tmp-32291-kNFkVo.patch

commit 481c822bc0eff8173be7788ca9b4acc48359c0c2
Author: Thomas Sibley <[email protected]>
Date:   Wed Nov 9 09:39:37 2022 -0800

    wip! remote download: not in manifest

diff --git a/nextstrain/cli/remote/nextstrain_dot_org.py b/nextstrain/cli/remote/nextstrain_dot_org.py
index 4c7f5c8..fd4c420 100644
--- a/nextstrain/cli/remote/nextstrain_dot_org.py
+++ b/nextstrain/cli/remote/nextstrain_dot_org.py
@@ -127,6 +127,20 @@ class SubResource(NamedTuple):
     file_extension: str
     primary: bool = False
 
+    def __str__(self) -> str:
+        type, subtype = self.media_type.split("/", 1)
+        subtype_tree = tuple(subtype.split("."))
+
+        resource = (
+            "dataset"   if subtype_tree[0:3] == ("vnd", "nextstrain", "dataset")   else
+            "narrative" if subtype_tree[0:3] == ("vnd", "nextstrain", "narrative") else
+            self.media_type
+        )
+
+        sidecar = sidecar_suffix(self.media_type)
+
+        return f"{resource} ({sidecar})" if sidecar else resource
+
 
 class Dataset(Resource):
     """
@@ -336,7 +350,18 @@ def download(url: urllib.parse.ParseResult, local_path: Path, recursively: bool
     with requests.Session() as http:
         http.auth = auth()
 
-        resources = _ls(path, recursively = recursively, http = http)
+        if recursively:
+            resources = _ls(path, recursively = recursively, http = http)
+        else:
+            # Avoid the query and just try to download the single resource.
+            # This saves a request for single-dataset (or narrative) downloads,
+            # but also allows downloading core datasets which aren't in the
+            # manifest.  (At least until the manifest goes away.)
+            #   -trs, 9 Nov 2022
+            if narratives_only(path):
+                resources = [Narrative({"request": path})]
+            else:
+                resources = [Dataset({"request": path})]
 
         if not resources:
             raise UserError(f"Path {path} does not seem to exist")
@@ -361,7 +386,9 @@ def download(url: urllib.parse.ParseResult, local_path: Path, recursively: bool
 
                     # Check for bad response
                     raise_for_status(response)
-                    assert content_media_type(response) == subresource.media_type
+
+                    if content_media_type(response) != subresource.media_type:
+                        raise UserError(f"Path {path} does not seem to be a {subresource}.")
 
                     # Local destination
                     if local_path.is_dir():
@@ -485,7 +512,7 @@ def remote_path(url: urllib.parse.ParseResult) -> NormalizedPath:
     return normalize_path(url.path)
 
 
-def normalize_path(path: str) -> NormalizedPath:
+def normalize_path(path: Union[str, NormalizedPath]) -> NormalizedPath:
     """
     Ensure the URL *path* starts with a single ``/`` and ends without one, then
     wrap in a :class:`PurePosixPath` subclass (:class:`NormalizedPath`), for
@@ -500,6 +527,8 @@ def normalize_path(path: str) -> NormalizedPath:
     >>> normalize_path("/")
     NormalizedPath('/')
     """
+    if isinstance(path, NormalizedPath):
+        return path
     return NormalizedPath("/" + path.strip("/"))