.ts
@@ -0,0 +1,71 @@
+import { SubjectMetadata } from '../types/validation-result.ts'
+const PARTICIPANT_ID = 'participantId'
+/**
+ * Go from tsv format string with participant_id as a required header to array of form
+ * [
+ *   {
+ *     participantId: 'participant_id_1'
+ *     foo: 'x',
+ *     ...
+ *   },
+ *   {
+ *     participantId: 'participant_id_2'
+ *     foo: 'y',
+ *     ...
+ *   }
+ *   ...
+ * ]
+ *
+ * returns null if participant_id is not a header or file contents do not exist
+ * @param {string} participantsTsvContent
+ */
+export const collectSubjectMetadata = (
+  participantsTsvContent: Uint8Array,
+): SubjectMetadata[] => {
+  if (!participantsTsvContent) {
+    return []
+  }
+
+  const contentTable = new TextDecoder()
+    .decode(participantsTsvContent)
+    .split(/\r?\n/)
+    .filter((row) => row !== '')
+    .map((row) => row.split('\t'))
+  const [snakeCaseHeaders, ...subjectData] = contentTable
+  const headers = snakeCaseHeaders.map((header) =>
+    header === 'participant_id' ? PARTICIPANT_ID : header,
+  )
+  const targetKeys = [PARTICIPANT_ID, 'age', 'sex', 'group']
+    .map((key) => ({
+      key,
+      index: headers.findIndex((targetKey) => targetKey === key),
+    }))
+    .filter(({ index }) => index !== -1)
+  const participantIdKey = targetKeys.find(({ key }) => key === PARTICIPANT_ID)
+  const ageKey = targetKeys.find(({ key }) => key === 'age')
+  if (participantIdKey === undefined) return [] as SubjectMetadata[]
+  else
+    return subjectData
+      .map((data) => {
+        // this first map is for transforming any data coming out of participants.tsv:
+        // strip subject ids to match metadata.subjects: 'sub-01' -> '01'
+        data[participantIdKey.index] = data[participantIdKey.index].replace(
+          /^sub-/,
+          '',
+        )
+        // make age an integer
+        // @ts-expect-error
+        if (ageKey) data[ageKey.index] = parseInt(data[ageKey.index])
+        return data
+      })
+      .map((data) =>
+        //extract all target metadata for each subject
+        targetKeys.reduce(
+          (subject, { key, index }) => ({
+            ...subject,
+            [key]: data[index],
+          }),
+          {},
+        ),
+      ) as SubjectMetadata[]
+}
diff --git a/bids-validator/src/summary/summary.ts b/bids-validator/src/summary/summary.ts
new file mode 100644
index 000000000..d12a82fba
--- /dev/null
+++ b/bids-validator/src/summary/summary.ts
@@ -0,0 +1,132 @@
+import { collectSubjectMetadata } from './collectSubjectMetadata.ts'
+import { readAll, readerFromStreamReader } from '../deps/stream.ts'
+import { Summary } from '../types/validation-result.ts'
+import { BIDSContext } from '../schema/context.ts'
+
+const modalitiesCount: Record<string, number> = {
+  mri: 0,
+  pet: 0,
+  meg: 0,
+  eeg: 0,
+  ieeg: 0,
+  microscopy: 0,
+}
+
+const secondaryModalitiesCount: Record<string, number> = {
+  MRI_Diffusion: 0,
+  MRI_Structural: 0,
+  MRI_Functional: 0,
+  MRI_Perfusion: 0,
+  PET_Static: 0,
+  PET_Dynamic: 0,
+  iEEG_ECoG: 0,
+  iEEG_SEEG: 0,
+}
+
+const modalityPrettyLookup: Record<string, string> = {
+  mri: 'MRI',
+  pet: 'PET',
+  meg: 'MEG',
+  eeg: 'EEG',
+  ieeg: 'iEEG',
+  micro: 'Microscopy',
+}
+
+const secondaryLookup: Record<string, string> = {
+  dwi: 'MRI_Diffusion',
+  anat: 'MRI_Structural',
+  bold: 'MRI_Functional',
+  perf: 'MRI_Perfusion',
+}
+
+function computeModalities(modalities: Record<string, number>): string[] {
+  // Order by matching file count
+  const nonZero = Object.keys(modalities).filter((a) => modalities[a] !== 0)
+  if (nonZero.length === 0) {
+    return []
+  }
+  const sortedModalities = nonZero.sort((a, b) => {
+    if (modalities[b] === modalities[a]) {
+      // On a tie, hand it to the non-MRI modality
+      if (b === 'MRI') {
+        return -1
+      } else {
+        return 0
+      }
+    }
+    return modalities[b] - modalities[a]
+  })
+  return sortedModalities.map((mod) =>
+    mod in modalityPrettyLookup ? modalityPrettyLookup[mod] : mod,
+  )
+}
+
+function computeSecondaryModalities(
+  secondary: Record<string, number>,
+): string[] {
+  const nonZeroSecondary = Object.keys(secondary).filter(
+    (a) => secondary[a] !== 0,
+  )
+  const sortedSecondary = nonZeroSecondary.sort(
+    (a, b) => secondary[b] - secondary[a],
+  )
+  return sortedSecondary
+}
+
+export const summary: Summary = {
+  dataProcessed: false,
+  totalFiles: -1,
+  size: 0,
+  sessions: new Set(),
+  subjects: new Set(),
+  subjectMetadata: [],
+  tasks: new Set(),
+  pet: {},
+  get modalities() {
+    return computeModalities(modalitiesCount)
+  },
+  get secondaryModalities() {
+    return computeSecondaryModalities(secondaryModalitiesCount)
+  },
+}
+
+export async function updateSummary(context: BIDSContext): Promise<void> {
+  if (context.file.path.startsWith('/derivatives')) {
+    return
+  }
+
+  summary.totalFiles++
+  summary.size += await context.file.size
+
+  if ('sub' in context.entities) {
+    summary.subjects.add(context.entities.sub)
+  }
+  if ('ses' in context.entities) {
+    summary.sessions.add(context.entities.ses)
+  }
+  if ('TaskName' in context.json) {
+    summary.tasks.add(context.json.TaskName)
+  }
+  if (context.modality) {
+    modalitiesCount[context.modality]++
+  }
+
+  if (context.datatype in secondaryLookup) {
+    const key = secondaryLookup[context.datatype]
+    secondaryModalitiesCount[key]++
+  } else if (context.datatype === 'pet' && 'rec' in context.entities) {
+    if (['acstat', 'nacstat'].includes(context.entities.rec)) {
+      secondaryModalitiesCount.PET_Static++
+    } else if (['acdyn', 'nacdyn'].includes(context.entities.rec)) {
+      secondaryModalitiesCount.PET_Dynamic++
+    }
+  }
+
+  if (context.file.path.includes('participants.tsv')) {
+    const stream = await context.file.stream
+    const streamReader = stream.getReader()
+    const denoReader = readerFromStreamReader(streamReader)
+    const fileBuffer = await readAll(denoReader)
+    summary.subjectMetadata = collectSubjectMetadata(fileBuffer)
+  }
+}
diff --git a/bids-validator/src/tests/local/common.ts b/bids-validator/src/tests/local/common.ts
index 464508260..9f17f51aa 100644
--- a/bids-validator/src/tests/local/common.ts
+++ b/bids-validator/src/tests/local/common.ts
@@ -3,13 +3,17 @@ import { FileTree } from '../../types/filetree.ts'
 import { validate } from '../../validators/bids.ts'
 import { ValidationResult } from '../../types/validation-result.ts'
 import { DatasetIssues } from '../../issues/datasetIssues.ts'
+import { summary } from '../../summary/summary.ts'
 
