mednotes-opencode 0.1.0
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- package/.opencode/agents/med-chat-triager.md +204 -0
- package/.opencode/agents/med-flashcard-maker.md +63 -0
- package/.opencode/agents/med-knowledge-architect.md +230 -0
- package/.opencode/agents/med-link-graph-curator.md +177 -0
- package/.opencode/agents/med-publish-guard.md +62 -0
- package/.opencode/commands/flashcards.md +25 -0
- package/.opencode/commands/mednotes/create.md +25 -0
- package/.opencode/commands/mednotes/enrich.md +27 -0
- package/.opencode/commands/mednotes/fix-wiki.md +27 -0
- package/.opencode/commands/mednotes/history.md +22 -0
- package/.opencode/commands/mednotes/link-body.md +25 -0
- package/.opencode/commands/mednotes/link-related.md +27 -0
- package/.opencode/commands/mednotes/link.md +27 -0
- package/.opencode/commands/mednotes/pdf-library.md +27 -0
- package/.opencode/commands/mednotes/process-chats.md +23 -0
- package/.opencode/commands/mednotes/setup.md +21 -0
- package/.opencode/commands/mednotes/status.md +27 -0
- package/.opencode/commands/mednotes/telemetry.md +27 -0
- package/.opencode/commands/report.md +26 -0
- package/.opencode/mednotes/AGENTS.md +57 -0
- package/.opencode/mednotes/agents/med-chat-triager.md +197 -0
- package/.opencode/mednotes/agents/med-flashcard-maker.md +56 -0
- package/.opencode/mednotes/agents/med-knowledge-architect.md +224 -0
- package/.opencode/mednotes/agents/med-link-graph-curator.md +171 -0
- package/.opencode/mednotes/agents/med-publish-guard.md +55 -0
- package/.opencode/mednotes/contracts/.gitkeep +1 -0
- package/.opencode/mednotes/contracts/agents.json +116 -0
- package/.opencode/mednotes/contracts/opencode-plugin.json +70 -0
- package/.opencode/mednotes/docs/agent-prompt-hardening.md +567 -0
- package/.opencode/mednotes/docs/agent-role-contracts.md +94 -0
- package/.opencode/mednotes/docs/anki-mcp-twenty-rules.md +214 -0
- package/.opencode/mednotes/docs/anki-templates/README.md +39 -0
- package/.opencode/mednotes/docs/anki-templates/cloze.back.html +23 -0
- package/.opencode/mednotes/docs/anki-templates/cloze.front.html +14 -0
- package/.opencode/mednotes/docs/anki-templates/qa.back.html +24 -0
- package/.opencode/mednotes/docs/anki-templates/qa.front.html +14 -0
- package/.opencode/mednotes/docs/anki-templates/style.css +182 -0
- package/.opencode/mednotes/docs/atomicity-splitting-policy.md +113 -0
- package/.opencode/mednotes/docs/extension-docs.md +40 -0
- package/.opencode/mednotes/docs/flashcard-ingestion.md +278 -0
- package/.opencode/mednotes/docs/knowledge-architect.md +208 -0
- package/.opencode/mednotes/docs/merge-policy.md +110 -0
- package/.opencode/mednotes/docs/public-vocabulary.md +104 -0
- package/.opencode/mednotes/docs/semantic-linker.md +141 -0
- package/.opencode/mednotes/docs/taxonomy-policy.md +90 -0
- package/.opencode/mednotes/docs/triage-policy.md +187 -0
- package/.opencode/mednotes/docs/vault-version-control.md +758 -0
- package/.opencode/mednotes/docs/vocabulary-db-recovery.md +58 -0
- package/.opencode/mednotes/docs/workflow-output-contract.md +779 -0
- package/.opencode/mednotes/hooks/hooks.json +79 -0
- package/.opencode/mednotes/package-lock.json +6361 -0
- package/.opencode/mednotes/package.json +15 -0
- package/.opencode/mednotes/pyproject.toml +48 -0
- package/.opencode/mednotes/scripts/bootstrap_windows_python_uv.cmd +13 -0
- package/.opencode/mednotes/scripts/bootstrap_windows_python_uv.ps1 +172 -0
- package/.opencode/mednotes/scripts/enrich_notes.py +23 -0
- package/.opencode/mednotes/scripts/full_reset_windows_python_uv.cmd +13 -0
- package/.opencode/mednotes/scripts/hooks/antigravity_hook_status.mjs +212 -0
- package/.opencode/mednotes/scripts/hooks/mednotes_hook/adapters/antigravity.mjs +169 -0
- package/.opencode/mednotes/scripts/hooks/mednotes_hook/adapters/harness_payload.mjs +103 -0
- package/.opencode/mednotes/scripts/hooks/mednotes_hook/adapters/opencode_plugin.mjs +341 -0
- package/.opencode/mednotes/scripts/hooks/mednotes_hook/adapters/opencode_user_config_sync.mjs +177 -0
- package/.opencode/mednotes/scripts/hooks/mednotes_hook/anki_preflight.mjs +214 -0
- package/.opencode/mednotes/scripts/hooks/mednotes_hook/cli.mjs +143 -0
- package/.opencode/mednotes/scripts/hooks/mednotes_hook/diagnostics.mjs +11 -0
- package/.opencode/mednotes/scripts/hooks/mednotes_hook/domain/agent_directive_core.mjs +160 -0
- package/.opencode/mednotes/scripts/hooks/mednotes_hook/fsm_directive.mjs +1470 -0
- package/.opencode/mednotes/scripts/hooks/mednotes_hook/hook_errors.mjs +120 -0
- package/.opencode/mednotes/scripts/hooks/mednotes_hook/retention.mjs +114 -0
- package/.opencode/mednotes/scripts/hooks/mednotes_hook/runtime.mjs +174 -0
- package/.opencode/mednotes/scripts/hooks/mednotes_hook/telemetry_capture.mjs +511 -0
- package/.opencode/mednotes/scripts/hooks/mednotes_hook/vault_guard.mjs +624 -0
- package/.opencode/mednotes/scripts/hooks/mednotes_hook.mjs +5 -0
- package/.opencode/mednotes/scripts/mednotes/_runtime_paths.py +24 -0
- package/.opencode/mednotes/scripts/mednotes/anki_model_validator.py +18 -0
- package/.opencode/mednotes/scripts/mednotes/capture_extension_diff.py +1562 -0
- package/.opencode/mednotes/scripts/mednotes/feedback_report.py +16 -0
- package/.opencode/mednotes/scripts/mednotes/flashcard_index.py +18 -0
- package/.opencode/mednotes/scripts/mednotes/flashcard_pipeline.py +18 -0
- package/.opencode/mednotes/scripts/mednotes/flashcard_report.py +18 -0
- package/.opencode/mednotes/scripts/mednotes/flashcard_sources.py +18 -0
- package/.opencode/mednotes/scripts/mednotes/obsidian/README.md +6 -0
- package/.opencode/mednotes/scripts/mednotes/obsidian_note_utils.py +20 -0
- package/.opencode/mednotes/scripts/mednotes/pdf_library/cli.py +16 -0
- package/.opencode/mednotes/scripts/mednotes/project_fsm.py +229 -0
- package/.opencode/mednotes/scripts/mednotes/setup_telemetry_email.py +404 -0
- package/.opencode/mednotes/scripts/mednotes/sync_anki_twenty_rules.py +18 -0
- package/.opencode/mednotes/scripts/mednotes/sync_opencode_user_config.py +36 -0
- package/.opencode/mednotes/scripts/mednotes/wiki/cli.py +20 -0
- package/.opencode/mednotes/scripts/mednotes/wiki_graph.py +18 -0
- package/.opencode/mednotes/scripts/mednotes/wiki_tree.py +134 -0
- package/.opencode/mednotes/scripts/reset_windows_python_uv.ps1 +625 -0
- package/.opencode/mednotes/scripts/run_python.mjs +109 -0
- package/.opencode/mednotes/scripts/vault/vault_commit.ps1 +19 -0
- package/.opencode/mednotes/scripts/vault/vault_commit.sh +18 -0
- package/.opencode/mednotes/scripts/vault/vault_git.ps1 +19 -0
- package/.opencode/mednotes/scripts/vault/vault_git.py +3107 -0
- package/.opencode/mednotes/scripts/vault/vault_git.sh +18 -0
- package/.opencode/mednotes/scripts/vault/vault_precommit.ps1 +19 -0
- package/.opencode/mednotes/scripts/vault/vault_precommit.sh +18 -0
- package/.opencode/mednotes/skills/THIRD_PARTY_NOTICES.md +45 -0
- package/.opencode/mednotes/skills/create-medical-flashcards/SKILL.md +113 -0
- package/.opencode/mednotes/skills/create-medical-note/SKILL.md +90 -0
- package/.opencode/mednotes/skills/enrich-medical-note/SKILL.md +120 -0
- package/.opencode/mednotes/skills/fix-medical-wiki/SKILL.md +559 -0
- package/.opencode/mednotes/skills/link-medical-wiki/SKILL.md +224 -0
- package/.opencode/mednotes/skills/obsidian-cli/SKILL.md +118 -0
- package/.opencode/mednotes/skills/obsidian-markdown/SKILL.md +207 -0
- package/.opencode/mednotes/skills/obsidian-markdown/references/CALLOUTS.md +58 -0
