Create notion of defaultSessionSpec for config.json files

GMOD · Dec 20, 2023 · 767d8ef · 767d8ef
1 parent d2f38c9
commit 767d8ef
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Showing 5 changed files with 100 additions and 48 deletions.
diff --git a/products/jbrowse-web/src/__snapshots__/jbrowseModel.test.ts.snap b/products/jbrowse-web/src/__snapshots__/jbrowseModel.test.ts.snap
@@ -470,34 +470,26 @@ exports[`JBrowse model creates with non-empty snapshot 1`] = `
   },
   "connections": [],
   "defaultSession": {
-    "activeWidgets": {
-      "hierarchicalTrackSelector": "hierarchicalTrackSelector",
-    },
-    "name": "Integration test example",
+    "name": "Session",
+    "type": "spec",
     "views": [
       {
-        "bpPerPx": 0.05,
-        "displayedRegions": [
-          {
-            "assemblyName": "volvox",
-            "end": 50001,
-            "refName": "ctgA",
-            "start": 0,
-          },
+        "assembly": "volvox",
+        "loc": "ctgA:1-100",
+        "tracks": [
+          "volvox_cram_pileup",
         ],
-        "id": "integration_test",
-        "offsetPx": 2000,
         "type": "LinearGenomeView",
       },
-    ],
-    "widgets": {
-      "hierarchicalTrackSelector": {
-        "filterText": "",
-        "id": "hierarchicalTrackSelector",
-        "type": "HierarchicalTrackSelectorWidget",
-        "view": "integration_test",
+      {
+        "assembly": "volvox",
+        "loc": "ctgB:1-100",
+        "tracks": [
+          "volvox_cram_pileup",
+        ],
+        "type": "LinearGenomeView",
       },
-    },
+    ],
   },
   "internetAccounts": [],
   "plugins": [

diff --git a/products/jbrowse-web/src/components/NoConfigMessage.tsx b/products/jbrowse-web/src/components/NoConfigMessage.tsx
@@ -23,6 +23,7 @@ export default function NoConfigMessage() {
     ['test_data/volvox/config_auth_main.json', 'Volvox (auth, mainthreadrpc)'],
     ['test_data/volvox/config_auth.json', 'Volvox (auth)'],
     ['test_data/volvoxhub/config.json', 'Volvox (with ucsc-hub)'],
+    ['test_data/volvox/spec.json', 'Volvox (with spec defaultsession)'],
   ]
   const { href, search } = window.location
   const { config, ...rest } = Object.fromEntries(new URLSearchParams(search))

diff --git a/products/jbrowse-web/src/createPluginManager.ts b/products/jbrowse-web/src/createPluginManager.ts
@@ -8,9 +8,9 @@ import corePlugins from './corePlugins'
 import { SessionLoaderModel, loadSessionSpec } from './SessionLoader'
 
 export function createPluginManager(self: SessionLoaderModel) {
-  // it is ready when a session has loaded and when there is no config
-  // error Assuming that the query changes self.sessionError or
-  // self.sessionSnapshot or self.blankSession
+  // it is ready when a session has loaded and when there is no config error
+  // Assuming that the query changes self.sessionError or self.sessionSnapshot
+  // or self.blankSession
   const pluginManager = new PluginManager([
     ...corePlugins.map(P => ({
       plugin: new P(),
@@ -47,43 +47,38 @@ export function createPluginManager(self: SessionLoaderModel) {
 
   // @ts-expect-error
   if (!self.configSnapshot?.configuration?.rpc?.defaultDriver) {
-    const { rpc } = rootModel.jbrowse.configuration
-    rpc.defaultDriver.set('WebWorkerRpcDriver')
+    rootModel.jbrowse.configuration.rpc.defaultDriver.set('WebWorkerRpcDriver')
   }
 
