feat(util.web.download_file): Add silent option for download.

magna/ncbi/web.py

@@ -88,13 +88,14 @@ class NcbiAssemblyFileType(str, Enum):
     fna = 'fna'
 
 
-def download_ncbi_assembly_file_to_disk(gid: str, target: str, file: NcbiAssemblyFileType):
+def download_ncbi_assembly_file_to_disk(gid: str, target: str, file: NcbiAssemblyFileType, silent: bool = False):
     """Download a file from the NCBI assembly directory to disk.
 
     Args:
         gid: The NCBI accession.
         target: The target path.
         file: The file type to download.
+        silent: True if the progress should be hidden.
 
     Examples:
         >>> download_ncbi_assembly_file_to_disk('GCA_003138775.1', '/tmp/foo.fna.gz', NcbiAssemblyFileType.fna)
@@ -118,7 +119,7 @@ def download_ncbi_assembly_file_to_disk(gid: str, target: str, file: NcbiAssembl
     # Download to a temporary location and verify the md5
     with tempfile.TemporaryDirectory() as tmpdir:
         target_tmp = os.path.join(tmpdir, name)
-        download_file(url, target_tmp, md5)
+        download_file(url, target_tmp, md5, silent=silent)
         move_file(target_tmp, target, checksum=True)
 
 

magna/util/web.py

@@ -5,13 +5,14 @@
 from magna.util.disk import TqdmUpTo, md5sum
 
 
-def download_file(url: str, path: str, md5: Optional[str] = None):
+def download_file(url: str, path: str, md5: Optional[str] = None, silent: bool = False):
     """Downloads a file to disk, optionally validating the md5 hash.
 
     Args:
         url: The url to download from.
         path: The path to save the file to.
         md5: The expected md5 hash of the file.
+        silent: True if the progress should be supressed.
 
     Raises:
         IOError: If the md5 hash doesn't match.
@@ -21,9 +22,12 @@ def download_file(url: str, path: str, md5: Optional[str] = None):
 
         >>> download_file('https://www.example.com/data.csv', '/tmp/data.csv')
     """
-    with TqdmUpTo(unit='B', unit_scale=True, unit_divisor=1024, miniters=1, desc=url.split('/')[-1]) as t:
-        urllib.request.urlretrieve(url, filename=path, reporthook=t.update_to, data=None)
-        t.total = t.n
+    if not silent:
+        with TqdmUpTo(unit='B', unit_scale=True, unit_divisor=1024, miniters=1, desc=url.split('/')[-1]) as t:
+            urllib.request.urlretrieve(url, filename=path, reporthook=t.update_to, data=None)
+            t.total = t.n
+    else:
+        urllib.request.urlretrieve(url, filename=path)
 
     if md5 and md5 != md5sum(path):
         raise IOError('Hash mismatch')