@jbrowse/plugin-data-management 2.2.2 → 2.3.0

package/src/HierarchicalTrackSelectorWidget/components/ToggleConnectionsDialog.tsx

@@ -68,7 +68,11 @@ function ToggleConnectionDialog({
                     color="primary"
                   />
                 }
-                label={`${name} (${ellipses(assemblyNames.join(','))})`}
+                label={`${name} ${
+                  assemblyNames.length
+                    ? '(' + ellipses(assemblyNames.join(',')) + ')'
+                    : ''
+                }`}
               />
             )
           })}

package/src/HierarchicalTrackSelectorWidget/components/__snapshots__/HierarchicalTrackSelector.test.tsx.snap

@@ -2,7 +2,7 @@
 
 exports[`HierarchicalTrackSelector widget renders nothing with no assembly 1`] = `
 <button
-  class="MuiButtonBase-root MuiFab-root MuiFab-circular MuiFab-sizeSmall MuiFab-secondary MuiFab-root MuiFab-circular MuiFab-sizeSmall MuiFab-secondary css-tbl9bo-MuiButtonBase-root-MuiFab-root-fab"
+  class="MuiButtonBase-root MuiFab-root MuiFab-circular MuiFab-sizeSmall MuiFab-secondary MuiFab-root MuiFab-circular MuiFab-sizeSmall MuiFab-secondary css-15opis6-MuiButtonBase-root-MuiFab-root-fab"
   tabindex="0"
   type="button"
 >

package/src/HierarchicalTrackSelectorWidget/model.ts

@@ -67,6 +67,7 @@ export function generateHierarchy(
   model: HierarchicalTrackSelectorModel,
   trackConfigurations: AnyConfigurationModel[],
   collapsed: { get: (arg: string) => boolean | undefined },
+  extra?: string,
 ) {
   const hierarchy = { children: [] as TreeNode[] } as TreeNode
   const { filterText, view } = model
@@ -91,7 +92,7 @@ export function generateHierarchy(
       for (let i = 0; i < categories.length; i++) {
         const category = categories[i]
         const ret = currLevel.children.find(c => c.name === category)
-        const id = categories.slice(0, i + 1).join(',')
+        const id = extra + '-' + categories.slice(0, i + 1).join(',')
         if (!ret) {
           const n = {
             children: [],
@@ -228,10 +229,7 @@ export default function stateTreeFactory(pluginManager: PluginManager) {
         const conns =
           (assembly &&
             connectionInstances
-              ?.filter(c =>
-                hasAnyOverlap(assembly.allAliases, getConf(c, 'assemblyNames')),
-              )
-              .map(c => ({
+              ?.map(c => ({
                 // @ts-ignore
                 id: getSnapshot(c).configuration,
                 name: getConf(c, 'name'),
@@ -239,7 +237,8 @@ export default function stateTreeFactory(pluginManager: PluginManager) {
                 state: {
                   expanded: true,
                 },
-              }))) ||
+              }))
+              .filter(f => f.children.length)) ||
           []
 
         return {
@@ -254,13 +253,14 @@ export default function stateTreeFactory(pluginManager: PluginManager) {
 
       connectionHierarchy(
         assemblyName: string,
-        connection: { tracks: AnyConfigurationModel[] },
+        connection: { name: string; tracks: AnyConfigurationModel[] },
       ) {
         return generateHierarchy(
           // eslint-disable-next-line @typescript-eslint/no-explicit-any
           self as any,
           self.connectionTrackConfigurations(assemblyName, connection),
           self.collapsed,
+          connection.name,
         )
       },
     }))

package/src/PluginStoreWidget/components/__snapshots__/PluginStoreWidget.test.js.snap