 export async function validatePath(
   t: Deno.TestContext,
   path: string,
 ): Promise<{ tree: FileTree; result: ValidationResult }> {
   let tree: FileTree = new FileTree('', '')
-  let result: ValidationResult = { issues: new DatasetIssues(), summary: {} }
+  let result: ValidationResult = {
+    issues: new DatasetIssues(),
+    summary: summary,
+  }
 
   await t.step('file tree is read', async () => {
     tree = await readFileTree(path)
diff --git a/bids-validator/src/tests/local/valid_headers.test.ts b/bids-validator/src/tests/local/valid_headers.test.ts
index d038ba6a8..bb86d5a22 100644
--- a/bids-validator/src/tests/local/valid_headers.test.ts
+++ b/bids-validator/src/tests/local/valid_headers.test.ts
@@ -19,7 +19,7 @@ Deno.test('valid_headers dataset', async (t) => {
   })
 
   await t.step('summary has correct dataProcessed', () => {
-    assertEquals(result.summary.dataProcessed, ['rhyme judgment'])
+    assertEquals(result.summary.dataProcessed, false)
   })
 
   await t.step('summary has correct dataProcessed', () => {
diff --git a/bids-validator/src/types/validation-result.ts b/bids-validator/src/types/validation-result.ts
index 4c5d8a2a0..8ce6e70f1 100644
--- a/bids-validator/src/types/validation-result.ts
+++ b/bids-validator/src/types/validation-result.ts
@@ -1,8 +1,8 @@
 import { DatasetIssues } from '../issues/datasetIssues.ts'
 
-interface SubjectMetadata {
+export interface SubjectMetadata {
   PARTICIPANT_ID: string
-  age: string
+  age: number
   sex: string
   group: string
 }
@@ -15,10 +15,10 @@ interface SubjectMetadata {
 */
 
 export interface Summary {
-  sessions: string[]
-  subjects: string[]
-  subjectMetadata: SubjectMetaData[]
-  tasks: string[]
+  sessions: Set<string>
+  subjects: Set<string>
+  subjectMetadata: SubjectMetadata[]
+  tasks: Set<string>
   modalities: string[]
   secondaryModalities: string[]
   totalFiles: number
diff --git a/bids-validator/src/validators/bids.ts b/bids-validator/src/validators/bids.ts
index 194680d88..69e1f5821 100644
--- a/bids-validator/src/validators/bids.ts
+++ b/bids-validator/src/validators/bids.ts
@@ -11,7 +11,7 @@ import {
 } from './filenames.ts'
 import { DatasetIssues } from '../issues/datasetIssues.ts'
 import { ValidationResult } from '../types/validation-result.ts'
-import { updateSummary } from '../summary.ts'
+import { summary, updateSummary } from '../summary/summary.ts'
 
 /**
  * Full BIDS schema validation entrypoint
@@ -37,5 +37,6 @@ export async function validate(fileTree: FileTree): Promise<ValidationResult> {
   }
   return {
     issues,
+    summary,
   }
 }

From dd88ba1c176798ec470653abb79a69dcd1c96055 Mon Sep 17 00:00:00 2001
From: Ross Blair <rosswilsonblair@gmail.com>
Date: Wed, 29 Jun 2022 16:20:25 -0500
Subject: [PATCH 03/13] await update to summary.

---
 bids-validator/src/validators/bids.ts | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/bids-validator/src/validators/bids.ts b/bids-validator/src/validators/bids.ts
index 69e1f5821..80e1ded39 100644
--- a/bids-validator/src/validators/bids.ts
+++ b/bids-validator/src/validators/bids.ts
@@ -33,7 +33,7 @@ export async function validate(fileTree: FileTree): Promise<ValidationResult> {
       checkLabelFormat(schema, context)
     }
     applyRules(schema, context)
-    updateSummary(context)
+    await updateSummary(context)
   }
   return {
     issues,

From 71bde4688dedd73e284b01b4006cc876e9b4031d Mon Sep 17 00:00:00 2001
From: Nell Hardcastle <nell@dev-nell.com>
Date: Wed, 29 Jun 2022 13:00:14 -0700
Subject: [PATCH 04/13] fix: Fix minor issues with valid_headers tests

---
 bids-validator/src/tests/local/valid_headers.test.ts | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/bids-validator/src/tests/local/valid_headers.test.ts b/bids-validator/src/tests/local/valid_headers.test.ts
index bb86d5a22..cf05feadf 100644
--- a/bids-validator/src/tests/local/valid_headers.test.ts
+++ b/bids-validator/src/tests/local/valid_headers.test.ts
@@ -22,7 +22,7 @@ Deno.test('valid_headers dataset', async (t) => {
     assertEquals(result.summary.dataProcessed, false)
   })
 
-  await t.step('summary has correct dataProcessed', () => {
+  await t.step('summary has correct modalities', () => {
     assertEquals(result.summary.modalities, ['MRI'])
   })
 

From c4025dac316afea63ba80d4cb39a551bbd398b3d Mon Sep 17 00:00:00 2001
From: Nell Hardcastle <nell@dev-nell.com>
Date: Wed, 29 Jun 2022 14:38:04 -0700
Subject: [PATCH 05/13] feat: Add .text() method to BIDSFile for quickly
 accessing full text

---
 bids-validator/src/files/deno.test.ts         |  7 ++-
 bids-validator/src/files/deno.ts              | 46 ++++++++++++-------
 bids-validator/src/files/ignore.ts            |  6 +--
 .../src/issues/datasetIssues.test.ts          | 11 +++--
 bids-validator/src/schema/entities.test.ts    |  5 +-
 bids-validator/src/tests/simple-dataset.ts    | 27 +++++++----
 bids-validator/src/types/file.ts              |  6 ++-
 7 files changed, 68 insertions(+), 40 deletions(-)

diff --git a/bids-validator/src/files/deno.test.ts b/bids-validator/src/files/deno.test.ts
index 5fb949a3d..3e6d71295 100644
--- a/bids-validator/src/files/deno.test.ts
+++ b/bids-validator/src/files/deno.test.ts
@@ -26,10 +26,15 @@ Deno.test('Deno implementation of BIDSFile', async (t) => {
   })
   await t.step('can be read as ReadableStream', async () => {
     const file = new BIDSFileDeno(testDir, testFilename, ignore)
-    const stream = await file.stream
+    const stream = file.stream
     const streamReader = stream.getReader()
     const denoReader = readerFromStreamReader(streamReader)
     const fileBuffer = await readAll(denoReader)
     assertEquals(await file.size, fileBuffer.length)
   })
+  await t.step('can be read with .text() method', async () => {
+    const file = new BIDSFileDeno(testDir, testFilename, ignore)
+    const text = await file.text()
+    assertEquals(await file.size, text.length)
+  })
 })
diff --git a/bids-validator/src/files/deno.ts b/bids-validator/src/files/deno.ts
index 3375e3cf4..de13285f2 100644
--- a/bids-validator/src/files/deno.ts
+++ b/bids-validator/src/files/deno.ts
@@ -14,7 +14,7 @@ export class BIDSFileDeno implements BIDSFile {
   #ignore: FileIgnoreRulesDeno
   name: string
   path: string
-  private _fileInfo: Deno.FileInfo | undefined
+  #fileInfo: Deno.FileInfo | undefined
   private _datasetAbsPath: string
 
   constructor(datasetPath: string, path: string, ignore: FileIgnoreRulesDeno) {
@@ -28,30 +28,44 @@ export class BIDSFileDeno implements BIDSFile {
     return join(this._datasetAbsPath, this.path)
   }
 
