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Remove --tracks and --view options from set-default-session CLI (#4146)
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@cmdcolin
cmdcolin committed Jan 10, 2024
1 parent 07b65e2 commit d38f511
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12 changes: 3 additions & 9 deletions products/jbrowse-cli/README.md
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Original file line number Diff line number Diff line change
Expand Up @@ -543,32 +543,26 @@ Set a default session with views and tracks

```
USAGE
$ jbrowse set-default-session [-s <value>] [-n <value>] [-v <value>] [--viewId <value>] [-t <value>] [-c] [--target
<value>] [--out <value>] [--delete] [-h]
$ jbrowse set-default-session [-s <value>] [-n <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 --view LinearGenomeView --tracks track1, track2, track3
$ jbrowse set-default-session --target /path/to/jb2/installation/config.json
$ jbrowse set-default-session --view LinearGenomeView, --name newName --viewId view-no-tracks
$ jbrowse set-default-session --view LinearGenomeView, --name newName
$ jbrowse set-default-session --currentSession # Prints out current default session
```
Expand Down
67 changes: 2 additions & 65 deletions products/jbrowse-cli/src/commands/set-default-session.test.ts
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Original file line number Diff line number Diff line change
Expand Up @@ -65,17 +65,8 @@ const simpleBam = dataDir('simple.bam')
const simpleDefaultSession = dataDir('sampleDefaultSession.json')
const testConfig = dataDir('test_config.json')

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
// Cleaning up exitCode in Node.js 20, xref
// https://github.com/jestjs/jest/issues/14501
afterAll(() => (process.exitCode = 0))

describe('set-default-session', () => {
Expand Down Expand Up @@ -130,28 +121,6 @@ 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)))
Expand Down Expand Up @@ -203,36 +172,4 @@ 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',
},
],
},
],
},
})
},
)
})
114 changes: 13 additions & 101 deletions products/jbrowse-cli/src/commands/set-default-session.ts
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Original file line number Diff line number Diff line change
Expand Up @@ -6,14 +6,11 @@ import JBrowseCommand from '../base'

const fsPromises = fs.promises

// 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>
type DefaultSession = Record<string, unknown>
type Track = Record<string, unknown>

interface Config {
// eslint-disable-next-line @typescript-eslint/no-explicit-any
assemblies?: { name: string; sequence: Record<string, any> }[]
assemblies?: { name: string; sequence: Record<string, unknown> }[]
configuration?: {}
connections?: unknown[]
defaultSession?: DefaultSession
Expand All @@ -28,8 +25,8 @@ 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 --view LinearGenomeView --tracks track1, track2, track3',
'$ jbrowse set-default-session --view LinearGenomeView, --name newName --viewId view-no-tracks',
'$ jbrowse set-default-session --target /path/to/jb2/installation/config.json',
'$ jbrowse set-default-session --view LinearGenomeView, --name newName',
'$ jbrowse set-default-session --currentSession # Prints out current default session',
]

Expand All @@ -43,19 +40,6 @@ 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',
Expand All @@ -77,102 +61,30 @@ export default class SetDefaultSession extends JBrowseCommand {

async run() {
const { flags: runFlags } = await this.parse(SetDefaultSession)
const {
session,
name,
tracks,
currentSession,
view,
viewId,
delete: deleteDefaultSession,
} = runFlags
const { session, currentSession, 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)
this.log(`Deleted defaultSession from ${this.target}`)
return
}

// if user passes current session flag, print out and exit
if (currentSession) {
} else if (currentSession) {
this.log(
`The current default session is ${JSON.stringify(
configContents.defaultSession,
)}`,
)
this.exit()
}

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) {
this.error(`Please either provide a default session file`, { exit: 120 })
} else if (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,
},
],
}
await this.writeJsonFile(this.target, {
...configContents,
defaultSession: await this.readDefaultSessionFile(session),
})
}
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) {
Expand Down

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