Merge pull request #916 from dandi/gh-892

Make `dandi upload` look for dandiset.yaml in parents of common path

dandi/cli/cmd_upload.py

@@ -10,11 +10,6 @@
 
 
 @click.command()
-# @dandiset_path_option(
-#     help="Top directory (local) of the dandiset.  Files will be uploaded with "
-#     "paths relative to that directory. If not specified, current or a parent "
-#     "directory containing dandiset.yaml file will be assumed "
-# )
 @click.option(
     "-e",
     "--existing",
@@ -69,7 +64,6 @@ def upload(
     dandi_instance,
     existing="refresh",
     validation="require",
-    dandiset_path=None,
     # Development options should come as kwargs
     allow_any_path=False,
     upload_dandiset_metadata=False,
@@ -79,7 +73,9 @@ def upload(
     Upload Dandiset files to DANDI Archive.
 
     The target Dandiset to upload to must already be registered in the archive,
-    and a `dandiset.yaml` file must exist in the local `--dandiset-path`.
+    and a `dandiset.yaml` file must exist in the common ancestor of the given
+    paths (or the current directory, if no paths are specified) or a parent
+    directory thereof.
 
     Local Dandiset should pass validation.  For that, the assets should first
     be organized using the `dandi organize` command.
@@ -100,7 +96,6 @@ def upload(
         paths,
         existing=existing,
         validation=validation,
-        dandiset_path=dandiset_path,
         dandi_instance=dandi_instance,
         allow_any_path=allow_any_path,
         upload_dandiset_metadata=upload_dandiset_metadata,

dandi/tests/fixtures.py

@@ -330,8 +330,7 @@ def upload(
         with pytest.MonkeyPatch().context() as m:
             m.setenv("DANDI_API_KEY", self.api.api_key)
             upload(
-                paths=paths,
-                dandiset_path=self.dspath,
+                paths=paths or [self.dspath],
                 dandi_instance=self.api.instance_id,
                 devel_debug=True,
                 **{**self.upload_kwargs, **kwargs},

dandi/upload.py

@@ -30,7 +30,6 @@ def upload(
     paths: Optional[List[Union[str, Path]]] = None,
     existing: str = "refresh",
     validation: str = "require",
-    dandiset_path: Union[str, Path, None] = None,
     dandi_instance: str = "dandi",
     allow_any_path: bool = False,
     upload_dandiset_metadata: bool = False,
@@ -42,11 +41,15 @@ def upload(
     from .dandiapi import DandiAPIClient
     from .dandiset import APIDandiset, Dandiset
 
-    dandiset_ = Dandiset.find(dandiset_path)
+    if paths:
+        paths = [Path(p).absolute() for p in paths]
+        dandiset_ = Dandiset.find(os.path.commonpath(paths))
+    else:
+        dandiset_ = Dandiset.find(None)
     if not dandiset_:
         raise RuntimeError(
-            f"Found no {dandiset_metadata_file} anywhere.  "
-            "Use 'dandi download' or 'organize' first"
+            f"Found no {dandiset_metadata_file} anywhere in common ancestor of"
+            " paths.  Use 'dandi download' or 'organize' first."
         )
 
     instance = get_instance(dandi_instance)
@@ -74,15 +77,9 @@ def upload(
 
     ignore_benign_pynwb_warnings()  # so validate doesn't whine
 
-    #
-    # Treat paths
-    #
     if not paths:
         paths = [dandiset.path]
-    original_paths = paths
 
-    # Expand and validate all paths -- they should reside within dandiset
-    paths = [Path(p).absolute() for p in paths]
     dandi_files = list(
         find_dandi_files(
             *paths,
@@ -335,7 +332,7 @@ def upload_agg(*ignored: Any) -> str:
 
     if sync:
         relpaths: List[str] = []
-        for p in original_paths:
+        for p in paths:
             rp = os.path.relpath(p, dandiset.path)
             relpaths.append("" if rp == "." else rp)
         path_prefix = reduce(os.path.commonprefix, relpaths)  # type: ignore[arg-type]

docs/source/cmdline/upload.rst

@@ -8,7 +8,9 @@
 Upload Dandiset files to DANDI Archive.
 
 The target Dandiset to upload to must already be registered in the archive, and
-a :file:`dandiset.yaml` file must exist in the local :option:`--dandiset-path`.
+a :file:`dandiset.yaml` file must exist in the common ancestor of the given
+paths (or the current directory, if no paths are specified) or a parent
+directory thereof.
 
 Local Dandisets should pass validation.  For that, the assets should first be
 organized using the :ref:`dandi_organize` command.