Merge pull request #114 from PRIDE-Archive/dev

Minor changes for existing folders projects.

Author: ypriverol

pridepy/pdc/client.py

@@ -139,7 +139,7 @@ def parse_accessions(accession: str) -> List[str]:
         raise ValueError("--accession must not be empty")
 
     source_path = Path(accession).expanduser()
-    if source_path.exists():
+    if source_path.is_file():
         if source_path.suffix.lower() != ".csv":
             raise ValueError(f"Only CSV accession files are supported: {source_path}")
         return _read_accessions_from_csv(source_path)
@@ -168,7 +168,7 @@ def parse_download_requests(accession: str, file_type: Optional[str] = None) ->
     command_file_type = normalize_file_type(file_type) if file_type else None
     source_path = Path(accession).expanduser()
 
-    if source_path.exists():
+    if source_path.is_file():
         if source_path.suffix.lower() != ".csv":
             raise ValueError(f"Only CSV accession files are supported: {source_path}")
 

pridepy/tests/test_pdc_client.py

@@ -60,6 +60,17 @@ class TestPDCAccessions(TestCase):
     def test_single_accession(self):
         assert parse_accessions("PDC000109") == ["PDC000109"]
 
+    def test_accession_not_confused_with_same_named_directory(self):
+        with tempfile.TemporaryDirectory() as tmp_dir:
+            old_cwd = os.getcwd()
+            os.chdir(tmp_dir)
+            try:
+                os.makedirs("PDC000714")
+                assert parse_accessions("PDC000714") == ["PDC000714"]
+                assert parse_download_requests("PDC000714") == [PDCDownloadRequest("PDC000714", None)]
+            finally:
+                os.chdir(old_cwd)
+
     def test_comma_accessions_are_deduped(self):
         assert parse_accessions("PDC000109,PDC000110,PDC000109") == [
             "PDC000109",

pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "pridepy"
-version = "0.0.16"
+version = "0.0.17"
 description = "Python Client library for PRIDE Rest API"
 readme = "README.md"
 requires-python = ">=3.9"