-  let afterInitializedCb = () => {}
+  let afterInitializedCallback = () => {}
 
-  // in order: saves the previous autosave for recovery, tries to
-  // load the local session if session in query, or loads the default
-  // session
+  // in order: saves the previous autosave for recovery, tries to load the
+  // local session if session in query, or loads the default session
   try {
-    if (self.sessionError) {
+    const { defaultSession } = rootModel.jbrowse
+    const { sessionError, sessionSnapshot, sessionSpec } = self
+    if (sessionError) {
       rootModel.setDefaultSession()
       rootModel.session.notify(
-        `Error loading session: ${self.sessionError}. If you
-                received this URL from another user, request that they send you
-                a session generated with the "Share" button instead of copying
-                and pasting their URL`,
+        `Error loading session: ${self.sessionError}. If you received this URL from another user, request that they send you a session generated with the "Share" button instead of copying and pasting their URL`,
       )
-    } else if (self.sessionSnapshot) {
-      rootModel.setSession(self.sessionSnapshot)
-    } else if (self.sessionSpec) {
+    } else if (sessionSnapshot) {
+      rootModel.setSession(sessionSnapshot)
+    } else if (sessionSpec) {
       // @ts-expect-error
-      afterInitializedCb = loadSessionSpec(self.sessionSpec, pluginManager)
-    } else if (rootModel.jbrowse.defaultSession?.views?.length) {
+      afterInitializedCallback = loadSessionSpec(sessionSpec, pluginManager)
+    } else if (defaultSession?.type === 'spec') {
+      afterInitializedCallback = loadSessionSpec(defaultSession, pluginManager)
+    } else if (defaultSession?.views?.length) {
       rootModel.setDefaultSession()
     }
   } catch (e) {
     rootModel.setDefaultSession()
     const str = `${e}`
-    const errorMessage = str
-      .replace('[mobx-state-tree] ', '')
-      .replace(/\(.+/, '')
+    const err = str.replace('[mobx-state-tree] ', '').replace(/\(.+/, '')
     rootModel.session?.notify(
       `Session could not be loaded. ${
-        errorMessage.length > 1000
-          ? `${errorMessage.slice(0, 1000)}...see more in console`
-          : errorMessage
+        err.length > 1000 ? `${err.slice(0, 1000)}...see more in console` : err
       }`,
     )
     console.error(e)
@@ -94,6 +89,6 @@ export function createPluginManager(self: SessionLoaderModel) {
 
   pluginManager.setRootModel(rootModel)
   pluginManager.configure()
-  afterInitializedCb()
+  afterInitializedCallback()
   return pluginManager
 }
diff --git a/products/jbrowse-web/src/rootModel/rootModel.ts b/products/jbrowse-web/src/rootModel/rootModel.ts
@@ -278,6 +278,7 @@ export default function RootModel({
 
         this.setSession(newSession)
       },
+
       /**
        * #action
        */

diff --git a/test_data/volvox/spec.json b/test_data/volvox/spec.json
@@ -0,0 +1,63 @@
+{
+  "assemblies": [
+    {
+      "name": "volvox",
+      "aliases": ["vvx"],
+      "sequence": {
+        "type": "ReferenceSequenceTrack",
+        "trackId": "volvox_refseq",
+        "adapter": {
+          "type": "TwoBitAdapter",
+          "twoBitLocation": {
+            "uri": "volvox.2bit",
+            "locationType": "UriLocation"
+          }
+        }
+      }
+    }
+  ],
+  "connections": [],
+  "defaultSession": {
+    "name": "Session",
+    "type": "spec",
+    "views": [
+      {
+        "type": "LinearGenomeView",
+        "tracks": ["volvox_cram_pileup"],
+        "loc": "ctgA:1-100",
+        "assembly": "volvox"
+      },
+      {
+        "type": "LinearGenomeView",
+        "tracks": ["volvox_cram_pileup"],
+        "loc": "ctgB:1-100",
+        "assembly": "volvox"
+      }
+    ]
+  },
+  "tracks": [
+    {
+      "type": "AlignmentsTrack",
+      "trackId": "volvox_cram_pileup",
+      "name": "volvox-sorted.cram",
+      "category": ["Integration test"],
+      "assemblyNames": ["volvox"],
+      "adapter": {
+        "type": "CramAdapter",
+        "cramLocation": {
+          "uri": "volvox-sorted-altname.cram"
+        },
+        "craiLocation": {
+          "uri": "volvox-sorted-altname.cram.crai"
+        },
+        "sequenceAdapter": {
+          "type": "TwoBitAdapter",
+          "twoBitLocation": {
+            "uri": "volvox.2bit"
+          }
+        },
+        "fetchSizeLimit": 1000
+      }
+    }
+  ]
+}