- package/.opencode/mednotes/skills/obsidian-markdown/references/EMBEDS.md +63 -0
- package/.opencode/mednotes/skills/obsidian-markdown/references/PROPERTIES.md +61 -0
- package/.opencode/mednotes/skills/obsidian-ops/SKILL.md +136 -0
- package/.opencode/mednotes/skills/pdf-library/SKILL.md +45 -0
- package/.opencode/mednotes/skills/process-medical-chats/SKILL.md +246 -0
- package/.opencode/mednotes/skills/workflow-report/SKILL.md +100 -0
- package/.opencode/mednotes/src/mednotes/__init__.py +5 -0
- package/.opencode/mednotes/src/mednotes/domains/__init__.py +5 -0
- package/.opencode/mednotes/src/mednotes/domains/flashcards/README.md +26 -0
- package/.opencode/mednotes/src/mednotes/domains/flashcards/__init__.py +2 -0
- package/.opencode/mednotes/src/mednotes/domains/flashcards/build_demo_apkg.py +177 -0
- package/.opencode/mednotes/src/mednotes/domains/flashcards/contracts.py +385 -0
- package/.opencode/mednotes/src/mednotes/domains/flashcards/flashcards_machine.py +522 -0
- package/.opencode/mednotes/src/mednotes/domains/flashcards/fsm.py +817 -0
- package/.opencode/mednotes/src/mednotes/domains/flashcards/index.py +630 -0
- package/.opencode/mednotes/src/mednotes/domains/flashcards/install_models.py +445 -0
- package/.opencode/mednotes/src/mednotes/domains/flashcards/model.py +359 -0
- package/.opencode/mednotes/src/mednotes/domains/flashcards/obsidian_links.py +135 -0
- package/.opencode/mednotes/src/mednotes/domains/flashcards/obsidian_note_utils.py +546 -0
- package/.opencode/mednotes/src/mednotes/domains/flashcards/pipeline.py +580 -0
- package/.opencode/mednotes/src/mednotes/domains/flashcards/report.py +510 -0
- package/.opencode/mednotes/src/mednotes/domains/flashcards/sources.py +682 -0
- package/.opencode/mednotes/src/mednotes/domains/flashcards/sync_rules.py +184 -0
- package/.opencode/mednotes/src/mednotes/domains/history/__init__.py +1 -0
- package/.opencode/mednotes/src/mednotes/domains/history/history_fsm.py +852 -0
- package/.opencode/mednotes/src/mednotes/domains/history/history_machine.py +453 -0
- package/.opencode/mednotes/src/mednotes/domains/setup/__init__.py +7 -0
- package/.opencode/mednotes/src/mednotes/domains/setup/setup_fsm.py +808 -0
- package/.opencode/mednotes/src/mednotes/domains/setup/setup_machine.py +973 -0
- package/.opencode/mednotes/src/mednotes/domains/wiki/README.md +64 -0
- package/.opencode/mednotes/src/mednotes/domains/wiki/__init__.py +1 -0
- package/.opencode/mednotes/src/mednotes/domains/wiki/api.py +668 -0
- package/.opencode/mednotes/src/mednotes/domains/wiki/batch_state.py +102 -0
- package/.opencode/mednotes/src/mednotes/domains/wiki/capabilities/__init__.py +1 -0
- package/.opencode/mednotes/src/mednotes/domains/wiki/capabilities/atomicity/__init__.py +1 -0
- package/.opencode/mednotes/src/mednotes/domains/wiki/capabilities/atomicity/atomicity.py +877 -0
- package/.opencode/mednotes/src/mednotes/domains/wiki/capabilities/body_link/__init__.py +1 -0
- package/.opencode/mednotes/src/mednotes/domains/wiki/capabilities/body_link/body_linker.py +1562 -0
- package/.opencode/mednotes/src/mednotes/domains/wiki/capabilities/effects/__init__.py +1 -0
- package/.opencode/mednotes/src/mednotes/domains/wiki/capabilities/effects/effect_adapters.py +949 -0
- package/.opencode/mednotes/src/mednotes/domains/wiki/capabilities/effects/fix_wiki_runtime_adapters.py +433 -0
- package/.opencode/mednotes/src/mednotes/domains/wiki/capabilities/graph/__init__.py +1 -0
- package/.opencode/mednotes/src/mednotes/domains/wiki/capabilities/graph/coverage.py +413 -0
- package/.opencode/mednotes/src/mednotes/domains/wiki/capabilities/graph/graph.py +396 -0
- package/.opencode/mednotes/src/mednotes/domains/wiki/capabilities/graph/graph_fixes.py +161 -0
- package/.opencode/mednotes/src/mednotes/domains/wiki/capabilities/hygiene/__init__.py +1 -0
- package/.opencode/mednotes/src/mednotes/domains/wiki/capabilities/hygiene/hygiene.py +483 -0
- package/.opencode/mednotes/src/mednotes/domains/wiki/capabilities/illustrate/__init__.py +2 -0
- package/.opencode/mednotes/src/mednotes/domains/wiki/capabilities/illustrate/anchors.py +185 -0
- package/.opencode/mednotes/src/mednotes/domains/wiki/capabilities/illustrate/core/__init__.py +0 -0
- package/.opencode/mednotes/src/mednotes/domains/wiki/capabilities/illustrate/core/cache.py +223 -0
- package/.opencode/mednotes/src/mednotes/domains/wiki/capabilities/illustrate/core/config.py +131 -0
- package/.opencode/mednotes/src/mednotes/domains/wiki/capabilities/illustrate/core/download.py +224 -0
- package/.opencode/mednotes/src/mednotes/domains/wiki/capabilities/illustrate/core/frontmatter.py +59 -0
- package/.opencode/mednotes/src/mednotes/domains/wiki/capabilities/illustrate/core/insert.py +227 -0
- package/.opencode/mednotes/src/mednotes/domains/wiki/capabilities/illustrate/core/local_import.py +54 -0
- package/.opencode/mednotes/src/mednotes/domains/wiki/capabilities/illustrate/sources/__init__.py +42 -0
- package/.opencode/mednotes/src/mednotes/domains/wiki/capabilities/illustrate/sources/web_profiles.py +99 -0
- package/.opencode/mednotes/src/mednotes/domains/wiki/capabilities/illustrate/sources/web_search.py +203 -0
- package/.opencode/mednotes/src/mednotes/domains/wiki/capabilities/illustrate/sources/wikimedia.py +102 -0
- package/.opencode/mednotes/src/mednotes/domains/wiki/capabilities/markdown/__init__.py +1 -0
- package/.opencode/mednotes/src/mednotes/domains/wiki/capabilities/markdown/markdown_db_adapter.mjs +434 -0
- package/.opencode/mednotes/src/mednotes/domains/wiki/capabilities/markdown/markdown_node_runtime.py +274 -0
- package/.opencode/mednotes/src/mednotes/domains/wiki/capabilities/markdown/markdown_query.py +227 -0
- package/.opencode/mednotes/src/mednotes/domains/wiki/capabilities/notes/__init__.py +1 -0
- package/.opencode/mednotes/src/mednotes/domains/wiki/capabilities/notes/artifacts.py +605 -0
- package/.opencode/mednotes/src/mednotes/domains/wiki/capabilities/notes/canonical_merge.py +277 -0
- package/.opencode/mednotes/src/mednotes/domains/wiki/capabilities/notes/markdown_zones.py +85 -0
- package/.opencode/mednotes/src/mednotes/domains/wiki/capabilities/notes/meaning_planner.py +307 -0
- package/.opencode/mednotes/src/mednotes/domains/wiki/capabilities/notes/note_iter.py +67 -0
- package/.opencode/mednotes/src/mednotes/domains/wiki/capabilities/notes/note_merge.py +278 -0
- package/.opencode/mednotes/src/mednotes/domains/wiki/capabilities/notes/note_plan.py +409 -0
- package/.opencode/mednotes/src/mednotes/domains/wiki/capabilities/notes/note_policy.py +22 -0
- package/.opencode/mednotes/src/mednotes/domains/wiki/capabilities/notes/note_style/__init__.py +79 -0
- package/.opencode/mednotes/src/mednotes/domains/wiki/capabilities/notes/note_style/fixes.py +264 -0
- package/.opencode/mednotes/src/mednotes/domains/wiki/capabilities/notes/note_style/frontmatter.py +435 -0
- package/.opencode/mednotes/src/mednotes/domains/wiki/capabilities/notes/note_style/models.py +208 -0
- package/.opencode/mednotes/src/mednotes/domains/wiki/capabilities/notes/note_style/prompts.py +37 -0
- package/.opencode/mednotes/src/mednotes/domains/wiki/capabilities/notes/note_style/tables.py +236 -0
- package/.opencode/mednotes/src/mednotes/domains/wiki/capabilities/notes/note_style/validate.py +404 -0
- package/.opencode/mednotes/src/mednotes/domains/wiki/capabilities/notes/provenance.py +478 -0
- package/.opencode/mednotes/src/mednotes/domains/wiki/capabilities/notes/raw_chats.py +273 -0
