`set-default-session --tracks` generates incomplete session

set-default-session --tracks generates tracks with minimal properties: “type” and “configuration”:

    "views": [
      {
        "id": "LinearGenomeView-12",
        "type": "LinearGenomeView",
        "tracks": [
          {
            "type": "QuantitativeTrack",
            "configuration": "monocot"
          },
          {
            "type": "AlignmentsTrack",
            "configuration": "zea_mays"
          },

This config.json results in a fatal error TypeError: Cannot read properties of undefined (reading 'height').

To Reproduce

1. jbrowse create
2. jbrowse add-assembly
3. jbrowse add-track
4. jbrowse set-default-session --tracks
5. Open the configured app in a web browser.

Expected behavior

• App should allow unset properties like height and show tracks with some default values.
• set-default-session should set all the required properties.

Screenshots

Version:

@jbrowse/cli/1.6.4 darwin-x64 node-v16.13.21

Additional context

I am trying to automate jbrowse configuration to handle many different conditions and data. I hope everything can be done via CLI.

[cmdcolin]

thanks for the continued patience with this. Indeed, --out was not working. I have proposed a fix that allows it to work in #2715

also changes the name of the flag to be --root instead of --out/–target because it is indeed inconsistent, and since --out was not working anyways, hopefully the change is not disruptive.

[cmdcolin]

@abretaud can you create a new issue or discussion for this? it’s hard to track too many branches on a thread 😃

just to try to address, I think displayCrossHatches is part of the “renderer” config. It is also part of the state model of the display to allow the user to select it via the UI. we could probably add it as a config of the display to make that easier