Allow 'hydrating' a defaultSession that does not specify the display type of a track

packages/core/pluggableElementTypes/models/BaseTrackModel.ts

@@ -1,10 +1,11 @@
-import { transaction } from 'mobx'
+import { autorun, transaction } from 'mobx'
 import {
   getRoot,
   resolveIdentifier,
   types,
   Instance,
   IAnyStateTreeNode,
+  addDisposer,
 } from 'mobx-state-tree'
 
 // locals
@@ -210,6 +211,19 @@ export function createBaseTrackModel(
             : []),
         ]
       },
+      afterAttach() {
+        addDisposer(
+          self,
+          autorun(() => {
+            if (!self.displays.length) {
+              const compatDisp = getCompatibleDisplays(self)
+              self.showDisplay(
+                self.configuration.trackId + '-' + compatDisp[0].type,
+              )
+            }
+          }),
+        )
+      },
     }))
 }
 

products/jbrowse-cli/README.md

@@ -543,26 +543,32 @@ Set a default session with views and tracks
 
 ```
 USAGE
-  $ jbrowse set-default-session [-s <value>] [-n <value>] [-c] [--target <value>] [--out <value>] [--delete] [-h]
+  $ jbrowse set-default-session [-s <value>] [-n <value>] [-v <value>] [--viewId <value>] [-t <value>] [-c] [--target
+    <value>] [--out <value>] [--delete] [-h]
 
 FLAGS
   -c, --currentSession   List out the current default session
   -h, --help             Show CLI help.
   -n, --name=<value>     [default: New Default Session] Give a name for the default session
   -s, --session=<value>  set path to a file containing session in json format
+  -t, --tracks=<value>   Track id or track ids as comma separated string to put into default session
+  -v, --view=<value>     View type in config to be added as default session, i.e LinearGenomeView, CircularView,
+                         DotplotView.
+                         Must be provided if no default session file provided
       --delete           Delete any existing default session.
       --out=<value>      synonym for target
       --target=<value>   path to config file in JB2 installation directory to write out to
+      --viewId=<value>   Identifier for the view. Will be generated on default
 
 DESCRIPTION
   Set a default session with views and tracks
 
 EXAMPLES
   $ jbrowse set-default-session --session /path/to/default/session.json
 
-  $ jbrowse set-default-session --target /path/to/jb2/installation/config.json
+  $ jbrowse set-default-session --target /path/to/jb2/installation/config.json --view LinearGenomeView --tracks track1, track2, track3
 
-  $ jbrowse set-default-session --view LinearGenomeView, --name newName
+  $ jbrowse set-default-session --view LinearGenomeView, --name newName --viewId view-no-tracks
 
   $ jbrowse set-default-session --currentSession # Prints out current default session
 ```

products/jbrowse-cli/src/commands/set-default-session.test.ts

@@ -65,8 +65,17 @@ const simpleBam = dataDir('simple.bam')
 const simpleDefaultSession = dataDir('sampleDefaultSession.json')
 const testConfig = dataDir('test_config.json')
 
-// Cleaning up exitCode in Node.js 20, xref
-// https://github.com/jestjs/jest/issues/14501
+const setupWithAddTrack = setup
+  .do(async ctx => {
+    await copyFile(testConfig, path.join(ctx.dir, path.basename(testConfig)))
+    await rename(
+      path.join(ctx.dir, path.basename(testConfig)),
+      path.join(ctx.dir, 'config.json'),
+    )
+  })
+  .command(['add-track', simpleBam, '--load', 'copy'])
+
+// Cleaning up exitCode in Node.js 20, xref https://github.com/jestjs/jest/issues/14501
 afterAll(() => (process.exitCode = 0))
 
 describe('set-default-session', () => {
@@ -121,6 +130,28 @@ describe('set-default-session', () => {
     .exit(160)
     .it('fails when file is does not have a default session to read')
 