- package/.opencode/mednotes/src/mednotes/domains/wiki/capabilities/notes/sources_backfill.py +235 -0
- package/.opencode/mednotes/src/mednotes/domains/wiki/capabilities/pdf/__init__.py +10 -0
- package/.opencode/mednotes/src/mednotes/domains/wiki/capabilities/pdf/anchors.py +16 -0
- package/.opencode/mednotes/src/mednotes/domains/wiki/capabilities/pdf/captions.py +47 -0
- package/.opencode/mednotes/src/mednotes/domains/wiki/capabilities/pdf/cli.py +179 -0
- package/.opencode/mednotes/src/mednotes/domains/wiki/capabilities/pdf/cloud.py +52 -0
- package/.opencode/mednotes/src/mednotes/domains/wiki/capabilities/pdf/config.py +196 -0
- package/.opencode/mednotes/src/mednotes/domains/wiki/capabilities/pdf/context_packets.py +76 -0
- package/.opencode/mednotes/src/mednotes/domains/wiki/capabilities/pdf/db.py +81 -0
- package/.opencode/mednotes/src/mednotes/domains/wiki/capabilities/pdf/doctor.py +102 -0
- package/.opencode/mednotes/src/mednotes/domains/wiki/capabilities/pdf/figure_ids.py +42 -0
- package/.opencode/mednotes/src/mednotes/domains/wiki/capabilities/pdf/ingest.py +326 -0
- package/.opencode/mednotes/src/mednotes/domains/wiki/capabilities/pdf/insert.py +316 -0
- package/.opencode/mednotes/src/mednotes/domains/wiki/capabilities/pdf/mentions.py +57 -0
- package/.opencode/mednotes/src/mednotes/domains/wiki/capabilities/pdf/ocr.py +71 -0
- package/.opencode/mednotes/src/mednotes/domains/wiki/capabilities/pdf/paths.py +35 -0
- package/.opencode/mednotes/src/mednotes/domains/wiki/capabilities/pdf/pdf_engine.py +77 -0
- package/.opencode/mednotes/src/mednotes/domains/wiki/capabilities/pdf/schema.py +155 -0
- package/.opencode/mednotes/src/mednotes/domains/wiki/capabilities/pdf/search.py +188 -0
- package/.opencode/mednotes/src/mednotes/domains/wiki/capabilities/pdf/tui/__init__.py +1 -0
- package/.opencode/mednotes/src/mednotes/domains/wiki/capabilities/pdf/tui/app.py +89 -0
- package/.opencode/mednotes/src/mednotes/domains/wiki/capabilities/pdf/tui/image_backend.py +29 -0
- package/.opencode/mednotes/src/mednotes/domains/wiki/capabilities/pdf/tui/state.py +65 -0
- package/.opencode/mednotes/src/mednotes/domains/wiki/capabilities/publish/__init__.py +1 -0
- package/.opencode/mednotes/src/mednotes/domains/wiki/capabilities/publish/publish.py +1139 -0
- package/.opencode/mednotes/src/mednotes/domains/wiki/capabilities/publish/publish_receipts.py +365 -0
- package/.opencode/mednotes/src/mednotes/domains/wiki/capabilities/publish/publish_recovery.py +240 -0
- package/.opencode/mednotes/src/mednotes/domains/wiki/capabilities/quality/__init__.py +1 -0
- package/.opencode/mednotes/src/mednotes/domains/wiki/capabilities/quality/agent_behavior_corpus.py +2069 -0
- package/.opencode/mednotes/src/mednotes/domains/wiki/capabilities/quality/agent_report_validation.py +4448 -0
- package/.opencode/mednotes/src/mednotes/domains/wiki/capabilities/quality/agent_run_audit.py +852 -0
- package/.opencode/mednotes/src/mednotes/domains/wiki/capabilities/quality/architect_prompt_eval.py +341 -0
- package/.opencode/mednotes/src/mednotes/domains/wiki/capabilities/quality/body_linker_eval.py +240 -0
- package/.opencode/mednotes/src/mednotes/domains/wiki/capabilities/quality/curator_output_validation.py +175 -0
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- package/.opencode/mednotes/src/mednotes/domains/wiki/capabilities/quality/triager_prompt_eval.py +1295 -0
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- package/.opencode/mednotes/src/mednotes/domains/wiki/capabilities/specialist/__init__.py +1 -0
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- package/.opencode/mednotes/src/mednotes/domains/wiki/capabilities/subagents/__init__.py +1 -0
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- package/.opencode/mednotes/src/mednotes/domains/wiki/capabilities/vocabulary/__init__.py +1 -0
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- package/.opencode/mednotes/src/mednotes/domains/wiki/capabilities/vocabulary/llm_disambiguation.py +182 -0
- package/.opencode/mednotes/src/mednotes/domains/wiki/capabilities/vocabulary/taxonomy/__init__.py +116 -0
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- package/.opencode/mednotes/src/mednotes/domains/wiki/capabilities/vocabulary/taxonomy/normalize.py +72 -0
- package/.opencode/mednotes/src/mednotes/domains/wiki/capabilities/vocabulary/taxonomy/policy.py +135 -0
- package/.opencode/mednotes/src/mednotes/domains/wiki/capabilities/vocabulary/taxonomy/resolve.py +413 -0
- package/.opencode/mednotes/src/mednotes/domains/wiki/capabilities/vocabulary/taxonomy/schema.py +157 -0
- package/.opencode/mednotes/src/mednotes/domains/wiki/capabilities/vocabulary/taxonomy/status.py +137 -0
- package/.opencode/mednotes/src/mednotes/domains/wiki/capabilities/vocabulary/vocabulary_bootstrap.py +509 -0
- package/.opencode/mednotes/src/mednotes/domains/wiki/capabilities/vocabulary/vocabulary_curator_batch.py +1115 -0
- package/.opencode/mednotes/src/mednotes/domains/wiki/capabilities/vocabulary/vocabulary_ingestion.py +632 -0
- package/.opencode/mednotes/src/mednotes/domains/wiki/capabilities/vocabulary/vocabulary_map.py +930 -0
- package/.opencode/mednotes/src/mednotes/domains/wiki/capabilities/vocabulary/vocabulary_recovery.py +1388 -0
- package/.opencode/mednotes/src/mednotes/domains/wiki/cli.py +6665 -0
- package/.opencode/mednotes/src/mednotes/domains/wiki/common.py +69 -0
- package/.opencode/mednotes/src/mednotes/domains/wiki/config.py +210 -0
- package/.opencode/mednotes/src/mednotes/domains/wiki/contracts/__init__.py +74 -0
- package/.opencode/mednotes/src/mednotes/domains/wiki/contracts/agent_report.py +242 -0
- package/.opencode/mednotes/src/mednotes/domains/wiki/contracts/agent_run_audit.py +196 -0
- package/.opencode/mednotes/src/mednotes/domains/wiki/contracts/agents.py +601 -0
- package/.opencode/mednotes/src/mednotes/domains/wiki/contracts/curator.py +256 -0
- package/.opencode/mednotes/src/mednotes/domains/wiki/contracts/effect_payloads.py +519 -0
- package/.opencode/mednotes/src/mednotes/domains/wiki/contracts/happy_path.py +190 -0
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- package/.opencode/mednotes/src/mednotes/domains/wiki/flows/fix_wiki/fix_wiki_machine.py +1588 -0
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- package/.opencode/mednotes/src/mednotes/domains/wiki/flows/fix_wiki/fix_wiki_problem.py +153 -0
- package/.opencode/mednotes/src/mednotes/domains/wiki/flows/fix_wiki/fix_wiki_receipt_evidence.py +306 -0
- package/.opencode/mednotes/src/mednotes/domains/wiki/flows/fix_wiki/fix_wiki_states.py +290 -0
- package/.opencode/mednotes/src/mednotes/domains/wiki/flows/fix_wiki/fix_wiki_user_report.py +342 -0
- package/.opencode/mednotes/src/mednotes/domains/wiki/flows/fix_wiki/health.py +6332 -0
- package/.opencode/mednotes/src/mednotes/domains/wiki/flows/link/__init__.py +1 -0
- package/.opencode/mednotes/src/mednotes/domains/wiki/flows/link/link_fsm.py +1119 -0
- package/.opencode/mednotes/src/mednotes/domains/wiki/flows/link/link_git.py +638 -0
- package/.opencode/mednotes/src/mednotes/domains/wiki/flows/link/link_machine.py +1106 -0
- package/.opencode/mednotes/src/mednotes/domains/wiki/flows/link/link_retry_governance.py +374 -0
- package/.opencode/mednotes/src/mednotes/domains/wiki/flows/link/link_runtime_result.py +485 -0
- package/.opencode/mednotes/src/mednotes/domains/wiki/flows/link/link_triggers.py +183 -0
- package/.opencode/mednotes/src/mednotes/domains/wiki/flows/link/linking.py +2758 -0
- package/.opencode/mednotes/src/mednotes/domains/wiki/flows/link/reference_repair.py +718 -0
