Misc

packages/core/configuration/util.ts

@@ -42,9 +42,8 @@ export function readConfObject<CONFMODEL extends AnyConfigurationModel>(
   args: Record<string, unknown> = {},
 ): any {
   if (!slotPath) {
-    return JSON.parse(JSON.stringify(getSnapshot(confObject)))
-  }
-  if (typeof slotPath === 'string') {
+    return structuredClone(getSnapshot(confObject))
+  } else if (typeof slotPath === 'string') {
     let slot = confObject[slotPath]
     // check for the subconf being a map if we don't find it immediately
     if (
@@ -66,15 +65,13 @@ export function readConfObject<CONFMODEL extends AnyConfigurationModel>(
       //     schemaType.name
       //   })`,
       // )
+    } else {
+      const val = slot.expr ? slot.expr.evalSync(args) : slot
+      return isStateTreeNode(val)
+        ? JSON.parse(JSON.stringify(getSnapshot(val)))
+        : val
     }
-
-    const val = slot.expr ? slot.expr.evalSync(args) : slot
-    return isStateTreeNode(val)
-      ? JSON.parse(JSON.stringify(getSnapshot(val)))
-      : val
-  }
-
-  if (Array.isArray(slotPath)) {
+  } else if (Array.isArray(slotPath)) {
     const slotName = slotPath[0]!
     if (slotPath.length > 1) {
       const newPath = slotPath.slice(1)
@@ -172,39 +169,35 @@ export function isBareConfigurationSchemaType(
 export function isConfigurationSchemaType(
   thing: unknown,
 ): thing is AnyConfigurationSchemaType {
-  if (!isType(thing)) {
-    return false
-  }
-
-  // written as a series of if-statements instead of a big logical OR
-  // because this construction gives much better debugging backtraces.
+  // written as a series of if-statements instead of a big logical because this
+  // construction gives much better debugging backtraces.
 
-  // also, note that the order of these statements matters, because
-  // for example some union types are also optional types
+  // also, note that the order of these statements matters, because for example
+  // some union types are also optional types
 
-  if (isBareConfigurationSchemaType(thing)) {
+  if (!isType(thing)) {
+    return false
+  } else if (isBareConfigurationSchemaType(thing)) {
     return true
-  }
-
-  if (isUnionType(thing)) {
+  } else if (isUnionType(thing)) {
     return getUnionSubTypes(thing).every(
       t => isConfigurationSchemaType(t) || t.name === 'undefined',
     )
-  }
-
-  if (isOptionalType(thing) && isConfigurationSchemaType(getSubType(thing))) {
+  } else if (
+    isOptionalType(thing) &&
+    isConfigurationSchemaType(getSubType(thing))
+  ) {
     return true
-  }
-
-  if (isArrayType(thing) && isConfigurationSchemaType(getSubType(thing))) {
+  } else if (
+    isArrayType(thing) &&
+    isConfigurationSchemaType(getSubType(thing))
+  ) {
     return true
-  }
-
-  if (isMapType(thing) && isConfigurationSchemaType(getSubType(thing))) {
+  } else if (isMapType(thing) && isConfigurationSchemaType(getSubType(thing))) {
     return true
+  } else {
+    return false
   }
-
-  return false
 }
 
 export function isConfigurationModel(

packages/core/package.json

@@ -31,6 +31,7 @@
   },
   "dependencies": {
     "@babel/runtime": "^7.17.9",
+    "@floating-ui/react": "^0.27.0",
     "@gmod/abortable-promise-cache": "^2.0.0",
     "@gmod/bgzf-filehandle": "^1.4.3",
     "@gmod/http-range-fetcher": "^3.0.4",

packages/core/pluggableElementTypes/RpcMethodTypeWithFiltersAndRenameRegions.ts

@@ -0,0 +1,40 @@
+import RpcMethodType from './RpcMethodType'
+import { renameRegionsIfNeeded } from '../util'
+import SerializableFilterChain from './renderers/util/serializableFilterChain'
+
+import type { RenderArgs } from '@jbrowse/core/rpc/coreRpcMethods'
+
+export default abstract class RpcMethodTypeWithFiltersAndRenameRegions extends RpcMethodType {
+  async deserializeArguments(args: any, rpcDriverClassName: string) {
+    const l = await super.deserializeArguments(args, rpcDriverClassName)
+    return {
+      ...l,
+      filters: args.filters
+        ? new SerializableFilterChain({
+            filters: args.filters,
+          })
+        : undefined,
+    }
+  }
+
+  async serializeArguments(
+    args: RenderArgs & {
+      stopToken?: string
+      statusCallback?: (arg: string) => void
+    },
+    rpcDriverClassName: string,
+  ) {
+    const pm = this.pluginManager
+    const assemblyManager = pm.rootModel?.session?.assemblyManager
+    if (!assemblyManager) {
+      throw new Error('no assembly manager')
+    }
+
+    const renamedArgs = await renameRegionsIfNeeded(assemblyManager, {
+      ...args,
+      filters: args.filters?.toJSON().filters,
+    })
+
+    return super.serializeArguments(renamedArgs, rpcDriverClassName)
+  }
+}

