Update strain_mappings_generator.py

GNPS file mappings file could be tsv or csv file.
- rename `gnps_file_mapping_tsv_file` to `gnps_file_mappings_file`
- rename `tsv_file` to `gnps_file_mappings_file`
- update relevant docstrings

src/nplinker/pairedomics/strain_mappings_generator.py

@@ -30,7 +30,7 @@ def podp_generate_strain_mappings(
     podp_project_json_file: str | PathLike,
     genome_status_json_file: str | PathLike,
     genome_bgc_mappings_file: str | PathLike,
-    gnps_file_mapping_tsv_file: str | PathLike,
+    gnps_file_mappings_file: str | PathLike,
     output_json_file: str | PathLike,
 ) -> StrainCollection:
     """Generate strain mappings JSON file for PODP pipeline.
@@ -44,7 +44,7 @@ def podp_generate_strain_mappings(
     - "original_genome_id <-> resolved_genome_id" is extracted from `genome_status_json_file`.
     - "resolved_genome_id <-> bgc_id" is extracted from `genome_bgc_mappings_file`.
     - "strain_id <-> MS_filename" is extracted from `podp_project_json_file`.
-    - "MS_filename <-> spectrum_id" is extracted from `gnps_file_mapping_tsv_file`.
+    - "MS_filename <-> spectrum_id" is extracted from `gnps_file_mappings_file`.
 
     Args:
         podp_project_json_file(str | PathLike): The path to the PODP project
@@ -53,8 +53,8 @@ def podp_generate_strain_mappings(
             JSON file.
         genome_bgc_mappings_file(str | PathLike): The path to the genome BGC
             mappings JSON file.
-        gnps_file_mapping_tsv_file(str | PathLike): The path to the GNPS file
-            mapping TSV file.
+        gnps_file_mappings_file(str | PathLike): The path to the GNPS file
+            mappings file (csv or tsv).
         output_json_file(str | PathLike): The path to the output JSON file.
 
     Returns:
@@ -84,7 +84,7 @@ def podp_generate_strain_mappings(
     # Get mappings strain_id <-> MS_filename <-> spectrum_id
     mappings_strain_id_spectrum_id = get_mappings_strain_id_spectrum_id(
         extract_mappings_strain_id_ms_filename(podp_project_json_file),
-        extract_mappings_ms_filename_spectrum_id(gnps_file_mapping_tsv_file),
+        extract_mappings_ms_filename_spectrum_id(gnps_file_mappings_file),
     )
 
     # Get mappings strain_id <-> bgc_id / spectrum_id
@@ -280,24 +280,26 @@ def extract_mappings_strain_id_ms_filename(
     return mappings_dict
 
 
-def extract_mappings_ms_filename_spectrum_id(tsv_file: str | PathLike) -> dict[str, set[str]]:
+def extract_mappings_ms_filename_spectrum_id(
+    gnps_file_mappings_file: str | PathLike
+) -> dict[str, set[str]]:
     """Extract mappings "MS_filename <-> spectrum_id".
 
     Args:
-        tsv_file(str | PathLike): The path to the GNPS file mapping TSV file.
+        gnps_file_mappings_file(str | PathLike): The path to the GNPS file mappings file (csv or
+            tsv).
 
     Returns:
         dict[str, set[str]]: Key is MS filename and value is a set of spectrum ids.
 
     Notes:
-        The `tsv_file` is generated by GNPS molecular networking. It's downloaded
-        from GNPS website to a file with a default name defined in
-        `GNPS_FILE_MAPPINGS_FILENAME`.
+        The `gnps_file_mappings_file` is generated by GNPS molecular networking. It's downloaded
+        from GNPS website to a file with a default name defined in `GNPS_FILE_MAPPINGS_FILENAME`.
 
     See Also:
-        `GNPSFileMappingLoader`: A class to load GNPS file mapping TSV file.
+        `GNPSFileMappingLoader`: A class to load GNPS file mappings file.
     """
-    loader = GNPSFileMappingLoader(tsv_file)
+    loader = GNPSFileMappingLoader(gnps_file_mappings_file)
     return loader.mapping_reversed