-  private async _getSize(): Promise<number> {
-    if (!this._fileInfo) {
-      this._fileInfo = await Deno.stat(this._getPath())
-    }
-    return this._fileInfo.size
-  }
-
-  get size(): Promise<number> {
-    return this._getSize()
+  /**
+   * Deferred stat to get size
+   */
+  get size(): number {
+    return (
+      this.#fileInfo?.size ||
+      (this.#fileInfo = Deno.statSync(this._getPath())).size
+    )
   }
 
-  private async _getStream(): Promise<ReadableStream<Uint8Array>> {
+  get stream(): ReadableStream<Uint8Array> {
     // Avoid asking for write access
     const openOptions = { read: true, write: false }
-    return (await Deno.open(this._getPath(), openOptions)).readable
-  }
-
-  get stream(): Promise<ReadableStream<Uint8Array>> {
-    return this._getStream()
+    return Deno.openSync(this._getPath(), openOptions).readable
   }
 
   get ignored(): boolean {
     return this.#ignore.test(this.path)
   }
+
+  /**
+   * Read the entire file and decode as utf-8 text
+   */
+  async text(): Promise<string> {
+    const streamReader = this.stream
+      .pipeThrough(new TextDecoderStream('utf-8'))
+      .getReader()
+    let data = ''
+    try {
+      while (true) {
+        const { done, value } = await streamReader.read()
+        if (done) return data
+        data += value
+      }
+    } finally {
+      streamReader.releaseLock()
+    }
+  }
 }
 
 export class FileTreeDeno extends FileTree {
diff --git a/bids-validator/src/files/ignore.ts b/bids-validator/src/files/ignore.ts
index 96f49b33b..aa2ad2c20 100644
--- a/bids-validator/src/files/ignore.ts
+++ b/bids-validator/src/files/ignore.ts
@@ -3,11 +3,7 @@ import { ignore, Ignore } from '../deps/ignore.ts'
 import { FileIgnoreRules } from '../types/ignore.ts'
 
 export async function readBidsIgnore(file: BIDSFile) {
-  const fileStream = await file.stream
-  const reader = fileStream
-    .pipeThrough(new TextDecoderStream('utf-8'))
-    .getReader()
-  const { value } = await reader.read()
+  const value = await file.text()
   if (value) {
     const lines = value.split('\n')
     return lines
diff --git a/bids-validator/src/issues/datasetIssues.test.ts b/bids-validator/src/issues/datasetIssues.test.ts
index 94452952a..10f99c650 100644
--- a/bids-validator/src/issues/datasetIssues.test.ts
+++ b/bids-validator/src/issues/datasetIssues.test.ts
@@ -16,20 +16,23 @@ Deno.test('DatasetIssues management class', async (t) => {
     // This mostly tests the issueFile mapping function
     const issues = new DatasetIssues()
     const testStream = new ReadableStream()
+    const text = () => Promise.resolve('')
     const files = [
       {
+        text,
         name: 'dataset_description.json',
         path: '/dataset_description.json',
-        size: Promise.resolve(500),
+        size: 500,
         ignored: false,
-        stream: Promise.resolve(testStream),
+        stream: testStream,
       } as BIDSFile,
       {
+        text,
         name: 'README',
         path: '/README',
-        size: Promise.resolve(500),
+        size: 500,
         ignored: false,
-        stream: Promise.resolve(testStream),
+        stream: testStream,
         line: 1,
         character: 5,
         severity: 'warning',
diff --git a/bids-validator/src/schema/entities.test.ts b/bids-validator/src/schema/entities.test.ts
index d5da7cee6..73516e0c7 100644
--- a/bids-validator/src/schema/entities.test.ts
+++ b/bids-validator/src/schema/entities.test.ts
@@ -6,9 +6,10 @@ Deno.test('test readEntities', async (t) => {
   const testFile = {
     name: 'task-rhymejudgment_bold.json',
     path: '/task-rhymejudgment_bold.json',
-    size: null as unknown as Promise<number>,
+    size: null as unknown as number,
     ignored: false,
-    stream: null as unknown as Promise<ReadableStream<Uint8Array>>,
+    stream: null as unknown as ReadableStream<Uint8Array>,
+    text: () => Promise.resolve(''),
   }
   const context = readEntities(testFile)
   assert(context.suffix === 'bold', 'failed to match suffix')
diff --git a/bids-validator/src/tests/simple-dataset.ts b/bids-validator/src/tests/simple-dataset.ts
index 659b2e011..0e10fdb09 100644
--- a/bids-validator/src/tests/simple-dataset.ts
+++ b/bids-validator/src/tests/simple-dataset.ts
@@ -1,48 +1,55 @@
 import { FileTree } from '../types/filetree.ts'
 
+const text = () => Promise.resolve('')
+
 // Very basic dataset modeled for tests
 const rootFileTree = new FileTree('/', '')
 const subjectFileTree = new FileTree('/sub-01', 'sub-01', rootFileTree)
 const anatFileTree = new FileTree('/sub-01/anat', 'anat', subjectFileTree)
 anatFileTree.files = [
   {
+    text,
     path: '/sub-01/anat/sub-01_T1w.nii.gz',
     name: 'sub-01_T1w.nii.gz',
-    size: Promise.resolve(311112),
+    size: 311112,
     ignored: false,
-    stream: Promise.resolve(new ReadableStream()),
+    stream: new ReadableStream<Uint8Array>(),
   },
 ]
 subjectFileTree.files = []
 subjectFileTree.directories = [anatFileTree]
 rootFileTree.files = [
   {
+    text,
     path: '/dataset_description.json',
     name: 'dataset_description.json',
-    size: Promise.resolve(240),
+    size: 240,
     ignored: false,
-    stream: Promise.resolve(new ReadableStream()),
+    stream: new ReadableStream(),
   },
   {
+    text,
     path: '/README',
     name: 'README',
-    size: Promise.resolve(709),
+    size: 709,
     ignored: false,
-    stream: Promise.resolve(new ReadableStream()),
+    stream: new ReadableStream(),
   },
   {
+    text,
     path: '/CHANGES',
     name: 'CHANGES',
-    size: Promise.resolve(39),
+    size: 39,
     ignored: false,
-    stream: Promise.resolve(new ReadableStream()),
+    stream: new ReadableStream(),
   },
   {
+    text,
     path: '/participants.tsv',
     name: 'participants.tsv',
-    size: Promise.resolve(36),
+    size: 36,
     ignored: false,
-    stream: Promise.resolve(new ReadableStream()),
+    stream: new ReadableStream(),
   },
 ]
 rootFileTree.directories = [subjectFileTree]
diff --git a/bids-validator/src/types/file.ts b/bids-validator/src/types/file.ts
index 886ded9e3..8dee16392 100644
--- a/bids-validator/src/types/file.ts
+++ b/bids-validator/src/types/file.ts
@@ -9,9 +9,11 @@ export interface BIDSFile {
   // Dataset relative path for the file
   path: string
   // File size in bytes
-  size: Promise<number>
+  size: number
   // BIDS ignore status of the file
   ignored: boolean
   // ReadableStream to file raw contents
-  stream: Promise<ReadableStream<Uint8Array>>
+  stream: ReadableStream<Uint8Array>
+  // Resolve stream to decoded utf-8 text
+  text: () => Promise<string>
 }

From 7e5ee73dd2a331720c17c21072b4dd237b475a36 Mon Sep 17 00:00:00 2001
From: Ross Blair <rosswilsonblair@gmail.com>
Date: Thu, 30 Jun 2022 13:27:25 -0500
Subject: [PATCH 06/13] use text() function for taskname and participants
 entries in summary