packages/core/ui/LoadingEllipses.tsx

@@ -40,9 +40,13 @@ export default function LoadingEllipses({
   variant = 'body2',
   ...rest
 }: Props) {
-  const { classes } = useStyles()
+  const { cx, classes } = useStyles()
   return (
-    <Typography className={classes.dots} {...rest} variant={variant}>
+    <Typography
+      className={cx(classes.dots, rest.className)}
+      {...rest}
+      variant={variant}
+    >
       {message || 'Loading'}
     </Typography>
   )

plugins/breakpoint-split-view/src/BreakpointAlignmentsFeatureDetail/BreakpointAlignmentsFeatureDetail.tsx

@@ -6,7 +6,8 @@ import {
 } from '@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail'
 import { Paper } from '@mui/material'
 import { observer } from 'mobx-react'
-import { SimpleFeatureSerialized } from '@jbrowse/core/util'
+
+import type { SimpleFeatureSerialized } from '@jbrowse/core/util'
 
 const BreakpointAlignmentsFeatureDetail = observer(function ({
   model,

plugins/dotplot-view/package.json

@@ -36,7 +36,6 @@
     "clean": "rimraf dist esm *.tsbuildinfo"
   },
   "dependencies": {
-    "@floating-ui/react": "^0.26.3",
     "@mui/icons-material": "^6.0.0",
     "@mui/x-data-grid": "^7.0.0",
     "@types/file-saver": "^2.0.1",

plugins/dotplot-view/src/ComparativeRenderer/index.ts

@@ -19,11 +19,6 @@ interface RenderArgsSerialized extends ComparativeRenderArgsSerialized {
   rendererType: string
 }
 
-/**
- * call a synteny renderer with the given args
- * param views: a set of views that each contain a set of regions
- * used instead of passing regions directly as in render()
- */
 export default class ComparativeRender extends RpcMethodType {
   name = 'ComparativeRender'
 

plugins/linear-comparative-view/package.json

@@ -36,7 +36,6 @@
     "clean": "rimraf dist esm *.tsbuildinfo"
   },
   "dependencies": {
-    "@floating-ui/react": "^0.26.3",
     "@mui/icons-material": "^6.0.0",
     "copy-to-clipboard": "^3.3.1",
     "file-saver": "^2.0.0"

plugins/linear-comparative-view/src/LGVSyntenyDisplay/configSchemaF.ts

@@ -2,20 +2,26 @@ import { ConfigurationSchema } from '@jbrowse/core/configuration'
 import { linearPileupDisplayConfigSchemaFactory } from '@jbrowse/plugin-alignments'
 
 import type PluginManager from '@jbrowse/core/PluginManager'
+import type { Feature } from '@jbrowse/core/util'
 
 /**
  * #config LGVSyntenyDisplay
  * extends config
  * - [LinearPileupDisplay](../linearpileupdisplay)
  */
 function configSchemaF(pluginManager: PluginManager) {
+  pluginManager.jexl.addFunction('lgvSyntenyTooltip', (f: Feature) => {
+    const m = f.get('mate')
+    return [f.get('name') || f.get('id'), m?.name || m?.id]
+      .filter(f => !!f)
+      .join('<br/>')
+  })
   return ConfigurationSchema(
     'LGVSyntenyDisplay',
     {
       mouseover: {
         type: 'string',
-        defaultValue:
-          'jexl:(get(feature,"name")||"")+ "<br/>" + (get(feature,"mate").name||"")',
+        defaultValue: 'jexl:lgvSyntenyTooltip(feature)',
       },
     },
     {

plugins/linear-genome-view/package.json

@@ -38,7 +38,6 @@
     "useSrc": "node ../../scripts/useSrc.js"
   },
   "dependencies": {
-    "@floating-ui/react": "^0.26.3",
     "@mui/icons-material": "^6.0.0",
     "@types/file-saver": "^2.0.1",
     "copy-to-clipboard": "^3.3.1",

