Add work-map Notebook refresh command

src/didactopus/main.py

@@ -12,6 +12,7 @@ from .archive_phrase_inventory import write_archive_phrase_inventory_report
 from .first_ring_batch_promotion import run_first_ring_batch_promotion
 from .hub_bundle_rebuild import rebuild_hub_bundle_from_binding
 from .notebook_promotion_pipeline import run_notebook_promotion_pipeline
+from .notebook_workmap_refresh import run_notebook_workmap_refresh
 from .notebook_page import export_notebook_page_from_groundrecall_bundle
 from .notebook_page import export_notebook_page_from_groundrecall_store
 from .review_loader import load_draft_pack
@@ -114,6 +115,15 @@ def build_parser() -> argparse.ArgumentParser:
     pipeline_parser.add_argument("--phrase-input", action="append", default=[])
     pipeline_parser.add_argument("--seed-term", action="append", default=[])
     pipeline_parser.add_argument("--top-n", type=int, default=50)
+
+    workmap_parser = subparsers.add_parser(
+        "notebook-workmap-refresh",
+        help="Run the Notebook promotion pipeline from a project work-map so active paths do not need to be reassembled by hand",
+    )
+    workmap_parser.add_argument("work_map_path")
+    workmap_parser.add_argument("--output-path")
+    workmap_parser.add_argument("--phrase-inventory-output")
+    workmap_parser.add_argument("--top-n", type=int, default=50)
     return parser
 
 
@@ -243,4 +253,13 @@ def main() -> None:
         )
         print(summary)
         return
+    if args.command == "notebook-workmap-refresh":
+        summary = run_notebook_workmap_refresh(
+            args.work_map_path,
+            output_path=args.output_path,
+            phrase_inventory_output=args.phrase_inventory_output,
+            top_n=args.top_n,
+        )
+        print(summary)
+        return
     build_parser().print_help()

src/didactopus/notebook_workmap_refresh.py

@@ -0,0 +1,93 @@
+from __future__ import annotations
+
+import json
+from pathlib import Path
+from typing import Any
+
+from .notebook_promotion_pipeline import run_notebook_promotion_pipeline
+
+
+def _load_json(path: Path) -> dict[str, Any]:
+    return json.loads(path.read_text(encoding="utf-8"))
+
+
+def _resolve(base: Path, value: str) -> Path:
+    path = Path(value)
+    return path if path.is_absolute() else (base / path).resolve()
+
+
+def run_notebook_workmap_refresh(
+    work_map_path: str | Path,
+    *,
+    output_path: str | Path | None = None,
+    phrase_inventory_output: str | Path | None = None,
+    top_n: int = 50,
+) -> dict[str, Any]:
+    work_map_file = Path(work_map_path).resolve()
+    work_root = work_map_file.parent.parent
+    work_map = _load_json(work_map_file)
+
+    binding_path = _resolve(work_root, str(work_map["primary_hub"]["binding_path"]))
+    canonical_dir = _resolve(work_root, str(work_map["groundrecall_paths"]["canonical_export_dir"]))
+    manifest_path = _resolve(work_root, str(work_map["groundrecall_paths"]["batch_manifest"]))
+
+    report_path = (
+        Path(output_path).resolve()
+        if output_path
+        else _resolve(work_root, str(work_map["groundrecall_paths"]["pipeline_report_json"]))
+    )
+    phrase_path = (
+        Path(phrase_inventory_output).resolve()
+        if phrase_inventory_output
+        else _resolve(work_root, str(work_map["groundrecall_paths"]["pipeline_phrase_inventory_json"]))
+    )
+
+    normalized_roots = [
+        _resolve(work_root, item)
+        for item in (work_map.get("canonical_sources", {}) or {}).get("normalized_roots", [])
+    ]
+
+    seed_terms = [
+        str(item.get("concept", "")).strip()
+        for items in (work_map.get("promotion_priority", {}) or {}).values()
+        for item in items or []
+        if str(item.get("concept", "")).strip()
+    ]
+
+    if not seed_terms:
+        manifest_data = _load_json(manifest_path) if manifest_path.suffix == ".json" else None
+        if manifest_data:
+            seed_terms = [
+                str(item.get("concept", "")).strip()
+                for items in (manifest_data.get("promotion_priority", {}) or {}).values()
+                for item in items or []
+                if str(item.get("concept", "")).strip()
+            ]
+        else:
+            import yaml  # local import to avoid unnecessary dependency at module import time
+
+            manifest_yaml = yaml.safe_load(manifest_path.read_text(encoding="utf-8")) or {}
+            seed_terms = [
+                str(item.get("concept", "")).strip()
+                for items in (manifest_yaml.get("promotion_priority", {}) or {}).values()
+                for item in items or []
+                if str(item.get("concept", "")).strip()
+            ]
+
+    summary = run_notebook_promotion_pipeline(
+        binding_path=binding_path,
+        manifest_path=manifest_path,
+        canonical_dir=canonical_dir,
+        output_path=report_path,
+        phrase_inventory_output=phrase_path,
+        phrase_inputs=normalized_roots,
+        seed_terms=seed_terms,
+        top_n=top_n,
+    )
+    return {
+        "work_map_path": str(work_map_file),
+        "work_root": str(work_root),
+        "report_path": summary["report_path"],
+        "markdown_path": summary["markdown_path"],
+        "report": summary["report"],
+    }