@@ -501,28 +501,6 @@ exports[`<PluginStoreWidget /> renders with the available plugins 1`] = `
                     SequencePlugin
                   </p>
                 </li>
-                <li
-                  class="MuiListItem-root MuiListItem-dense MuiListItem-gutters MuiListItem-padding css-ypie1g-MuiListItem-root"
-                >
-                  <svg
-                    aria-hidden="true"
-                    aria-label="This plugin was installed by an administrator, you cannot remove it."
-                    class="MuiSvgIcon-root MuiSvgIcon-fontSizeMedium css-1a34d00-MuiSvgIcon-root-lockedPluginTooltip"
-                    data-mui-internal-clone-element="true"
-                    data-testid="LockIcon"
-                    focusable="false"
-                    viewBox="0 0 24 24"
-                  >
-                    <path
-                      d="M18 8h-1V6c0-2.76-2.24-5-5-5S7 3.24 7 6v2H6c-1.1 0-2 .9-2 2v10c0 1.1.9 2 2 2h12c1.1 0 2-.9 2-2V10c0-1.1-.9-2-2-2zm-6 9c-1.1 0-2-.9-2-2s.9-2 2-2 2 .9 2 2-.9 2-2 2zm3.1-9H8.9V6c0-1.71 1.39-3.1 3.1-3.1 1.71 0 3.1 1.39 3.1 3.1v2z"
-                    />
-                  </svg>
-                  <p
-                    class="MuiTypography-root MuiTypography-body1 css-k0xfey-MuiTypography-root"
-                  >
-                    TrackHubRegistryPlugin
-                  </p>
-                </li>
                 <li
                   class="MuiListItem-root MuiListItem-dense MuiListItem-gutters MuiListItem-padding css-ypie1g-MuiListItem-root"
                 >

package/src/ucsc-trackhub/model.ts

@@ -0,0 +1,119 @@
+import PluginManager from '@jbrowse/core/PluginManager'
+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'
+
+// locals
+import configSchema from './configSchema'
+import {
+  fetchGenomesFile,
+  fetchHubFile,
+  fetchTrackDbFile,
+  generateTracks,
+} from './ucscTrackHub'
+
+export default function UCSCTrackHubConnection(pluginManager: PluginManager) {
+  return types
+    .compose(
+      'UCSCTrackHubConnection',
+      BaseConnectionModelFactory(pluginManager),
+      types.model({
+        configuration: ConfigurationReference(configSchema),
+        type: types.literal('UCSCTrackHubConnection'),
+      }),
+    )
+    .actions(self => ({
+      async connect() {
+        const session = getSession(self)
+        try {
+          const connectionName = getConf(self, 'name')
+          const hubFileLocation = getConf(self, 'hubTxtLocation')
+          const hubFile = await fetchHubFile(hubFileLocation)
+          const genomeFile = hubFile.get('genomesFile')
+          if (!genomeFile) {
+            throw new Error('genomesFile not found on hub')
+          }
+
+          const hubUri = new URL(hubFileLocation.uri, hubFileLocation.baseUri)
+          const genomesFileLocation = hubUri
+            ? {
+                uri: new URL(genomeFile, hubUri).href,
+                locationType: 'UriLocation',
+              }
+            : {
+                localPath: genomeFile,
+                locationType: 'LocalPathLocation',
+              }
+          const genomesFile = await fetchGenomesFile(genomesFileLocation)
+          const trackDbData = []
+          for (const [genomeName, genome] of genomesFile) {
+            const assemblyNames = getConf(self, 'assemblyNames')
+            if (
+              assemblyNames.length > 0 &&
+              !assemblyNames.includes(genomeName)
+            ) {
+              continue
+            }
+            const conf = session.assemblies.find(
+              a => readConfObject(a, 'name') === genomeName,
+            )
+            if (!conf) {
+              throw new Error(
+                `Cannot find assembly for "${genomeName}" from the genomes file for connection "${connectionName}"`,
+              )
+            }
+            const trackDb = genome.get('trackDb')
+            if (!trackDb) {
+              throw new Error('genomesFile not found on hub')
+            }
+            const trackDbFileLocation = hubUri
+              ? {
+                  uri: new URL(trackDb, new URL(genomeFile, hubUri)).href,
+                  locationType: 'UriLocation',
+                }
+              : {
+                  localPath: trackDb,
+                  locationType: 'LocalPathLocation',
+                }
+            trackDbData.push([
+              trackDbFileLocation,
+              await fetchTrackDbFile(trackDbFileLocation),
+              genomeName,
+              conf,
+            ] as const)
+          }
+          for (const [
+            trackDbFileLocation,
+            trackDbFile,
+            genomeName,
+            conf,
+          ] of trackDbData) {
+            const sequenceAdapter = readConfObject(conf, [
+              'sequence',
+              'adapter',
+            ])
+            self.addTrackConfs(
+              generateTracks(
+                trackDbFile,
+                trackDbFileLocation,
+                genomeName,
+                sequenceAdapter,
+              ),
+            )
+          }
+        } catch (e) {
+          console.error(e)
+          session.notify(
+            `There was a problem connecting to the UCSC Track Hub "${self.configuration.name}". Please make sure you have entered a valid hub.txt file. The error that was thrown is: "${e}"`,
+            'error',
+          )
+          session.breakConnection(self.configuration)
+        }
+      },
+    }))
+}

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)
-            })
-        },
-      })),
-  )
-}