mednotes-opencode 0.1.0

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Files changed (430) hide show
  1. package/.opencode/agents/med-chat-triager.md +204 -0
  2. package/.opencode/agents/med-flashcard-maker.md +63 -0
  3. package/.opencode/agents/med-knowledge-architect.md +230 -0
  4. package/.opencode/agents/med-link-graph-curator.md +177 -0
  5. package/.opencode/agents/med-publish-guard.md +62 -0
  6. package/.opencode/commands/flashcards.md +25 -0
  7. package/.opencode/commands/mednotes/create.md +25 -0
  8. package/.opencode/commands/mednotes/enrich.md +27 -0
  9. package/.opencode/commands/mednotes/fix-wiki.md +27 -0
  10. package/.opencode/commands/mednotes/history.md +22 -0
  11. package/.opencode/commands/mednotes/link-body.md +25 -0
  12. package/.opencode/commands/mednotes/link-related.md +27 -0
  13. package/.opencode/commands/mednotes/link.md +27 -0
  14. package/.opencode/commands/mednotes/pdf-library.md +27 -0
  15. package/.opencode/commands/mednotes/process-chats.md +23 -0
  16. package/.opencode/commands/mednotes/setup.md +21 -0
  17. package/.opencode/commands/mednotes/status.md +27 -0
  18. package/.opencode/commands/mednotes/telemetry.md +27 -0
  19. package/.opencode/commands/report.md +26 -0
  20. package/.opencode/mednotes/AGENTS.md +57 -0
  21. package/.opencode/mednotes/agents/med-chat-triager.md +197 -0
  22. package/.opencode/mednotes/agents/med-flashcard-maker.md +56 -0
  23. package/.opencode/mednotes/agents/med-knowledge-architect.md +224 -0
  24. package/.opencode/mednotes/agents/med-link-graph-curator.md +171 -0
  25. package/.opencode/mednotes/agents/med-publish-guard.md +55 -0
  26. package/.opencode/mednotes/contracts/.gitkeep +1 -0
  27. package/.opencode/mednotes/contracts/agents.json +116 -0
  28. package/.opencode/mednotes/contracts/opencode-plugin.json +70 -0
  29. package/.opencode/mednotes/docs/agent-prompt-hardening.md +567 -0
  30. package/.opencode/mednotes/docs/agent-role-contracts.md +94 -0
  31. package/.opencode/mednotes/docs/anki-mcp-twenty-rules.md +214 -0
  32. package/.opencode/mednotes/docs/anki-templates/README.md +39 -0
  33. package/.opencode/mednotes/docs/anki-templates/cloze.back.html +23 -0
  34. package/.opencode/mednotes/docs/anki-templates/cloze.front.html +14 -0
  35. package/.opencode/mednotes/docs/anki-templates/qa.back.html +24 -0
  36. package/.opencode/mednotes/docs/anki-templates/qa.front.html +14 -0
  37. package/.opencode/mednotes/docs/anki-templates/style.css +182 -0
  38. package/.opencode/mednotes/docs/atomicity-splitting-policy.md +113 -0
  39. package/.opencode/mednotes/docs/extension-docs.md +40 -0
  40. package/.opencode/mednotes/docs/flashcard-ingestion.md +278 -0
  41. package/.opencode/mednotes/docs/knowledge-architect.md +208 -0
  42. package/.opencode/mednotes/docs/merge-policy.md +110 -0
  43. package/.opencode/mednotes/docs/public-vocabulary.md +104 -0
  44. package/.opencode/mednotes/docs/semantic-linker.md +141 -0
  45. package/.opencode/mednotes/docs/taxonomy-policy.md +90 -0
  46. package/.opencode/mednotes/docs/triage-policy.md +187 -0
  47. package/.opencode/mednotes/docs/vault-version-control.md +758 -0
  48. package/.opencode/mednotes/docs/vocabulary-db-recovery.md +58 -0
  49. package/.opencode/mednotes/docs/workflow-output-contract.md +779 -0
  50. package/.opencode/mednotes/hooks/hooks.json +79 -0
  51. package/.opencode/mednotes/package-lock.json +6361 -0
