Misc updates

GMOD · Jun 1, 2023 · 71e7c68 · 71e7c68
1 parent c93c7de
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Showing 5 changed files with 63 additions and 103 deletions.
diff --git a/plugins/legacy-jbrowse/src/JBrowse1Connection/model.tsx b/plugins/legacy-jbrowse/src/JBrowse1Connection/model.tsx
@@ -30,10 +30,7 @@ export default function (pluginManager: PluginManager) {
           const { fetchJb1 } = await import('./jb1ConfigLoad')
           const { convertTrackConfig } = await import('./jb1ToJb2')
           const config = await fetchJb1(dataDirLocation)
-          const assemblyName = readConfObject(
-            self.configuration,
-            'assemblyNames',
-          )[0]
+          const assemblyName = getConf(self, 'assemblyNames')[0]
           if (!assemblyName) {
             throw new Error('assembly name required for JBrowse 1 connection')
           }

diff --git a/products/jbrowse-cli/README.md b/products/jbrowse-cli/README.md
@@ -189,8 +189,8 @@ ARGUMENTS
                        For JBrowse 1, location of JB1 data directory similar to http://mysite.com/jbrowse/data/
 
 OPTIONS
-  -a, --assemblyNames=assemblyNames  Comma separated list of assembly name(s) to filter from this connection. Optional,
-                                     will show all assemblies from connection if unspecified
+  -a, --assemblyNames=assemblyNames  For UCSC, optional: Comma separated list of assembly name(s) to filter from this
+                                     connection. For JBrowse: a single assembly name
 
   -c, --config=config                Any extra config settings to add to connection in JSON object format, such as
                                      '{"uri":"url":"https://sample.com"}, "locationType": "UriLocation"}'
@@ -216,13 +216,12 @@ OPTIONS
   --target=target                    path to config file in JB2 installation directory to write out to.
 
