diff --git a/doc/data_structures.md b/doc/data_structures.md index d684a03..4149446 100644 --- a/doc/data_structures.md +++ b/doc/data_structures.md @@ -1,4 +1,4 @@ -# database.pkl +## database.pkl - **iid** (int)ernal structure id (can change at any update) - **tid** (int): taxon id (wikidata id) @@ -19,7 +19,7 @@ | tc2r | dict[tuple[tid, cid], set[rid]] | References of couple tid/cid | | taxonomy_direct_parents | dict[tid, set[tid]] | Direct taxonomic parents | | taxonomy_names | dict[tid, str] | Name of taxon tid | -| taxonomy_ranks | dict[tid, rank_id] | Rank of taxon tid | +| taxonomy_ranks | dict[tid, set[rank_id]] | Rank of taxon tid | | taxonomy_children | dict[tid, set[tid]] | All the children of taxon tid | | taxonomy_parents_with_distance | dict[tid, dict[tid, int]] | All the parents of taxon tid with an arbitrary taxonomic distance | | taxonomy_ranks_names | dict[tid, str] | Name of rank | diff --git a/update/generate_database_chemo.py b/update/generate_database_chemo.py index 8a6c99b..09157da 100644 --- a/update/generate_database_chemo.py +++ b/update/generate_database_chemo.py @@ -81,7 +81,7 @@ def run(path: Path) -> None: t2c: dict[int, set[int]] = {} c2t: dict[int, set[int]] = {} - tc2r: dict[tuple, set[str]] = {} + tc2r: dict[tuple[int, int], set[str]] = {} logging.info("Finished generating the chemical libraries")