  52. package/.opencode/mednotes/package.json +15 -0
  53. package/.opencode/mednotes/pyproject.toml +48 -0
  54. package/.opencode/mednotes/scripts/bootstrap_windows_python_uv.cmd +13 -0
  55. package/.opencode/mednotes/scripts/bootstrap_windows_python_uv.ps1 +172 -0
  56. package/.opencode/mednotes/scripts/enrich_notes.py +23 -0
  57. package/.opencode/mednotes/scripts/full_reset_windows_python_uv.cmd +13 -0
  58. package/.opencode/mednotes/scripts/hooks/antigravity_hook_status.mjs +212 -0
  59. package/.opencode/mednotes/scripts/hooks/mednotes_hook/adapters/antigravity.mjs +169 -0
  60. package/.opencode/mednotes/scripts/hooks/mednotes_hook/adapters/harness_payload.mjs +103 -0
  61. package/.opencode/mednotes/scripts/hooks/mednotes_hook/adapters/opencode_plugin.mjs +341 -0
  62. package/.opencode/mednotes/scripts/hooks/mednotes_hook/adapters/opencode_user_config_sync.mjs +177 -0
  63. package/.opencode/mednotes/scripts/hooks/mednotes_hook/anki_preflight.mjs +214 -0
  64. package/.opencode/mednotes/scripts/hooks/mednotes_hook/cli.mjs +143 -0
  65. package/.opencode/mednotes/scripts/hooks/mednotes_hook/diagnostics.mjs +11 -0
  66. package/.opencode/mednotes/scripts/hooks/mednotes_hook/domain/agent_directive_core.mjs +160 -0
  67. package/.opencode/mednotes/scripts/hooks/mednotes_hook/fsm_directive.mjs +1470 -0
  68. package/.opencode/mednotes/scripts/hooks/mednotes_hook/hook_errors.mjs +120 -0
  69. package/.opencode/mednotes/scripts/hooks/mednotes_hook/retention.mjs +114 -0
  70. package/.opencode/mednotes/scripts/hooks/mednotes_hook/runtime.mjs +174 -0
  71. package/.opencode/mednotes/scripts/hooks/mednotes_hook/telemetry_capture.mjs +511 -0
  72. package/.opencode/mednotes/scripts/hooks/mednotes_hook/vault_guard.mjs +624 -0
  73. package/.opencode/mednotes/scripts/hooks/mednotes_hook.mjs +5 -0
  74. package/.opencode/mednotes/scripts/mednotes/_runtime_paths.py +24 -0
  75. package/.opencode/mednotes/scripts/mednotes/anki_model_validator.py +18 -0
  76. package/.opencode/mednotes/scripts/mednotes/capture_extension_diff.py +1562 -0
  77. package/.opencode/mednotes/scripts/mednotes/feedback_report.py +16 -0
  78. package/.opencode/mednotes/scripts/mednotes/flashcard_index.py +18 -0
  79. package/.opencode/mednotes/scripts/mednotes/flashcard_pipeline.py +18 -0
  80. package/.opencode/mednotes/scripts/mednotes/flashcard_report.py +18 -0
  81. package/.opencode/mednotes/scripts/mednotes/flashcard_sources.py +18 -0
  82. package/.opencode/mednotes/scripts/mednotes/obsidian/README.md +6 -0
  83. package/.opencode/mednotes/scripts/mednotes/obsidian_note_utils.py +20 -0
  84. package/.opencode/mednotes/scripts/mednotes/pdf_library/cli.py +16 -0
  85. package/.opencode/mednotes/scripts/mednotes/project_fsm.py +229 -0
  86. package/.opencode/mednotes/scripts/mednotes/setup_telemetry_email.py +404 -0
  87. package/.opencode/mednotes/scripts/mednotes/sync_anki_twenty_rules.py +18 -0
  88. package/.opencode/mednotes/scripts/mednotes/sync_opencode_user_config.py +36 -0
  89. package/.opencode/mednotes/scripts/mednotes/wiki/cli.py +20 -0
  90. package/.opencode/mednotes/scripts/mednotes/wiki_graph.py +18 -0
  91. package/.opencode/mednotes/scripts/mednotes/wiki_tree.py +134 -0
  92. package/.opencode/mednotes/scripts/reset_windows_python_uv.ps1 +625 -0
  93. package/.opencode/mednotes/scripts/run_python.mjs +109 -0
  94. package/.opencode/mednotes/scripts/vault/vault_commit.ps1 +19 -0