 EXAMPLES
-  $ jbrowse add-connection http://mysite.com/jbrowse/data/
-  $ jbrowse add-connection http://mysite.com/jbrowse/custom_data_folder/ --type JBrowse1Connection
-  $ jbrowse add-connection http://mysite.com/path/to/hub.txt --assemblyName hg19
-  $ jbrowse add-connection http://mysite.com/path/to/custom_hub_name.txt --type UCSCTrackHubConnection --assemblyName
-  hg19
+  $ jbrowse add-connection http://mysite.com/jbrowse/data/ -a hg19
+  $ jbrowse add-connection http://mysite.com/jbrowse/custom_data_folder/ --type JBrowse1Connection -a hg38
+  $ jbrowse add-connection http://mysite.com/path/to/hub.txt
+  $ jbrowse add-connection http://mysite.com/path/to/custom_hub_name.txt --type UCSCTrackHubConnection
   $ jbrowse add-connection http://mysite.com/path/to/custom --type custom --config
-  '{"uri":{"url":"https://mysite.com/path/to/custom"}, "locationType": "UriLocation"}' --assemblyName hg19
+  '{"uri":{"url":"https://mysite.com/path/to/custom"}, "locationType": "UriLocation"}' -a hg19
   $ jbrowse add-connection https://mysite.com/path/to/hub.txt --connectionId newId --name newName --target
   /path/to/jb2/installation/config.json
 ```

diff --git a/products/jbrowse-cli/src/base.ts b/products/jbrowse-cli/src/base.ts
@@ -152,7 +152,7 @@ export default abstract class JBrowseCommand extends Command {
     return fsPromises.readFile(location, { encoding: 'utf8' })
   }
 
-  async readJsonFile(location: string): Promise<Record<string, unknown>> {
+  async readJsonFile<T>(location: string): Promise<T> {
     let contents
     try {
       contents = await fsPromises.readFile(location, { encoding: 'utf8' })

diff --git a/products/jbrowse-cli/src/commands/add-connection.test.ts b/products/jbrowse-cli/src/commands/add-connection.test.ts
@@ -108,7 +108,7 @@ describe('add-connection', () => {
       )
     })
     .command(['add-connection', 'https://mysite.com/jbrowse/data'])
-    .it('adds an JBrowse1 connection from a url', async ctx => {
+    .it('adds JBrowse1 connection from a url', async ctx => {
       const contents = readConf(ctx)
       expect(contents).toEqual({
         ...defaultConfig,
@@ -125,28 +125,7 @@ describe('add-connection', () => {
         ],
       })
     })
-  setup
-    .nock('https://mysite.com', site => site.head('/custom').reply(200))
-    .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-connection',
-      'https://mysite.com/custom',
-      '--type',
-      'newType',
-      '--connectionId',
-      'newConnectionId',
-      '--name',
-      'newName',
-    ])
-    .exit(140)
-    .it('fails if custom without a config object')
   setup
     .nock('https://mysite.com', site => site.head('/custom').reply(200))
     .do(async ctx => {

diff --git a/products/jbrowse-cli/src/commands/add-connection.ts b/products/jbrowse-cli/src/commands/add-connection.ts
@@ -1,16 +1,23 @@
 import { flags } from '@oclif/command'
-import fetch from '../fetchWithProxy'
 import fs from 'fs'
 import path from 'path'
 import parseJSON from 'json-parse-better-errors'
+
+// locals
+import fetch from '../fetchWithProxy'
 import JBrowseCommand from '../base'
 
 interface Connection {
   [key: string]: unknown
 }
 
+interface Assembly {
+  name: string
+  sequence: { [key: string]: unknown }
+}
+
 interface Config {
-  assemblies?: { name: string; sequence: { [key: string]: unknown } }[]
+  assemblies?: Assembly[]
   configuration?: {}
   connections?: Connection[]
   defaultSession?: {}
@@ -24,11 +31,11 @@ export default class AddConnection extends JBrowseCommand {
   static description = 'Add a connection to a JBrowse 2 configuration'
 
   static examples = [
-    '$ jbrowse add-connection http://mysite.com/jbrowse/data/',
-    '$ jbrowse add-connection http://mysite.com/jbrowse/custom_data_folder/ --type JBrowse1Connection',
-    '$ jbrowse add-connection http://mysite.com/path/to/hub.txt --assemblyName hg19',
-    '$ jbrowse add-connection http://mysite.com/path/to/custom_hub_name.txt --type UCSCTrackHubConnection --assemblyName hg19',
-    `$ jbrowse add-connection http://mysite.com/path/to/custom --type custom --config '{"uri":{"url":"https://mysite.com/path/to/custom"}, "locationType": "UriLocation"}' --assemblyName hg19`,
+    '$ jbrowse add-connection http://mysite.com/jbrowse/data/ -a hg19',
+    '$ jbrowse add-connection http://mysite.com/jbrowse/custom_data_folder/ --type JBrowse1Connection -a hg38',
+    '$ jbrowse add-connection http://mysite.com/path/to/hub.txt',
+    '$ jbrowse add-connection http://mysite.com/path/to/custom_hub_name.txt --type UCSCTrackHubConnection',
+    `$ jbrowse add-connection http://mysite.com/path/to/custom --type custom --config '{"uri":{"url":"https://mysite.com/path/to/custom"}, "locationType": "UriLocation"}' -a hg19`,
     '$ jbrowse add-connection https://mysite.com/path/to/hub.txt --connectionId newId --name newName --target /path/to/jb2/installation/config.json',
   ]
 