- package/.opencode/mednotes/src/mednotes/domains/wiki/flows/link/related_notes_fsm.py +1855 -0
- package/.opencode/mednotes/src/mednotes/domains/wiki/flows/link_related/__init__.py +1 -0
- package/.opencode/mednotes/src/mednotes/domains/wiki/flows/link_related/link_related_machine.py +834 -0
- package/.opencode/mednotes/src/mednotes/domains/wiki/flows/process_chats/__init__.py +1 -0
- package/.opencode/mednotes/src/mednotes/domains/wiki/flows/process_chats/process_chats_fsm.py +1592 -0
- package/.opencode/mednotes/src/mednotes/domains/wiki/flows/process_chats/process_chats_machine.py +3097 -0
- package/.opencode/mednotes/src/mednotes/domains/wiki/flows/process_chats/process_chats_primary_objective.py +28 -0
- package/.opencode/mednotes/src/mednotes/domains/wiki/flows/process_chats/process_chats_runtime_result.py +185 -0
- package/.opencode/mednotes/src/mednotes/domains/wiki/performance.py +97 -0
- package/.opencode/mednotes/src/mednotes/kernel/__init__.py +6 -0
- package/.opencode/mednotes/src/mednotes/kernel/agent_directive.py +336 -0
- package/.opencode/mednotes/src/mednotes/kernel/base.py +51 -0
- package/.opencode/mednotes/src/mednotes/kernel/blockers.py +39 -0
- package/.opencode/mednotes/src/mednotes/kernel/effect_executor.py +55 -0
- package/.opencode/mednotes/src/mednotes/kernel/effect_intent.py +69 -0
- package/.opencode/mednotes/src/mednotes/kernel/effects.py +160 -0
- package/.opencode/mednotes/src/mednotes/kernel/errors.py +38 -0
- package/.opencode/mednotes/src/mednotes/kernel/fsm_event.py +35 -0
- package/.opencode/mednotes/src/mednotes/kernel/fsm_model.py +55 -0
- package/.opencode/mednotes/src/mednotes/kernel/fsm_transition_result.py +75 -0
- package/.opencode/mednotes/src/mednotes/kernel/guardrails.py +188 -0
- package/.opencode/mednotes/src/mednotes/kernel/progress.py +319 -0
- package/.opencode/mednotes/src/mednotes/kernel/public_report.py +346 -0
- package/.opencode/mednotes/src/mednotes/kernel/state_machine.py +164 -0
- package/.opencode/mednotes/src/mednotes/kernel/workflow.py +619 -0
- package/.opencode/mednotes/src/mednotes/platform/__init__.py +5 -0
- package/.opencode/mednotes/src/mednotes/platform/backup_policy.py +382 -0
- package/.opencode/mednotes/src/mednotes/platform/feedback/__init__.py +62 -0
- package/.opencode/mednotes/src/mednotes/platform/feedback/cli.py +275 -0
- package/.opencode/mednotes/src/mednotes/platform/feedback/contracts.py +83 -0
- package/.opencode/mednotes/src/mednotes/platform/feedback/core.py +4168 -0
- package/.opencode/mednotes/src/mednotes/platform/feedback/integrity.py +989 -0
- package/.opencode/mednotes/src/mednotes/platform/feedback/operational_contract.py +2293 -0
- package/.opencode/mednotes/src/mednotes/platform/feedback/telemetry.py +875 -0
- package/.opencode/mednotes/src/mednotes/platform/feedback/telemetry_config.py +65 -0
- package/.opencode/mednotes/src/mednotes/platform/opencode_runtime_config.py +182 -0
- package/.opencode/mednotes/src/mednotes/platform/paths/__init__.py +1560 -0
- package/.opencode/mednotes/src/mednotes/platform/secrets.py +89 -0
- package/.opencode/mednotes/src/mednotes/platform/user_config.py +103 -0
- package/.opencode/mednotes/src/mednotes/platform/vault_guard.py +214 -0
- package/.opencode/mednotes/uv.lock +932 -0
- package/.opencode/mednotes.generated.json +395 -0
- package/.opencode/opencode.json +31 -0
- package/.opencode/plugins/mednotes-fsm.mjs +7 -0
- package/.opencode/plugins/mednotes_hook/adapters/antigravity.mjs +169 -0
- package/.opencode/plugins/mednotes_hook/adapters/harness_payload.mjs +103 -0
- package/.opencode/plugins/mednotes_hook/adapters/opencode_plugin.mjs +341 -0
- package/.opencode/plugins/mednotes_hook/adapters/opencode_user_config_sync.mjs +177 -0
- package/.opencode/plugins/mednotes_hook/anki_preflight.mjs +214 -0
- package/.opencode/plugins/mednotes_hook/cli.mjs +143 -0
- package/.opencode/plugins/mednotes_hook/diagnostics.mjs +11 -0
- package/.opencode/plugins/mednotes_hook/domain/agent_directive_core.mjs +160 -0
- package/.opencode/plugins/mednotes_hook/fsm_directive.mjs +1470 -0
- package/.opencode/plugins/mednotes_hook/hook_errors.mjs +120 -0
- package/.opencode/plugins/mednotes_hook/retention.mjs +114 -0
- package/.opencode/plugins/mednotes_hook/runtime.mjs +174 -0
- package/.opencode/plugins/mednotes_hook/telemetry_capture.mjs +511 -0
- package/.opencode/plugins/mednotes_hook/vault_guard.mjs +624 -0
- package/AGENTS.md +57 -0
- package/README.md +194 -0
- package/adapters/antigravity/agents.json +80 -0
- package/adapters/antigravity/templates/med-chat-triager.md +214 -0
- package/adapters/antigravity/templates/med-flashcard-maker.md +72 -0
- package/adapters/antigravity/templates/med-knowledge-architect.md +241 -0
- package/adapters/antigravity/templates/med-link-graph-curator.md +187 -0
- package/adapters/antigravity/templates/med-publish-guard.md +71 -0
- package/adapters/gemini-cli/gemini-extension.json +14 -0
- package/adapters/gemini-cli/package.json +15 -0
- package/adapters/gemini-cli/pyproject.toml +48 -0
- package/bin/mednotes-opencode.mjs +155 -0
- package/contracts/agents.json +116 -0
- package/core/agents/med-chat-triager.md +197 -0
- package/core/agents/med-flashcard-maker.md +56 -0
- package/core/agents/med-knowledge-architect.md +224 -0
- package/core/agents/med-link-graph-curator.md +171 -0
- package/core/agents/med-publish-guard.md +55 -0
- package/core/commands/flashcards.toml +22 -0
- package/core/commands/mednotes/create.toml +22 -0
- package/core/commands/mednotes/enrich.toml +24 -0
- package/core/commands/mednotes/fix-wiki.toml +24 -0
- package/core/commands/mednotes/history.toml +19 -0
- package/core/commands/mednotes/link-body.toml +22 -0
- package/core/commands/mednotes/link-related.toml +24 -0
- package/core/commands/mednotes/link.toml +24 -0
- package/core/commands/mednotes/pdf-library.toml +24 -0
- package/core/commands/mednotes/process-chats.toml +20 -0
- package/core/commands/mednotes/setup.toml +18 -0
- package/core/commands/mednotes/status.toml +24 -0
- package/core/commands/mednotes/telemetry.toml +24 -0
- package/core/commands/report.toml +23 -0
- package/core/skills/THIRD_PARTY_NOTICES.md +45 -0
- package/core/skills/create-medical-flashcards/SKILL.md +113 -0
- package/core/skills/create-medical-note/SKILL.md +90 -0
- package/core/skills/enrich-medical-note/SKILL.md +120 -0
- package/core/skills/fix-medical-wiki/SKILL.md +559 -0
- package/core/skills/link-medical-wiki/SKILL.md +224 -0
- package/core/skills/obsidian-cli/SKILL.md +118 -0
- package/core/skills/obsidian-markdown/SKILL.md +207 -0
- package/core/skills/obsidian-markdown/references/CALLOUTS.md +58 -0
- package/core/skills/obsidian-markdown/references/EMBEDS.md +63 -0
- package/core/skills/obsidian-markdown/references/PROPERTIES.md +61 -0
- package/core/skills/obsidian-ops/SKILL.md +136 -0
- package/core/skills/pdf-library/SKILL.md +45 -0
- package/core/skills/process-medical-chats/SKILL.md +246 -0
- package/core/skills/workflow-report/SKILL.md +100 -0
- package/package.json +45 -0
package/.opencode/mednotes/src/mednotes/domains/wiki/capabilities/vocabulary/taxonomy/__init__.py
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"""Wiki_Medicina taxonomy public API.
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The canonical taxonomy policy is defined in ``wiki.taxonomy.policy``; schema
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constants are compatibility projections derived from that single source.