---
 bids-validator/src/schema/context.ts               |  2 +-
 .../src/summary/collectSubjectMetadata.ts          |  5 ++---
 bids-validator/src/summary/summary.ts              | 14 +++++++-------
 .../src/tests/local/valid_headers.test.ts          |  2 +-
 4 files changed, 11 insertions(+), 12 deletions(-)

diff --git a/bids-validator/src/schema/context.ts b/bids-validator/src/schema/context.ts
index 77ec8de22..bca20d67b 100644
--- a/bids-validator/src/schema/context.ts
+++ b/bids-validator/src/schema/context.ts
@@ -42,8 +42,8 @@ export class BIDSContext implements Context {
     this.modality = ''
     this.sidecar = {}
     this.associations = {} as ContextAssociations
-    this.columns = {}
     this.json = {}
+    this.columns = {}
     this.nifti_header = {} as ContextNiftiHeader
   }
 
diff --git a/bids-validator/src/summary/collectSubjectMetadata.ts b/bids-validator/src/summary/collectSubjectMetadata.ts
index 41e728200..b5e4db934 100644
--- a/bids-validator/src/summary/collectSubjectMetadata.ts
+++ b/bids-validator/src/summary/collectSubjectMetadata.ts
@@ -20,14 +20,13 @@ const PARTICIPANT_ID = 'participantId'
  * @param {string} participantsTsvContent
  */
 export const collectSubjectMetadata = (
-  participantsTsvContent: Uint8Array,
+  participantsTsvContent: string,
 ): SubjectMetadata[] => {
   if (!participantsTsvContent) {
     return []
   }
 
-  const contentTable = new TextDecoder()
-    .decode(participantsTsvContent)
+  const contentTable = participantsTsvContent
     .split(/\r?\n/)
     .filter((row) => row !== '')
     .map((row) => row.split('\t'))
diff --git a/bids-validator/src/summary/summary.ts b/bids-validator/src/summary/summary.ts
index d12a82fba..0a2a3a2ac 100644
--- a/bids-validator/src/summary/summary.ts
+++ b/bids-validator/src/summary/summary.ts
@@ -104,8 +104,11 @@ export async function updateSummary(context: BIDSContext): Promise<void> {
   if ('ses' in context.entities) {
     summary.sessions.add(context.entities.ses)
   }
-  if ('TaskName' in context.json) {
-    summary.tasks.add(context.json.TaskName)
+  if (context.extension === '.json') {
+    const parsedJson = JSON.parse(await context.file.text())
+    if ('TaskName' in parsedJson) {
+      summary.tasks.add(parsedJson.TaskName)
+    }
   }
   if (context.modality) {
     modalitiesCount[context.modality]++
@@ -123,10 +126,7 @@ export async function updateSummary(context: BIDSContext): Promise<void> {
   }
 
   if (context.file.path.includes('participants.tsv')) {
-    const stream = await context.file.stream
-    const streamReader = stream.getReader()
-    const denoReader = readerFromStreamReader(streamReader)
-    const fileBuffer = await readAll(denoReader)
-    summary.subjectMetadata = collectSubjectMetadata(fileBuffer)
+    let tsvContents = await context.file.text()
+    summary.subjectMetadata = collectSubjectMetadata(tsvContents)
   }
 }
diff --git a/bids-validator/src/tests/local/valid_headers.test.ts b/bids-validator/src/tests/local/valid_headers.test.ts
index cf05feadf..de863c9ca 100644
--- a/bids-validator/src/tests/local/valid_headers.test.ts
+++ b/bids-validator/src/tests/local/valid_headers.test.ts
@@ -15,7 +15,7 @@ Deno.test('valid_headers dataset', async (t) => {
   })
 
   await t.step('summary has correct tasks', () => {
-    assertEquals(result.summary.tasks, ['rhyme judgment'])
+    assertEquals(Array.from(result.summary.tasks), ['rhyme judgment'])
   })
 
   await t.step('summary has correct dataProcessed', () => {

From be14d463a401db536ddf98da95be48de5748bf0c Mon Sep 17 00:00:00 2001
From: Ross Blair <rosswilsonblair@gmail.com>
Date: Thu, 30 Jun 2022 13:44:43 -0500
Subject: [PATCH 07/13] add nellh's getter to parse json for context class

---
 bids-validator/src/schema/context.ts  | 9 ++++++---
 bids-validator/src/summary/summary.ts | 2 +-
 2 files changed, 7 insertions(+), 4 deletions(-)

diff --git a/bids-validator/src/schema/context.ts b/bids-validator/src/schema/context.ts
index bca20d67b..1e80c4063 100644
--- a/bids-validator/src/schema/context.ts
+++ b/bids-validator/src/schema/context.ts
@@ -25,7 +25,6 @@ export class BIDSContext implements Context {
   sidecar: object
   associations: ContextAssociations
   columns: object
-  json: Record<string, any>
   nifti_header: ContextNiftiHeader
 
   constructor(fileTree: FileTree, file: BIDSFile, issues: DatasetIssues) {
@@ -42,11 +41,15 @@ export class BIDSContext implements Context {
     this.modality = ''
     this.sidecar = {}
     this.associations = {} as ContextAssociations
-    this.json = {}
     this.columns = {}
     this.nifti_header = {} as ContextNiftiHeader
   }
-
+  get json(): Promise<Record<string, any>> {
+    return this.file
+      .text()
+      .then((text) => JSON.parse(text))
+      .catch((error) => {})
+  }
   get path(): string {
     return this.datasetPath
   }
diff --git a/bids-validator/src/summary/summary.ts b/bids-validator/src/summary/summary.ts
index 0a2a3a2ac..0f5a8464a 100644
--- a/bids-validator/src/summary/summary.ts
+++ b/bids-validator/src/summary/summary.ts
@@ -105,7 +105,7 @@ export async function updateSummary(context: BIDSContext): Promise<void> {
     summary.sessions.add(context.entities.ses)
   }
   if (context.extension === '.json') {
-    const parsedJson = JSON.parse(await context.file.text())
+    const parsedJson = await context.json
     if ('TaskName' in parsedJson) {
       summary.tasks.add(parsedJson.TaskName)
     }

From 362ca76eb557d0f20047a55fe206462916e95295 Mon Sep 17 00:00:00 2001
From: Ross Blair <rosswilsonblair@gmail.com>
Date: Fri, 1 Jul 2022 09:39:55 -0500
Subject: [PATCH 08/13] get summary modalities and secondary modalites going