tests/test_notebook_workmap_refresh.py

@@ -0,0 +1,163 @@
+from __future__ import annotations
+
+import json
+from pathlib import Path
+
+from didactopus.notebook_workmap_refresh import run_notebook_workmap_refresh
+
+
+def test_notebook_workmap_refresh_runs_from_work_map(tmp_path: Path) -> None:
+    pilot = tmp_path / "pilot"
+    docs_dir = pilot / "normalized" / "seed-bundle" / "documents" / "source-one"
+    docs_dir.mkdir(parents=True)
+    (docs_dir / "document.md").write_text(
+        "# Source One\n\nEvolution is a change in the gene pool of a population over time.\n",
+        encoding="utf-8",
+    )
+
+    export_dir = pilot / "groundrecall" / "export" / "canonical"
+    export_dir.mkdir(parents=True)
+    notebook_dir = pilot / "didactopus" / "notebook-page"
+    notebook_dir.mkdir(parents=True)
+    workmap_dir = pilot / ".groundrecall"
+    workmap_dir.mkdir(parents=True)
+
+    hub = {
+        "bundle_kind": "groundrecall_query_bundle",
+        "query_type": "concept",
+        "concept": {
+            "concept_id": "concept::hub",
+            "title": "Hub",
+            "aliases": [],
+            "description": "Hub concept",
+            "source_artifact_ids": ["ia_hub"],
+            "current_status": "reviewed",
+        },
+        "relevant_claims": [{"claim_id": "hc1", "claim_text": "Hub claim."}],
+        "relations": [],
+        "supporting_observations": [],
+        "source_artifacts": [],
+        "related_concepts": [],
+        "review_candidates": [],
+        "suggested_next_actions": [],
+        "bundle_notes": [],
+    }
+    source_bundle = {
+        "bundle_kind": "groundrecall_query_bundle",
+        "query_type": "concept",
+        "concept": {
+            "concept_id": "concept::source",
+            "title": "Source Concept",
+            "aliases": [],
+            "description": "Source concept",
+            "source_artifact_ids": ["ia_src"],
+            "current_status": "reviewed",
+        },
+        "relevant_claims": [
+            {
+                "claim_id": "c1",
+                "claim_text": "Evolution is a change in the gene pool of a population over time.",
+                "source_observation_ids": ["o1"],
+                "metadata": {},
+            }
+        ],
+        "relations": [],
+        "supporting_observations": [
+            {
+                "observation_id": "o1",
+                "artifact_id": "ia_src",
+                "text": "Evolution is a change in the gene pool of a population over time.",
+                "role": "claim",
+                "origin_path": "documents/source-one/document.md",
+                "grounding_status": "grounded",
+            }
+        ],
+        "source_artifacts": [
+            {
+                "artifact_id": "ia_src",
+                "artifact_kind": "doclift_bundle_artifact",
+                "title": "document",
+                "path": "documents/source-one/document.md",
+                "current_status": "reviewed",
+            }
+        ],
+        "related_concepts": [],
+    }
+    placeholder = {
+        "bundle_kind": "groundrecall_query_bundle",