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"""
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from __future__ import annotations
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from mednotes.domains.wiki.capabilities.vocabulary.taxonomy.audit import (
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_canonical_directory_paths,
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taxonomy_audit,
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taxonomy_tree,
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)
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from mednotes.domains.wiki.capabilities.vocabulary.taxonomy.migration import (
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_default_migration_receipt_path,
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_join_wiki_relative_dir,
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_load_json_file,
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_missing_parent_dirs,
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_plan_wiki_dir,
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_write_json_atomic,
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apply_taxonomy_migration,
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rollback_taxonomy_migration,
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taxonomy_migration_plan,
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)
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from mednotes.domains.wiki.capabilities.vocabulary.taxonomy.normalize import (
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_DRIVE_RE,
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_UNSAFE_TAXONOMY_RE,
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_UNSAFE_TITLE_RE,
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_fold_taxonomy_segment,
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_safe_relative_dir,
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normalize_taxonomy,
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safe_title,
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)
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from mednotes.domains.wiki.capabilities.vocabulary.taxonomy.policy import (
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CANONICAL_TAXONOMY_POLICY,
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TaxonomyAreaPolicy,
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TaxonomySpecialtyPolicy,
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)
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from mednotes.domains.wiki.capabilities.vocabulary.taxonomy.resolve import (
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_NEAR_DUPLICATE_CUTOFF,
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TaxonomyDecisionRequired,
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_canonicalize_taxonomy_parts,
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_format_suggestions,
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_match_existing_segment,
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_suggest_existing_segments,
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_validate_taxonomy_not_title,
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_visible_child_dirs,
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resolve_target_for_note,
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resolve_taxonomy,
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target_for_note,
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)
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from mednotes.domains.wiki.capabilities.vocabulary.taxonomy.schema import (
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CANONICAL_AREA_ALIASES,
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CANONICAL_TAXONOMY,
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CANONICAL_TAXONOMY_ALIASES,
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TaxonomyResolution,
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_canonical_area_aliases_by_fold,
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_canonical_roots_by_fold,
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_canonical_specialties_by_fold,
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_canonical_specialties_for_root,
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canonical_taxonomy_invariants,
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canonical_taxonomy_tree,
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)
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63
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from mednotes.domains.wiki.capabilities.vocabulary.taxonomy.status import (
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TAXONOMY_STATUS_SCHEMA,
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render_taxonomy_status_markdown,
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taxonomy_status,
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)
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__all__ = [
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"CANONICAL_TAXONOMY",
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"CANONICAL_TAXONOMY_POLICY",
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"CANONICAL_AREA_ALIASES",
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"CANONICAL_TAXONOMY_ALIASES",
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74
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"TaxonomyAreaPolicy",
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75
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"TaxonomyResolution",
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"TaxonomySpecialtyPolicy",
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"TaxonomyDecisionRequired",
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"TAXONOMY_STATUS_SCHEMA",
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"_DRIVE_RE",
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80
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"_NEAR_DUPLICATE_CUTOFF",
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"_UNSAFE_TAXONOMY_RE",
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"_UNSAFE_TITLE_RE",
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"_canonical_directory_paths",
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"_canonical_area_aliases_by_fold",
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"_canonical_roots_by_fold",
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"_canonical_specialties_by_fold",
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"_canonical_specialties_for_root",
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"_canonicalize_taxonomy_parts",
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"_default_migration_receipt_path",
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"_fold_taxonomy_segment",
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"_format_suggestions",
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92
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"_join_wiki_relative_dir",
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93
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"_load_json_file",
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94
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"_match_existing_segment",
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95
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"_missing_parent_dirs",
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"_plan_wiki_dir",
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"_safe_relative_dir",
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"_suggest_existing_segments",
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"_validate_taxonomy_not_title",
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"_visible_child_dirs",
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"_write_json_atomic",
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"apply_taxonomy_migration",
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"canonical_taxonomy_tree",
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"canonical_taxonomy_invariants",
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"normalize_taxonomy",
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"resolve_target_for_note",
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"resolve_taxonomy",
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"render_taxonomy_status_markdown",
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"rollback_taxonomy_migration",
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"safe_title",
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"target_for_note",
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112
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"taxonomy_audit",
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"taxonomy_migration_plan",
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114
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"taxonomy_status",
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"taxonomy_tree",
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116
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]
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package/.opencode/mednotes/src/mednotes/domains/wiki/capabilities/vocabulary/taxonomy/audit.py
ADDED
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@@ -0,0 +1,201 @@
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"""Taxonomy tree and dry-run audit helpers."""
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from __future__ import annotations
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4
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from pathlib import Path
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from typing import Any
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from mednotes.domains.wiki.capabilities.notes import note_style
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8
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from mednotes.domains.wiki.capabilities.notes.note_iter import is_note_markdown
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9
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from mednotes.domains.wiki.capabilities.notes.note_policy import is_operational_index_note
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10
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from mednotes.domains.wiki.capabilities.vocabulary.taxonomy.normalize import _fold_taxonomy_segment
|
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11
|
+
from mednotes.domains.wiki.capabilities.vocabulary.taxonomy.resolve import _visible_child_dirs
|
|
12
|
+
from mednotes.domains.wiki.capabilities.vocabulary.taxonomy.schema import (
|
|
13
|
+
CANONICAL_TAXONOMY,
|
|
14
|
+
_canonical_area_aliases_by_fold,
|
|
15
|
+
_canonical_roots_by_fold,
|
|
16
|
+
_canonical_specialties_by_fold,
|
|
17
|
+
canonical_taxonomy_tree,
|
|
18
|
+
)
|
|
19
|
+
from mednotes.domains.wiki.common import MissingPathError, ValidationError
|
|
20
|
+
|
|
21
|
+
IGNORED_TOP_LEVEL_DIRS = {"attachments", "_Mock_Embeds"}
|
|
22
|
+
IGNORED_ROOT_NOTES = {"_Índice_Medicina.md"}
|
|
23
|
+
|
|
24
|
+
|
|
25
|
+
def taxonomy_tree(wiki_dir: Path, max_depth: int = 0) -> dict[str, Any]:
|
|
26
|
+
if not wiki_dir.exists():
|
|
27
|
+
raise MissingPathError(f"Wiki dir not found: {wiki_dir}")
|
|
28
|
+
if not wiki_dir.is_dir():
|
|
29
|
+
raise ValidationError(f"Wiki dir is not a directory: {wiki_dir}")
|
|
30
|
+
|
|
31
|
+
directories: list[dict[str, Any]] = []
|
|
32
|
+
for path in sorted((p for p in wiki_dir.rglob("*") if p.is_dir() and not p.name.startswith(".")), key=lambda p: p.as_posix()):
|
|
33
|
+
rel = path.relative_to(wiki_dir)
|
|
34
|
+
if any(part.startswith(".") for part in rel.parts):
|
|
35
|
+
continue
|
|
36
|
+
depth = len(rel.parts)
|
|
37
|
+
if max_depth and depth > max_depth:
|
|
38
|
+
continue
|
|
39
|
+
direct_notes = sum(1 for child in path.glob("*.md") if is_note_markdown(wiki_dir, child))
|
|
40
|
+
child_dirs = sum(1 for child in path.iterdir() if child.is_dir() and not child.name.startswith("."))