plugins/linear-genome-view/src/BaseLinearDisplay/components/BlockError.tsx

@@ -0,0 +1,47 @@
+import React from 'react'
+
+import ErrorMessageStackTraceDialog from '@jbrowse/core/ui/ErrorMessageStackTraceDialog'
+import { getSession } from '@jbrowse/core/util'
+import RefreshIcon from '@mui/icons-material/Refresh'
+import ReportIcon from '@mui/icons-material/Report'
+import { IconButton, Tooltip } from '@mui/material'
+import { observer } from 'mobx-react'
+
+import BlockMsg from './BlockMsg'
+
+const BlockError = observer(function ({ model }: { model: any }) {
+  return (
+    <BlockMsg
+      message={`${model.error}`}
+      severity="error"
+      action={
+        <>
+          <Tooltip title="Reload track">
+            <IconButton
+              data-testid="reload_button"
+              onClick={() => {
+                model.reload()
+              }}
+            >
+              <RefreshIcon />
+            </IconButton>
+          </Tooltip>
+          <Tooltip title="Show stack trace">
+            <IconButton
+              onClick={() => {
+                getSession(model).queueDialog(onClose => [
+                  ErrorMessageStackTraceDialog,
+                  { onClose, error: model.error as Error },
+                ])
+              }}
+            >
+              <ReportIcon />
+            </IconButton>
+          </Tooltip>
+        </>
+      }
+    />
+  )
+})
+
+export default BlockError

plugins/linear-genome-view/src/BaseLinearDisplay/components/BlockMsg.tsx

@@ -24,6 +24,9 @@ export default function BlockMsg({
   const { classes } = useStyles()
   return (
     <Alert
+      onClick={event => {
+        event.stopPropagation()
+      }}
       severity={severity}
       action={action}
       classes={{ message: classes.ellipses }}

plugins/linear-genome-view/src/BaseLinearDisplay/components/ServerSideRenderedBlockContent.tsx

@@ -1,19 +1,14 @@
-import React, { lazy } from 'react'
+import React, { Suspense, lazy } from 'react'
 
 import { LoadingEllipses } from '@jbrowse/core/ui'
-import { getSession } from '@jbrowse/core/util'
-import RefreshIcon from '@mui/icons-material/Refresh'
-import ReportIcon from '@mui/icons-material/Report'
-import { IconButton, Tooltip } from '@mui/material'
 import { observer } from 'mobx-react'
 import { getParent } from 'mobx-state-tree'
 import { makeStyles } from 'tss-react/mui'
 
 import BlockMsg from './BlockMsg'
 
-const ErrorMessageStackTraceDialog = lazy(
-  () => import('@jbrowse/core/ui/ErrorMessageStackTraceDialog'),
-)
+// lazies
+const BlockError = lazy(() => import('./BlockError'))
 
 const useStyles = makeStyles()(theme => {
   const bg = theme.palette.action.disabledBackground
@@ -53,39 +48,13 @@ const ServerSideRenderedBlockContent = observer(function ({
 }) {
   if (model.error) {
     return (
-      <BlockMsg
-        message={`${model.error}`}
-        severity="error"
-        action={
-          <>
-            <Tooltip title="Reload track">
-              <IconButton
-                data-testid="reload_button"
-                onClick={() => {
-                  model.reload()
-                }}
-              >
-                <RefreshIcon />
-              </IconButton>
-            </Tooltip>
-            <Tooltip title="Show stack trace">
-              <IconButton
-                onClick={() => {
-                  getSession(model).queueDialog(onClose => [
-                    ErrorMessageStackTraceDialog,
-                    { onClose, error: model.error as Error },
-                  ])
-                }}
-              >
-                <ReportIcon />
-              </IconButton>
-            </Tooltip>
-          </>
-        }
-      />
+      <Suspense fallback={null}>
+        <BlockError model={model} />
+      </Suspense>
     )
   } else if (model.message) {
-    // the message can be a fully rendered react component, e.g. the region too large message
+    // the message can be a fully rendered react component, e.g. the region too
+    // large message
     return React.isValidElement(model.message) ? (
       model.message
     ) : (

plugins/linear-genome-view/src/BaseLinearDisplay/models/autorunFeatureDensityStats.ts

@@ -1,4 +1,4 @@
-import { getContainingView } from '@jbrowse/core/util'
+import { getContainingView, isAbortException } from '@jbrowse/core/util'
 import { isAlive } from 'mobx-state-tree'
 
 import type { BaseLinearDisplayModel } from './BaseLinearDisplayModel'
@@ -40,7 +40,7 @@ export default async function autorunFeatureDensityStats(
     }
   } catch (e) {
     console.error(e)
-    if (isAlive(self)) {
+    if (isAlive(self) && !isAbortException(e)) {
       self.setError(e)
     }
   }