---
 bids-validator/src/files/deno.ts              |  4 ++--
 bids-validator/src/main.ts                    |  2 +-
 bids-validator/src/summary/summary.ts         | 15 +++++++++++++--
 bids-validator/src/tests/local/common.ts      |  4 ++--
 bids-validator/src/types/validation-result.ts | 15 ++++++++++++++-
 bids-validator/src/validators/bids.ts         |  4 ++--
 bids-validator/src/validators/filenames.ts    |  2 ++
 7 files changed, 36 insertions(+), 10 deletions(-)

diff --git a/bids-validator/src/files/deno.ts b/bids-validator/src/files/deno.ts
index de13285f2..6f0bc35fa 100644
--- a/bids-validator/src/files/deno.ts
+++ b/bids-validator/src/files/deno.ts
@@ -93,7 +93,7 @@ export async function _readFileTree(
   const tree = new FileTreeDeno(relativePath, name, parent, rootPath)
 
   for await (const dirEntry of Deno.readDir(join(rootPath, relativePath))) {
-    if (dirEntry.isFile) {
+    if (dirEntry.isFile || dirEntry.isSymlink) {
       const file = new BIDSFileDeno(
         rootPath,
         join(relativePath, dirEntry.name),
@@ -122,6 +122,6 @@ export async function _readFileTree(
  * Read in the target directory structure and return a FileTree
  */
 export function readFileTree(rootPath: string): Promise<FileTree> {
-  const ignore = new FileIgnoreRulesDeno([])
+  const ignore = new FileIgnoreRulesDeno(['.git**'])
   return _readFileTree(rootPath, '/', ignore)
 }
diff --git a/bids-validator/src/main.ts b/bids-validator/src/main.ts
index 6e7748884..ae407fa55 100644
--- a/bids-validator/src/main.ts
+++ b/bids-validator/src/main.ts
@@ -22,7 +22,7 @@ async function main() {
   const schemaResult = await validate(tree)
 
   if (options.schemaOnly) {
-    inspect(schemaResult.issues.issues)
+    inspect(schemaResult)
     // TODO - generate a summary without the old validator
   } else {
     const output = schemaResult.issues.formatOutput()
diff --git a/bids-validator/src/summary/summary.ts b/bids-validator/src/summary/summary.ts
index 0f5a8464a..52cb44bfd 100644
--- a/bids-validator/src/summary/summary.ts
+++ b/bids-validator/src/summary/summary.ts
@@ -1,6 +1,6 @@
 import { collectSubjectMetadata } from './collectSubjectMetadata.ts'
 import { readAll, readerFromStreamReader } from '../deps/stream.ts'
-import { Summary } from '../types/validation-result.ts'
+import { Summary, SummaryOutput } from '../types/validation-result.ts'
 import { BIDSContext } from '../schema/context.ts'
 
 const modalitiesCount: Record<string, number> = {
@@ -35,7 +35,7 @@ const modalityPrettyLookup: Record<string, string> = {
 const secondaryLookup: Record<string, string> = {
   dwi: 'MRI_Diffusion',
   anat: 'MRI_Structural',
-  bold: 'MRI_Functional',
+  func: 'MRI_Functional',
   perf: 'MRI_Perfusion',
 }
 
@@ -130,3 +130,14 @@ export async function updateSummary(context: BIDSContext): Promise<void> {
     summary.subjectMetadata = collectSubjectMetadata(tsvContents)
   }
 }
+
+export function formatSummary(summary: Summary): SummaryOutput {
+  return {
+    ...summary,
+    sessions: Array.from(summary.sessions),
+    subjects: Array.from(summary.subjects),
+    tasks: Array.from(summary.tasks),
+    modalities: summary.modalities,
+    secondaryModalities: summary.secondaryModalities,
+  }
+}
diff --git a/bids-validator/src/tests/local/common.ts b/bids-validator/src/tests/local/common.ts
index 9f17f51aa..ebe7d168a 100644
--- a/bids-validator/src/tests/local/common.ts
+++ b/bids-validator/src/tests/local/common.ts
@@ -3,7 +3,7 @@ import { FileTree } from '../../types/filetree.ts'
 import { validate } from '../../validators/bids.ts'
 import { ValidationResult } from '../../types/validation-result.ts'
 import { DatasetIssues } from '../../issues/datasetIssues.ts'
-import { summary } from '../../summary/summary.ts'
+import { summary, formatSummary } from '../../summary/summary.ts'
 
 export async function validatePath(
   t: Deno.TestContext,
@@ -12,7 +12,7 @@ export async function validatePath(
   let tree: FileTree = new FileTree('', '')
   let result: ValidationResult = {
     issues: new DatasetIssues(),
-    summary: summary,
+    summary: formatSummary(summary),
   }
 
   await t.step('file tree is read', async () => {
diff --git a/bids-validator/src/types/validation-result.ts b/bids-validator/src/types/validation-result.ts
index 8ce6e70f1..d229bf40c 100644
--- a/bids-validator/src/types/validation-result.ts
+++ b/bids-validator/src/types/validation-result.ts
@@ -27,10 +27,23 @@ export interface Summary {
   pet: Record<string, any>
 }
 
+export interface SummaryOutput {
+  sessions: string[]
+  subjects: string[]
+  subjectMetadata: SubjectMetadata[]
+  tasks: string[]
+  modalities: string[]
+  secondaryModalities: string[]
+  totalFiles: number
+  size: number
+  dataProcessed: boolean
+  pet: Record<string, any>
+}
+
 /**
  * The output of a validation run
  */
 export interface ValidationResult {
   issues: DatasetIssues
-  summary: Summary
+  summary: SummaryOutput
 }
diff --git a/bids-validator/src/validators/bids.ts b/bids-validator/src/validators/bids.ts
index 80e1ded39..8e178dbd8 100644
--- a/bids-validator/src/validators/bids.ts
+++ b/bids-validator/src/validators/bids.ts
@@ -11,7 +11,7 @@ import {
 } from './filenames.ts'
 import { DatasetIssues } from '../issues/datasetIssues.ts'
 import { ValidationResult } from '../types/validation-result.ts'
-import { summary, updateSummary } from '../summary/summary.ts'
+import { summary, formatSummary, updateSummary } from '../summary/summary.ts'
 
 /**
  * Full BIDS schema validation entrypoint
@@ -37,6 +37,6 @@ export async function validate(fileTree: FileTree): Promise<ValidationResult> {
   }
   return {
     issues,
-    summary,
+    summary: formatSummary(summary),
   }
 }
diff --git a/bids-validator/src/validators/filenames.ts b/bids-validator/src/validators/filenames.ts
index 1880dc415..65a748022 100644
--- a/bids-validator/src/validators/filenames.ts
+++ b/bids-validator/src/validators/filenames.ts
@@ -13,6 +13,7 @@ export function checkDatatypes(schema: Schema, context: BIDSContext) {
   datatypeFromDirectory(schema, context)
   if (schema.rules.datatypes.hasOwnProperty(context.datatype)) {
     const rules = schema.rules.datatypes[context.datatype]
+
     for (const key of Object.keys(rules)) {
       if (validateFilenameAgainstRule(rules[key], schema, context)) {
         matchedRule = key
@@ -180,6 +181,7 @@ export function datatypeFromDirectory(schema: Schema, context: BIDSContext) {
     if (schema.rules.modalities[key].datatypes.includes(dirDatatype)) {
       context.modality = key
       context.datatype = dirDatatype
+
       return
     }
   }

From cb91bb50b71df99007109105beaf35fb8b3a7010 Mon Sep 17 00:00:00 2001
From: Ross Blair <rosswilsonblair@gmail.com>
Date: Fri, 1 Jul 2022 10:42:59 -0500
Subject: [PATCH 09/13] convert summary and related functions to a class

---
 bids-validator/src/summary/summary.ts         | 174 ++++++++++--------
 bids-validator/src/tests/local/common.ts      |   4 +-
 bids-validator/src/types/validation-result.ts |  14 +-
 bids-validator/src/validators/bids.ts         |   6 +-
 4 files changed, 104 insertions(+), 94 deletions(-)

diff --git a/bids-validator/src/summary/summary.ts b/bids-validator/src/summary/summary.ts
index 52cb44bfd..e6bc390d2 100644
--- a/bids-validator/src/summary/summary.ts
+++ b/bids-validator/src/summary/summary.ts
@@ -1,28 +1,8 @@
 import { collectSubjectMetadata } from './collectSubjectMetadata.ts'
 import { readAll, readerFromStreamReader } from '../deps/stream.ts'
-import { Summary, SummaryOutput } from '../types/validation-result.ts'
+import { SummaryOutput, SubjectMetadata } from '../types/validation-result.ts'
 import { BIDSContext } from '../schema/context.ts'
 
