change datas to data

src/nplinker/genomics/mibig/mibig_loader.py

@@ -28,7 +28,7 @@ def __init__(self, data_dir: str):
         """
         self.data_dir = data_dir
         self._file_dict = self.parse_data_dir(self.data_dir)
-        self._metadata_dict = self._parse_metadatas()
+        self._metadata_dict = self._parse_metadata()
         self._bgcs = self._parse_bgcs()
 
     def get_files(self) -> dict[str, str]:
@@ -58,15 +58,15 @@ def parse_data_dir(data_dir: str) -> dict[str, str]:
             file_dict[fname] = file
         return file_dict
 
-    def get_metadatas(self) -> dict[str, MibigMetadata]:
+    def get_metadata(self) -> dict[str, MibigMetadata]:
         """Get MibigMetadata objects.
 
         Returns:
             The key is BGC accession (file name) and the value is MibigMetadata object
         """
         return self._metadata_dict
 
-    def _parse_metadatas(self) -> dict[str, MibigMetadata]:
+    def _parse_metadata(self) -> dict[str, MibigMetadata]:
         """Parse all metadata files and return MibigMetadata objects.
 
         Returns:

tests/unit/genomics/test_mibig_downloader.py

@@ -2,7 +2,7 @@
 from nplinker.genomics import mibig
 
 
-class TestDownloadAndExtractMibigMetadatas:
+class TestDownloadAndExtractMibigMetadata:
     def test_default(self, tmp_path):
         download_path = tmp_path / "download"
         extract_path = tmp_path / "metadata"

tests/unit/genomics/test_mibig_loader.py

@@ -48,13 +48,13 @@ def test_parse_data_dir(self, data_dir):
         assert isinstance(files["BGC0000001"], str)
         assert os.path.exists(files["BGC0000001"])
 
-    def test_get_metadatas(self, loader):
-        metadatas = loader.get_metadatas()
-        assert isinstance(metadatas, dict)
-        assert len(metadatas) == 2502  # MIBiG v3.1 has 2502 BGCs
-        assert "BGC0000001" in metadatas
-        assert "BGC0000246" not in metadatas
-        assert isinstance(metadatas["BGC0000001"], MibigMetadata)
+    def test_get_metadata(self, loader):
+        metadata = loader.get_metadata()
+        assert isinstance(metadata, dict)
+        assert len(metadata) == 2502  # MIBiG v3.1 has 2502 BGCs
+        assert "BGC0000001" in metadata
+        assert "BGC0000246" not in metadata
+        assert isinstance(metadata["BGC0000001"], MibigMetadata)
 
     def test_get_bgcs(self, loader):
         bgcs = loader.get_bgcs()

tests/unit/test_utils.py

@@ -17,7 +17,7 @@ def test_find_delimiter(filename, expected):
 
 
 BGC_GBK_URL = "https://mibig.secondarymetabolites.org/repository/BGC0000001/BGC0000001.gbk"
-MIBIG_METADATAS_URL = "https://dl.secondarymetabolites.org/mibig/mibig_json_3.1.tar.gz"
+MIBIG_METADATA_URL = "https://dl.secondarymetabolites.org/mibig/mibig_json_3.1.tar.gz"
 ROOT = Path(__file__).parent
 
 
@@ -47,7 +47,7 @@ class TestExtractArchive:
     @pytest.fixture
     def archive(self):
         temppath = mkdtemp()
-        utils.download_url(MIBIG_METADATAS_URL, temppath)
+        utils.download_url(MIBIG_METADATA_URL, temppath)
         archive = Path(temppath) / "mibig_json_3.1.tar.gz"
         yield archive
 
@@ -82,7 +82,7 @@ def temppath2(self):
         rmtree(temppath)
 
     def test_defaults(self, temppath1):
-        utils.download_and_extract_archive(url=MIBIG_METADATAS_URL, download_root=temppath1)
+        utils.download_and_extract_archive(url=MIBIG_METADATA_URL, download_root=temppath1)
 
         fdownload = Path(temppath1) / "mibig_json_3.1.tar.gz"
         fextract = Path(temppath1) / "mibig_json_3.1"
@@ -92,7 +92,7 @@ def test_defaults(self, temppath1):
 
     def test_optional_args(self, temppath1, temppath2):
         utils.download_and_extract_archive(
-            url=MIBIG_METADATAS_URL,
+            url=MIBIG_METADATA_URL,
             download_root=temppath1,
             extract_root=temppath2,
             filename="example.tar.gz",
@@ -108,7 +108,7 @@ def test_optional_args(self, temppath1, temppath2):
 
     def test_arg_remove_finished(self, temppath1):
         utils.download_and_extract_archive(
-            url=MIBIG_METADATAS_URL, download_root=temppath1, remove_finished=True
+            url=MIBIG_METADATA_URL, download_root=temppath1, remove_finished=True
         )
 
         fdownload = Path(temppath1) / "mibig_json_3.1.tar.gz"