Link to download loom file

[slinnarsson]

I made a new endpoint "/clone/..:" to download the actual .loom file for a dataset. This makes it easy to download a dataset from a public server, and then work with it locally.

In the client, each dataset should have a "Download" button. This should be visible but not take too much visual space, so an icon would make sense. Maybe a cloud with arrow.

When clicked, this downloads the file to the user's computer.

[slinnarsson]

And the icon should have a tooltip, e.g. "Download this .loom file" so that the purpose is clear.

[slinnarsson]

Even better: "Download Midbrain_20160601.loom" i.e. using the actual name of the file.

[JobLeonard]

Ok, this should be simple enough. It's just an addition to the list of datasets we currently have in the client, right? That is to say: I can just take the projects from the /loom/ endpoint and find all available loom files as /clone/<transcriptome>__<project>__<dataset>.loom?

(not yet taking into account your earlier remark that we are likely to relax the naming convention for loom files)

[slinnarsson]

The endpoint is GET /clone/{project}/{filename}. From /loom you'll now get a list of datasets, each of which is a list with two items: project and filename. For example:

[
   ["Midbrain", "midbrain_20160801.loom"],
   ["Cortex", "astrocytes_final.loom"],
   ["Cortex", "oligos_final.loom"]
]

The link to download the last of those datasets would be /clone/Cortex/oligos_final.loom and the tooltip would show as Download oligos_final.loom.

The concept of transcriptome is gone because it was only ever needed to support uploads.

[slinnarsson]

Actually, maybe I should make /loom return a dictionary instead? It would be easier then to add fields later on and they would not rely on the order of fields in a list:

[
   {"project": "Midbrain", "filename": "midbrain_20160801.loom"},
   {"project": "Cortex", "filename": "astrocytes_final.loom"},
   {"project": "Cortex", "filename": "oligos_final.loom"}
]

[slinnarsson]

I made the change to the /loom endpoint, and updated the docs.

[JobLeonard]

Isn't that the existing method of listing projects you had before, with a "filename" field added and all the loom-pipeline-related fields stripped? This is what /loom returned before:

[
    {
        "project": "midbrain",
        "status": "created",
        "cluster_method": "AP",
        "transcriptome": "hg19_sUCSC",
        "message": "Ready to browse.",
        "regression_label": "_Cluster",
        "n_features": 1000,
        "dataset": "human_sten_May29"
    },
    {
        "project": "Published",
        "status": "created",
        "cluster_method": "AP",
        "transcriptome": "mm10_sUCSC",
        "message": "Ready to browse.",
        "regression_label": "_Cluster",
        "n_features": 1000,
        "dataset": "Oligodendrocytes_Science_2016"
    }
]

The client side currently relies on a number of these fields - "status" is used to determine if projects can be opened and message is displayed as an explanation. Since that is all loom-pipeline specific that needs to be stripped out as well.

Also, I showed the react-router branch version of Loom to Gioelle and Lars, in part to test the browser code, and they got a bit confused by the UI, not understanding where to click to get to a datavisualisation. I need to re-arrange it to be more intuitive; might as well do that while I implement the download button.

• [x] remove loom-pipeline related code from datasets.js
• [x] reorganise dataset list UI
• [x] add download button
• [x] tooltip instruction on button

[slinnarsson]

Exactly. We might want to add metadata such as "title", "description", "authors", "reference" etc. in the future. These would be stored in the loom file itself, and not related to the pipeline.

[JobLeonard]

Well, that was even easier than expected. Nice when issues take only half an hour to implement ;)

[JobLeonard]

Forgot the tooltip