  95. package/.opencode/mednotes/scripts/vault/vault_commit.sh +18 -0
  96. package/.opencode/mednotes/scripts/vault/vault_git.ps1 +19 -0
  97. package/.opencode/mednotes/scripts/vault/vault_git.py +3107 -0
  98. package/.opencode/mednotes/scripts/vault/vault_git.sh +18 -0
  99. package/.opencode/mednotes/scripts/vault/vault_precommit.ps1 +19 -0
  100. package/.opencode/mednotes/scripts/vault/vault_precommit.sh +18 -0
  101. package/.opencode/mednotes/skills/THIRD_PARTY_NOTICES.md +45 -0
  102. package/.opencode/mednotes/skills/create-medical-flashcards/SKILL.md +113 -0
  103. package/.opencode/mednotes/skills/create-medical-note/SKILL.md +90 -0
  104. package/.opencode/mednotes/skills/enrich-medical-note/SKILL.md +120 -0
  105. package/.opencode/mednotes/skills/fix-medical-wiki/SKILL.md +559 -0
  106. package/.opencode/mednotes/skills/link-medical-wiki/SKILL.md +224 -0
  107. package/.opencode/mednotes/skills/obsidian-cli/SKILL.md +118 -0
  108. package/.opencode/mednotes/skills/obsidian-markdown/SKILL.md +207 -0
  109. package/.opencode/mednotes/skills/obsidian-markdown/references/CALLOUTS.md +58 -0
  110. package/.opencode/mednotes/skills/obsidian-markdown/references/EMBEDS.md +63 -0
  111. package/.opencode/mednotes/skills/obsidian-markdown/references/PROPERTIES.md +61 -0
  112. package/.opencode/mednotes/skills/obsidian-ops/SKILL.md +136 -0
  113. package/.opencode/mednotes/skills/pdf-library/SKILL.md +45 -0
  114. package/.opencode/mednotes/skills/process-medical-chats/SKILL.md +246 -0
  115. package/.opencode/mednotes/skills/workflow-report/SKILL.md +100 -0
  116. package/.opencode/mednotes/src/mednotes/__init__.py +5 -0
  117. package/.opencode/mednotes/src/mednotes/domains/__init__.py +5 -0
  118. package/.opencode/mednotes/src/mednotes/domains/flashcards/README.md +26 -0
  119. package/.opencode/mednotes/src/mednotes/domains/flashcards/__init__.py +2 -0
  120. package/.opencode/mednotes/src/mednotes/domains/flashcards/build_demo_apkg.py +177 -0
  121. package/.opencode/mednotes/src/mednotes/domains/flashcards/contracts.py +385 -0
  122. package/.opencode/mednotes/src/mednotes/domains/flashcards/flashcards_machine.py +522 -0
  123. package/.opencode/mednotes/src/mednotes/domains/flashcards/fsm.py +817 -0
  124. package/.opencode/mednotes/src/mednotes/domains/flashcards/index.py +630 -0
  125. package/.opencode/mednotes/src/mednotes/domains/flashcards/install_models.py +445 -0
  126. package/.opencode/mednotes/src/mednotes/domains/flashcards/model.py +359 -0
  127. package/.opencode/mednotes/src/mednotes/domains/flashcards/obsidian_links.py +135 -0
  128. package/.opencode/mednotes/src/mednotes/domains/flashcards/obsidian_note_utils.py +546 -0
  129. package/.opencode/mednotes/src/mednotes/domains/flashcards/pipeline.py +580 -0
  130. package/.opencode/mednotes/src/mednotes/domains/flashcards/report.py +510 -0
  131. package/.opencode/mednotes/src/mednotes/domains/flashcards/sources.py +682 -0
  132. package/.opencode/mednotes/src/mednotes/domains/flashcards/sync_rules.py +184 -0
  133. package/.opencode/mednotes/src/mednotes/domains/history/__init__.py +1 -0
  134. package/.opencode/mednotes/src/mednotes/domains/history/history_fsm.py +852 -0
  135. package/.opencode/mednotes/src/mednotes/domains/history/history_machine.py +453 -0
  136. package/.opencode/mednotes/src/mednotes/domains/setup/__init__.py +7 -0
