Updates

GMOD · Apr 6, 2023 · c2e0c95 · c2e0c95
1 parent a6f5f5c
commit c2e0c95
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Showing 14 changed files with 19,732 additions and 230 deletions.
diff --git a/packages/core/rpc/coreRpcMethods.ts b/packages/core/rpc/coreRpcMethods.ts
@@ -5,5 +5,5 @@ export { default as CoreGetFileInfo } from './methods/CoreGetFileInfo'
 export { default as CoreGetFeatures } from './methods/CoreGetFeatures'
 export { default as CoreRender } from './methods/CoreRender'
 export { default as CoreFreeResources } from './methods/CoreFreeResources'
+export { default as CoreGetFeatureDensityStats } from './methods/CoreGetFeatureDensityStats'
 export { type RenderArgs } from './methods/util'
-export { default as CoreEstimateRegionStats } from './methods/CoreEstimateRegionStats'
diff --git a/...re/rpc/methods/CoreEstimateRegionStats.ts → ...rpc/methods/CoreGetFeatureDensityStats.ts b/...re/rpc/methods/CoreEstimateRegionStats.ts → ...rpc/methods/CoreGetFeatureDensityStats.ts
@@ -6,8 +6,8 @@ import { RemoteAbortSignal } from '../remoteAbortSignals'
 import { isFeatureAdapter } from '../../data_adapters/BaseAdapter'
 import { renameRegionsIfNeeded, Region } from '../../util'
 
-export default class CoreEstimateRegionStats extends RpcMethodType {
-  name = 'CoreEstimateRegionStats'
+export default class CoreGetFeatureDensityStats extends RpcMethodType {
+  name = 'CoreGetFeatureDensityStats'
 
   async serializeArguments(
     args: RenderArgs & {

diff --git a/plugins/linear-genome-view/src/BaseLinearDisplay/models/BaseLinearDisplayModel.tsx b/plugins/linear-genome-view/src/BaseLinearDisplay/models/BaseLinearDisplayModel.tsx
@@ -318,7 +318,7 @@ function stateModelFactory() {
       /**
        * #action
        */
-      clearRegionsStats() {
+      clearFeatureDensityStats() {
         self.featureDensityStatsP = undefined
         self.featureDensityStats = undefined
       },
@@ -534,7 +534,7 @@ function stateModelFactory() {
                 return
               }
 
-              self.clearRegionsStats()
+              self.clearFeatureDensityStats()
               self.setCurrBpPerPx(view.bpPerPx)
               const featureDensityStats = await self.getFeatureDensityStats()
               if (isAlive(self)) {

diff --git a/plugins/linear-genome-view/src/BaseLinearDisplay/models/util.ts b/plugins/linear-genome-view/src/BaseLinearDisplay/models/util.ts
@@ -54,7 +54,7 @@ export async function getFeatureDensityStatsPre(
   }
   const sessionId = getRpcSessionId(self)
 
-  return rpcManager.call(sessionId, 'CoreEstimateRegionStats', {
+  return rpcManager.call(sessionId, 'CoreGetFeatureDensityStats', {
     sessionId,
     regions,
     adapterConfig,

diff --git a/plugins/wiggle/src/LinearWiggleDisplay/models/model.tsx b/plugins/wiggle/src/LinearWiggleDisplay/models/model.tsx
@@ -17,15 +17,14 @@ import {
   LinearGenomeViewModel,
 } from '@jbrowse/plugin-linear-genome-view'
 import { when } from 'mobx'
-import { isAlive, types, Instance } from 'mobx-state-tree'
+import { types, Instance } from 'mobx-state-tree'
 import PluginManager from '@jbrowse/core/PluginManager'
 
 import { axisPropsFromTickScale } from 'react-d3-axis-mod'
 import {
   getNiceDomain,
   getScale,
-  getStats,
-  statsAutorun,
+  quantitativeStatsAutorun,
   YSCALEBAR_LABEL_OFFSET,
 } from '../../util'
 
