fix tabular file header detection (#264)

* change the way to detect header columns

the new approach is reliable and faster

* remove unused utils

src/nplinker/metabolomics/gnps/gnps_format.py

@@ -1,12 +1,12 @@
 from __future__ import annotations
+import re
 import zipfile
 from enum import Enum
 from enum import unique
 from os import PathLike
 from pathlib import Path
 import httpx
 from bs4 import BeautifulSoup
-from nplinker.utils import get_headers
 
 
 GNPS_TASK_URL = "https://gnps.ucsd.edu/ProteoSAFe/status.jsp?task={}"
@@ -118,11 +118,13 @@ def gnps_format_from_file_mapping(file: str | PathLike) -> GNPSFormat:
     Returns:
         GNPS format identified in the file.
     """
-    headers = get_headers(file)
-    if "AllFiles" in headers:
+    with open(file, "r") as f:
+        header = f.readline().strip()
+
+    if re.search(r"\bAllFiles\b", header):
         return GNPSFormat.SNETS
-    if "UniqueFileSources" in headers:
+    if re.search(r"\bUniqueFileSources\b", header):
         return GNPSFormat.SNETSV2
-    if "row ID" in headers:
+    if re.search(r"\b{}\b".format(re.escape("row ID")), header):
         return GNPSFormat.FBMN
     return GNPSFormat.Unknown

src/nplinker/utils.py

@@ -59,39 +59,6 @@ def wrapper_check_disk_space(*args, **kwargs):
 #
 
 
-def find_delimiter(file: str | PathLike) -> str:
-    """Detect the delimiter for the given tabular file.
-
-    Args:
-        file: Path to tabular file.
-
-    Returns:
-        Detected delimiter character.
-
-    Examples:
-        >>> delim = find_delimiter("~/table.csv")
-    """
-    sniffer = csv.Sniffer()
-    with open(file, mode="rt", encoding="utf-8") as fp:
-        delimiter = sniffer.sniff(fp.read(5000)).delimiter
-    return delimiter
-
-
-def get_headers(file: str | PathLike) -> list[str]:
-    """Read headers from the given tabular file.
-
-    Args:
-        file: Path to the file to read the header from.
-
-    Returns:
-        A list of column names from the header.
-    """
-    with open(file) as f:
-        headers = f.readline().strip()
-        dl = find_delimiter(file)
-        return headers.split(dl)
-
-
 def is_file_format(file: str | PathLike, format: str = "tsv") -> bool:
     """Check if the file is in the given format.
 

tests/unit/test_utils.py

@@ -3,17 +3,6 @@
 from tempfile import mkdtemp
 import pytest
 from nplinker import utils
-from nplinker.utils import find_delimiter
-from . import GNPS_DATA_DIR
-
-
-@pytest.mark.parametrize(
-    "filename, expected",
-    [[GNPS_DATA_DIR / "nodes.tsv", "\t"], [GNPS_DATA_DIR / "nodes_mwe.csv", ","]],
-)
-def test_find_delimiter(filename, expected):
-    actual = find_delimiter(filename)
-    assert actual == expected
 
 
 BGC_GBK_URL = "https://mibig.secondarymetabolites.org/repository/BGC0000001/BGC0000001.gbk"