|
|
41
|
+
directories.append(
|
|
42
|
+
{
|
|
43
|
+
"path": rel.as_posix(),
|
|
44
|
+
"parts": list(rel.parts),
|
|
45
|
+
"depth": depth,
|
|
46
|
+
"direct_note_count": direct_notes,
|
|
47
|
+
"child_dir_count": child_dirs,
|
|
48
|
+
}
|
|
49
|
+
)
|
|
50
|
+
return {"wiki_dir": str(wiki_dir), "directory_count": len(directories), "directories": directories}
|
|
51
|
+
|
|
52
|
+
|
|
53
|
+
def _canonical_directory_paths() -> list[tuple[str, ...]]:
|
|
54
|
+
paths: list[tuple[str, ...]] = []
|
|
55
|
+
for root, specialties in CANONICAL_TAXONOMY:
|
|
56
|
+
paths.append((root,))
|
|
57
|
+
paths.extend((root, specialty) for specialty in specialties)
|
|
58
|
+
return paths
|
|
59
|
+
|
|
60
|
+
|
|
61
|
+
def taxonomy_audit(wiki_dir: Path) -> dict[str, Any]:
|
|
62
|
+
if not wiki_dir.exists():
|
|
63
|
+
raise MissingPathError(f"Wiki dir not found: {wiki_dir}")
|
|
64
|
+
if not wiki_dir.is_dir():
|
|
65
|
+
raise ValidationError(f"Wiki dir is not a directory: {wiki_dir}")
|
|
66
|
+
|
|
67
|
+
roots = _canonical_roots_by_fold()
|
|
68
|
+
area_aliases = _canonical_area_aliases_by_fold()
|
|
69
|
+
specialties = _canonical_specialties_by_fold()
|
|
70
|
+
canonical_paths = _canonical_directory_paths()
|
|
71
|
+
missing_canonical_dirs = [
|
|
72
|
+
"/".join(parts)
|
|
73
|
+
for parts in canonical_paths
|
|
74
|
+
if not wiki_dir.joinpath(*parts).exists()
|
|
75
|
+
]
|
|
76
|
+
|
|
77
|
+
proposed_moves: list[dict[str, Any]] = []
|
|
78
|
+
compliant_top_level_dirs: list[str] = []
|
|
79
|
+
unmapped_top_level_dirs: list[str] = []
|
|
80
|
+
top_level_dirs = _visible_child_dirs(wiki_dir)
|
|
81
|
+
destinations: dict[str, list[str]] = {}
|
|
82
|
+
|
|
83
|
+
for directory in top_level_dirs:
|
|
84
|
+
if directory.name in IGNORED_TOP_LEVEL_DIRS:
|
|
85
|
+
continue
|
|
86
|
+
folded = _fold_taxonomy_segment(directory.name)
|
|
87
|
+
rel_source = directory.relative_to(wiki_dir).as_posix()
|
|
88
|
+
if folded in roots:
|
|
89
|
+
compliant_top_level_dirs.append(rel_source)
|
|
90
|
+
continue
|
|
91
|
+
if folded in area_aliases:
|
|
92
|
+
destination = area_aliases[folded]
|
|
93
|
+
destinations.setdefault(destination, []).append(rel_source)
|
|
94
|
+
proposed_moves.append(
|
|
95
|
+
{
|
|
96
|
+
"source": rel_source,
|
|
97
|
+
"destination": destination,
|
|
98
|
+
"reason": "known_area_alias",
|
|
99
|
+
"destination_exists": wiki_dir.joinpath(destination).exists(),
|
|
100
|
+
}
|
|
101
|
+
)
|
|
102
|
+
continue
|
|
103
|
+
if folded in specialties:
|
|
104
|
+
root, specialty = specialties[folded]
|
|
105
|
+
destination = f"{root}/{specialty}"
|
|
106
|
+
destinations.setdefault(destination, []).append(rel_source)
|
|
107
|
+
proposed_moves.append(
|
|
108
|
+
{
|
|
109
|
+
"source": rel_source,
|
|
110
|
+
"destination": destination,
|
|
111
|
+
"reason": "known_specialty_or_alias",
|
|
112
|
+
"destination_exists": wiki_dir.joinpath(root, specialty).exists(),
|
|
113
|
+
}
|
|
114
|
+
)
|
|
115
|
+
else:
|
|
116
|
+
unmapped_top_level_dirs.append(rel_source)
|
|
117
|
+
|
|
118
|
+
duplicate_destinations = [
|
|
119
|
+
{"destination": destination, "sources": sources}
|
|
120
|
+
for destination, sources in sorted(destinations.items())
|
|
121
|
+
if len(sources) > 1
|
|
122
|
+
]
|
|
123
|
+
duplicate_directory_groups: list[dict[str, Any]] = []
|
|
124
|
+
by_folded: dict[str, list[str]] = {}
|
|
125
|
+
for path in sorted((p for p in wiki_dir.rglob("*") if p.is_dir() and not p.name.startswith(".")), key=lambda p: p.as_posix()):
|
|
126
|
+
rel = path.relative_to(wiki_dir)
|
|
127
|
+
if any(part.startswith(".") for part in rel.parts):
|
|
128
|
+
continue
|
|
129
|
+
if len(rel.parts) == 1 and path.name in IGNORED_TOP_LEVEL_DIRS:
|
|
130
|
+
continue
|
|
131
|
+
by_folded.setdefault(_fold_taxonomy_segment(path.name), []).append(rel.as_posix())
|
|
132
|
+
for folded, paths in sorted(by_folded.items()):
|
|
133
|
+
if len(paths) > 1:
|
|
134
|
+
duplicate_directory_groups.append({"key": folded, "paths": paths})
|
|
135
|
+
|
|
136
|
+
empty_root_notes = sorted(
|
|
137
|
+
path.name
|
|
138
|
+
for path in wiki_dir.glob("*.md")
|
|
139
|
+
if is_note_markdown(wiki_dir, path)
|
|
140
|
+
and path.name not in IGNORED_ROOT_NOTES
|
|
141
|
+
and not _is_operational_index_note(path)
|
|
142
|
+
and _is_strictly_empty(path)
|
|
143
|
+
)
|
|
144
|
+
invalid_root_notes = sorted(
|
|
145
|
+
path.name
|
|
146
|
+
for path in wiki_dir.glob("*.md")
|
|
147
|
+
if is_note_markdown(wiki_dir, path)
|
|
148
|
+
and path.name not in IGNORED_ROOT_NOTES
|
|
149
|
+
and not _is_operational_index_note(path)
|
|
150
|
+
and not _is_strictly_empty(path)
|
|
151
|
+
and not _is_valid_root_note(path)
|
|
152
|
+
)
|
|
153
|
+
root_notes = sorted(
|
|
154
|
+
path.name
|
|
155
|
+
for path in wiki_dir.glob("*.md")
|
|
156
|
+
if is_note_markdown(wiki_dir, path)
|
|
157
|
+
and path.name not in IGNORED_ROOT_NOTES
|
|
158
|
+
and not _is_operational_index_note(path)
|
|
159
|
+
and not _is_strictly_empty(path)
|
|
160
|
+
and _is_valid_root_note(path)
|
|
161
|
+
)
|
|
162
|
+
return {
|
|
163
|
+
"wiki_dir": str(wiki_dir),
|
|
164
|
+
"canonical_taxonomy": canonical_taxonomy_tree(),
|
|
165
|
+
"missing_canonical_dirs": missing_canonical_dirs,
|
|
166
|
+
"compliant_top_level_dirs": compliant_top_level_dirs,
|
|
167
|
+
"proposed_moves": proposed_moves,
|
|
168
|
+
"unmapped_top_level_dirs": unmapped_top_level_dirs,
|
|
169
|
+
"duplicate_destinations": duplicate_destinations,
|
|
170
|
+
"duplicate_directory_groups": duplicate_directory_groups,
|
|
171
|
+
"root_notes": root_notes,
|
|
172
|
+
"empty_root_notes": empty_root_notes,
|
|
173
|
+
"invalid_root_notes": invalid_root_notes,
|
|
174
|
+
"requires_review": bool(unmapped_top_level_dirs or duplicate_destinations or root_notes),
|
|
175
|
+
"dry_run_only": True,
|
|
176
|
+
}
|
|
177
|
+
|
|
178
|
+
|
|
179
|
+
def _is_strictly_empty(path: Path) -> bool:
|
|
180
|
+
try:
|
|
181
|
+
return path.read_text(encoding="utf-8").strip() == ""
|
|
182
|
+
except OSError:
|
|
183
|
+
return False
|
|
184
|
+
|
|
185
|
+
|
|
186
|
+
def _is_valid_root_note(path: Path) -> bool:
|
|
187
|
+
try:
|
|
188
|
+
content = path.read_text(encoding="utf-8")
|
|
189
|
+
except OSError:
|
|
190
|
+
return False
|
|
191
|
+
title = note_style.infer_title(content, path)
|
|
192
|
+
report = note_style.validate_note_style(content, title=title, path=str(path))
|
|
193
|
+
return bool(report.get("ok"))
|
|
194
|
+
|
|
195
|
+
|
|
196
|
+
def _is_operational_index_note(path: Path) -> bool:
|
|
197
|
+
try:
|
|
198
|
+
content = path.read_text(encoding="utf-8")
|
|
199
|
+
except OSError:
|
|
200
|
+
return False
|
|
201
|
+
return is_operational_index_note(path, content)
|
package/.opencode/mednotes/src/mednotes/domains/wiki/capabilities/vocabulary/taxonomy/migration.py
ADDED
|
@@ -0,0 +1,314 @@
|
|
|
1
|
+
"""Conservative taxonomy migration planning, apply and rollback."""
