Changelog

Changelog

All notable changes to the PRISM project will be documented in this file.

The format is based on Keep a Changelog, and this project adheres to Semantic Versioning.

[Unreleased]

[1.12.0] - 2026-03-08

Changed

  • Scripts Canonicalization: Reorganized utility scripts into domain folders (scripts/ci, scripts/data, scripts/dev, scripts/maintenance, scripts/release, scripts/setup) and updated internal docs/examples to canonical paths.

  • Setup Test Script Placement: Moved setup-related test utilities to scripts/ci/ and retained setup-path compatibility wrappers for transition.

  • Procedure Validation Session Source: Session existence checks now rely only on on-disk dataset structure (sub-*/ses-*). PRISM702 is deprecated and retained only for backward compatibility in the issue catalog.

Added

  • Wrapper Retirement Playbook: Added docs/WRAPPER_CLEANUP_CHECKLIST.md with explicit exit criteria, removal sequence, validation commands, and rollback plan for controlled wrapper removal.

  • Scripts Inventory Guide: Added scripts/README.md to classify active script domains (build, ci, setup) versus future_feature and _archive paths after cleanup.

Removed

  • Legacy Root Script Wrappers: Removed old root-level scripts/*.py|*.sh|*.bat|*.ps1 wrappers and standardized execution on canonical script locations under scripts/{ci,data,dev,maintenance,release,setup}.

[1.11.0] - 2026-02-26

Added

  • Examples in Build Distribution: Examples folder now included in PyInstaller bundles for Windows/macOS/Linux distributions. Users get sample datasets immediately upon extraction.

  • Decimal Separator Support: Enhanced numeric parsing to better support different decimal separators in survey data and participant information across locales.

Fixed

  • Settings Management: Corrected last project path and name persistence in application settings.

  • AND Export Metadata: Fixed date format handling in AND export for better compatibility with external tools.

[1.10.1] - 2026-02-25

Fixed

  • Logo Display in Executable: Added PRISM logo to app/static/img/ to ensure it displays correctly in bundled Windows executable. The logo now resolves from the bundled static assets rather than requiring parent directory traversal.

[1.10.0] - 2026-02-25

Added

  • Survey Customizer β€” LimeSurvey Survey Settings: New collapsible accordion with three sections for LimeSurvey-specific survey configuration (closes #9):

    • Text & Messages: Welcome message, end message, end URL, and end URL description with template dropdowns (Standard, Academic, Brief for welcome; Standard, Academic, Brief, Redirect for end message).

    • Data Policy / Ethics: Enable data policy toggle, policy notice with 5 consent templates (Standard Ethics, GDPR Data Protection, Anonymous Survey, Longitudinal Study, Minimal), policy error message, and checkbox label.

    • Presentation & Navigation: 14 survey-level settings including progress bar, backward navigation, question index, group info display, question numbering, β€œno answer” option, on-screen keyboard, print answers, auto-redirect, and public statistics/graphs.

  • Survey Customizer β€” Text Templates: Built-in HTML templates for welcome messages, end messages, and data policy consent text with [BRACKET] placeholders for easy customization.

  • Template Editor β€” Language Overview Bar: Shows detected languages, primary language badge, and warning indicator when Technical.Language mismatches content. β€œAdd Language” and β€œRemove Language” buttons batch-update all question Descriptions and Levels consistently.

  • Template Editor β€” Preview Tab: New β€œPreview” tab renders questions as a mock survey form with language switcher. Missing translations highlighted with warning styling. Shows Reversed/Required badges and response options (radio buttons or text input).

  • Language Consistency Validation: Backend _validate_language_consistency() detects fake translations (identical content across languages), inconsistent language keys across items, Technical.Language vs content key mismatches, and complementary/disjoint language sets. All warnings shown during template validation without blocking saves.

Fixed

  • Template Editor β€” Global Template Access: Fixed initializeLibraryPath() incorrectly setting the library path to project directory, which caused refreshTemplateList() to use the non-merged API and hide global templates. Now uses merged API when a project is active, showing both [Global] and [Project] templates.

[1.9.2] - 2026-02-05

Security

  • MD5 Hash Security: Fixed all MD5 hash usage by adding usedforsecurity=False parameter (HIGH severity - Bandit B324). MD5 is only used for generating short identifier suffixes, not for cryptographic purposes.

  • XML Parsing Vulnerability: Replaced insecure xml.etree.ElementTree with defusedxml to protect against XML bomb attacks (MEDIUM severity - Bandit B314, B405, B408, B318).

  • Code Injection Prevention: Added explicit # nosec B307 annotations to sandboxed eval() calls that use restricted SAFE_GLOBALS dictionary for formula evaluation in survey recipes.

