Protein files from an input path - regex name parsing

README.md

@@ -86,6 +86,8 @@ PYTHONPATH='.' python3 -u ${FRIDATA_PATH}/fridata.py \
  -e ${EMBEDDER_TYPE}
 ```
 
+For subset runs with `--input-path`, new datasets store canonical keys as `{line_from_ids_file}_{chain}` (for example `A0A2K6V5L6_A`), not the full AlphaFold CIF filename stem. The dataset’s `input_structures.idx` maps each canonical key to the source structure filename. Older datasets created before this convention may still use long AF-style keys.
+
 ## Running as a CLI tool
 
 Assuming all `Instalation and activation` steps succeeded.
@@ -106,7 +108,7 @@ python3 -m pip install -e .
 
 ```
 $ fridata <...>
-```
+```3dc54 (Use ids_file tokens (e.g. plain UniProt) plus chain as the canonical dataset index keys)
 
 ## Running on HPC
 

tests/test_input_path_resolution.py

@@ -0,0 +1,138 @@
+"""Tests for input_path ID resolution (exact stem + AF model version / isoform)."""
+
+from pathlib import Path
+
+from toolbox.models.manage_dataset.extract_archive import (
+    build_stem_to_paths,
+    pick_single_path_for_canonical_id,
+    resolve_id,
+    retrieve_single_file,
+)
+
+
+def _touch(path: Path) -> None:
+    path.parent.mkdir(parents=True, exist_ok=True)
+    path.write_text("", encoding="utf-8")
+
+
+def test_build_stem_to_paths_empty(tmp_path: Path) -> None:
+    assert build_stem_to_paths(tmp_path) == {}
+
+
+def test_resolve_exact_cif_only(tmp_path: Path) -> None:
+    f = tmp_path / "Q5VSL9-2.cif"
+    _touch(f)
+    inv = build_stem_to_paths(tmp_path)
+    out = resolve_id("Q5VSL9-2", inv)
+    assert len(out) == 1
+    assert out[0].resolve() == f.resolve()
+
+
+def test_resolve_prefers_cif_over_pdb_same_stem(tmp_path: Path) -> None:
+    cif = tmp_path / "Q5VSL9-2.cif"
+    pdb = tmp_path / "Q5VSL9-2.pdb"
+    _touch(pdb)
+    _touch(cif)
+    inv = build_stem_to_paths(tmp_path)
+    out = resolve_id("Q5VSL9-2", inv)
+    assert len(out) == 1
+    assert out[0].suffix.lower() == ".cif"
+
+
+def test_resolve_af_latest_version(tmp_path: Path) -> None:
+    _touch(tmp_path / "AF-Q5VSL9-2-F1-model_v4.cif")
+    v6 = tmp_path / "AF-Q5VSL9-2-F1-model_v6.cif"
+    _touch(v6)
+    inv = build_stem_to_paths(tmp_path)
+    out = resolve_id("Q5VSL9-2", inv)
+    assert len(out) == 1
+    assert out[0].resolve() == v6.resolve()
+
+
+def test_resolve_af_multi_fragment_same_version(tmp_path: Path) -> None:
+    f1 = tmp_path / "AF-Q5VSL9-F1-model_v4.cif"
+    f2 = tmp_path / "AF-Q5VSL9-F2-model_v4.cif"
+    _touch(f1)
+    _touch(f2)
+    inv = build_stem_to_paths(tmp_path)
+    out = resolve_id("Q5VSL9", inv)
+    assert len(out) == 2
+    assert {p.resolve() for p in out} == {f1.resolve(), f2.resolve()}
+
+
+def test_pick_single_path_prefers_lowest_af_fragment(tmp_path: Path) -> None:
+    f1 = tmp_path / "AF-Q5VSL9-F1-model_v4.cif"
+    f2 = tmp_path / "AF-Q5VSL9-F2-model_v4.cif"
+    _touch(f1)
+    _touch(f2)
+    chosen = pick_single_path_for_canonical_id([f2, f1])
+    assert chosen.resolve() == f1.resolve()
+
+
+def test_pick_single_path_non_af_tiebreak_by_path(tmp_path: Path) -> None:
+    a = tmp_path / "a" / "x.cif"
+    b = tmp_path / "b" / "y.cif"
+    _touch(a)
+    _touch(b)
+    chosen = pick_single_path_for_canonical_id([b, a])
+    assert chosen.resolve() == a.resolve()
+
+
+def test_retrieve_single_file_canonical_pdb_code(tmp_path: Path) -> None:
+    f = tmp_path / "AF-A0A2K6V5L6-F1-model_v6.cif"
+    f.write_text("dummy", encoding="utf-8")
+    data, pdb_code, ext = retrieve_single_file((str(f), "A0A2K6V5L6"))
+    assert data == "dummy"
+    assert pdb_code == "A0A2K6V5L6"
+    assert ext == ".cif"
+
+
+def test_retrieve_single_file_plain_path_uses_stem(tmp_path: Path) -> None:
+    f = tmp_path / "AF-A0A2K6V5L6-F1-model_v6.cif"
+    f.write_text("z", encoding="utf-8")
+    _, pdb_code, _ = retrieve_single_file(str(f))
+    assert pdb_code == "AF-A0A2K6V5L6-F1-model_v6"
+
+
+def test_resolve_exact_wins_over_af_pattern(tmp_path: Path) -> None:
+    exact = tmp_path / "Q5VSL9-2.cif"
+    _touch(exact)
+    _touch(tmp_path / "AF-Q5VSL9-2-F1-model_v6.cif")
+    inv = build_stem_to_paths(tmp_path)
+    out = resolve_id("Q5VSL9-2", inv)
+    assert len(out) == 1
+    assert out[0].resolve() == exact.resolve()
+
+
+def test_resolve_loose_isoform_fallback(tmp_path: Path) -> None:
+    iso = tmp_path / "AF-Q5VSL9-2-F1-model_v6.cif"
+    _touch(iso)
+    inv = build_stem_to_paths(tmp_path)
+    out = resolve_id("Q5VSL9", inv)
+    assert len(out) == 1
+    assert out[0].resolve() == iso.resolve()
+
+
+def test_resolve_af_exact_takes_precedence_over_loose_higher_version(tmp_path: Path) -> None:
+    base_v4 = tmp_path / "AF-Q5VSL9-F1-model_v4.cif"
+    iso_v6 = tmp_path / "AF-Q5VSL9-2-F1-model_v6.cif"
+    _touch(base_v4)
+    _touch(iso_v6)
+    inv = build_stem_to_paths(tmp_path)
+    out = resolve_id("Q5VSL9", inv)
+    assert len(out) == 1
+    assert out[0].resolve() == base_v4.resolve()
+
+
+def test_resolve_missing_returns_empty(tmp_path: Path) -> None:
+    _touch(tmp_path / "OTHER.cif")
+    inv = build_stem_to_paths(tmp_path)
+    assert resolve_id("Q5VSL9", inv) == []
+
+
+def test_resolve_strips_id_not_applied_use_raw_match(tmp_path: Path) -> None:
+    """Whitespace is stripped by caller in save_extracted_files; resolver is strict."""
+    _touch(tmp_path / "Q5VSL9.cif")
+    inv = build_stem_to_paths(tmp_path)
+    assert resolve_id(" Q5VSL9", inv) == []
+    assert resolve_id("Q5VSL9", inv) != []