  137. package/.opencode/mednotes/src/mednotes/domains/setup/setup_fsm.py +808 -0
  138. package/.opencode/mednotes/src/mednotes/domains/setup/setup_machine.py +973 -0
  139. package/.opencode/mednotes/src/mednotes/domains/wiki/README.md +64 -0
  140. package/.opencode/mednotes/src/mednotes/domains/wiki/__init__.py +1 -0
  141. package/.opencode/mednotes/src/mednotes/domains/wiki/api.py +668 -0
  142. package/.opencode/mednotes/src/mednotes/domains/wiki/batch_state.py +102 -0
  143. package/.opencode/mednotes/src/mednotes/domains/wiki/capabilities/__init__.py +1 -0
  144. package/.opencode/mednotes/src/mednotes/domains/wiki/capabilities/atomicity/__init__.py +1 -0
  145. package/.opencode/mednotes/src/mednotes/domains/wiki/capabilities/atomicity/atomicity.py +877 -0
  146. package/.opencode/mednotes/src/mednotes/domains/wiki/capabilities/body_link/__init__.py +1 -0
  147. package/.opencode/mednotes/src/mednotes/domains/wiki/capabilities/body_link/body_linker.py +1562 -0
  148. package/.opencode/mednotes/src/mednotes/domains/wiki/capabilities/effects/__init__.py +1 -0
  149. package/.opencode/mednotes/src/mednotes/domains/wiki/capabilities/effects/effect_adapters.py +949 -0
  150. package/.opencode/mednotes/src/mednotes/domains/wiki/capabilities/effects/fix_wiki_runtime_adapters.py +433 -0
  151. package/.opencode/mednotes/src/mednotes/domains/wiki/capabilities/graph/__init__.py +1 -0
  152. package/.opencode/mednotes/src/mednotes/domains/wiki/capabilities/graph/coverage.py +413 -0
  153. package/.opencode/mednotes/src/mednotes/domains/wiki/capabilities/graph/graph.py +396 -0
  154. package/.opencode/mednotes/src/mednotes/domains/wiki/capabilities/graph/graph_fixes.py +161 -0
  155. package/.opencode/mednotes/src/mednotes/domains/wiki/capabilities/hygiene/__init__.py +1 -0
  156. package/.opencode/mednotes/src/mednotes/domains/wiki/capabilities/hygiene/hygiene.py +483 -0
  157. package/.opencode/mednotes/src/mednotes/domains/wiki/capabilities/illustrate/__init__.py +2 -0
  158. package/.opencode/mednotes/src/mednotes/domains/wiki/capabilities/illustrate/anchors.py +185 -0
  159. package/.opencode/mednotes/src/mednotes/domains/wiki/capabilities/illustrate/core/__init__.py +0 -0
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  161. package/.opencode/mednotes/src/mednotes/domains/wiki/capabilities/illustrate/core/config.py +131 -0
  162. package/.opencode/mednotes/src/mednotes/domains/wiki/capabilities/illustrate/core/download.py +224 -0
  163. package/.opencode/mednotes/src/mednotes/domains/wiki/capabilities/illustrate/core/frontmatter.py +59 -0
  164. package/.opencode/mednotes/src/mednotes/domains/wiki/capabilities/illustrate/core/insert.py +227 -0
  165. package/.opencode/mednotes/src/mednotes/domains/wiki/capabilities/illustrate/core/local_import.py +54 -0
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  167. package/.opencode/mednotes/src/mednotes/domains/wiki/capabilities/illustrate/sources/web_profiles.py +99 -0
  168. package/.opencode/mednotes/src/mednotes/domains/wiki/capabilities/illustrate/sources/web_search.py +203 -0
  169. package/.opencode/mednotes/src/mednotes/domains/wiki/capabilities/illustrate/sources/wikimedia.py +102 -0
  170. package/.opencode/mednotes/src/mednotes/domains/wiki/capabilities/markdown/__init__.py +1 -0
  171. package/.opencode/mednotes/src/mednotes/domains/wiki/capabilities/markdown/markdown_db_adapter.mjs +434 -0