+  setupWithAddTrack
+    .do(async ctx => {
+      await copyFile(testConfig, path.join(ctx.dir, path.basename(testConfig)))
+
+      await rename(
+        path.join(ctx.dir, path.basename(testConfig)),
+        path.join(ctx.dir, 'config.json'),
+      )
+    })
+    .command(['set-default-session', '--tracks', 'simple'])
+    .exit(130)
+    .it('fails when specifying a track without specifying a view')
+  setupWithAddTrack
+    .command([
+      'set-default-session',
+      '--view',
+      'LinearGenomeView',
+      '--tracks',
+      'track-non-exist',
+    ])
+    .exit(140)
+    .it('fails when specifying a track that does not exist')
   setup
     .do(async ctx => {
       await copyFile(testConfig, path.join(ctx.dir, path.basename(testConfig)))
@@ -172,4 +203,36 @@ describe('set-default-session', () => {
         },
       })
     })
+  setupWithAddTrack
+    .command([
+      'set-default-session',
+      '--view',
+      'LinearGenomeView',
+      '--tracks',
+      'simple',
+    ])
+    .it(
+      'adds a default session that is a linear genome view and a simple track',
+      async ctx => {
+        const contents = readConf(ctx)
+        expect(contents).toEqual({
+          ...defaultConfig,
+          defaultSession: {
+            name: 'New Default Session',
+            views: [
+              {
+                id: 'LinearGenomeView-1',
+                type: 'LinearGenomeView',
+                tracks: [
+                  {
+                    type: 'AlignmentsTrack',
+                    configuration: 'simple',
+                  },
+                ],
+              },
+            ],
+          },
+        })
+      },
+    )
 })

products/jbrowse-cli/src/commands/set-default-session.ts

@@ -6,11 +6,14 @@ import JBrowseCommand from '../base'
 
 const fsPromises = fs.promises
 
-type DefaultSession = Record<string, unknown>
-type Track = Record<string, unknown>
+// eslint-disable-next-line @typescript-eslint/no-explicit-any
+type DefaultSession = Record<string, any>
+// eslint-disable-next-line @typescript-eslint/no-explicit-any
+type Track = Record<string, any>
 
 interface Config {
-  assemblies?: { name: string; sequence: Record<string, unknown> }[]
+  // eslint-disable-next-line @typescript-eslint/no-explicit-any
+  assemblies?: { name: string; sequence: Record<string, any> }[]
   configuration?: {}
   connections?: unknown[]
   defaultSession?: DefaultSession
@@ -25,8 +28,8 @@ export default class SetDefaultSession extends JBrowseCommand {
 
   static examples = [
     '$ jbrowse set-default-session --session /path/to/default/session.json',
-    '$ jbrowse set-default-session --target /path/to/jb2/installation/config.json',
-    '$ jbrowse set-default-session --view LinearGenomeView, --name newName',
+    '$ jbrowse set-default-session --target /path/to/jb2/installation/config.json --view LinearGenomeView --tracks track1, track2, track3',
+    '$ jbrowse set-default-session --view LinearGenomeView, --name newName --viewId view-no-tracks',
     '$ jbrowse set-default-session --currentSession # Prints out current default session',
   ]
 
@@ -40,6 +43,19 @@ export default class SetDefaultSession extends JBrowseCommand {
       description: 'Give a name for the default session',
       default: 'New Default Session',
     }),
+    view: Flags.string({
+      char: 'v',
+      description:
+        'View type in config to be added as default session, i.e LinearGenomeView, CircularView, DotplotView.\nMust be provided if no default session file provided',
+    }),
+    viewId: Flags.string({
+      description: 'Identifier for the view. Will be generated on default',
+    }),
+    tracks: Flags.string({
+      char: 't',
+      description:
+        'Track id or track ids as comma separated string to put into default session',
+    }),
     currentSession: Flags.boolean({
       char: 'c',
       description: 'List out the current default session',
@@ -61,30 +77,102 @@ export default class SetDefaultSession extends JBrowseCommand {
 
   async run() {
     const { flags: runFlags } = await this.parse(SetDefaultSession)
-    const { session, currentSession, delete: deleteDefaultSession } = runFlags
+    const {
+      session,
+      name,
+      tracks,
+      currentSession,
+      view,
+      viewId,
+      delete: deleteDefaultSession,
+    } = runFlags
     const output = runFlags.target || runFlags.out || '.'
     const isDir = (await fsPromises.lstat(output)).isDirectory()
     this.target = isDir ? `${output}/config.json` : output
     const configContents: Config = await this.readJsonFile(this.target)
 