@@ -49,7 +56,7 @@ export default class AddConnection extends JBrowseCommand {
     assemblyNames: flags.string({
       char: 'a',
       description:
-        'Comma separated list of assembly name(s) to filter from this connection. Optional, will show all assemblies from connection if unspecified',
+        'For UCSC, optional: Comma separated list of assembly name(s) to filter from this connection. For JBrowse: a single assembly name',
     }),
     config: flags.string({
       char: 'c',
@@ -91,15 +98,14 @@ export default class AddConnection extends JBrowseCommand {
     const isDir = fs.lstatSync(output).isDirectory()
     this.target = isDir ? `${output}/config.json` : output
 
-    const { connectionUrlOrPath: argsPath } = runArgs as {
-      connectionUrlOrPath: string
-    }
-    const { config, assemblyNames } = runFlags
-    let { type, name, connectionId } = runFlags
+    const { connectionUrlOrPath } = runArgs
+    const { assemblyNames, type, name, config, connectionId } = runFlags
     const { skipCheck, force } = runFlags
-    const url = await this.resolveURL(argsPath, !(skipCheck || force))
-
-    const configContents: Config = await this.readJsonFile(this.target)
+    const url = await this.resolveURL(
+      connectionUrlOrPath,
+      !(skipCheck || force),
+    )
+    const configContents = await this.readJsonFile<Config>(this.target)
     this.debug(`Using config file ${this.target}`)
 
     if (!configContents.assemblies?.length) {
@@ -109,62 +115,46 @@ export default class AddConnection extends JBrowseCommand {
       )
     }
 
-    type = type || this.determineConnectionType(url, config)
-    connectionId =
+    const configType = type || this.determineConnectionType(url)
+    const id =
       connectionId ||
-      [type, assemblyNames, +Date.now()].filter(f => !!f).join('-')
-    name = name || connectionId
-
-    let configObj = {}
-    if (config) {
-      configObj = parseJSON(config)
-    }
-    const connectionConfig: Connection = {
-      type,
-      connectionId,
-      name: name || connectionId,
-      assemblyNames: assemblyNames?.split(','),
-      ...configObj,
-    }
-
-    switch (type) {
-      case 'UCSCTrackHubConnection': {
-        connectionConfig.hubTxtLocation = {
-          uri: url,
-          locationType: 'UriLocation',
-        }
-        break
-      }
-      case 'JBrowse1Connection': {
-        connectionConfig.dataDirLocation = {
-          uri: url,
-          locationType: 'UriLocation',
-        }
-        break
-      }
-      default: {
-        if (!config || !this.isValidJSON(config)) {
-          this.error(
-            'When type is not UCSCTrackHubConnection or JBrowse1Connection, config object must be provided.\nPlease enter a config object using --config',
-            { exit: 140 },
-          )
-        }
-
-        break
-      }
+      [configType, assemblyNames, +Date.now()].filter(f => !!f).join('-')
+    const connectionConfig = {
+      type: configType,
+      name: name || id,
+      ...(configType === 'UCSCTrackHubConnection'
+        ? {
+            hubTxtLocation: {
+              uri: url,
+              locationType: 'UriLocation',
+            },
+          }
+        : {}),
+      ...(configType === 'JBrowse1Connection'
+        ? {
+            dataDirLocation: {
+              uri: url,
+              locationType: 'UriLocation',
+            },
+          }
+        : {}),
+      connectionId: id,
+      assemblyNames:
+        assemblyNames || type === 'JBrowse1Connection'
+          ? [configContents.assemblies[0]?.name]
+          : undefined,
+      ...(config ? parseJSON(config) : {}),
     }
 
     if (!configContents.connections) {
       configContents.connections = []
     }
     const idx = configContents.connections.findIndex(
-      configConnection => configConnection.connectionId === connectionId,
+      c => c.connectionId === connectionId,
     )
 
     if (idx !== -1) {
-      this.debug(`Found existing connectionId ${connectionId} in configuration`)
       if (runFlags.force || runFlags.overwrite) {
-        this.debug(`Overwriting connection ${connectionId} in configuration`)
         configContents.connections[idx] = connectionConfig
       } else {
         this.error(
@@ -213,19 +203,14 @@ export default class AddConnection extends JBrowseCommand {
     })
   }
 
-  determineConnectionType(url: string, config: string | undefined) {
+  determineConnectionType(url: string) {
     if (path.basename(url) === 'hub.txt') {
       return 'UCSCTrackHubConnection'
     }
     if (url.includes('jbrowse/data')) {
       return 'JBrowse1Connection'
     }
-    if (config && this.isValidJSON(config)) {
-      return 'custom'
-    }
-    return this.error(
-      `Unable to determine a specific connection from URL given.\nPlease specify a type with --type.\nIf you want a custom type, please provide the config object with --config`,
-    )
+    return 'custom'
   }
 
   isValidJSON(str: string) {