[skip ci] 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/rpc/BaseRpcDriver.ts

@@ -158,7 +158,6 @@ export default abstract class BaseRpcDriver {
     if (!sessionId) {
       throw new TypeError('sessionId is required')
     }
-    let done = false
     const unextendedWorker = await this.getWorker(sessionId)
     const worker = pluginManager.evaluateExtensionPoint(
       'Core-extendWorker',
@@ -172,41 +171,13 @@ export default abstract class BaseRpcDriver {
     const filteredAndSerializedArgs = this.filterArgs(serializedArgs, sessionId)
 
     // now actually call the worker
-    const callP = worker
-      .call(functionName, filteredAndSerializedArgs, {
-        timeout: 5 * 60 * 1000, // 5 minutes
-        statusCallback: args.statusCallback,
-        rpcDriverClassName: this.name,
-        ...options,
-      })
-      .finally(() => {
-        done = true
-      })
-
-    // check every 5 seconds to see if the worker has been killed, and reject
-    // the killedP promise if it has
-    let killedCheckInterval: ReturnType<typeof setInterval>
-    const killedP = new Promise((resolve, reject) => {
-      killedCheckInterval = setInterval(() => {
-        // must've been killed
-        if (worker.status === 'killed') {
-          reject(
-            new Error(
-              `operation timed out, worker process stopped responding, ${worker.error}`,
-            ),
-          )
-        } else if (done) {
-          resolve(true)
-        }
-      }, this.workerCheckFrequency)
-    }).finally(() => {
-      clearInterval(killedCheckInterval)
+    const call = await worker.call(functionName, filteredAndSerializedArgs, {
+      timeout: 5 * 60 * 1000, // 5 minutes
+      statusCallback: args.statusCallback,
+      rpcDriverClassName: this.name,
+      ...options,
     })
 
-    // the result is a race between the actual result promise, and the "killed"
-    // promise. the killed promise will only actually win if the worker was
-    // killed before the call could return
-    const resultP = Promise.race([callP, killedP])
-    return rpcMethod.deserializeReturn(resultP, args, this.name)
+    return rpcMethod.deserializeReturn(call, args, this.name)
   }
 }

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 }}