Changelog

v2.0.6

Phenopacket Export Pipeline:

• Fixed camelCase serialization in Phenopacket JSON output (preserving_proto_field_name=False), producing valid GA4GH Phenopacket v2 JSON (#205)

• Integrated validate.py into the export pipeline with a two-tier approach: Python-native structural checks (required fields, CURIE format, schema version) plus optional phenopacket-tools CLI fallback when available on PATH

• Added ontology-prefix placement checks as soft validation warnings (e.g. HP: terms outside phenotypicFeatures, MONDO: terms outside diseases)

• Improved CLI export with Rich progress bars: sequential two-phase display (creation bar completes before validation bar appears)

• Added structured warnings system: mapper warnings (e.g. “No diagnosis ID found”) now use warnings.warn() consistently, are captured per-record with record ID context, and displayed in the export summary

• Added warnings.json output file alongside failures.json for detailed warning inspection

• Export summary now includes a Warnings column for both creation and validation stages with deduplicated counts

RD-CDM v2.0.3 Integration:

• Updated to rd-cdm v2.0.3 with eleven updated ontology/code system versions and the replacement of the deprecated SNOMED CT Sex at Birth concept with LOINC 76689-9

• Updated the RareLink-CDM REDCap data dictionary and instruments to reflect rd-cdm v2.0.3 changes

• Updated Phenopacket and FHIR export pipelines to use the revised code systems and data element definitions

Ontology Routing Adapter:

• Designed ontology_routing_adapter.py for use cases where single repeated elements contain mixed ontology prefixes (e.g. HP and MONDO codes in the same instrument), enabling automatic routing of HP codes to phenotypicFeatures and MONDO/OMIM/ORDO codes to diseases (#207)

Package & Dependencies:

• Reduced core dependencies from ~20 to ~10 by moving test, docs, Docker, numpy, and pandas to optional extras ([test], [docs], [fhir], [data], [dev])

• Removed unused dependencies: node, npm, config, schema-automator, tqdm

• Removed the rarelink_cdm/rd_cdm/ codegen subfolder (unused at runtime); future versions will import directly from the rd-cdm PyPI package

Infrastructure:

• Fixed toFHIR Docker Compose: updated Kafka image references from deprecated bitnami/kafka:latest to bitnamilegacy/kafka:3.7.0 following Bitnami’s August 2025 image deprecation (#210)

• Added .DS_Store to .gitignore (#202)

Documentation & Tests:

• Updated installation docs to document optional extras (pip install rarelink[fhir], pip install rarelink[data], etc.)

• Updated tests to work with PipelineResult dataclass return type and corrected mock patch paths

• Removed unused numpy/pandas references from Sphinx conf.py

v2.0.5 (2025-12-12)

• Fixed a few of bugs

• enhanced versioning and refactored repo folders

• improved the functionality of MedicalActions for Phenopackets export

• included MaXo as a novel coding system into the LinkML schema, Python classes, REDCap data dictionary and for Phenopackets export.

• See release notes here for more detail: https://github.com/BIH-CEI/rarelink/releases/tag/v2.0.5

v2.0.4 (2025-09-25)

• FHIR Export: fixed CLI export and tofhir config .yml and docker files for the FHIR export and module

• FHIR IG: fixed image paths in the FHIR IG to correctly display the RD-CDM image

v2.0.3 (2025-09-24)

• FHIR-IG: Fixed RareLink FHIR IG version label back to 2.0.0

• PyPi package: Excluded the entire FHIR IG from the PyPi package to reduce package size (in a future version the RareLink FHIR IG will be published as a separate Git repo and package)

• Figure: Updated overview Figure in the README and documentation to reflect the current state of the RareLink framework

• RareLink-Phenopacket engine: fixed Metadata mapper to correctly include the ontologies within the VariationDescriptors

• RareLink-Phenopacket engine: fixed label fetching from local JSONs for pipeline

• Warnings: fixed DeprecationWarnings in code and tests

v2.0.2 (including v2.0.1)

The current version now published is v2.0.1.

The following changes have been made since the last version:

Dynamic versioning for code systems:

• Implemented dynamic retrieval of the latest CodeSystemsContainer definitions from the RD-CDM PyPi package so that the RareLink-CDM always reflects the most current ontology/code system versions.

• The RareLink/CDM engine also updates the entire RareLink-CDM and its toFHIR mappings when updates of element codes or ontology versions were made to the RD-CDM package.

• The MetaData mapper of the Phenopacket Engine now scans actual Phenopacket content to detect which code systems (e.g., MONDO, HPO, LOINC, HGVS, GENO) are used and inserts only those resources with their correct, up-to-date version identifiers to ensure generated Phenopackets remain consistent with the latest controlled vocabularies without manual version updates.

Phenopacket Pipeline:

• included automatic conversion the zygosity LOINC codes from the RareLink-CDM to the GENO ontologies. This ensures compliance with Phenopacket-analysis algorithms such as `GPSEA<https://www.medrxiv.org/content/10.1101/2025.03.05.25323315.abstract>`_.

• deacivated for the Phenopacket pipeline because the HGVS variant remains required for the pipeline and includes the structural variant information.

• included automatic transversion syntax code from hgvs to hgvs.c, hgvs.g, hgvs.p, and hgvs.m for HGVS variants depending on the variant type. This ensures compliance with Phenopacket-analysis algorithms such as GPSEA.

• Fixed serialization of vital_status so that in the case of an empty or unknown (3.1) Vital Status within the RareLink-CDM, the default Phenopacket status ``UNKNOWN_STATUS``is passed to the Phenopacket.

Updated _rarelink_redcap_validate_hgvs command:

• Added –hgvs-variable (-v) option to the validate-hgvs CLI command

• Users can now supply one or more custom HGVS field names; if omitted, the default HGVS_VARIABLES list is used.

• Enhanced validate_and_encode_hgvs to recursively scan nested dicts and lists for HGVS variables at any depth

• Refactored the CLI command to pass the user-provided hgvs_variables list (or fall back to defaults) into the validator

• Documentation updated to reflect the new hgvs-variable option and the improved nesting behavior

Customising the RareLink-CDM data dictionary:

• Added a section on how to customise the RareLink-CDM data dictionary to suit your specific needs or simplify manual data capture: Customise the Data Dictionary.

• This includes guidelines on how to hide fields, change field labels and descriptions, and add new fields and instruments as extensions to the RareLink-CDM.

• Added the hint on the REDCap Multi-languag Management for the RareLink-CDM

Published on PyPi

• The RareLink package is now available on PyPi, making it easier to install and use: https://pypi.org/project/rarelink/.

Fixed bugs:

• Fixed the Windows bug within the masked_input CLI tool function for the CLI command rarelink setup keys.

v2.0.0

First published and stable version of RareLink. This version includes the initial set of features and functionalities that were developed and tested.

Also, the FHIR Implementation Guide is finished, validated through the IG publisher including the test instances, and is available at: https://bih-cei.github.io/rarelink/.

v2.0.0.dev1 (Under Development)

This version was unstable and was used for testing and development purposes. It is not recommended for production use.

Previous versions (up to v2.0):

• The ERKER project was the previous version of RareLink and can still be found in the ERKER GitHub repository. However, the ERKER project is no longer maintained and has been replaced by RareLink.