@@ -677,23 +676,11 @@ function stateModelFactory(
          */
         async reload() {
           self.setError()
-          const aborter = new AbortController()
-          self.setLoading(aborter)
-          try {
-            const stats = await getStats(self, {
-              signal: aborter.signal,
-              ...self.renderProps(),
-            })
-            if (isAlive(self)) {
-              self.updateQuantitativeStats(stats)
-              superReload()
-            }
-          } catch (e) {
-            self.setError(e)
-          }
+          superReload()
         },
+
         afterAttach() {
-          statsAutorun(self)
+          quantitativeStatsAutorun(self)
         },
         /**
          * #action

diff --git a/plugins/wiggle/src/MultiLinearWiggleDisplay/models/model.tsx b/plugins/wiggle/src/MultiLinearWiggleDisplay/models/model.tsx
@@ -30,8 +30,7 @@ import {
 import {
   getNiceDomain,
   getScale,
-  getStats,
-  statsAutorun,
+  quantitativeStatsAutorun,
   YSCALEBAR_LABEL_OFFSET,
 } from '../../util'
 
@@ -662,27 +661,12 @@ const stateModelFactory = (
       type ExportSvgOpts = Parameters<typeof superRenderSvg>[0]
 
       return {
-        // re-runs stats and refresh whole display on reload
         async reload() {
           self.setError()
-          const aborter = new AbortController()
-          let stats
-          try {
-            self.setLoading(aborter)
-            stats = await getStats(self, {
-              signal: aborter.signal,
-              ...self.renderProps(),
-            })
-            if (isAlive(self)) {
-              self.updateQuantitativeStats(stats)
-              superReload()
-            }
-          } catch (e) {
-            self.setError(e)
-          }
+          superReload()
         },
         afterAttach() {
-          statsAutorun(self)
+          quantitativeStatsAutorun(self)
           addDisposer(
             self,
             autorun(async () => {