-const modalitiesCount: Record<string, number> = {
-  mri: 0,
-  pet: 0,
-  meg: 0,
-  eeg: 0,
-  ieeg: 0,
-  microscopy: 0,
-}
-
-const secondaryModalitiesCount: Record<string, number> = {
-  MRI_Diffusion: 0,
-  MRI_Structural: 0,
-  MRI_Functional: 0,
-  MRI_Perfusion: 0,
-  PET_Static: 0,
-  PET_Dynamic: 0,
-  iEEG_ECoG: 0,
-  iEEG_SEEG: 0,
-}
-
 const modalityPrettyLookup: Record<string, string> = {
   mri: 'MRI',
   pet: 'PET',
@@ -73,71 +53,113 @@ function computeSecondaryModalities(
   return sortedSecondary
 }
 
-export const summary: Summary = {
-  dataProcessed: false,
-  totalFiles: -1,
-  size: 0,
-  sessions: new Set(),
-  subjects: new Set(),
-  subjectMetadata: [],
-  tasks: new Set(),
-  pet: {},
+class Summary {
+  sessions: Set<string>
+  subjects: Set<string>
+  subjectMetadata: SubjectMetadata[]
+  tasks: Set<string>
+  totalFiles: number
+  size: number
+  dataProcessed: boolean
+  pet: Record<string, any>
+  modalitiesCount: Record<string, number>
+  secondaryModalitiesCount: Record<string, number>
+  datatypes: Set<string>
+  constructor() {
+    this.dataProcessed = false
+    this.totalFiles = -1
+    this.size = 0
+    this.sessions = new Set()
+    this.subjects = new Set()
+    this.subjectMetadata = []
+    this.tasks = new Set()
+    this.pet = {}
+    this.datatypes = new Set()
+    this.modalitiesCount = {
+      mri: 0,
+      pet: 0,
+      meg: 0,
+      eeg: 0,
+      ieeg: 0,
+      microscopy: 0,
+    }
+    this.secondaryModalitiesCount = {
+      MRI_Diffusion: 0,
+      MRI_Structural: 0,
+      MRI_Functional: 0,
+      MRI_Perfusion: 0,
+      PET_Static: 0,
+      PET_Dynamic: 0,
+      iEEG_ECoG: 0,
+      iEEG_SEEG: 0,
+    }
+  }
   get modalities() {
-    return computeModalities(modalitiesCount)
-  },
+    return computeModalities(this.modalitiesCount)
+  }
   get secondaryModalities() {
-    return computeSecondaryModalities(secondaryModalitiesCount)
-  },
-}
-
-export async function updateSummary(context: BIDSContext): Promise<void> {
-  if (context.file.path.startsWith('/derivatives')) {
-    return
+    return computeSecondaryModalities(this.secondaryModalitiesCount)
   }
+  async update(context: BIDSContext): Promise<void> {
+    if (context.file.path.startsWith('/derivatives')) {
+      return
+    }
 
-  summary.totalFiles++
-  summary.size += await context.file.size
+    this.totalFiles++
+    this.size += await context.file.size
 
-  if ('sub' in context.entities) {
-    summary.subjects.add(context.entities.sub)
-  }
-  if ('ses' in context.entities) {
-    summary.sessions.add(context.entities.ses)
-  }
-  if (context.extension === '.json') {
-    const parsedJson = await context.json
-    if ('TaskName' in parsedJson) {
-      summary.tasks.add(parsedJson.TaskName)
+    if ('sub' in context.entities) {
+      this.subjects.add(context.entities.sub)
+    }
+    if ('ses' in context.entities) {
+      this.sessions.add(context.entities.ses)
     }
-  }
-  if (context.modality) {
-    modalitiesCount[context.modality]++
-  }
 
-  if (context.datatype in secondaryLookup) {
-    const key = secondaryLookup[context.datatype]
-    secondaryModalitiesCount[key]++
-  } else if (context.datatype === 'pet' && 'rec' in context.entities) {
-    if (['acstat', 'nacstat'].includes(context.entities.rec)) {
-      secondaryModalitiesCount.PET_Static++
-    } else if (['acdyn', 'nacdyn'].includes(context.entities.rec)) {
-      secondaryModalitiesCount.PET_Dynamic++
+    if (context.datatype) {
+      this.datatypes.add(context.datatype)
+    }
+    if (context.extension === '.json') {
+      const parsedJson = await context.json
+      if ('TaskName' in parsedJson) {
+        this.tasks.add(parsedJson.TaskName)
+      }
+    }
+    if (context.modality) {
+      this.modalitiesCount[context.modality]++
     }
-  }
 
-  if (context.file.path.includes('participants.tsv')) {
-    let tsvContents = await context.file.text()
-    summary.subjectMetadata = collectSubjectMetadata(tsvContents)
+    if (context.datatype in secondaryLookup) {
+      const key = secondaryLookup[context.datatype]
+      this.secondaryModalitiesCount[key]++
+    } else if (context.datatype === 'pet' && 'rec' in context.entities) {
+      if (['acstat', 'nacstat'].includes(context.entities.rec)) {
+        this.secondaryModalitiesCount.PET_Static++
+      } else if (['acdyn', 'nacdyn'].includes(context.entities.rec)) {
+        this.secondaryModalitiesCount.PET_Dynamic++
+      }
+    }
+
+    if (context.file.path.includes('participants.tsv')) {
+      let tsvContents = await context.file.text()
+      this.subjectMetadata = collectSubjectMetadata(tsvContents)
+    }
   }
-}
 
-export function formatSummary(summary: Summary): SummaryOutput {
-  return {
-    ...summary,
-    sessions: Array.from(summary.sessions),
-    subjects: Array.from(summary.subjects),
-    tasks: Array.from(summary.tasks),
-    modalities: summary.modalities,
-    secondaryModalities: summary.secondaryModalities,
+  formatOutput(): SummaryOutput {
+    return {
+      sessions: Array.from(this.sessions),
+      subjects: Array.from(this.subjects),
+      subjectMetadata: this.subjectMetadata,
+      tasks: Array.from(this.tasks),
+      modalities: this.modalities,
+      secondaryModalities: this.secondaryModalities,
+      totalFiles: this.totalFiles,
+      size: this.size,
+      dataProcessed: this.dataProcessed,
+      pet: this.pet,
+      datatypes: Array.from(this.datatypes),
+    }
   }
 }
+
+export const summary = new Summary()
diff --git a/bids-validator/src/tests/local/common.ts b/bids-validator/src/tests/local/common.ts
index ebe7d168a..b6aa65317 100644
--- a/bids-validator/src/tests/local/common.ts
+++ b/bids-validator/src/tests/local/common.ts
@@ -3,7 +3,7 @@ import { FileTree } from '../../types/filetree.ts'
 import { validate } from '../../validators/bids.ts'
 import { ValidationResult } from '../../types/validation-result.ts'
 import { DatasetIssues } from '../../issues/datasetIssues.ts'
-import { summary, formatSummary } from '../../summary/summary.ts'
+import { summary } from '../../summary/summary.ts'
 
 export async function validatePath(
   t: Deno.TestContext,
@@ -12,7 +12,7 @@ export async function validatePath(
   let tree: FileTree = new FileTree('', '')
   let result: ValidationResult = {
     issues: new DatasetIssues(),
-    summary: formatSummary(summary),
+    summary: summary.formatOutput(),
   }
 
   await t.step('file tree is read', async () => {
diff --git a/bids-validator/src/types/validation-result.ts b/bids-validator/src/types/validation-result.ts
index d229bf40c..0c7a113c0 100644
--- a/bids-validator/src/types/validation-result.ts
+++ b/bids-validator/src/types/validation-result.ts
@@ -14,19 +14,6 @@ export interface SubjectMetadata {
     TracerRadionuclide: {},
 */
 