+        "query_type": "concept",
+        "concept": {
+            "concept_id": "concept::gene-pool",
+            "title": "Gene Pool",
+            "aliases": [],
+            "description": "Placeholder",
+            "source_artifact_ids": [],
+            "current_status": "reviewed",
+        },
+        "relevant_claims": [],
+        "relations": [],
+        "supporting_observations": [],
+        "source_artifacts": [],
+        "related_concepts": [],
+        "review_candidates": [],
+        "suggested_next_actions": [],
+        "bundle_notes": [],
+    }
+    (export_dir / "groundrecall_query_bundle__hub.json").write_text(json.dumps(hub), encoding="utf-8")
+    (export_dir / "query_bundle__source.json").write_text(json.dumps(source_bundle), encoding="utf-8")
+    (export_dir / "query_bundle__gene-pool.json").write_text(json.dumps(placeholder), encoding="utf-8")
+    (notebook_dir / "notebook_page__hub.json").write_text(json.dumps({"concept": {"concept_id": "concept::hub"}, "summary": {}}), encoding="utf-8")
+
+    binding = {
+        "primary_artifacts": {
+            "groundrecall_query_bundle": "../../groundrecall/export/canonical/groundrecall_query_bundle__hub.json",
+            "notebook_page": "./notebook_page__hub.json",
+        },
+        "supporting_artifacts": {
+            "gene_pool_bundle": "../../groundrecall/export/canonical/query_bundle__gene-pool.json",
+        },
+    }
+    (notebook_dir / "binding.json").write_text(json.dumps(binding), encoding="utf-8")
+
+    manifest = pilot / "manifests" / "first-ring-promotion-batch.yaml"
+    manifest.parent.mkdir(parents=True)
+    manifest.write_text(
+        """
+promotion_priority:
+  tier_3:
+    - concept: gene-pool
+      label: Gene Pool
+      compose_from:
+        bundle_refs:
+          - query_bundle__source.json
+        keyword_phrases:
+          - gene pool
+""",
+        encoding="utf-8",
+    )
+
+    work_map = {
+        "project": "pilot",
+        "primary_hub": {
+            "binding_path": "didactopus/notebook-page/binding.json",
+        },
+        "canonical_sources": {
+            "normalized_roots": ["normalized/seed-bundle"],
+        },
+        "groundrecall_paths": {
+            "canonical_export_dir": "groundrecall/export/canonical",
+            "batch_manifest": "manifests/first-ring-promotion-batch.yaml",
+            "pipeline_report_json": "groundrecall/report.json",
+            "pipeline_phrase_inventory_json": "groundrecall/phrases.json",
+        },
+    }
+    work_map_path = workmap_dir / "work-map.json"
+    work_map_path.write_text(json.dumps(work_map), encoding="utf-8")
+
+    result = run_notebook_workmap_refresh(work_map_path, top_n=10)
+
+    report = json.loads(Path(result["report_path"]).read_text(encoding="utf-8"))
+    rebuilt_bundle = json.loads((export_dir / "query_bundle__gene-pool.json").read_text(encoding="utf-8"))
+    assert report["batch_promotion"]["weak_node_count"] == 1
+    assert report["delta"]["hub"]["related_concept_count"] == 1
+    assert len(rebuilt_bundle["relevant_claims"]) == 1