Changed

  • Security Documentation: Added clarifying comments for temp directory usage patterns to document that they are read-only validation operations.

Fixed

  • Import Safety: Updated XML imports in pavlovia.py, limesurvey_exporter.py, and prism_to_limesurvey.py to use defusedxml with safe fallbacks.

  • Code Quality: Applied Black formatting and Ruff linting fixes across codebase.

[1.9.1] - 2026-01-21

Fixed

  • Windows Stability: Additional Windows-specific stability improvements and bug fixes.

[1.9.0] - 2026-01-21

Added

  • Cross-Platform: Native folder picker for Windows and Linux using tkinter with graceful fallbacks.

  • Windows Support: Platform-specific browser launching with Windows fallback (cmd /c start).

  • Logging: Comprehensive logging system for compiled Windows builds (prism_studio.log in user home directory).

  • Windows UI: Startup notification dialog showing application URL when browser doesn’t auto-launch.

  • Code Signing: Integrated free SignPath.io code signing for Windows executables in GitHub Actions.

  • Path Handling: Added Windows-specific temp path recognition in error messages.

  • Error Feedback: Enhanced error alerts for failed folder picker operations in all templates.

  • Documentation: Added comprehensive cross-platform development guides (CROSS_PLATFORM.md, DEVELOPING_FOR_WINDOWS_ON_MACOS.md, CODE_SIGNING_SETUP.md).

  • Setup Scripts: Added tkinter availability checks with installation instructions in setup.ps1 and setup.sh.

Changed

  • Folder Picker: Improved platform detection and error handling in /api/browse-folder endpoint.

  • Windows Compatibility: All templates (projects.html, recipes.html, survey_generator.html, converter.html) now show error messages when folder picker fails.

  • Build Workflow: GitHub Actions now automatically signs Windows executables when SignPath credentials are configured.

Fixed

  • Windows Paths: Removed all hardcoded Unix paths (/Users/karl/work/) from codebase.

  • Temp Paths: Fixed Windows temp directory patterns in path_utils.py (\Temp, \AppData, C:\Users).

  • Browser Launch: Fixed browser not opening on Windows compiled version.

  • Silent Errors: Fixed folder picker failing silently without user feedback.

  • Console Output: Fixed missing console output in Windows compiled builds using log redirection.

Security

  • Code Signing: Windows executables are now digitally signed by trusted CA (SignPath) for IT department compliance.

[1.8.1] - 2026-01-15

Fixed

  • Build: Fixed PyInstaller --add-data syntax error on Unix-based systems.

  • Build: Corrected --target-architecture flag for macOS Silicon builds.

  • Build: Fixed missing icon source path in build script.

[1.8.0] - 2026-01-15

Added

  • Project Tab: Enhanced participants.json management with required field highlighting and star indicators.

  • NeuroBagel Widget: Improved error handling instructions when the widget cannot be loaded.

  • CI/CD: Added multi-platform build support for macOS (Intel/Silicon), Linux, and Windows in GitHub Actions.

  • Conversion: Added file head preview in terminal and logs for TSV/CSV debugging to help diagnose delimiter issues.

Changed

  • UI: Removed confusing red error styling for mandatory fields in Project Tab.

  • Workflow: Updated build pipeline to generate specific artifacts for different architectures.

[1.7.1] - 2026-01-12

Added

  • Custom Recipes: Added support for custom recipe folders in survey and biometrics commands.

  • Project UI: Added dataset description API endpoints and metadata management.

  • Converter UI: Option to save conversion outputs directly to the project.

  • Logging: New logging helper for file previews and streamlined log processing in the converter UI.

Changed

  • BIDS Compatibility: Enhanced .bidsignore rules and integrated automatic updates during survey conversion.

  • Refactoring: Updated imports in the web module for improved organization.

Removed

  • Examples: Removed outdated example files.

[1.7.0] - 2026-01-12

Added

  • Workshop Materials: New PRISM workshop exercises and materials for data conversion, metadata creation, and SPSS export.

  • Alias Support: Implemented AliasOf and Aliases resolution in sidecar data and schemas for better handling of redundant definitions.

  • UI Enhancements: Added server shutdown functionality and quit button in the Web UI.

  • Project Management: Enhanced project selection enforcement and project management workflows.

Changed

  • Validation: Enhanced validation logic and reporting for eyetracking, physiological, func, and eeg modalities.

  • Reporting: Improved dataset statistics and task reporting in summaries.

  • Architecture: Refactored survey recipes and core code structure for improved maintainability and readability.

  • Logic: Updated participants.json resolution logic to be more robust across modules.

