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- Refactor generate_data_entry_excel(): replace example_data bool with prefill_metadata param (NULL | data.frame | CSV/TSV path); default loads inst/extdata/cMD_prefill_example.csv - Add load_prefill_metadata() and split_prefill_values() internal helpers - Add inst/extdata/cMD_prefill_example.csv (4 example rows) - Update man/, inst/scripts/generate_excel_template.R, README_EXCEL_GENERATION.md - Update tests: example_data=FALSE -> prefill_metadata=NULL; add data.frame prefill test - Add .github/ISSUE_TEMPLATE/cMD_sra_curation.yml (BioProject, attachment, DOI fields) - Add .github/workflows/metadata-curation-agent.yml (HITL loop: intake-and-map + process-curator-response jobs; ubuntu-latest + r-lib/actions; state on curation-state/issue-N branch; LLM via GitHub Models API gpt-4o-mini) - Add inst/scripts/agent_state.R (init/update_mapping/apply_response/status) - Add inst/scripts/agent_metadata_lookup.R (SRA/BioSample fetch + attachment join) - Add inst/scripts/agent_column_mapping.R (LLM + adist heuristic fallback) - Add inst/scripts/agent_prefill_excel.R (state -> prefill df -> Excel) - Add tests/testthat/test-agent-scripts.R (46 tests, 0 failures)
Metadata Validation ReportDate: $(date -u +"%Y-%m-%d %H:%M:%S UTC") Schema Information
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Title
feat: issue-triggered metadata curation agent + Excel prefill API
Summary
This PR adds an issue-triggered GitHub Actions curation flow with human-in-the-loop (HITL) mapping review, and refactors Excel template generation to use explicit metadata prefilling.
What changed
example_dataingenerate_data_entry_excel()withprefill_metadataNULL,data.frame, or CSV/TSV pathinst/extdatacMD_prefill_example.csv)gpt-4o-mini) with heuristic fallbackcuration-state/issue-<N>branchagent_state.Ragent_metadata_lookup.Ragent_column_mapping.Ragent_prefill_excel.Rprefill_metadataAPITesting
devtools::test(filter = "excel-generation")passeddevtools::test(filter = "agent-scripts")passed (46 passed, 0 failed, 0 warnings)Notes
ubuntu-latest+r-lib/actionssetup (no Bioconductor Docker).GITHUB_TOKENis available; otherwise heuristic mapping is used.AI Attribution
This PR was developed with assistance from GitHub Copilot (GPT-5.3-Codex) "Planning" Agent.
These changes have NOT yet been manually tested - only the AI-generated machine tests. Many features require GitHub Actions and Issues for testing.