Wrapper to upload dataset

src/scrnaseq/upload_dataset.py

@@ -0,0 +1,88 @@
+from gypsum_client import cache_directory, rest_url, upload_directory
+
+__author__ = "Jayaram Kancherla"
+__copyright__ = "Jayaram Kancherla"
+__license__ = "MIT"
+
+
+def upload_dataset(
+    name: str,
+    version: str,
+    directory: str = None,
+    package: str = "scRNAseq",
+    cache_dir: str = cache_directory(),
+    deduplicate: bool = True,
+    probation: bool = False,
+    url: str = rest_url(),
+    token: str = None,
+    concurrent: int = 1,
+    abort_failed: bool = True,
+):
+    """Upload the dataset to the gypsum bucket.
+
+    This is a wrapper around
+    :py:func:`~gypsum_client.upload_file_actions.upload_directory`
+    specific to the `scRNAseq` package.
+
+    See Also:
+        :py:func:`~gypsum_client.upload_file_actions.upload_directory`,
+        to upload a directory to the gypsum backend.
+
+    Args:
+        Name:
+            Dataset name.
+
+        version:
+            Version name.
+
+        directory:
+            Path to a directory containing the ``files`` to be uploaded.
+            This directory is assumed to correspond to a version of an asset.
+
+        cache_dir:
+            Path to the cache for saving files, e.g., in
+            :py:func:`~gypsum_client.save_operations.save_version`.
+
+            Used to convert symbolic links to upload links,see
+            :py:func:`~gypsum_client.prepare_directory_for_upload.prepare_directory_upload`.
+
+        deduplicate:
+            Whether the backend should attempt deduplication of ``files``
+            in the immediately previous version.
+            Defaults to True.
+
+        probation:
+            Whether to perform a probational upload.
+            Defaults to False.
+
+        url:
+            URL of the gypsum REST API.
+
+        token:
+            GitHub access token to authenticate to the gypsum REST API.
+
+        concurrent:
+            Number of concurrent downloads.
+            Defaults to 1.
+
+        abort_failed:
+            Whether to abort the upload on any failure.
+
+            Setting this to `False` can be helpful for diagnosing upload problems.
+
+    Returns:
+        `True` if successfull, otherwise `False`.
+    """
+    return upload_directory(
+        directory,
+        package,
+        name,
+        version,
+        cache_dir=cache_dir,
+        deduplicate=deduplicate,
+        probation=probation,
+        url=url,
+        token=token,
+        concurrent=concurrent,
+        abort_failed=abort_failed,
+    )