Cleanup IO utils

Author: cthoyt

pyproject.toml

@@ -1,5 +1,5 @@
 [build-system]
-requires = ["uv_build>=0.6.6,<0.7"]
+requires = ["uv_build>=0.6.6,<1.0"]
 build-backend = "uv_build"
 
 [project]
@@ -69,7 +69,7 @@ dependencies = [
     "humanize",
     "tabulate",
     "cachier",
-    "pystow>=0.7.0",
+    "pystow>=0.7.5",
     "bioversions>=0.8.101",
     "bioregistry>=0.12.30",
     "bioontologies>=0.7.2",

src/pyobo/getters.py

@@ -367,10 +367,14 @@ def iter_helper_helper(
             logger.warning("[%s] HTTP %s: unable to download %s", prefix, e.getcode(), e.geturl())
             if strict and not bioregistry.is_deprecated(prefix):
                 raise
-        except (urllib.error.URLError, requests.exceptions.ConnectTimeout) as e:
+        except urllib.error.URLError as e:
             logger.warning("[%s] unable to download - %s", prefix, e.reason)
             if strict and not bioregistry.is_deprecated(prefix):
                 raise
+        except requests.exceptions.ConnectTimeout as e:
+            logger.warning("[%s] unable to download - %s", prefix, e)
+            if strict and not bioregistry.is_deprecated(prefix):
+                raise
         except ParseError as e:
             if not e.node:
                 logger.warning("[%s] %s", prefix, e)

src/pyobo/sources/uniprot/uniprot.py

@@ -4,6 +4,7 @@
 from pathlib import Path
 from typing import cast
 
+from pystow.utils import safe_open_reader
 from tqdm.auto import tqdm
 
 from pyobo import Obo, Reference
@@ -22,7 +23,6 @@
     participates_in,
 )
 from pyobo.struct.typedef import gene_product_of, located_in, molecularly_interacts_with
-from pyobo.utils.io import open_reader
 
 PREFIX = "uniprot"
 BASE_URL = "https://rest.uniprot.org/uniprotkb/stream"
@@ -78,7 +78,7 @@ def iter_terms(self, force: bool = False) -> Iterable[Term]:
 
 def iter_terms(version: str | None = None) -> Iterable[Term]:
     """Iterate over UniProt Terms."""
-    with open_reader(ensure(version=version)) as reader:
+    with safe_open_reader(ensure(version=version)) as reader:
         _ = next(reader)  # header
         for (
             uniprot_id,

src/pyobo/utils/io.py

@@ -9,9 +9,11 @@
 from collections.abc import Generator, Iterable, Mapping
 from contextlib import contextmanager
 from pathlib import Path
-from typing import Literal, TextIO, TypeVar
+from typing import Literal, TextIO, TypeVar, cast
 
 import pandas as pd
+import pystow.utils
+from pystow.utils import safe_open_reader, safe_open_writer
 from tqdm.auto import tqdm
 
 __all__ = [
@@ -20,7 +22,6 @@
     "multisetdict",
     "open_map_tsv",
     "open_multimap_tsv",
-    "open_reader",
     "safe_open",
     "safe_open_writer",
     "write_iterable_tsv",
@@ -34,14 +35,6 @@
 Y = TypeVar("Y")
 
 
-@contextmanager
-def open_reader(path: str | Path, sep: str = "\t"):
-    """Open a file and get a reader for it."""
-    path = Path(path)
-    with safe_open(path, read=True) as file:
-        yield get_reader(file, sep=sep)
-
-
 def get_reader(x, sep: str = "\t"):
     """Get a :func:`csv.reader` with PyOBO default settings."""
     return csv.reader(x, delimiter=sep, quoting=csv.QUOTE_MINIMAL)
@@ -51,18 +44,18 @@ def open_map_tsv(
     path: str | Path, *, use_tqdm: bool = False, has_header: bool = True
 ) -> Mapping[str, str]:
     """Load a mapping TSV file into a dictionary."""
-    with safe_open(path, read=True) as file:
+    rv = {}
+    with pystow.utils.safe_open_reader(path) as reader:
         if has_header:
-            next(file)  # throw away header
+            next(reader)  # throw away header
         if use_tqdm:
-            file = tqdm(file, desc=f"loading TSV from {path}")
-        rv = {}
-        for row in get_reader(file):
+            reader = tqdm(reader, desc=f"loading TSV from {path}")
+        for row in reader:
             if len(row) != 2:
                 logger.warning("[%s] malformed row can not be put in dict: %s", path, row)
                 continue
             rv[row[0]] = row[1]
-        return rv
+    return rv
 
 
 def open_multimap_tsv(
@@ -72,24 +65,27 @@ def open_multimap_tsv(
     has_header: bool = True,
 ) -> Mapping[str, list[str]]:
     """Load a mapping TSV file that has multiple mappings for each."""
-    return multidict(_help_multimap_tsv(path=path, use_tqdm=use_tqdm, has_header=has_header))
+    with _help_multimap_tsv(path=path, use_tqdm=use_tqdm, has_header=has_header) as file:
+        return multidict(file)
 
 
+@contextmanager
 def _help_multimap_tsv(
     path: str | Path,
     *,
     use_tqdm: bool = False,
     has_header: bool = True,
-) -> Iterable[tuple[str, str]]:
-    with safe_open(path, read=True) as file:
+) -> Generator[Iterable[tuple[str, str]], None, None]:
+    with safe_open_reader(path) as reader:
         if has_header:
             try:
-                next(file)  # throw away header
+                next(reader)  # throw away header
             except gzip.BadGzipFile as e:
                 raise ValueError(f"could not open file {path}") from e
         if use_tqdm:
-            file = tqdm(file, desc=f"loading TSV from {path}")
-        yield from get_reader(file)
+            yield tqdm(reader, desc=f"loading TSV from {path}")
+        else:
+            yield cast(Iterable[tuple[str, str]], reader)
 
 
 def multidict(pairs: Iterable[tuple[X, Y]]) -> Mapping[X, list[Y]]:
@@ -156,6 +152,7 @@ def safe_open(
     path: str | Path, read: bool, encoding: str | None = None
 ) -> Generator[TextIO, None, None]:
     """Safely open a file for reading or writing text."""
+    # TODO replace me!
     path = Path(path).expanduser().resolve()
     mode: Literal["rt", "wt"] = "rt" if read else "wt"
     if path.suffix.endswith(".gz"):
@@ -164,13 +161,3 @@ def safe_open(
     else:
         with open(path, mode=mode) as file:
             yield file
-
-
-@contextlib.contextmanager
-def safe_open_writer(f: str | Path | TextIO, *, delimiter: str = "\t"):  # type:ignore
-    """Open a CSV writer, wrapping :func:`csv.writer`."""
-    if isinstance(f, str | Path):
-        with safe_open(f, read=False) as file:
-            yield csv.writer(file, delimiter=delimiter)
-    else:
-        yield csv.writer(f, delimiter=delimiter)