     if (deleteDefaultSession) {
       delete configContents.defaultSession
+      this.debug(`Writing configuration to file ${this.target}`)
       await this.writeJsonFile(this.target, configContents)
-    } else if (currentSession) {
+      this.log(`Deleted defaultSession from ${this.target}`)
+      return
+    }
+
+    // if user passes current session flag, print out and exit
+    if (currentSession) {
       this.log(
         `The current default session is ${JSON.stringify(
           configContents.defaultSession,
         )}`,
       )
       this.exit()
-    } else if (!session) {
-      this.error(`Please either provide a default session file`, { exit: 120 })
+    }
+
+    const foundTracks: Track[] = []
+    const existingDefaultSession = configContents.defaultSession?.length > 0
+
+    // must provide default session, or view, or tracks + view
+    if (!session && !view && !tracks) {
+      this.error(
+        `No default session information provided, Please either provide a default session file or enter information to build a default session`,
+        { exit: 120 },
+      )
     } else if (session) {
-      await this.writeJsonFile(this.target, {
-        ...configContents,
-        defaultSession: await this.readDefaultSessionFile(session),
-      })
+      // if user provides a file, process and set as default session and exit
+      const defaultJson = await this.readDefaultSessionFile(session)
+      configContents.defaultSession = defaultJson
+    } else {
+      // use trackids if any to match to tracks in the config
+      let trackIds = []
+      if (tracks && configContents.tracks) {
+        if (!view) {
+          this.error(
+            'Tracks must have a view type specified. Please rerun using the --view flag',
+            { exit: 130 },
+          )
+        }
+        trackIds = tracks.split(',').map(c => c.trim())
+        trackIds.forEach(trackId => {
+          this.log(trackId)
+          const matchingTrack = configContents.tracks?.find(
+            track => trackId === track.trackId,
+          )
+          if (!matchingTrack) {
+            this.error(
+              `Track ${trackId} has not been added to config yet.\nPlease add the track with the add-track command before adding to the default session`,
+              { exit: 140 },
+            )
+          } else {
+            foundTracks.push({
+              type: matchingTrack.type,
+              configuration: matchingTrack.trackId,
+            })
+          }
+        })
+      }
+
+      configContents.defaultSession = {
+        name,
+        views: [
+          {
+            id: viewId || `${view}-${foundTracks.length}`,
+            type: view,
+            tracks: foundTracks,
+          },
+        ],
+      }
     }
+    this.debug(`Writing configuration to file ${this.target}`)
+    await this.writeJsonFile(this.target, configContents)
+
+    this.log(
+      `${
+        existingDefaultSession ? 'Overwrote' : 'Added'
+      } defaultSession "${name}" ${existingDefaultSession ? 'in' : 'to'} ${
+        this.target
+      }`,
+    )
   }
 
   async readDefaultSessionFile(defaultSessionFile: string) {

test_data/volvox/config.json

@@ -218,34 +218,19 @@
   },
   "connections": [],
   "defaultSession": {
-    "name": "Integration test example",
+    "name": "New Default Session",
     "views": [
       {
-        "id": "integration_test",
+        "id": "LinearGenomeView-1",
         "type": "LinearGenomeView",
-        "offsetPx": 2000,
-        "bpPerPx": 0.05,
-        "displayedRegions": [
+        "tracks": [
           {
-            "refName": "ctgA",
-            "start": 0,
-            "end": 50001,
-            "assemblyName": "volvox"
+            "type": "FeatureTrack",
+            "configuration": "gff3tabix_genes"
           }
         ]
       }
-    ],
-    "widgets": {
-      "hierarchicalTrackSelector": {
-        "id": "hierarchicalTrackSelector",
-        "type": "HierarchicalTrackSelectorWidget",
-        "filterText": "",
-        "view": "integration_test"
-      }
-    },
-    "activeWidgets": {
-      "hierarchicalTrackSelector": "hierarchicalTrackSelector"
-    }
+    ]
   },
   "tracks": [
     {