Annotations Files

In 0.12, Cellxgene included support for additional annotations in a file specificd with the --experimental-label-file flag. This requires some changes to the server launching model, since now the server is determined by the annotation file as well as the dataset.

User Interface

From a user interface perspective, the file crawler currently outputs a tree of directories ending with a terminal file name. In order to support annotation files, we could have available annotations listed after the file name

• example_files
  • pbmc3k.h5ad | annotations: myann1, shared1, [New Name] (Create)

If there are existing annotations, they are rendered as links that will launch a new server. The brackets indicate a text entry box, and the Create button are intended to allow users to add new annotation file.

Implementation

• The view endpoint will require support for a labelFile parameter.
• A new createLabelFile endpoint will have to be introduced. This endpoint will require the dataset to exist before creating the label file. We may be able to simply specify the label file name and leave the creation to the cellxgene program. We can whitelist only [0-9A-Za-z_-.].
• Internally we will need to define cache entries by dataset and an optional labelFile (can be None)