[1.6.6] - 2026-01-02

Changed

  • Documentation: Updated ReadTheDocs specifications with new schema keys and features.

  • Consistency: Synchronized version numbers across all project files (codemeta.json, CITATION.cff, etc.).

[1.6.5] - 2025-12-25

Added

  • Template Editor (Web UI): Create and edit Survey/Biometrics JSON templates with schema-derived field help.

  • Value-only editing: Keys are fixed; users edit values via form controls (no raw JSON/brackets for typical fields).

  • Item workflows: Add/select items (questions/metrics), edit per-item fields, validate, and download templates.

[1.6.2] - 2025-12-24

Added

  • Biometrics Support: Enhanced biometrics conversion and validation UI.

  • Methods Boilerplate: Added API endpoint and UI for generating methods boilerplate text.

  • Internationalization: Enhanced metadata structure for internationalization support.

  • Build Tools: Added macOS build script and enhanced Windows build version metadata.

  • Schemas: Added new PRISM schemas and example templates for survey and biometrics.

Changed

  • Refactoring: Improved output directory handling and validation for survey and biometrics imports.

  • Demo Data: Restructured demo dataset paths and related scripts.

[1.6.1] - 2025-12-22

Added

  • Survey Generator UI: Added display of response scales (levels), units, and value ranges for items in the Survey Export tool.

  • Metadata Extraction: Enhanced template info extraction to include item-level metadata (Scale, Units, Min/Max values).

  • Rebranding: Renamed repository to prism-studio and updated all internal/external references.

Fixed

  • Version Consistency: Synchronized version numbers across setup.py, src/__init__.py, prism.py, and API endpoints.

  • Documentation: Updated all documentation links and script names to reflect the new prism-studio branding.

[1.6.0] - 2025-12-20

Added

Survey Data Processing (PRISM Studio)

  • Survey import wizard with TSV/CSV/Excel support

  • Library-based conversion using template JSON schemas

  • Automatic participant detection from data columns

  • Value validation against library definitions (min/max/levels)

  • Missing value handling with configurable strategies

  • Detailed import logs with row-by-row feedback

Derivatives System

  • Survey scoring recipes in JSON format (derivatives/surveys/*.json)

  • Reverse coding support for inverted items

  • Subscale computation (sum, mean methods)

  • Multi-format export: CSV, Excel (with Codebook sheet), SPSS (.save), R/Feather

  • Rich metadata in exports: Variable labels, value labels, score details

  • Codebook generation: JSON and TSV codebooks with full documentation

  • Participant variables merge: Age, sex, education included in derivatives

PRISM Naming Conventions

  • Strict suffix validation for survey (_survey) and biometrics (_biometrics)

  • Physio and eyetrack suffixes added to BIDS regex

  • Task-based sidecar naming (task-<name>_survey.json)

Structured Issue System

  • PRISM error codes (PRISM001-PRISM9xx) with severity levels and categories

  • Error categories: dataset structure, file naming, sidecar/metadata, schema validation, content validation, BIDS compatibility, plugin errors

  • Comprehensive src/issues.py module for consistent error reporting

  • Updated docs/ERROR_CODES.md with complete error code reference

Output Formats

  • JSON output (--json, --json-pretty) for CI/CD integration

  • SARIF format (--format sarif) for GitHub Code Scanning

  • JUnit XML (--format junit) for test runners

  • Markdown (--format markdown) for documentation

  • CSV export (--format csv) for spreadsheet analysis

  • Output file redirection (-o, --output)

Auto-Fix System

  • Automatic fixing of common issues (--fix)

  • Dry-run mode (--dry-run) to preview fixes

  • Fixable issues: missing dataset_description.json, missing sidecars, .bidsignore updates

  • List all fixable issues (--list-fixes)

Plugin System

  • Custom validators via Python plugins in <dataset>/validators/

  • Plugin template generator (--init-plugin <name>)

  • Plugin discovery and loading (--list-plugins)

  • Plugin disable flag (--no-plugins)

  • Context-aware API with access to files, subjects, modalities

REST API

  • Blueprint-based API at /api/v1/

  • Endpoints: /health, /schemas, /schemas/<version>, /validate

  • JSON request/response format

  • Async validation with progress tracking

New Schemas

  • Physiological (physio) schema: ECG, EDA, respiration, PPG, EMG support

  • Eyetracking schema: gaze tracking, fixations, saccades

Survey Library

  • Bilingual survey templates (German + English in single JSON)

  • i18n system for compile-time language selection

  • Surveys: PHQ-9, GAD-7, PSS-10, WHO-5, Rosenberg, MAIA, PSQI, BDI, DANCEQ, HFerst, GoldDSI