|
|
2
|
+
from __future__ import annotations
|
|
3
|
+
|
|
4
|
+
import json
|
|
5
|
+
import shutil
|
|
6
|
+
from datetime import UTC, datetime
|
|
7
|
+
from pathlib import Path
|
|
8
|
+
from typing import Any, Literal
|
|
9
|
+
|
|
10
|
+
from pydantic import Field
|
|
11
|
+
from pydantic import ValidationError as PydanticValidationError
|
|
12
|
+
|
|
13
|
+
from mednotes.domains.wiki.capabilities.notes.raw_chats import atomic_write_text
|
|
14
|
+
from mednotes.domains.wiki.capabilities.vocabulary.taxonomy.audit import taxonomy_audit
|
|
15
|
+
from mednotes.domains.wiki.capabilities.vocabulary.taxonomy.normalize import _safe_relative_dir
|
|
16
|
+
from mednotes.domains.wiki.capabilities.vocabulary.taxonomy.policy import TAXONOMY_POLICY_VERSION
|
|
17
|
+
from mednotes.domains.wiki.common import (
|
|
18
|
+
MIGRATION_PLAN_SCHEMA,
|
|
19
|
+
MIGRATION_RECEIPT_SCHEMA,
|
|
20
|
+
CollisionError,
|
|
21
|
+
MedOpsError,
|
|
22
|
+
MissingPathError,
|
|
23
|
+
ValidationError,
|
|
24
|
+
_now_iso,
|
|
25
|
+
)
|
|
26
|
+
from mednotes.domains.wiki.config import MedConfig, _path
|
|
27
|
+
from mednotes.kernel.base import ContractModel, JsonObject, JsonObjectAdapter, contract_error
|
|
28
|
+
|
|
29
|
+
|
|
30
|
+
class _TaxonomyRollbackOperationFields(ContractModel):
|
|
31
|
+
action: Literal["move_dir"]
|
|
32
|
+
source: str = Field(min_length=1)
|
|
33
|
+
destination: str = Field(min_length=1)
|
|
34
|
+
source_path: str = Field(default="")
|
|
35
|
+
destination_path: str = Field(default="")
|
|
36
|
+
created_parent_dirs: list[str] = Field(default_factory=list)
|
|
37
|
+
applied_at: str = Field(default="")
|
|
38
|
+
|
|
39
|
+
|
|
40
|
+
class _TaxonomyRollbackFields(ContractModel):
|
|
41
|
+
strategy: Literal["taxonomy_receipt"]
|
|
42
|
+
receipt_path: str = Field(min_length=1)
|
|
43
|
+
|
|
44
|
+
|
|
45
|
+
class _TaxonomyMigrationReceiptFields(ContractModel):
|
|
46
|
+
schema_id: str = Field(alias="schema", serialization_alias="schema")
|
|
47
|
+
status: Literal["running", "completed", "failed"]
|
|
48
|
+
plan_path: str = Field(default="")
|
|
49
|
+
wiki_dir: str = Field(min_length=1)
|
|
50
|
+
taxonomy_policy_version: str = Field(default="")
|
|
51
|
+
started_at: str = Field(default="")
|
|
52
|
+
completed_at: str | None = None
|
|
53
|
+
failed_at: str = Field(default="")
|
|
54
|
+
error: str = Field(default="")
|
|
55
|
+
applied_operations: list[_TaxonomyRollbackOperationFields] = Field(default_factory=list)
|
|
56
|
+
rollback: _TaxonomyRollbackFields
|
|
57
|
+
|
|
58
|
+
|
|
59
|
+
def _taxonomy_receipt_fields(receipt: JsonObject) -> _TaxonomyMigrationReceiptFields:
|
|
60
|
+
try:
|
|
61
|
+
return _TaxonomyMigrationReceiptFields.model_validate(receipt)
|
|
62
|
+
except PydanticValidationError as exc:
|
|
63
|
+
raise contract_error(exc, prefix="taxonomy migration receipt") from exc
|
|
64
|
+
|
|
65
|
+
|
|
66
|
+
def _join_wiki_relative_dir(wiki_dir: Path, value: str) -> Path:
|
|
67
|
+
return wiki_dir.joinpath(*_safe_relative_dir(value))
|
|
68
|
+
|
|
69
|
+
|
|
70
|
+
def _missing_parent_dirs(wiki_dir: Path, destination: Path) -> list[str]:
|
|
71
|
+
missing: list[str] = []
|
|
72
|
+
parents = []
|
|
73
|
+
current = destination.parent
|
|
74
|
+
while current != wiki_dir and current != current.parent:
|
|
75
|
+
parents.append(current)
|
|
76
|
+
current = current.parent
|
|
77
|
+
for parent in reversed(parents):
|
|
78
|
+
if not parent.exists():
|
|
79
|
+
missing.append(parent.relative_to(wiki_dir).as_posix())
|
|
80
|
+
return missing
|
|
81
|
+
|
|
82
|
+
|
|
83
|
+
def _default_migration_receipt_path() -> Path:
|
|
84
|
+
stamp = datetime.now(UTC).strftime("%Y%m%dT%H%M%SZ")
|
|
85
|
+
return _path(f"~/.mednotes/taxonomy-migrations/{stamp}.json")
|
|
86
|
+
|
|
87
|
+
|
|
88
|
+
def render_taxonomy_migration_plan_markdown(plan: dict[str, Any]) -> str:
|
|
89
|
+
lines = [
|
|
90
|
+
"# Taxonomy Migration Plan",
|
|
91
|
+
"",
|
|
92
|
+
f"taxonomy_policy_version: {plan['taxonomy_policy_version']}",
|
|
93
|
+
f"wiki_dir: {plan['wiki_dir']}",
|
|
94
|
+
"",
|
|
95
|
+
"## Operations",
|
|
96
|
+
"",
|
|
97
|
+
]
|
|
98
|
+
if plan["operations"]:
|
|
99
|
+
for item in plan["operations"]:
|
|
100
|
+
lines.append(f"- `{item['source']}` -> `{item['destination']}` ({item['reason']})")
|
|
101
|
+
else:
|
|
102
|
+
lines.append("- none")
|
|
103
|
+
lines.extend(["", "## Blocked", ""])
|
|
104
|
+
if plan["blocked_items"]:
|
|
105
|
+
for item in plan["blocked_items"]:
|
|
106
|
+
lines.append(f"- `{item['source']}`: {item['blocked_reason']}")
|
|
107
|
+
else:
|
|
108
|
+
lines.append("- none")
|
|
109
|
+
return "\n".join(lines) + "\n"
|
|
110
|
+
|
|
111
|
+
|
|
112
|
+
def taxonomy_migration_plan(wiki_dir: Path) -> dict[str, Any]:
|
|
113
|
+
audit = taxonomy_audit(wiki_dir)
|
|
114
|
+
duplicate_destinations = {item["destination"] for item in audit["duplicate_destinations"]}
|
|
115
|
+
operations: list[JsonObject] = []
|
|
116
|
+
blocked: list[JsonObject] = []
|
|
117
|
+
|
|
118
|
+
for item in audit["proposed_moves"]:
|
|
119
|
+
source_rel = item["source"]
|
|
120
|
+
destination_rel = item["destination"]
|
|
121
|
+
source = _join_wiki_relative_dir(wiki_dir, source_rel)
|
|
122
|
+
destination = _join_wiki_relative_dir(wiki_dir, destination_rel)
|
|
123
|
+
base = {
|
|
124
|
+
"action": "move_dir",
|
|
125
|
+
"source": source_rel,
|
|
126
|
+
"destination": destination_rel,
|
|
127
|
+
"source_path": str(source),
|
|
128
|
+
"destination_path": str(destination),
|
|
129
|
+
"reason": item.get("reason", ""),
|
|
130
|
+
}
|
|
131
|
+
if destination_rel in duplicate_destinations:
|
|
132
|
+
blocked.append({**base, "blocked_reason": "duplicate_destination"})
|
|
133
|
+
elif not source.exists():
|
|
134
|
+
blocked.append({**base, "blocked_reason": "source_missing"})
|
|
135
|
+
elif not source.is_dir():
|
|
136
|
+
blocked.append({**base, "blocked_reason": "source_not_directory"})
|
|
137
|
+
elif destination.exists():
|
|
138
|
+
blocked.append({**base, "blocked_reason": "destination_exists"})
|
|
139
|
+
elif source in destination.parents or source == destination:
|
|
140
|
+
blocked.append({**base, "blocked_reason": "destination_inside_source"})
|
|
141
|
+
else:
|
|
142
|
+
operations.append({**base, "created_parent_dirs": _missing_parent_dirs(wiki_dir, destination)})
|
|
143
|
+
|
|
144
|
+
for source_rel in audit["unmapped_top_level_dirs"]:
|
|
145
|
+
blocked.append({"action": "review_dir", "source": source_rel, "blocked_reason": "unmapped_top_level_dir"})
|
|
146
|
+
for filename in audit["root_notes"]:
|
|
147
|
+
blocked.append({"action": "review_file", "source": filename, "blocked_reason": "root_note"})
|
|
148
|
+
|
|
149
|
+
plan = {
|
|
150
|
+
"schema": MIGRATION_PLAN_SCHEMA,
|
|
151
|
+
"wiki_dir": str(wiki_dir),
|
|
152
|
+
"taxonomy_policy_version": TAXONOMY_POLICY_VERSION,
|
|
153
|
+
"generated_at": _now_iso(),
|
|
154
|
+
"dry_run": True,
|
|
155
|
+
"operations": operations,
|
|
156
|
+
"blocked_items": blocked,
|
|
157
|
+
"summary": {
|
|
158
|
+
"operation_count": len(operations),
|
|
159
|
+
"blocked_count": len(blocked),
|
|
160
|
+
"requires_review": bool(blocked),
|
|
161
|
+
},
|
|
162
|
+
"audit": audit,
|
|
163
|
+
}
|
|
164
|
+
plan["human_report_markdown"] = render_taxonomy_migration_plan_markdown(plan)
|
|
165
|
+
return plan
|
|
166
|
+
|
|
167
|
+
|
|
168
|
