"""Tests for the Proteostasis Network tree browser renderer.""" from pathlib import Path from ai_gene_review.tools import render_pn_tree_browser as browser from ai_gene_review.tools.report_pn_projected_annotations import PNWorkbookRow def test_tree_browser_embeds_leaf_iba_annotations_and_gene_accessions( monkeypatch, tmp_path: Path, ) -> None: """Leaf-node details should carry existing IBA rows and external-link accessions.""" pn_code = ( "Autophagy-Lysosome Pathway|Autophagic lysosome reformation|" "Efflux of autophagy products" ) workbook_row = PNWorkbookRow( order=1, gene_symbol="SPNS1", gene_name="spinster homolog 1", branch="Autophagy-Lysosome Pathway", class_name="Autophagic lysosome reformation", group="Efflux of autophagy products", type_name="", subtype="", uniprot_id="Q9H2V7", notes="Lysosome efflux permease required for ALR after starvation.", references=( "Membrane Trafficking in Autophagy - ScienceDirect", "Spinster is required for autophagic lysosome reformation and mTOR reactivation following starvation | PNAS", ), ) def fake_workbook_context(workbook_path: Path | None, workbook_sheet: str): return ( [workbook_row], {"SPNS1": "Q9H2V7"}, {"SPNS1": "spinster homolog 1"}, {pn_code: [workbook_row]}, ) def fake_iba_annotations(workbook_rows, duckdb_path): return { ("SPNS1", "Q9H2V7"): [ { "go_id": "GO:0033700", "go_label": "phospholipid efflux", "aspect": "BP", "references": "GO_REF:0000033", } ] } monkeypatch.setattr(browser, "build_workbook_context", fake_workbook_context) monkeypatch.setattr(browser, "load_existing_iba_annotations", fake_iba_annotations) review_path = tmp_path / "genes" / "human" / "SPNS1" / "SPNS1-ai-review.html" review_path.parent.mkdir(parents=True) review_path.write_text("SPNS1 review", encoding="utf-8") data = browser.build_data( coverage_rows=[ { "level": "group", "code": pn_code, "status": "mapped", "curation_files": "", "curation_subjects": "", } ], projection_rows=[ { "gene_symbol": "SPNS1", "gene_name": "spinster homolog 1", "pn_code": pn_code, "target_go_id": "GO:0007041", "target_go_label": "lysosomal transport", "goa_status": "new_to_goa", "mapping_scope": "ok_for_propagation_to_go", "mapping_subject_code": pn_code, } ], audit_rows=[], mapping_dir=tmp_path, review_root=tmp_path / "genes", ) node = data["nodes"][pn_code] assert data["projection_rows"][0]["uniprot_id"] == "Q9H2V7" assert data["projection_rows"][0]["review_path"].endswith( "genes/human/SPNS1/SPNS1-ai-review.html" ) assert node["source_evidence_row_count"] == 1 assert node["source_reference_count"] == 2 assert node["source_workbook_evidence"][0]["notes"].startswith("Lysosome efflux") assert node["existing_iba_gene_count"] == 1 assert node["existing_iba_annotation_count"] == 1 assert node["existing_iba_by_gene"][0]["terms"][0]["go_id"] == "GO:0033700" html = browser.render_html(data, Path("projects/PROTEOSTASIS/pn.html")) assert "Source Workbook Evidence" in html assert "Spinster is required for autophagic lysosome reformation" in html assert 'const REPO_ROOT_HREF = "../../";' in html assert '"review_path":"genes/human/SPNS1/SPNS1-ai-review.html"' in html assert ">Review" in html assert "functionome.geneontology.org" in html assert "Q9H2V7" in html def test_render_html_targets_served_deploy_path() -> None: """Hrefs must resolve from where the page is served, not where it is written. The committed page lives at ``projects/PROTEOSTASIS/pn.html`` but is copied verbatim into ``pages/projects/PROTEOSTASIS/pn.html`` (one level deeper) for deployment. ``served_path`` lets href computation target the deployed depth so repo-root links (gene reviews) and the project-page link resolve correctly. """ data = {"root_codes": [], "tree": [], "summary": {}} html = browser.render_html( data, Path("projects/PROTEOSTASIS/pn.html"), served_path=Path("pages/projects/PROTEOSTASIS/pn.html"), ) # Repo-root prefix for gene-review links: three levels up from # pages/projects/PROTEOSTASIS/ reaches the deployed repo root. assert 'const REPO_ROOT_HREF = "../../../";' in html # Project page sits beside the PROTEOSTASIS/ folder in pages/projects/. assert 'href="../PROTEOSTASIS.html"' in html # Report TSVs live in the repo-root projects/ tree, not under pages/. assert ( 'href="../../../projects/PROTEOSTASIS/reports/' 'pn_mapping_coverage/pn_mapping_code_coverage.tsv"' in html ) assert ( 'href="../../../projects/PROTEOSTASIS/reports/' 'pn_mapping_audit/unusual_propagations.tsv"' in html ) def test_render_html_defaults_served_path_to_output_path() -> None: """Without served_path, hrefs are computed relative to the output path.""" data = {"root_codes": [], "tree": [], "summary": {}} html = browser.render_html(data, Path("projects/PROTEOSTASIS/pn.html")) assert 'const REPO_ROOT_HREF = "../../";' in html