-export interface Summary {
-  sessions: Set<string>
-  subjects: Set<string>
-  subjectMetadata: SubjectMetadata[]
-  tasks: Set<string>
-  modalities: string[]
-  secondaryModalities: string[]
-  totalFiles: number
-  size: number
-  dataProcessed: boolean
-  pet: Record<string, any>
-}
-
 export interface SummaryOutput {
   sessions: string[]
   subjects: string[]
@@ -38,6 +25,7 @@ export interface SummaryOutput {
   size: number
   dataProcessed: boolean
   pet: Record<string, any>
+  datatypes: string[]
 }
 
 /**
diff --git a/bids-validator/src/validators/bids.ts b/bids-validator/src/validators/bids.ts
index 8e178dbd8..fc869eab5 100644
--- a/bids-validator/src/validators/bids.ts
+++ b/bids-validator/src/validators/bids.ts
@@ -11,7 +11,7 @@ import {
 } from './filenames.ts'
 import { DatasetIssues } from '../issues/datasetIssues.ts'
 import { ValidationResult } from '../types/validation-result.ts'
-import { summary, formatSummary, updateSummary } from '../summary/summary.ts'
+import { summary } from '../summary/summary.ts'
 
 /**
  * Full BIDS schema validation entrypoint
@@ -33,10 +33,10 @@ export async function validate(fileTree: FileTree): Promise<ValidationResult> {
       checkLabelFormat(schema, context)
     }
     applyRules(schema, context)
-    await updateSummary(context)
+    await summary.update(context)
   }
   return {
     issues,
-    summary: formatSummary(summary),
+    summary: summary.formatOutput(),
   }
 }

From e01105c854b1be05615803d845beee04b6fb769a Mon Sep 17 00:00:00 2001
From: Ross Blair <rosswilsonblair@gmail.com>
Date: Fri, 1 Jul 2022 11:09:47 -0500
Subject: [PATCH 10/13] add test to check summary modality sorting works

---
 bids-validator/src/summary/summary.test.ts | 15 +++++++++++++++
 1 file changed, 15 insertions(+)
 create mode 100644 bids-validator/src/summary/summary.test.ts

diff --git a/bids-validator/src/summary/summary.test.ts b/bids-validator/src/summary/summary.test.ts
new file mode 100644
index 000000000..aacf91d3c
--- /dev/null
+++ b/bids-validator/src/summary/summary.test.ts
@@ -0,0 +1,15 @@
+import { computeModalities, modalityPrettyLookup, Summary } from './summary.ts'
+import { assertEquals, assertObjectMatch } from '../deps/asserts.ts'
+
+Deno.test('Summary class and helper functions', async (t) => {
+  await t.step('Constructor succeeds', () => {
+    new Summary()
+  })
+  await t.step('computeModalities properly sorts modality counts', () => {
+    const modalitiesIn = { eeg: 5, mri: 6, pet: 6 }
+    const modalitiesOut = ['pet', 'mri', 'eeg'].map(
+      (x) => modalityPrettyLookup[x],
+    )
+    assertEquals(computeModalities(modalitiesIn), modalitiesOut)
+  })
+})

From 28078bf9f58c76e8cc9a6c196d824ac743f208c6 Mon Sep 17 00:00:00 2001
From: Ross Blair <rosswilsonblair@gmail.com>
Date: Fri, 1 Jul 2022 11:16:35 -0500
Subject: [PATCH 11/13] forgot to add changes to summary for tests to work

---
 bids-validator/src/summary/summary.ts | 12 +++++++-----
 1 file changed, 7 insertions(+), 5 deletions(-)

diff --git a/bids-validator/src/summary/summary.ts b/bids-validator/src/summary/summary.ts
index e6bc390d2..530e561f2 100644
--- a/bids-validator/src/summary/summary.ts
+++ b/bids-validator/src/summary/summary.ts
@@ -3,7 +3,7 @@ import { readAll, readerFromStreamReader } from '../deps/stream.ts'
 import { SummaryOutput, SubjectMetadata } from '../types/validation-result.ts'
 import { BIDSContext } from '../schema/context.ts'
 
-const modalityPrettyLookup: Record<string, string> = {
+export const modalityPrettyLookup: Record<string, string> = {
   mri: 'MRI',
   pet: 'PET',
   meg: 'MEG',
@@ -19,7 +19,9 @@ const secondaryLookup: Record<string, string> = {
   perf: 'MRI_Perfusion',
 }
 
-function computeModalities(modalities: Record<string, number>): string[] {
+export function computeModalities(
+  modalities: Record<string, number>,
+): string[] {
   // Order by matching file count
   const nonZero = Object.keys(modalities).filter((a) => modalities[a] !== 0)
   if (nonZero.length === 0) {
@@ -28,7 +30,7 @@ function computeModalities(modalities: Record<string, number>): string[] {
   const sortedModalities = nonZero.sort((a, b) => {
     if (modalities[b] === modalities[a]) {
       // On a tie, hand it to the non-MRI modality
-      if (b === 'MRI') {
+      if (b === 'mri') {
         return -1
       } else {
         return 0
@@ -41,7 +43,7 @@ function computeModalities(modalities: Record<string, number>): string[] {
   )
 }
 
-function computeSecondaryModalities(
+export function computeSecondaryModalities(
   secondary: Record<string, number>,
 ): string[] {
   const nonZeroSecondary = Object.keys(secondary).filter(
@@ -53,7 +55,7 @@ function computeSecondaryModalities(
   return sortedSecondary
 }
 
-class Summary {
+export class Summary {
   sessions: Set<string>
   subjects: Set<string>
   subjectMetadata: SubjectMetadata[]

From 0ce659ff8388950f0efcb223488b351be08a728a Mon Sep 17 00:00:00 2001
From: Ross Blair <rosswilsonblair@gmail.com>
Date: Fri, 1 Jul 2022 13:28:10 -0500
Subject: [PATCH 12/13] Set default ignore rules in ignores constructor. Use
 exported summary class instead of singleton. Add additional filenames test

---
 bids-validator/src/files/deno.ts              |  2 +-
 bids-validator/src/files/ignore.ts            |  3 ++
 bids-validator/src/summary/summary.ts         |  9 +++--
 bids-validator/src/tests/local/common.ts      |  3 +-
 bids-validator/src/validators/bids.ts         |  3 +-
 .../src/validators/filenames.test.ts          | 36 +++++++++++++++----
 6 files changed, 41 insertions(+), 15 deletions(-)

diff --git a/bids-validator/src/files/deno.ts b/bids-validator/src/files/deno.ts
index 6f0bc35fa..ee6509d40 100644
--- a/bids-validator/src/files/deno.ts
+++ b/bids-validator/src/files/deno.ts
@@ -122,6 +122,6 @@ export async function _readFileTree(
  * Read in the target directory structure and return a FileTree
  */
 export function readFileTree(rootPath: string): Promise<FileTree> {
-  const ignore = new FileIgnoreRulesDeno(['.git**'])
+  const ignore = new FileIgnoreRulesDeno([])
   return _readFileTree(rootPath, '/', ignore)
 }
diff --git a/bids-validator/src/files/ignore.ts b/bids-validator/src/files/ignore.ts
index aa2ad2c20..c02fce640 100644
--- a/bids-validator/src/files/ignore.ts
+++ b/bids-validator/src/files/ignore.ts
@@ -12,6 +12,8 @@ export async function readBidsIgnore(file: BIDSFile) {
   }
 }
 
