fixup! Add functionality for setting custom names

src/resdk/resolwe.py

@@ -466,7 +466,6 @@ def _download_files(
         files: List[Union[str, Path]],
         download_dir=None,
         show_progress=True,
-        custom_file_names: Optional[List[str]] = None,
     ):
         """Download files.
 
@@ -475,7 +474,6 @@ def _download_files(
 
         :param files: files to download
         :param download_dir: download directory
-        :param custom_file_names: list of file names to save the downloaded files as
 
         """
         if not download_dir:
@@ -486,14 +484,6 @@ def _download_files(
                 "Download directory does not exist: {}".format(download_dir)
             )
 
-        if not custom_file_names:
-            custom_file_names = len(files) * [None]
-        else:
-            if not len(files) == len(custom_file_names):
-                raise ValueError(
-                    "Number of files and their corresponding custom file names must be equal."
-                )
-
         if not files:
             self.logger.info("No files to download.")
         else:
@@ -503,7 +493,7 @@ def _download_files(
             sizes: dict[str, dict[str, int]] = defaultdict(lambda: defaultdict(int))
             checksums: dict[str, dict[str, int]] = defaultdict(lambda: defaultdict(int))
 
-            for file_uri, custom_file_name in zip(files, custom_file_names):
+            for file_uri in files:
                 file_name = os.path.basename(file_uri)
                 file_path = os.path.dirname(file_uri)
                 file_url = urljoin(self.url, "data/{}".format(file_uri))
@@ -527,19 +517,12 @@ def _download_files(
 
                 file_size = sizes[file_directory][file_name]
 
-                if custom_file_name:
-                    desc = f"Downloading file {file_name} as {custom_file_name}"
-                    actual_file_name = custom_file_name
-                else:
-                    desc = f"Downloading file {file_name}"
-                    actual_file_name = file_name
-
                 with tqdm.tqdm(
                     total=file_size,
                     disable=not show_progress,
-                    desc=desc,
+                    desc=f"Downloading file {file_name}",
                 ) as progress_bar, open(
-                    os.path.join(download_dir, file_path, actual_file_name), "wb"
+                    os.path.join(download_dir, file_path, file_name), "wb"
                 ) as file_handle:
                     response = self.session.get(file_url, stream=True, auth=self.auth)
 
@@ -556,12 +539,10 @@ def _download_files(
                     # checksums that are difficult to reproduce here.
                     return
                 expected_md5 = checksums[file_directory][file_name]
-                computed_md5 = md5(
-                    os.path.join(download_dir, file_path, actual_file_name)
-                )
+                computed_md5 = md5(os.path.join(download_dir, file_path, file_name))
                 if expected_md5 != computed_md5:
                     raise ValueError(
-                        f"Checksum ({computed_md5}) of downloaded file {actual_file_name} does not match the expected value of {expected_md5}."
+                        f"Checksum ({computed_md5}) of downloaded file {file_name} does not match the expected value of {expected_md5}."
                     )
 
     def data_usage(self, **query_params):

src/resdk/resources/collection.py

@@ -140,7 +140,7 @@ def download(self, file_name=None, field_name=None, download_dir=None):
             data_files = data.files(file_name, field_name)
             files.extend("{}/{}".format(data.id, file_name) for file_name in data_files)
 
-        self.resolwe._download_files(files=files, download_dir=download_dir)
+        self.resolwe._download_files(files, download_dir)
 
 
 class Collection(CollectionRelationsMixin, BaseCollection):

src/resdk/resources/data.py

@@ -2,6 +2,7 @@
 
 import json
 import logging
+import os
 from typing import Optional
 from urllib.parse import urljoin
 
@@ -16,6 +17,12 @@
 from .sample import Sample
 from .utils import flatten_field, parse_resolwe_datetime
 
+logging.basicConfig(
+    level=logging.INFO,
+    format="%(asctime)s - %(levelname)s - %(message)s",
+    datefmt="%d-%b-%y %H:%M:%S",
+)
+
 
 class Data(BaseResolweResource):
     """Resolwe Data resource.
@@ -329,7 +336,6 @@ def download(
         file_name: Optional[str] = None,
         field_name: Optional[str] = None,
         download_dir: Optional[str] = None,
-        custom_file_name: Optional[str] = None,
     ):
         """Download Data object's files and directories.
 
@@ -343,9 +349,6 @@ def download(
         * re.data.get(42).download(file_name='alignment7.bam')
         * re.data.get(42).download(field_name='bam')
 
-        If custom_file_name is provided, the file will be saved with that name,
-        provided that either field_name or file_name is also specified.
-
         """
         if file_name and field_name:
             raise ValueError("Only one of file_name or field_name may be given.")
@@ -354,20 +357,48 @@ def download(
             "{}/{}".format(self.id, fname)
             for fname in self.files(file_name, field_name)
         ]
+        file_names = [fname for fname in self.files(file_name, field_name)]
 
-        # Only applies if downloading a single file
-        custom_file_names = None
-        if custom_file_name:
-            if file_name or field_name:
-                custom_file_names = [custom_file_name] * len(files)
-            else:
-                raise ValueError(
-                    "Setting a custom file name is not supported "
-                    "without specifying file name or field name."
-                )
+        self.resolwe._download_files(files=files, download_dir=download_dir)
+
+        return file_names
+
+    def download_and_rename(
+        self,
+        custom_file_name: str,
+        field_name: Optional[str] = None,
+        file_name: Optional[str] = None,
+        download_dir: Optional[str] = None,
+    ):
+        """Download and rename a single file from data object."""
+
+        if download_dir is None:
+            download_dir = os.getcwd()
+
+        new_file_path = os.path.join(download_dir, custom_file_name)
+
+        if os.path.exists(new_file_path):
+            logging.warning(
+                f"File with path '{new_file_path}' already exists. Skipping download."
+            )
+            return
+
+        file_names = self.download(
+            file_name=file_name,
+            field_name=field_name,
+            download_dir=download_dir,
+        )
+        if len(file_names) != 1:
+            raise ValueError(
+                f"Expected one file to be downloaded, but got {len(file_names)}"
+            )
+        og_file_name = file_names[0]
+        og_file_path = os.path.join(download_dir, og_file_name)
 
-        self.resolwe._download_files(
-            files=files, download_dir=download_dir, custom_file_names=custom_file_names
+        logging.info(f"Renaming file '{og_file_name}' to '{custom_file_name}'.")
+        os.rename(
+            og_file_path,
+            new_file_path,
         )
 
     def stdout(self):

tests/unit/test_data.py

@@ -193,16 +193,14 @@ def test_download_ok(self, data_mock):
 
         data_mock.reset_mock()
         data_mock.files.return_value = ["file1.txt"]
-        Data.download(
+        Data.download_and_rename(
             data_mock,
             custom_file_name="text_file1.txt",
             field_name="txt",
             download_dir="/some/path/",
         )
-        data_mock.resolwe._download_files.assert_called_once_with(
-            files=["123/file1.txt"],
-            download_dir="/some/path/",
-            custom_file_names=["text_file1.txt"],
+        data_mock.download.assert_called_once_with(
+            file_name=None, field_name="txt", download_dir="/some/path/"
         )
 
     @patch("resdk.resolwe.Resolwe")