  • Migration tools: prism_tools.py survey i18n-migrate and i18n-build

Project Configuration

  • .prismrc.json project config file support

  • Settings: default schema version, output format, strict mode, ignored patterns

  • Per-dataset configuration

Testing

  • pytest unit tests covering core functionality

  • Test coverage for issues, validators, config, formatters

  • Demo folder used for integration testing

Web Interface Enhancements

  • Derivatives page with terminal output log

  • Progress tracking with percentage and current file

  • Navbar links to Derivatives and ReadTheDocs

  • Server-Sent Events for real-time updates

  • API blueprint integration

Changed

  • Renamed entry script to prism-studio.py

  • CLI now uses structured error codes instead of free-form messages

  • Validation results include severity levels (error, warning, info)

  • Improved error messages with fix hints

Fixed

  • Fixed .gitignore to properly track test files

  • Fixed modality patterns to include JSON sidecars for physio/eyetrack

  • Fixed BIDS regex to accept physio, eyetrack, events suffixes

1.0.0 - 2025-10-09

Added - Major Release πŸŽ‰οƒ

This is the first major release of PRISM with comprehensive features for validating psychological research datasets.

Schema Versioning System

  • Docker-like schema versioning (stable, v0.1, etc.)

  • --schema-version CLI flag to specify validation schema version

  • --list-versions command to display available schema versions

  • Schema version selector in web interface (dropdown menu)

  • Version information included in all validation results

  • Automatic version normalization (supports both 0.1 and v0.1 formats)

  • Default to stable version when not specified

  • Comprehensive documentation for schema versioning

Web Interface Improvements

  • Schema version dropdown in upload form

  • Schema version selector for local folder validation

  • Updated results page to display schema version used

  • Improved logo display with correct aspect ratio

  • Enhanced user experience with clear version selection

Core Features

  • Multi-modal validation support (image, movie, audio, EEG, eye-tracking, behavior, physiological)

  • BIDS-inspired filename validation

  • JSON schema validation for metadata files

  • Cross-subject consistency checking

  • Comprehensive validation reports

  • Support for session-based and direct subject organization

  • Local folder validation (no upload required)

  • DataLad-style upload (metadata only, placeholders for large files)

Documentation

  • Added SCHEMA_VERSIONING_GUIDE.md - Complete user guide

  • Added SCHEMA_VERSIONING_IMPLEMENTATION.md - Technical details

  • Added SCHEMA_VERSIONING_QUICKREF.md - Quick reference

  • Added SCHEMA_VERSIONING_COMPLETE.md - Implementation summary

  • Added SCHEMA_VERSIONING_CHECKLIST.md - Development checklist

  • Added SCHEMA_VERSIONING_VISUAL.md - Visual documentation

  • Updated README.md with versioning information

Infrastructure

  • Created schemas/stable/ directory for stable schema version

  • Created schemas/v0.1/ directory for version 0.1

  • Enhanced schema_manager.py with version-aware loading

  • Updated runner.py to support schema version parameter

  • Improved web interface validation workflow

Changed

  • Updated main validator to accept schema_version parameter

  • Modified web interface to pass schema version through validation pipeline

  • Enhanced templates with schema version UI elements

  • Updated README with new features and examples

Technical Details

  • Python 3.10+ compatible

  • Flask-based web interface

  • JSON Schema validation

  • Cross-platform support (Windows, macOS, Linux)

  • Zero-dependency validation core

Migration Guide

For existing users:

  • No breaking changes - all existing code continues to work

  • Default behavior uses stable schema version

  • Explicitly specify version only if needed for specific use cases

  • See docs/SCHEMA_VERSIONING_GUIDE.md for detailed migration instructions

Release Notes

v1.0.0 Highlights

πŸŽ‰ First Major Release - PRISM is now production-ready!

Key Features:

  • βœ… Schema versioning system (Docker-like)

  • βœ… Web interface with schema selection

  • βœ… Command-line tools with version support

  • βœ… Comprehensive validation for psychological datasets

  • βœ… Complete documentation suite

What’s Next:

  • Schema diff utilities

  • Auto-migration tools

  • Enhanced modality support

  • CI/CD integration examples

Acknowledgments

  • Developed at MRI-Lab Graz, University of Graz

  • Maintained by Karl Koschutnig

  • Built for the research community ❀️

[1.3.0] - 2025-11-28

Changed

  • Project Rename: Renamed project from prism-studio to prism.

  • Repository Restructuring: Moved helper scripts to helpers/ directory.

  • Documentation: Updated all documentation to reflect the new name.