orfdata 0.44.0__tar.gz → 0.45.0__tar.gz

{orfdata-0.44.0/orfdata.egg-info → orfdata-0.45.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: orfdata
-Version: 0.44.0
+Version: 0.45.0
 Summary: Reference proteomes with evidence-backed noncanonical ORFs on PyEnsembl genomes
 Author: OpenVax
 License-Expression: Apache-2.0

{orfdata-0.44.0 → orfdata-0.45.0}/orfdata/cli.py

@@ -102,14 +102,27 @@ def run(argv=None, prog=None, *, catalog_loader=load_catalog):
         argv = argv[1:]
     elif not argv[0].startswith("-"):
         _command_guide(prog).error(f"Unknown command {argv[0]!r}")
+    return query(argv, prog + " query", catalog_loader=catalog_loader)
+
+
+def query(argv=None, prog="orfdata query", *, catalog_loader=load_catalog):
+    """Run the ``query`` command on its own, under ``prog``.
+
+    Another tool can expose ORF queries as one of its commands with its own catalogue loader. Its help,
+    errors and examples name ``prog``, and exit statuses follow :func:`run`. Any ``catalog_loader`` other
+    than :func:`~orfdata.load_catalog` reads one catalogue, so ``--species`` is not offered.
+    """
+    argv = list(sys.argv[1:] if argv is None else argv)
+    default = catalog_loader is load_catalog
+    epilog = (f"Examples:\n  {prog} --gene TP53\n"
+              f"  {prog} --orf-id c7riboseqorf56 --json\n")
+    if default:
+        epilog += (f"  {prog} --species mouse --format fasta\n\n"
+                   "Find optional sources with 'orfdata catalogs list'.")
     parser = ArgumentParser(
         description="Query an installed ORF catalogue; preview records or export them explicitly.",
-        prog=prog + " query",
-        epilog="Examples:\n  orfdata query --gene TP53\n"
-               "  orfdata query --orf-id c7riboseqorf56 --json\n"
-               "  orfdata query --species mouse --format fasta\n\n"
-               "Find optional sources with 'orfdata catalogs list'.")
-    _add_query_arguments(parser)
+        prog=prog, epilog=epilog)
+    _add_query_arguments(parser, species=default)
     args = parser.parse_args(argv)
     return _query(args, parser, catalog_loader)
 
@@ -154,13 +167,16 @@ def _catalog_names(value):
     return value if value == "all" else [name for name in value.split(",") if name]
 
 
-def _add_query_arguments(parser, *, catalog_path=True):
+def _add_query_arguments(parser, *, catalog_path=True, species=True):
     if catalog_path:
         parser.add_argument("--catalog", action="append",
                             help="Use a compatible local JSON/JSON.gz catalogue; repeat to merge several")
+    else:
+        parser.set_defaults(catalog=None)
+    if catalog_path and species:
         parser.add_argument("--species", help="Use this species' catalogue, e.g. human or mouse (default human)")
     else:
-        parser.set_defaults(catalog=None, species=None)
+        parser.set_defaults(species=None)
     parser.add_argument("--gene", help="Exact source gene symbol or identifier")
     parser.add_argument("--transcript", help="Exact source transcript ID, including its version when supplied")
     parser.add_argument("--orf-id", help="Exact catalogue ORF identifier")
@@ -310,8 +326,6 @@ def _query(args, parser, catalog_loader):
             options.update(contig=match.group(1), start=start, end=end)
         if args.min_protein_length is not None and args.min_protein_length < 1:
             raise UsageError("--min-protein-length must be a positive number of amino acids")
-        if args.species and catalog_loader is not load_catalog:
-            raise UsageError("--species is not available here: this command reads one catalogue")
         paths = args.catalog or [None]
         if args.species or (args.genome_build and not args.catalog and catalog_loader is load_catalog):
             # The assembly picks the catalogue too, not only checks it.

orfdata-0.45.0/orfdata/version.py

@@ -0,0 +1 @@
+__version__ = "0.45.0"

{orfdata-0.44.0 → orfdata-0.45.0/orfdata.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: orfdata
-Version: 0.44.0
+Version: 0.45.0
 Summary: Reference proteomes with evidence-backed noncanonical ORFs on PyEnsembl genomes
 Author: OpenVax
 License-Expression: Apache-2.0

{orfdata-0.44.0 → orfdata-0.45.0}/tests/test_exit_statuses.py

@@ -175,7 +175,26 @@ def test_species_selection_needs_the_species_catalogue_loader(offline, capsys):
     with pytest.raises(SystemExit) as error:
         run(["query", "--species", "mouse"], catalog_loader=load_uorf_catalog)
     err = capsys.readouterr().err
-    assert error.value.code == 2 and "--species is not available here" in err
+    assert error.value.code == 2 and "unrecognized arguments: --species mouse" in err
+
+
+def test_query_runs_alone_under_another_program(offline, capsys):
+    from orfdata.catalog import load_uorf_catalog
+    from orfdata.cli import query
+
+    with pytest.raises(SystemExit) as error:
+        query(["--help"], "tool orfs", catalog_loader=load_uorf_catalog)
+    assert error.value.code == 0
+    text = capsys.readouterr().out
+    assert text.startswith("usage: tool orfs ") and "  tool orfs --gene TP53" in text
+    assert "--species" not in text and "catalogs list" not in text and "orfdata" not in text
+    with pytest.raises(SystemExit) as error:
+        query(["--not-an-option"], "tool orfs", catalog_loader=load_uorf_catalog)
+    assert error.value.code == 2
+    assert capsys.readouterr().err.startswith("tool orfs: error: unrecognized arguments: --not-an-option\n"
+                                              "Try 'tool orfs --help' for usage.")
+    query(["--orf-id", "c7riboseqorf56", "--json"], "tool orfs", catalog_loader=load_uorf_catalog)
+    assert json.loads(capsys.readouterr().out)["records"][0]["orf_id"] == "c7riboseqorf56"
 
 
 @pytest.mark.parametrize("argv", [

orfdata-0.44.0/orfdata/version.py

@@ -1 +0,0 @@
-__version__ = "0.44.0"