+
def _load_json_file(path: Path) -> JsonObject:
|
|
169
|
+
if not path.exists():
|
|
170
|
+
raise MissingPathError(f"JSON file not found: {path}")
|
|
171
|
+
try:
|
|
172
|
+
data = json.loads(path.read_text(encoding="utf-8"))
|
|
173
|
+
except json.JSONDecodeError as exc:
|
|
174
|
+
raise ValidationError(f"Invalid JSON file: {path}: {exc}") from exc
|
|
175
|
+
if not isinstance(data, dict):
|
|
176
|
+
raise ValidationError(f"JSON file must contain an object: {path}")
|
|
177
|
+
return JsonObjectAdapter.validate_python(data)
|
|
178
|
+
|
|
179
|
+
|
|
180
|
+
def _plan_wiki_dir(plan: dict[str, Any], config: MedConfig) -> Path:
|
|
181
|
+
if plan.get("schema") != MIGRATION_PLAN_SCHEMA:
|
|
182
|
+
raise ValidationError("Invalid taxonomy migration plan schema")
|
|
183
|
+
plan_wiki = _path(str(plan.get("wiki_dir", "")))
|
|
184
|
+
if plan_wiki.resolve() != config.wiki_dir.resolve():
|
|
185
|
+
raise ValidationError(f"Plan wiki_dir does not match configured wiki_dir: {plan_wiki} != {config.wiki_dir}")
|
|
186
|
+
return plan_wiki
|
|
187
|
+
|
|
188
|
+
|
|
189
|
+
def _write_json_atomic(path: Path, data: dict[str, Any]) -> None:
|
|
190
|
+
atomic_write_text(path, json.dumps(data, ensure_ascii=False, indent=2) + "\n")
|
|
191
|
+
|
|
192
|
+
|
|
193
|
+
def apply_taxonomy_migration(plan_path: Path, config: MedConfig, receipt_path: Path | None = None) -> dict[str, Any]:
|
|
194
|
+
plan = _load_json_file(plan_path)
|
|
195
|
+
wiki_dir = _plan_wiki_dir(plan, config)
|
|
196
|
+
plan_version = plan.get("taxonomy_policy_version")
|
|
197
|
+
if plan_version != TAXONOMY_POLICY_VERSION:
|
|
198
|
+
raise ValidationError(
|
|
199
|
+
f"taxonomy policy version mismatch: plan={plan_version!r} current={TAXONOMY_POLICY_VERSION!r}"
|
|
200
|
+
)
|
|
201
|
+
blocked = plan.get("blocked_items", [])
|
|
202
|
+
if blocked:
|
|
203
|
+
raise ValidationError("Taxonomy migration plan has blockers; refusing partial apply")
|
|
204
|
+
operations = plan.get("operations", [])
|
|
205
|
+
if not isinstance(operations, list):
|
|
206
|
+
raise ValidationError("Migration plan operations must be a list")
|
|
207
|
+
receipt_path = receipt_path or _default_migration_receipt_path()
|
|
208
|
+
|
|
209
|
+
receipt = {
|
|
210
|
+
"schema": MIGRATION_RECEIPT_SCHEMA,
|
|
211
|
+
"status": "running",
|
|
212
|
+
"plan_path": str(plan_path),
|
|
213
|
+
"wiki_dir": str(wiki_dir),
|
|
214
|
+
"taxonomy_policy_version": TAXONOMY_POLICY_VERSION,
|
|
215
|
+
"started_at": _now_iso(),
|
|
216
|
+
"completed_at": None,
|
|
217
|
+
"applied_operations": [],
|
|
218
|
+
"rollback": {
|
|
219
|
+
"strategy": "taxonomy_receipt",
|
|
220
|
+
"receipt_path": str(receipt_path),
|
|
221
|
+
},
|
|
222
|
+
}
|
|
223
|
+
receipt_path.parent.mkdir(parents=True, exist_ok=True)
|
|
224
|
+
_write_json_atomic(receipt_path, receipt)
|
|
225
|
+
|
|
226
|
+
try:
|
|
227
|
+
for raw_op in operations:
|
|
228
|
+
if not isinstance(raw_op, dict) or raw_op.get("action") != "move_dir":
|
|
229
|
+
raise ValidationError("Unsupported migration operation")
|
|
230
|
+
source_rel = str(raw_op["source"])
|
|
231
|
+
destination_rel = str(raw_op["destination"])
|
|
232
|
+
source = _join_wiki_relative_dir(wiki_dir, source_rel)
|
|
233
|
+
destination = _join_wiki_relative_dir(wiki_dir, destination_rel)
|
|
234
|
+
if not source.exists():
|
|
235
|
+
raise MissingPathError(f"Migration source missing: {source}")
|
|
236
|
+
if not source.is_dir():
|
|
237
|
+
raise ValidationError(f"Migration source is not a directory: {source}")
|
|
238
|
+
if destination.exists():
|
|
239
|
+
raise CollisionError(f"Migration destination already exists: {destination}")
|
|
240
|
+
created_parent_dirs = _missing_parent_dirs(wiki_dir, destination)
|
|
241
|
+
destination.parent.mkdir(parents=True, exist_ok=True)
|
|
242
|
+
shutil.move(str(source), str(destination))
|
|
243
|
+
applied = {
|
|
244
|
+
"action": "move_dir",
|
|
245
|
+
"source": source_rel,
|
|
246
|
+
"destination": destination_rel,
|
|
247
|
+
"source_path": str(source),
|
|
248
|
+
"destination_path": str(destination),
|
|
249
|
+
"created_parent_dirs": created_parent_dirs,
|
|
250
|
+
"applied_at": _now_iso(),
|
|
251
|
+
}
|
|
252
|
+
receipt["applied_operations"].append(applied)
|
|
253
|
+
_write_json_atomic(receipt_path, receipt)
|
|
254
|
+
except Exception as exc:
|
|
255
|
+
receipt.update({"status": "failed", "failed_at": _now_iso(), "error": str(exc)})
|
|
256
|
+
_write_json_atomic(receipt_path, receipt)
|
|
257
|
+
raise MedOpsError(f"Taxonomy migration failed. Receipt: {receipt_path}. Error: {exc}") from exc
|
|
258
|
+
|
|
259
|
+
receipt.update({"status": "completed", "completed_at": _now_iso()})
|
|
260
|
+
_write_json_atomic(receipt_path, receipt)
|
|
261
|
+
return {
|
|
262
|
+
"status": "completed",
|
|
263
|
+
"applied": True,
|
|
264
|
+
"receipt_path": str(receipt_path),
|
|
265
|
+
"applied_count": len(receipt["applied_operations"]),
|
|
266
|
+
"applied_operations": receipt["applied_operations"],
|
|
267
|
+
"rollback": receipt["rollback"],
|
|
268
|
+
}
|
|
269
|
+
|
|
270
|
+
|
|
271
|
+
def rollback_taxonomy_migration(receipt_path: Path, config: MedConfig) -> dict[str, Any]:
|
|
272
|
+
receipt = _load_json_file(receipt_path)
|
|
273
|
+
receipt_fields = _taxonomy_receipt_fields(receipt)
|
|
274
|
+
if receipt_fields.schema_id != MIGRATION_RECEIPT_SCHEMA:
|
|
275
|
+
raise ValidationError("Invalid taxonomy migration receipt schema")
|
|
276
|
+
wiki_dir = _path(receipt_fields.wiki_dir)
|
|
277
|
+
if wiki_dir.resolve() != config.wiki_dir.resolve():
|
|
278
|
+
raise ValidationError(f"Receipt wiki_dir does not match configured wiki_dir: {wiki_dir} != {config.wiki_dir}")
|
|
279
|
+
operations = receipt_fields.applied_operations
|
|
280
|
+
|
|
281
|
+
rolled_back: list[JsonObject] = []
|
|
282
|
+
for raw_op in reversed(operations):
|
|
283
|
+
source_rel = raw_op.source
|
|
284
|
+
destination_rel = raw_op.destination
|
|
285
|
+
source = _join_wiki_relative_dir(wiki_dir, source_rel)
|
|
286
|
+
destination = _join_wiki_relative_dir(wiki_dir, destination_rel)
|
|
287
|
+
if not destination.exists():
|
|
288
|
+
raise MissingPathError(f"Rollback source missing: {destination}")
|
|
289
|
+
if source.exists():
|
|
290
|
+
raise CollisionError(f"Rollback destination already exists: {source}")
|
|
291
|
+
source.parent.mkdir(parents=True, exist_ok=True)
|
|
292
|
+
shutil.move(str(destination), str(source))
|
|
293
|
+
removed_parent_dirs: list[str] = []
|
|
294
|
+
for rel_parent in reversed(raw_op.created_parent_dirs):
|
|
295
|
+
parent = _join_wiki_relative_dir(wiki_dir, rel_parent)
|
|
296
|
+
try:
|
|
297
|
+
parent.rmdir()
|
|
298
|
+
except OSError:
|
|
299
|
+
continue
|
|
300
|
+
removed_parent_dirs.append(str(rel_parent))
|
|
301
|
+
rolled_back.append(
|
|
302
|
+
{
|
|
303
|
+
"action": "move_dir",
|
|
304
|
+
"source": destination_rel,
|
|
305
|
+
"destination": source_rel,
|
|
306
|
+
"rolled_back_at": _now_iso(),
|
|
307
|
+
"removed_parent_dirs": removed_parent_dirs,
|
|
308
|
+
}
|
|
309
|
+
)
|
|
310
|
+
|
|
311
|
+
receipt["rolled_back_at"] = _now_iso()
|
|
312
|
+
receipt["rollback_operations"] = rolled_back
|
|
313
|
+
_write_json_atomic(receipt_path, receipt)
|
|
314
|
+
return {"rolled_back": True, "receipt_path": str(receipt_path), "rolled_back_count": len(rolled_back), "rollback_operations": rolled_back}
|