@jbrowse/plugin-data-management 2.2.1 → 2.3.0

package/src/ucsc-trackhub/model.js

@@ -1,125 +0,0 @@
-import { BaseConnectionModelFactory } from '@jbrowse/core/pluggableElementTypes/models'
-import {
-  ConfigurationReference,
-  readConfObject,
-  getConf,
-} from '@jbrowse/core/configuration'
-import { getSession } from '@jbrowse/core/util'
-import { types } from 'mobx-state-tree'
-import configSchema from './configSchema'
-import {
-  fetchGenomesFile,
-  fetchHubFile,
-  fetchTrackDbFile,
-  generateTracks,
-} from './ucscTrackHub'
-
-export default function UCSCTrackHubConnection(pluginManager) {
-  return types.compose(
-    'UCSCTrackHubConnection',
-    BaseConnectionModelFactory(pluginManager),
-    types
-      .model({
-        configuration: ConfigurationReference(configSchema),
-        type: types.literal('UCSCTrackHubConnection'),
-      })
-      .actions(self => ({
-        connect() {
-          const connectionName = getConf(self, 'name')
-          const hubFileLocation = getConf(self, 'hubTxtLocation')
-          const session = getSession(self)
-          fetchHubFile(hubFileLocation)
-            .then(hubFile => {
-              const genomesFileLocation = hubFileLocation.uri
-                ? {
-                    uri: new URL(
-                      hubFile.get('genomesFile'),
-                      hubFileLocation.uri,
-                    ).href,
-                    locationType: 'UriLocation',
-                  }
-                : {
-                    localPath: hubFile.get('genomesFile'),
-                    locationType: 'LocalPathLocation',
-                  }
-              return Promise.all([
-                hubFile,
-                fetchGenomesFile(genomesFileLocation),
-              ])
-            })
-            .then(([hubFile, genomesFile]) => {
-              const trackDbData = []
-              for (const [genomeName, genome] of genomesFile) {
-                const assemblyNames = getConf(self, 'assemblyNames')
-                if (
-                  assemblyNames.length > 0 &&
-                  !assemblyNames.includes(genomeName)
-                ) {
-                  break
-                }
-                const assemblyConf = session.assemblies.find(
-                  assembly => readConfObject(assembly, 'name') === genomeName,
-                )
-                if (!assemblyConf) {
-                  throw new Error(
-                    `Cannot find assembly for "${genomeName}" from the genomes file for connection "${connectionName}"`,
-                  )
-                }
-                const trackDbFileLocation = hubFileLocation.uri
-                  ? {
-                      uri: new URL(
-                        genome.get('trackDb'),
-                        new URL(
-                          hubFile.get('genomesFile'),
-                          hubFileLocation.uri,
-                        ),
-                      ).href,
-                      locationType: 'UriLocation',
-                    }
-                  : {
-                      localPath: genome.get('trackDb'),
-                      locationType: 'LocalPathLocation',
-                    }
-                trackDbData.push(
-                  Promise.all([
-                    trackDbFileLocation,
-                    fetchTrackDbFile(trackDbFileLocation),
-                    genomeName,
-                    assemblyConf,
-                  ]),
-                )
-              }
-              return Promise.all([...trackDbData])
-            })
-            .then(trackDbData => {
-              for (const [
-                trackDbFileLocation,
-                trackDbFile,
-                genomeName,
-                assemblyConf,
-              ] of trackDbData) {
-                const sequenceAdapter = readConfObject(assemblyConf, [
-                  'sequence',
-                  'adapter',
-                ])
-                const tracks = generateTracks(
-                  trackDbFile,
-                  trackDbFileLocation,
-                  genomeName,
-                  sequenceAdapter,
-                )
-                self.addTrackConfs(tracks)
-              }
-            })
-            .catch(error => {
-              console.error(error)
-              session.notify(
-                `There was a problem connecting to the UCSC Track Hub "${self.name}". Please make sure you have entered a valid hub.txt file. The error that was thrown is: "${error}"`,
-                'error',
-              )
-              session.breakConnection(self.configuration)
-            })
-        },
-      })),
-  )
-}