diff --git a/plugins/wiggle/src/WiggleRPC/MultiWiggleGetSources.ts b/plugins/wiggle/src/WiggleRPC/MultiWiggleGetSources.ts
@@ -0,0 +1,68 @@
+import RpcMethodType from '@jbrowse/core/pluggableElementTypes/RpcMethodType'
+import SerializableFilterChain from '@jbrowse/core/pluggableElementTypes/renderers/util/serializableFilterChain'
+import { getAdapter } from '@jbrowse/core/data_adapters/dataAdapterCache'
+import { RenderArgs } from '@jbrowse/core/rpc/coreRpcMethods'
+import { renameRegionsIfNeeded, Region } from '@jbrowse/core/util'
+import { RemoteAbortSignal } from '@jbrowse/core/rpc/remoteAbortSignals'
+import { AnyConfigurationModel } from '@jbrowse/core/configuration'
+
+export class MultiWiggleGetSources extends RpcMethodType {
+  name = 'MultiWiggleGetSources'
+
+  // eslint-disable-next-line @typescript-eslint/no-explicit-any
+  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 & {
+      signal?: AbortSignal
+      statusCallback?: (arg: string) => void
+    },
+    rpcDriverClassName: string,
+  ) {
+    const pm = this.pluginManager
+    const assemblyManager = pm.rootModel?.session?.assemblyManager
+    if (!assemblyManager) {
+      return args
+    }
+
+    const renamedArgs = await renameRegionsIfNeeded(assemblyManager, {
+      ...args,
+      filters: args.filters?.toJSON().filters,
+    })
+
+    return super.serializeArguments(renamedArgs, rpcDriverClassName)
+  }
+
+  async execute(
+    args: {
+      adapterConfig: AnyConfigurationModel
+      signal?: RemoteAbortSignal
+      sessionId: string
+      headers?: Record<string, string>
+      regions: Region[]
+      bpPerPx: number
+    },
+    rpcDriverClassName: string,
+  ) {
+    const pm = this.pluginManager
+    const deserializedArgs = await this.deserializeArguments(
+      args,
+      rpcDriverClassName,
+    )
+    const { regions, adapterConfig, sessionId } = deserializedArgs
+    const { dataAdapter } = await getAdapter(pm, sessionId, adapterConfig)
+
+    // @ts-expect-error
+    return dataAdapter.getSources(regions, deserializedArgs)
+  }
+}
diff --git a/plugins/wiggle/src/WiggleRPC/WiggleGetGlobalQuantitativeStats.ts b/plugins/wiggle/src/WiggleRPC/WiggleGetGlobalQuantitativeStats.ts
@@ -0,0 +1,44 @@
+import RpcMethodType from '@jbrowse/core/pluggableElementTypes/RpcMethodType'
+import SerializableFilterChain from '@jbrowse/core/pluggableElementTypes/renderers/util/serializableFilterChain'
+import { getAdapter } from '@jbrowse/core/data_adapters/dataAdapterCache'
+import { RemoteAbortSignal } from '@jbrowse/core/rpc/remoteAbortSignals'
+import { QuantitativeStats } from '@jbrowse/core/util/stats'
+import { AnyConfigurationModel } from '@jbrowse/core/configuration'
+
+export class WiggleGetGlobalQuantitativeStats extends RpcMethodType {
+  name = 'WiggleGetGlobalQuantitativeStats'
+
+  // eslint-disable-next-line @typescript-eslint/no-explicit-any
+  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 execute(
+    args: {
+      adapterConfig: AnyConfigurationModel
+      signal?: RemoteAbortSignal
+      headers?: Record<string, string>
+      sessionId: string
+    },
+    rpcDriverClassName: string,
+  ): Promise<QuantitativeStats> {
+    const pm = this.pluginManager
+    const deserializedArgs = await this.deserializeArguments(
+      args,
+      rpcDriverClassName,
+    )
+    const { adapterConfig, sessionId } = deserializedArgs
+    const { dataAdapter } = await getAdapter(pm, sessionId, adapterConfig)
+
+    // @ts-expect-error
+    return dataAdapter.getGlobalStats(deserializedArgs)
+  }
+}
diff --git a/plugins/wiggle/src/WiggleRPC/WiggleGetMultiRegionQuantitativeStats.ts b/plugins/wiggle/src/WiggleRPC/WiggleGetMultiRegionQuantitativeStats.ts
@@ -0,0 +1,73 @@
+import RpcMethodType from '@jbrowse/core/pluggableElementTypes/RpcMethodType'
+import SerializableFilterChain from '@jbrowse/core/pluggableElementTypes/renderers/util/serializableFilterChain'
+import { RenderArgs } from '@jbrowse/core/rpc/coreRpcMethods'
+import { getAdapter } from '@jbrowse/core/data_adapters/dataAdapterCache'
+import { RemoteAbortSignal } from '@jbrowse/core/rpc/remoteAbortSignals'
+import { Region, renameRegionsIfNeeded } from '@jbrowse/core/util'
+import { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter'
+
+export class WiggleGetMultiRegionQuantitativeStats extends RpcMethodType {
+  name = 'WiggleGetMultiRegionQuantitativeStats'
+
+  // eslint-disable-next-line @typescript-eslint/no-explicit-any
+  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 & {
+      signal?: AbortSignal
+      statusCallback?: (arg: string) => void
+    },
+    rpcDriverClassName: string,
+  ) {
+    const pm = this.pluginManager
+    const assemblyManager = pm.rootModel?.session?.assemblyManager
+    if (!assemblyManager) {
+      return args
+    }
+
+    const renamedArgs = await renameRegionsIfNeeded(assemblyManager, {
+      ...args,
+      filters: args.filters?.toJSON().filters,
+    })
+
+    return super.serializeArguments(renamedArgs, rpcDriverClassName)
+  }
+
+  async execute(
+    args: {
+      adapterConfig: {}
+      signal?: RemoteAbortSignal
+      sessionId: string
+      headers?: Record<string, string>
+      regions: Region[]
+      bpPerPx: number
+    },
+    rpcDriverClassName: string,
+  ) {
+    const pm = this.pluginManager
+    const deserializedArgs = await this.deserializeArguments(
+      args,
+      rpcDriverClassName,
+    )
+    const { regions, adapterConfig, sessionId } = deserializedArgs
+    const { dataAdapter } = await getAdapter(pm, sessionId, adapterConfig)
+
+    if (dataAdapter instanceof BaseFeatureDataAdapter) {
+      return dataAdapter.getMultiRegionQuantitativeStats(
+        regions,
+        deserializedArgs,
+      )
+    }
+    throw new Error('Data adapter not found')
+  }
+}