  172. package/.opencode/mednotes/src/mednotes/domains/wiki/capabilities/markdown/markdown_node_runtime.py +274 -0
  173. package/.opencode/mednotes/src/mednotes/domains/wiki/capabilities/markdown/markdown_query.py +227 -0
  174. package/.opencode/mednotes/src/mednotes/domains/wiki/capabilities/notes/__init__.py +1 -0
  175. package/.opencode/mednotes/src/mednotes/domains/wiki/capabilities/notes/artifacts.py +605 -0
  176. package/.opencode/mednotes/src/mednotes/domains/wiki/capabilities/notes/canonical_merge.py +277 -0
  177. package/.opencode/mednotes/src/mednotes/domains/wiki/capabilities/notes/markdown_zones.py +85 -0
  178. package/.opencode/mednotes/src/mednotes/domains/wiki/capabilities/notes/meaning_planner.py +307 -0
  179. package/.opencode/mednotes/src/mednotes/domains/wiki/capabilities/notes/note_iter.py +67 -0
  180. package/.opencode/mednotes/src/mednotes/domains/wiki/capabilities/notes/note_merge.py +278 -0
  181. package/.opencode/mednotes/src/mednotes/domains/wiki/capabilities/notes/note_plan.py +409 -0
  182. package/.opencode/mednotes/src/mednotes/domains/wiki/capabilities/notes/note_policy.py +22 -0
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  186. package/.opencode/mednotes/src/mednotes/domains/wiki/capabilities/notes/note_style/models.py +208 -0
  187. package/.opencode/mednotes/src/mednotes/domains/wiki/capabilities/notes/note_style/prompts.py +37 -0
  188. package/.opencode/mednotes/src/mednotes/domains/wiki/capabilities/notes/note_style/tables.py +236 -0
  189. package/.opencode/mednotes/src/mednotes/domains/wiki/capabilities/notes/note_style/validate.py +404 -0
  190. package/.opencode/mednotes/src/mednotes/domains/wiki/capabilities/notes/provenance.py +478 -0
  191. package/.opencode/mednotes/src/mednotes/domains/wiki/capabilities/notes/raw_chats.py +273 -0
  192. package/.opencode/mednotes/src/mednotes/domains/wiki/capabilities/notes/sources_backfill.py +235 -0
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  195. package/.opencode/mednotes/src/mednotes/domains/wiki/capabilities/pdf/captions.py +47 -0
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  239. package/.opencode/mednotes/src/mednotes/domains/wiki/capabilities/subagents/agents.py +1767 -0
  240. package/.opencode/mednotes/src/mednotes/domains/wiki/capabilities/vocabulary/__init__.py +1 -0
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  243. package/.opencode/mednotes/src/mednotes/domains/wiki/capabilities/vocabulary/llm_disambiguation.py +182 -0
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  430. package/package.json +45 -0
@@ -0,0 +1,116 @@
1
+ """Wiki_Medicina taxonomy public API.
2
+
3
+ The canonical taxonomy policy is defined in ``wiki.taxonomy.policy``; schema
4
+ constants are compatibility projections derived from that single source.
5
+ """
6
+ from __future__ import annotations
7
+
8
+ from mednotes.domains.wiki.capabilities.vocabulary.taxonomy.audit import (
9
+ _canonical_directory_paths,
10
+ taxonomy_audit,
11
+ taxonomy_tree,
12
+ )
13
+ from mednotes.domains.wiki.capabilities.vocabulary.taxonomy.migration import (
14
+ _default_migration_receipt_path,
15
+ _join_wiki_relative_dir,
16
+ _load_json_file,
17
+ _missing_parent_dirs,
18
+ _plan_wiki_dir,
19
+ _write_json_atomic,
20
+ apply_taxonomy_migration,
21
+ rollback_taxonomy_migration,
22
+ taxonomy_migration_plan,
23
+ )
24
+ from mednotes.domains.wiki.capabilities.vocabulary.taxonomy.normalize import (
