Add Frictionless Data Table Schema for libBIDS.sh output

[gdevenyi]

Define a comprehensive table_schema.json following the Frictionless Data Table Schema specification, enriched with metadata from the official BIDS schema (bids-standard/bids-schema). Includes titles, descriptions, format annotations (label/index), and constraints (enum, pattern, required, unique) for all 36 output fields.

Fixes #14

Summary by CodeRabbit

• Chores
  • Added a new tabular data schema to standardize BIDS-like metadata for derivatives and raw files.
  • Provides built-in validation: required fields, allowed suffixes/extensions, label and numeric format checks, unique path primary key, and missing-value handling to improve data integrity and interoperability.

[coderabbitai]

No actionable comments were generated in the recent review. 🎉

ℹ️ Recent review info

⚙️ Run configuration

Configuration used: defaults

Review profile: CHILL

Plan: Pro

Run ID: a3e70de4-7446-4dce-a4e6-0935d9f69efb

📥 Commits

Reviewing files that changed from the base of the PR and between eda36da and fcfe745.

📒 Files selected for processing (1)

• table_schema.json

✅ Files skipped from review due to trivial changes (1)

• table_schema.json

---

📝 Walkthrough

Walkthrough

Added table_schema.json, a declarative tabular-data-schema JSON file that sets primaryKey: "path", missingValues: ["NA", ""], and declares 30+ validated fields (enums, regexes, numeric constraints) for BIDS-like tabular metadata including suffix, extension, entity labels, and index fields.

Changes

Cohort / File(s)	Summary
Table Schema Definition table_schema.json	New JSON schema (profile: "tabular-data-schema") added. Declares path as the primary key, missingValues: ["NA", ""], required fields data_type, suffix, extension, and ~30+ fields with types and validations (regex for entity labels, enums for categorical fields, numeric minimums for index fields).

Estimated code review effort

🎯 2 (Simple) | ⏱️ ~12 minutes

Possibly related PRs

• Manual update from schema.json #19: Updates/parses many of the same BIDS-like tokens (data_type, suffixes, extensions) enumerated by this schema.

Poem

🐰 I hopped a schema through the glade,
Rows in order, columns arrayed,
Paths are loyal, tokens bright,
Regex guards them through the night,
A rabbit stamps the table "made."

🚥 Pre-merge checks | ✅ 5

✅ Passed checks (5 passed)

Check name	Status	Explanation
Description Check	✅ Passed	Check skipped - CodeRabbit’s high-level summary is enabled.
Title check	✅ Passed	The title clearly and specifically summarizes the main change: adding a Frictionless Data Table Schema for libBIDS.sh output.
Linked Issues check	✅ Passed	The PR addresses issue #14 by providing the table format specification as a Frictionless Data Table Schema with comprehensive field definitions and validation rules.
Out of Scope Changes check	✅ Passed	All changes are in-scope: the PR adds only table_schema.json with declarative schema definitions directly relevant to formalizing libBIDS.sh output structure per issue #14.
Docstring Coverage	✅ Passed	No functions found in the changed files to evaluate docstring coverage. Skipping docstring coverage check.

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✨ Finishing Touches

🧪 Generate unit tests (beta)

• Create PR with unit tests
• Commit unit tests in branch add-frictionless-table-schema

📝 Coding Plan

• Generate coding plan for human review comments

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[coderabbitai]

Actionable comments posted: 1

🧹 Nitpick comments (2)

table_schema.json (2)

8-14: Consider adding pattern constraint for derivatives.

The derivatives field currently has no pattern constraint. For consistency with other label-type fields and to ensure valid pipeline names, consider adding an alphanumeric pattern constraint.

📋 Proposed enhancement

 {
   "name": "derivatives",
   "title": "Derivative Pipeline",
   "type": "string",
-  "description": "Pipeline name extracted from the derivatives/ folder path. NA if the file is not in a derivatives directory."
+  "description": "Pipeline name extracted from the derivatives/ folder path. NA if the file is not in a derivatives directory.",
+  "constraints": {
+    "pattern": "^[a-zA-Z0-9]+$"
+  }
 }

🤖 Prompt for AI Agents

Verify each finding against the current code and only fix it if needed.

In `@table_schema.json` around lines 8 - 14, The "derivatives" field in the schema
has no pattern constraint; update the field object for "derivatives" (inside the
"fields" array) to include a "pattern" property that enforces valid pipeline
names (e.g., an alphanumeric pattern such as "^[A-Za-z0-9_-]+$" or your
preferred variant) and optionally add a "patternMessage" or "error" description
to explain invalid values; ensure the "type": "string" remains and that the new
pattern aligns with other label-type fields in the schema.

---

45-45: Replace non-standard format values with custom properties or document the extension.

The schema uses "format": "label" (25 fields) and "format": "index" (6 fields) throughout, but these are not standard Frictionless Data Table Schema format values. The official specification defines formats like default, email, uri, binary, and uuid. While non-standard formats may be ignored by Frictionless validators rather than causing errors, using custom properties (e.g., "bidsFormat": "label") or explicitly documenting this extension would improve clarity and standards compliance.

🤖 Prompt for AI Agents

Verify each finding against the current code and only fix it if needed.

In `@table_schema.json` at line 45, The schema uses non-standard "format" values
("label"/"index") across many field definitions; replace those custom usages
with a namespaced custom property (e.g., "bidsFormat": "label" or "x-format":
"label") wherever the "format" key is currently set, and update any code that
reads these fields to look for the new property instead of "format";
alternatively, if you must keep "format", add a top-level schema extension
comment or metadata entry documenting this non-standard extension so
validators/users know "label" and "index" are custom conventions.

🤖 Prompt for all review comments with AI agents

Verify each finding against the current code and only fix it if needed.

Inline comments:
In `@table_schema.json`:
- Around line 358-376: The suffix enum in the JSON schema is missing three valid
BIDS suffixes; update the "enum" array (the suffix enumeration block shown) to
include "description", "emg", and "physioevents" so it matches the official BIDS
suffixes (referenced in src/schema/objects/suffixes.yaml); ensure you add the
three strings to the existing list alongside entries like "descriptions" and
"physio".

---

Nitpick comments:
In `@table_schema.json`:
- Around line 8-14: The "derivatives" field in the schema has no pattern
constraint; update the field object for "derivatives" (inside the "fields"
array) to include a "pattern" property that enforces valid pipeline names (e.g.,
an alphanumeric pattern such as "^[A-Za-z0-9_-]+$" or your preferred variant)
and optionally add a "patternMessage" or "error" description to explain invalid
values; ensure the "type": "string" remains and that the new pattern aligns with
other label-type fields in the schema.
- Line 45: The schema uses non-standard "format" values ("label"/"index") across
many field definitions; replace those custom usages with a namespaced custom
property (e.g., "bidsFormat": "label" or "x-format": "label") wherever the
"format" key is currently set, and update any code that reads these fields to
look for the new property instead of "format"; alternatively, if you must keep
"format", add a top-level schema extension comment or metadata entry documenting
this non-standard extension so validators/users know "label" and "index" are
custom conventions.

---

ℹ️ Review info

⚙️ Run configuration

Configuration used: defaults

Review profile: CHILL

Plan: Pro

Run ID: 18ccbbc4-7844-4932-a3bb-5dd0b923485a

📥 Commits

Reviewing files that changed from the base of the PR and between ad2a0f7 and b19176e.

📒 Files selected for processing (1)

• table_schema.json