STU4 draft as R6 IG - #117
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October 13, 2025 13:01
- Updated sushi-config.yaml: version 4.0.0-cibuild, copyright 2025+, release label 'CI Build', fixed page filename cases - Updated publication-request.json: version 4.0.0-cibuild, path STU4-snapshot, R4-specific descriptions - Improved fsh.ini: removed duplicate [FSH] section - Enhanced input/ignoreWarnings.txt: added R4-appropriate suppressions, improved wildcard patterns - Updated build scripts: improved text descriptions - Fixed case sensitivity issues: molecularsequence.html, groupingguidance.html, glossary.html - Cleaned up obsolete continuous build scripts
- CGCodeSystem.fsh: Restored complete descriptions for biomarker-category, protein-ref-seq, and conservation-score codes - CGValueSets.fsh: Applied full LOINC display names and added documentation comments for better readability - CGConceptMaps.fsh: Improved structure with dynamic FSH syntax, better spacing, and full URLs
- Applied R4-compatible enhancements including: * Component-level extensions and improved spacing * Array indexing improvements and consistent formatting * Extension naming standardization (workflow-relatedArtifact) * Quote consistency and documentation improvements - Modernized extension usage: * Replaced local RelatedArtifactComponent extension with standard workflow-relatedArtifact * Removed redundant extension definition (now supported in FHIR Extension pack) * Updated all example instances to use standardized extension references - Updated ignoreWarnings.txt to reflect modern extension usage
- Added comprehensive artifacts page with better organization - Separates artifacts into logical sections: * Abstract Profiles, Resource Profiles, Data Type Profiles * Extensions, Code Systems, Value Sets, Concept Maps * Operations, Parameters, and Examples grouped by profile - Enabled artifacts page in navigation menu
- Added local HLA extensions that were deprecated in FHIR Extensions pack - Updated ignoreWarnings.txt with additional suppressed warnings - Updated concept maps and general profiles - Enhanced artifacts.md page formatting and organization
Major Changes: - Converted all pages XML pages to Markdown format - Updated sushi-config.yaml with generation: markdown for all converted pages
Complete Conversion:
- Converted all 51 XML intro-notes files to Markdown format
Formatting Enhancements:
- Applied proper STU Note formatting using markdown blockquotes with {:.stu-note}
- Converted HTTP request examples to pre blocks with proper styling
- Added {:.grid} styling to all tables (19 files) for consistent presentation
- Enhanced responsive image styling with proper div containers
Make changes to be compatible with R6. Convert all XML/HTML files to markdown (for easier changes and tracking).
…here the error msg changed
The 'workflow-relatedArtifact' extension now allows Observation.component as a context, so we don't need our local extension any longer.
…'s with 'updated content' css class.
See here for the error report: https://jira.hl7.org/browse/FHIR-53272
…ges, some text updates).Clean up of some old images
remove extraneous tracking file
Revert references to use standard FHIR extension URLs, even though they are deprecateded.
commit 630a304 Author: sirkyp <sirkyp@gmail.com> Date: Fri Nov 7 15:13:31 2025 -0600 Revert HLA extensions Revert references to use standard FHIR extension URLs, even though they are deprecateded.
* Fix grammar and spelling errors in Markdown files Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com> Co-authored-by: sirkyp <18217553+sirkyp@users.noreply.github.com>
Introduces build-local-tx.sh and test-local-tx.sh for building and validating the IG against a local terminology server. Adds README-LOCAL-TX.md and copilot-instructions.md to document local terminology workflows. Updates ignoreWarnings.txt to remove legacy code system warnings and clarify suppression rationale.
Removed the $GTR alias from Aliases.fsh and updated example Bundle files to use method.text instead of referencing $GTR. The examples were not valid GTR codes anyway, so we don't need to support GTR for now.
Standardizes coding values and identifiers across multiple FSH example files for consistency with external vocabularies (e.g., PharmVar, HGNC, Sequence Ontology, HLA, ClinVar). Updates include correcting gene studied codes, refining coding-change-type and changeType values, improving valueCodeableConcept structures, and updating documentation to reflect new coding conventions.
merge corrections.
…ions - Updated HLA allele codes in multiple FSH examples to use new accession numbers. - Enhanced descriptions for valueCodeableConcept in various examples to provide clearer context. - Removed deprecated coding.version fields and replaced them with appropriate coding references. - Consolidated genetic variant representations for clarity and consistency across examples. - Removed the local terminology server check script as it is no longer needed.
Standardize and correct HLA allele valueCodeableConcept strings in multiple FSH example files. Removed parenthetical gene annotations (e.g., " (A*)") and updated several allele identifiers across input/fsh/examples/* (bundle-CG-IG-HLA-FullBundle-01.fsh, bundle-cgexample.fsh, bundle-cgexample-withGrouping.fsh, haplotype-hla-a-1-r4.fsh, somaticReportPDFexamples.fsh) to normalize allele formatting and fix mismatched example values.
…n using local tx server).
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First draft of converting to an R6 based IG. Fixed all breaking changes from R4 -> R6, including commenting out examples of MolSeq and remove profiles of GenomicStudy while changing examples over to new GenomicStudy resource. Lastly to help better manage and track documentation changes, converted all XML/HTML files to markdown.
This does NOT include any documentation changes (other than a few tweaks to help with the conversion to markdown), including no diagram updates. This also does not change of the MolSeq guidance over to MolDef.
In short, this isn't usable yet, but is a starting point as we move towards R6.