Getting 400 error when updating existing annotations file

[alokito]

I am able to open existing annotations with the following command:

~/code/nsnx/cellxgene-gateway/.cellxgene-gateway/bin/cellxgene launch ../cellxgene_data/somedir/pbmc3k.h5ad --port 8002 --host 127.0.0.1 --experimental-annotations --experimental-annotations-file ../cellxgene_data/somedir/pbmc3k_annotations/somedirAnno1-MW36MWBW.csv

However, if I edit the annotations, I get a series of 400 errors in the Chrome Developer Tools. The request is a PUT to http://localhost:8002/api/v0.2/annotations/obs?annotation-collection-name=somedirAnno1-MW36MWBW. The error message is:

Error, bad annotation collection name

[bkmartinjr]

Hi @alokito - the collection name test is more-or-less a test for path name safety, and worst case is the regex [0-9][a-Z][A-Z]_. You collection name would appear to satisfy that test.

The error occurs when running cellxgene behind the proxy, right? Any chance the proxy is somehow modifying the query params on the request? Ideas on debugging: either run cellxgene directly (no proxy) and see if it works, or alternatively, run in --debug mode and see what request it actually receives. One of those should shed some light on what is occurring.

[alokito]

Hi Bruce! Sorry about the confusing command line, I am actually running cellxgene v0.13.0 directly from a venv named .cellxgene-gateway. If I read the regex correctly, the hyphen character is not allowed in the collection name, which is unfortunate since it is automatically added when new collections are made. The use case here is to allow users to open each other's annotations.

If I add --debug, it complains with:

Error: --port and --debug may not be used together (try --verbose for error logging).

if I add --verbose, it says that it is receiving the following request:

127.0.0.1 - - [22/Dec/2019 19:34:39] "PUT /api/v0.2/annotations/obs?annotation-collection-name=somedirAnno1-MW36MWBW HTTP/1.1" 400 -

[bkmartinjr]

Oh, darn - you are right. This is simply a use case we did not think through correctly.

Short-term work-around: rename the file.

I'll get it fixed in the next release. I think the simplest fix is to only use legal characters (turn the hyphen into an underscore).