Updated Tests to comply with pdb.gz

Author: jauy123

package/MDAnalysis/web/downloaders.py

@@ -19,6 +19,19 @@ def __init__(self,
 
         super().__init__(message)
 
+# Dict to convert file name arguments for Universe(topology_format="")
+TOPOLOGY_FORMAT_CONVERTER = {
+    "physical_file_extension": tuple([["pdb.gz", "pdb"]],
+                            ) ,
+    "topology_format": tuple(["PDB",],
+                             )
+    }
+
+def _file_format_to_topology_string(file_extension):
+    """Converts file names to a string usable by Universe(topology_format=)"""
+    for valid_file_extensions, valid_topology_string in zip(*TOPOLOGY_FORMAT_CONVERTER.values(), strict=True):
+        if file_extension in valid_file_extensions:
+            return valid_topology_string
 
 class BaseDownloader(ABC):
     """Abstract Base Class for all Downloaders. Not meant to be directly initalized!"""
@@ -51,14 +64,17 @@ def convert_to_universe(self, **kwargs):
             raise RuntimeError("File not set. Run download() to set file before convert_to_universe()")
 
         try:
-            return Universe(self._file.name, topology_format=self.file_format.upper(), **kwargs)
+            return Universe(self._file.name,
+                            topology_format=_file_format_to_topology_string(self.file_format),
+                            **kwargs)
         finally:
             self._file.close() 
 
 class PdbDownloader(BaseDownloader):
     """Class to handle download PDBs from the RCSB"""
 
-    def __init__(self, PDB_ID, file_format="pdb"):
+    def __init__(self, PDB_ID, file_format="pdb.gz"):
+
         super().__init__(PDB_ID, file_format)
 
         self._download = False

package/MDAnalysis/web/functions.py

@@ -1,10 +1,8 @@
 from .downloaders import PdbDownloader
 
-
-def fetch_pdb(PDB_ID, download_path=None, timeout=None, **kwargs):
+def fetch_pdb(PDB_ID, file_format="pdb.gz", download_path=None, timeout=None, **kwargs):
     """Fetchs PDB from RCSB"""
 
-    downloader = PdbDownloader(PDB_ID).download(download_path,
-                                                timeout=timeout)
+    downloader = PdbDownloader(PDB_ID, file_format).download(download_path, timeout=timeout)
 
     return downloader.convert_to_universe(**kwargs)

testsuite/MDAnalysisTests/web/test_web.py

@@ -5,7 +5,7 @@
 import requests
 
 working_PDB_ID = '1DPX' # egg white lysozyme 
-file_format = "pdb"
+file_format = "pdb.gz"
 
 
 @pytest.fixture(scope="function")
@@ -16,12 +16,18 @@ def shared_cache_directory(tmp_path_factory):
 
 class Test_Pdb_Downloader_BaseFunctionality():
     """Test Public API of Pdb_Downloader()"""
-   
-    def test_base_functionality(self):
-        """Test keywords in convert_to_universe()"""
-        downloader =  mda.web.PdbDownloader(PDB_ID=working_PDB_ID).download()
 
-        assert(isinstance(downloader.convert_to_universe(in_memory=True), mda.Universe))
+    valid_file_formats = ("pdb.gz", "pdb")
+
+    def test_base_functionality(self):
+        """Test file_formats and keywords in convert_to_universe()"""
+
+        universe_list = []
+        for file_format in self.valid_file_formats:
+            downloader =  mda.web.PdbDownloader(PDB_ID=working_PDB_ID, file_format=file_format).download()
+            universe_list.append(downloader.convert_to_universe(in_memory=True))
+
+        assert all(isinstance(universe, mda.Universe) for universe in universe_list)
 
     def test_timeout(self):
         """Checks requests timeout Exception for fetch_pdb and PdbDownloader"""
@@ -32,7 +38,7 @@ def test_invalid_id(self):
         """Test invalid id for PdbDownloader"""
 
         with pytest.raises(mda.web.downloaders.FileDownloadPDBError):
-            mda.web.PdbDownloader(PDB_ID='BananaBoat').download()
+            mda.web.PdbDownloader(PDB_ID='BananaBoat').download()       
 
 class Test_Pdb_Downloader_Cache():
     ### Cache Test underneath