change parameter output_dir to file for to_json method

NPLinker · Jul 5, 2023 · 6f4e123 · 6f4e123
1 parent b2d88d0
commit 6f4e123
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Showing 2 changed files with 5 additions and 6 deletions.
diff --git a/src/nplinker/pairedomics/podp_antismash_downloader.py b/src/nplinker/pairedomics/podp_antismash_downloader.py
@@ -72,7 +72,7 @@ def read_json(file: str | PathLike) -> dict[str, 'GenomeStatus']:
 
     @staticmethod
     def to_json(genome_status_dict: dict[str, 'GenomeStatus'],
-                     output_dir: str | PathLike) -> None:
+                file: str | PathLike) -> None:
         """Save the given genome status dictionary to a JSON file.
 
         The JSON file will be saved to the given output directory with the name
@@ -82,15 +82,14 @@ def to_json(genome_status_dict: dict[str, 'GenomeStatus'],
         Args:
             genome_status_dict (dict[str, 'GenomeStatus']): A dictionary of genome
                 status objects to be saved to a JSON file.
-            output_dir(str | PathLike): The path to the directory where the JSON
-                file will be saved.
+            file(str | PathLike): The path to the output JSON file.
         """
         json_data = {
             "genome_status":
             [gs._to_dict() for gs in genome_status_dict.values()],
             "version": "1.0"
         }
-        with open(Path(output_dir) / GENOME_STATUS_FILENAME, "w") as f:
+        with open(file, "w") as f:
             json.dump(json_data, f)
 
     def _to_dict(self) -> dict:
@@ -192,7 +191,7 @@ def podp_download_and_extract_antismash_data(
                 f' (from a total of {len(genome_records)}).')
 
     # save updated genome status to json file
-    GenomeStatus.to_json(gs_dict, project_download_root)
+    GenomeStatus.to_json(gs_dict, gs_file)
 
     if missing == len(genome_records):
         logger.warning('Failed to successfully retrieve ANY genome data!')

diff --git a/tests/pairedomics/test_podp_antismash_downloader.py b/tests/pairedomics/test_podp_antismash_downloader.py
@@ -74,7 +74,7 @@ def test_genome_status_to_json(tmp_path):
         "genome1": GenomeStatus("genome1", "refseq1", True, "/path/to/bgc1"),
         "genome2": GenomeStatus("genome2", "", False, "")
     }
-    GenomeStatus.to_json(genome_status_dict, tmp_path)
+    GenomeStatus.to_json(genome_status_dict, tmp_path / GENOME_STATUS_FILENAME)
     with open(tmp_path / GENOME_STATUS_FILENAME, "r") as f:
         loaded_data = json.load(f)