Copy feature from evidence track

[garrettjstevens]

Given a JBrowse FeatureTrack such as this:

Add an entry the right-click menu so that part or all of the feature can by copied to Apollo.

The two top priority copy actions are:

• Copy whole gene to Apollo
• Copy a transcript to an existing gene in Apollo

Other copy actions may be implemented on further discussion.

[garrettjstevens]

We can use the feature we already have that creates an Apollo feature from a JBrowse alignment feature as a template for this.

In packages/jbrowse-plugin-apollo/src/index.ts, add to an extension point like this:

pluginManager.addToExtensionPoint(
  'Core-extendPluggableElement',
  annotationFromJBrowseFeature,
)

Then the annotationFromJBrowseFeature function would look something like this:

export function annotationFromJBrowseFeature(pluggableElement: PluggableElementBase) {
  if (pluggableElement.name !== 'BasicFeatureDisplay') {
    return pluggableElement
  }
  const { stateModel } = pluggableElement as DisplayType
  const newStateModel = stateModel
    .views((self) => ({

      async createFeature() {
        const feature = self.contextMenuFeature
        // create the feature...
        const change = new AddFeatureChange({
          changedIds: [newFeature._id],
          typeName: 'AddFeatureChange',
          assembly: assemblyId,
          addedFeature: newFeature,
        })
        const session = getSession(self)
        await (
          session as unknown as ApolloSessionModel
        ).apolloDataStore.changeManager.submit(change)
        session.notify('Annotation added successfully', 'success')
      },
    }))
    .views((self) => {
      const superContextMenuItems = self.contextMenuItems
      return {
        contextMenuItems() {
          const feature = self.contextMenuFeature
          if (!feature) {
            return superContextMenuItems()
          }
          return [
            ...superContextMenuItems(),
            {
              label: 'Create Apollo annotation',
              icon: AddIcon,
              onClick: self.createFeature,
            },
          ]
        },
      }
    })
  ;(pluggableElement as DisplayType).stateModel = newStateModel
  return pluggableElement
}

If you need to create a dialog instead of immediately copying the feature, the onClick can be changed to call session.queueDialog, see packages/jbrowse-plugin-apollo/src/ApolloInternetAccount/addMenuItems.ts for examples.

Let's start with a "Copy whole feature to Apollo" menu item that doesn't need a dialog. Once this works, we can figure out what a "Copy subfeature to Apollo" dialog might look like, but in general it should list all the subfeature in the JBrowse feature and ask which one(s) to copy, and ask for a destination gene in Apollo (or have a option to add them to a new gene?). The destination genes can be any in the Apollo track that overlap the coordinates of the JBrowse feature.