25
+ _DRIVE_RE,
26
+ _UNSAFE_TAXONOMY_RE,
27
+ _UNSAFE_TITLE_RE,
28
+ _fold_taxonomy_segment,
29
+ _safe_relative_dir,
30
+ normalize_taxonomy,
31
+ safe_title,
32
+ )
33
+ from mednotes.domains.wiki.capabilities.vocabulary.taxonomy.policy import (
34
+ CANONICAL_TAXONOMY_POLICY,
35
+ TaxonomyAreaPolicy,
36
+ TaxonomySpecialtyPolicy,
37
+ )
38
+ from mednotes.domains.wiki.capabilities.vocabulary.taxonomy.resolve import (
39
+ _NEAR_DUPLICATE_CUTOFF,
40
+ TaxonomyDecisionRequired,
41
+ _canonicalize_taxonomy_parts,
42
+ _format_suggestions,
43
+ _match_existing_segment,
44
+ _suggest_existing_segments,
45
+ _validate_taxonomy_not_title,
46
+ _visible_child_dirs,
47
+ resolve_target_for_note,
48
+ resolve_taxonomy,
49
+ target_for_note,
50
+ )
51
+ from mednotes.domains.wiki.capabilities.vocabulary.taxonomy.schema import (
52
+ CANONICAL_AREA_ALIASES,
53
+ CANONICAL_TAXONOMY,
54
+ CANONICAL_TAXONOMY_ALIASES,
55
+ TaxonomyResolution,
56
+ _canonical_area_aliases_by_fold,
57
+ _canonical_roots_by_fold,
58
+ _canonical_specialties_by_fold,
59
+ _canonical_specialties_for_root,
60
+ canonical_taxonomy_invariants,
61
+ canonical_taxonomy_tree,
62
+ )
63
+ from mednotes.domains.wiki.capabilities.vocabulary.taxonomy.status import (
64
+ TAXONOMY_STATUS_SCHEMA,
65
+ render_taxonomy_status_markdown,
66
+ taxonomy_status,
67
+ )
68
+
69
+ __all__ = [
70
+ "CANONICAL_TAXONOMY",
71
+ "CANONICAL_TAXONOMY_POLICY",
72
+ "CANONICAL_AREA_ALIASES",
73
+ "CANONICAL_TAXONOMY_ALIASES",
74
+ "TaxonomyAreaPolicy",
75
+ "TaxonomyResolution",
76
+ "TaxonomySpecialtyPolicy",
77
+ "TaxonomyDecisionRequired",
78
+ "TAXONOMY_STATUS_SCHEMA",
79
+ "_DRIVE_RE",
80
+ "_NEAR_DUPLICATE_CUTOFF",
81
+ "_UNSAFE_TAXONOMY_RE",
82
+ "_UNSAFE_TITLE_RE",
83
+ "_canonical_directory_paths",
84
+ "_canonical_area_aliases_by_fold",
85
+ "_canonical_roots_by_fold",
86
+ "_canonical_specialties_by_fold",
87
+ "_canonical_specialties_for_root",
88
+ "_canonicalize_taxonomy_parts",
89
+ "_default_migration_receipt_path",
90
+ "_fold_taxonomy_segment",
91
+ "_format_suggestions",
92
+ "_join_wiki_relative_dir",
93
+ "_load_json_file",
94
+ "_match_existing_segment",
95
+ "_missing_parent_dirs",
96
+ "_plan_wiki_dir",
97
+ "_safe_relative_dir",
98
+ "_suggest_existing_segments",
99
+ "_validate_taxonomy_not_title",
100
+ "_visible_child_dirs",
101
+ "_write_json_atomic",
102
+ "apply_taxonomy_migration",
103
+ "canonical_taxonomy_tree",
104
+ "canonical_taxonomy_invariants",
105
+ "normalize_taxonomy",
106
+ "resolve_target_for_note",
107
+ "resolve_taxonomy",
108
+ "render_taxonomy_status_markdown",
109
+ "rollback_taxonomy_migration",
110
+ "safe_title",
111
+ "target_for_note",
112
+ "taxonomy_audit",
113
+ "taxonomy_migration_plan",
114
+ "taxonomy_status",
115
+ "taxonomy_tree",
116
+ ]
@@ -0,0 +1,201 @@
1
+ """Taxonomy tree and dry-run audit helpers."""
2
+ from __future__ import annotations
3
+
4
+ from pathlib import Path
5
+ from typing import Any
6
+
7
+ from mednotes.domains.wiki.capabilities.notes import note_style
8
+ from mednotes.domains.wiki.capabilities.notes.note_iter import is_note_markdown
9
+ from mednotes.domains.wiki.capabilities.notes.note_policy import is_operational_index_note
10
+ from mednotes.domains.wiki.capabilities.vocabulary.taxonomy.normalize import _fold_taxonomy_segment
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)
@@ -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}