+const defaultIgnores = ['.git**', '.datalad']
+
 /**
  * Deno implementation of .bidsignore style rules
  */
@@ -20,6 +22,7 @@ export class FileIgnoreRulesDeno implements FileIgnoreRules {
 
   constructor(config: string[]) {
     this.#ignore = ignore({ allowRelativePaths: true })
+    this.#ignore.add(defaultIgnores)
     this.#ignore.add(config)
   }
 
diff --git a/bids-validator/src/summary/summary.ts b/bids-validator/src/summary/summary.ts
index 530e561f2..4312ad769 100644
--- a/bids-validator/src/summary/summary.ts
+++ b/bids-validator/src/summary/summary.ts
@@ -117,9 +117,10 @@ export class Summary {
       this.sessions.add(context.entities.ses)
     }
 
-    if (context.datatype) {
+    if (context.datatype.length) {
       this.datatypes.add(context.datatype)
     }
+
     if (context.extension === '.json') {
       const parsedJson = await context.json
       if ('TaskName' in parsedJson) {
@@ -141,8 +142,8 @@ export class Summary {
       }
     }
 
-    if (context.file.path.includes('participants.tsv')) {
-      let tsvContents = await context.file.text()
+    if (context.file.path.endsWith('participants.tsv')) {
+      const tsvContents = await context.file.text()
       this.subjectMetadata = collectSubjectMetadata(tsvContents)
     }
   }
@@ -163,5 +164,3 @@ export class Summary {
     }
   }
 }
-
-export const summary = new Summary()
diff --git a/bids-validator/src/tests/local/common.ts b/bids-validator/src/tests/local/common.ts
index b6aa65317..dc4baaa8e 100644
--- a/bids-validator/src/tests/local/common.ts
+++ b/bids-validator/src/tests/local/common.ts
@@ -3,13 +3,14 @@ import { FileTree } from '../../types/filetree.ts'
 import { validate } from '../../validators/bids.ts'
 import { ValidationResult } from '../../types/validation-result.ts'
 import { DatasetIssues } from '../../issues/datasetIssues.ts'
-import { summary } from '../../summary/summary.ts'
+import { Summary } from '../../summary/summary.ts'
 
 export async function validatePath(
   t: Deno.TestContext,
   path: string,
 ): Promise<{ tree: FileTree; result: ValidationResult }> {
   let tree: FileTree = new FileTree('', '')
+  let summary = new Summary()
   let result: ValidationResult = {
     issues: new DatasetIssues(),
     summary: summary.formatOutput(),
diff --git a/bids-validator/src/validators/bids.ts b/bids-validator/src/validators/bids.ts
index fc869eab5..54d89fa4e 100644
--- a/bids-validator/src/validators/bids.ts
+++ b/bids-validator/src/validators/bids.ts
@@ -11,13 +11,14 @@ import {
 } from './filenames.ts'
 import { DatasetIssues } from '../issues/datasetIssues.ts'
 import { ValidationResult } from '../types/validation-result.ts'
-import { summary } from '../summary/summary.ts'
+import { Summary } from '../summary/summary.ts'
 
 /**
  * Full BIDS schema validation entrypoint
  */
 export async function validate(fileTree: FileTree): Promise<ValidationResult> {
   const issues = new DatasetIssues()
+  const summary = new Summary()
   // TODO - summary should be implemented in pure schema mode
   const schema = await loadSchema()
   for await (const context of walkFileTree(fileTree, issues)) {
diff --git a/bids-validator/src/validators/filenames.test.ts b/bids-validator/src/validators/filenames.test.ts
index 12771b666..51c50349c 100644
--- a/bids-validator/src/validators/filenames.test.ts
+++ b/bids-validator/src/validators/filenames.test.ts
@@ -42,13 +42,35 @@ Deno.test('test datatypeFromDirectory', (t) => {
   })
 })
 
-Deno.test('test checkDatatype', (t) => {
-  const filesToTest = [['/sub-01/func/sub-01_task-taskname_bold.json', []]]
-  filesToTest.map((test) => {
-    let context = newContext(test[0])
-    context = { ...context, ...readEntities(context.file) }
-    checkDatatypes(schema, context)
-    assertEquals(context.issues.fileInIssues(test[0]), test[1])
+Deno.test('test checkDatatype', async (t) => {
+  await t.step('Check no errors on good file', () => {
+    const filesToTest = [['/sub-01/func/sub-01_task-taskname_bold.json', []]]
+    filesToTest.map((test) => {
+      let context = newContext(test[0])
+      context = { ...context, ...readEntities(context.file) }
+      checkDatatypes(schema, context)
+      assertEquals(context.issues.fileInIssues(test[0]), test[1])
+    })
+  })
+
+  await t.step('Check for correct issues generated', () => {
+    const filesToTest = [
+      ['/sub-01/anat/sub-01_task-taskname_bold.json', 'DATATYPE_MISMATCH'],
+      ['/sub-01/func/task-taskname_bold.json', 'MISSING_REQUIRED_ENTITY'],
+      [
+        '/sub-01/func/sub-01_task-taskname_bad-ent_bold.json',
+        'ENTITY_NOT_IN_RULE',
+      ],
+    ]
+    filesToTest.map((test) => {
+      let context = newContext(test[0])
+      context = { ...context, ...readEntities(context.file) }
+      checkDatatypes(schema, context)
+      assertEquals(
+        context.issues.getFileIssueKeys(test[0]).includes(test[1]),
+        true,
+      )
+    })
   })
 })
 

From ac2aa22a667e093c8fcd0560cf99a2c1e64da5a1 Mon Sep 17 00:00:00 2001
From: Ross Blair <rosswilsonblair@gmail.com>
Date: Fri, 8 Jul 2022 12:16:07 -0500
Subject: [PATCH 13/13] pluralize datatype in checkdatatypes function. Reorder
 modalities in testing modality ranking in summary

---
 bids-validator/src/summary/summary.test.ts | 4 ++--
 bids-validator/src/validators/filenames.ts | 2 +-
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/bids-validator/src/summary/summary.test.ts b/bids-validator/src/summary/summary.test.ts
index aacf91d3c..9e0fbe886 100644
--- a/bids-validator/src/summary/summary.test.ts
+++ b/bids-validator/src/summary/summary.test.ts
@@ -6,8 +6,8 @@ Deno.test('Summary class and helper functions', async (t) => {
     new Summary()
   })
   await t.step('computeModalities properly sorts modality counts', () => {
-    const modalitiesIn = { eeg: 5, mri: 6, pet: 6 }
-    const modalitiesOut = ['pet', 'mri', 'eeg'].map(
+    const modalitiesIn = { eeg: 5, pet: 6, mri: 6, ieeg: 6 }
+    const modalitiesOut = ['pet', 'ieeg', 'mri', 'eeg'].map(
       (x) => modalityPrettyLookup[x],
     )
     assertEquals(computeModalities(modalitiesIn), modalitiesOut)
diff --git a/bids-validator/src/validators/filenames.ts b/bids-validator/src/validators/filenames.ts
index 65a748022..93496df25 100644
--- a/bids-validator/src/validators/filenames.ts
+++ b/bids-validator/src/validators/filenames.ts
@@ -34,7 +34,7 @@ export function checkDatatypes(schema: Schema, context: BIDSContext) {
       for (const key of Object.keys(rules)) {
         if (validateFilenameAgainstRule(rules[key], schema, context)) {
           matchedRule = key
-          possibleDatatypes.add(rules[key].datatype)
+          possibleDatatypes.add(rules[key].datatypes)
           break
         }
       }