Paper2Agent_decoupleRpy

Running

Standalone, non-agent-facing upload gate (quarantine -> validate -> admin register). Inert until wired to a UI: no MCP tool, no server.py change, no new dependency. See docs/adr/ADR-0011-upload-safety-gate.md. 24 new tests green. This PR does NOT deploy until merged into main.

feat(uploads): ADR-0011 manual-upload safety gate (Now slice)74d4e89e

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This branch has merge conflicts in the following files:

.gitattributes
.gitignore
README.md
app.py
docs/adr/ADR-0003-spaces-dev-mode.md
docs/adr/ADR-0005-private-storage-persistence.md
docs/adr/ADR-0006-loveless-single-cell-serving.md
docs/adr/ADR-0010-dataset-integrity-verification.md
docs/adr/ADR-0011-upload-safety-gate.md
gradio_ui.py
prompts.yaml
requirements.in
requirements.txt
scripts/_gse205154_sears_common.py
scripts/_investigate_gpl6244.py
scripts/_precompute_common.py
scripts/_verify_precompute.py
scripts/assemble_cptac_pda.py
scripts/assemble_cptac_pda_counts.py
scripts/assemble_gse15471.py
scripts/assemble_gse16515_mayo.py
scripts/assemble_gse17891.py
scripts/assemble_gse205154_sears.py
scripts/assemble_gse205154_sears_counts.py
scripts/assemble_gse205154_sears_tmm.py
scripts/assemble_gse21501.py
scripts/assemble_gse28735_pdac.py
scripts/assemble_gse57495.py
scripts/assemble_gse62165_jiang.py
scripts/assemble_gse71729_moffitt.py
scripts/assemble_gse71989_chen.py
scripts/assemble_nones.py
scripts/assemble_paca_ca.py
scripts/fix_gse50827_nones_symbols.py
scripts/load_and_validate_geo.py
scripts/requirements-dev.txt
scripts/security_scan.sh
scripts/verify_s3_sink.py
security/.gitignore
security/sbom.json
server.py
src/agent.py
src/cache.py
src/core/__init__.py
src/core/combine.py
src/core/constants.py
src/core/data_io.py
src/core/integrity.py
src/core/perf.py
src/core/types.py
src/datasets/manifest_schema.py
src/datasets/registry.py
src/logging_sink.py
src/managers/__init__.py
src/managers/execution/__init__.py
src/managers/execution/python_executor.py
src/managers/hf_storage.py
src/managers/support/__init__.py
src/managers/support/console_display.py
src/managers/support/package_manager.py
src/managers/tools/__init__.py
src/managers/tools/builtin_tools.py
src/managers/tools/mcp_manager.py
src/managers/tools/tool_manager.py
src/managers/tools/tool_registry.py
src/managers/workflow/__init__.py
src/managers/workflow/plan_manager.py
src/managers/workflow/state_manager.py
src/managers/workflow/workflow_engine.py
src/mcp_server/dependencies/r_dependencies.py
src/semantic/__init__.py
src/semantic/gene_sets.py
src/semantic/gene_symbols.py
src/semantic/regulators.py
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src/semantic/semantic_audit.py
src/tools/bulk_dataset_tools.py
src/tools/bulk_rnaseq/__init__.py
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src/tools/bulk_rnaseq/tools.py
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src/tools/dataset_tools/_base.py
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src/tools/dataset_tools/metadata.py
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src/tools/licenses.py
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src/tools/rna_pstime.py
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src/tools/rna_visium.py
src/uploads/__init__.py
src/uploads/promotion.py
src/uploads/records.py
src/uploads/staging.py
src/uploads/validation.py
src/workflows/activity_scoring.py
src/workflows/activity_stats.py
src/workflows/concordance.py
src/workflows/geo.py
src/workflows/integration.py
src/workflows/manifest_data_validation.py
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src/workflows/metadata_validation.py
src/workflows/microarray.py
src/workflows/sanity_checks.py
src/workflows/signatures.py
src/workflows/survival.py
tests/test_activity_scoring.py
tests/test_bulk_dataset_url_loading.py
tests/test_clinical_join.py
tests/test_combine_conformance.py
tests/test_compare_activity_by_group.py
tests/test_concordance.py
tests/test_concordance_tool.py
tests/test_curated_sample_filter.py
tests/test_data_type_detection.py
tests/test_dataset_manifest_contract.py
tests/test_dataset_registry.py
tests/test_de_batch_covariate.py
tests/test_deseq2_workflow.py
tests/test_enrichment_contamination_wiring.py
tests/test_gdc_star_counts.py
tests/test_geo_workflow.py
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tests/test_loading_plan_url.py
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tests/test_manifest_data_validation.py
tests/test_meta_analysis.py
tests/test_meta_analyze_tool.py
tests/test_metadata_validation.py
tests/test_metadata_validation_helpers.py
tests/test_microarray_workflow.py
tests/test_moffitt_integration.py
tests/test_planner_tool.py
tests/test_pool_cohorts_tool.py
tests/test_rna_sc_loader.py
tests/test_sanity_checks.py
tests/test_semantic_audit.py
tests/test_semantic_gene_symbols.py
tests/test_semantic_regulators.py
tests/test_semantic_result_annotation.py
tests/test_signatures.py
tests/test_tcga_paad_integration.py
tests/test_tool_registry.py
tests/test_tool_response_schemas.py
tests/test_upload_gate.py
tests/test_url_counts_loader.py
ui_formatting.py

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