Merge remote-tracking branch 'origin/master' into remove_toggle_track…

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GMOD · Nov 25, 2020 · 39e1db4 · 39e1db4
2 parents 981ca94 + 34eddf1
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diff --git a/.github/workflows/pull_request.yml b/.github/workflows/pull_request.yml
@@ -1,6 +1,6 @@
 name: Pull Request
 
-on: [pull_request]
+on: pull_request
 
 jobs:
   lint:

diff --git a/.github/workflows/push.yml b/.github/workflows/push.yml
@@ -0,0 +1,53 @@
+name: Push
+
+on: push
+
+jobs:
+  test:
+    name: Test and typecheck on node 10.x and ubuntu-latest
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v2
+      - name: Use Node.js 10.x
+        uses: actions/setup-node@v1
+        with:
+          node-version: 10.x
+      - name: Install deps and build (with cache)
+        uses: bahmutov/npm-install@v1
+      - name: Test codebase
+        run: yarn test-ci
+      - name: Upload coverage
+        run: bash <(curl -s https://codecov.io/bash)
+      - name: Typecheck codebase
+        run: yarn typecheck
+
+  build:
+    name: Build on node 10.x and ubuntu-latest
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v2
+      - name: Use Node.js 10.x
+        uses: actions/setup-node@v1
+        with:
+          node-version: 10.x
+      - name: Install deps and build (with cache)
+        uses: bahmutov/npm-install@v1
+      - name: Build codebase
+        run: yarn build
+      - name: Test build
+        run: BUILT_TESTS=1 yarn built-test-ci
+      - name: Build website
+        run: |
+          cd website/
+          yarn
+          yarn build
+      - name: Configure AWS credentials
+        uses: aws-actions/configure-aws-credentials@v1
+        with:
+          aws-access-key-id: ${{ secrets.AWS_ACCESS_KEY_ID }}
+          aws-secret-access-key: ${{ secrets.AWS_SECRET_ACCESS_KEY }}
+          aws-region: us-east-1
+      - name: Copy branch build to S3
+        run: |
+          cp products/jbrowse-web/build/test_data/config.json products/jbrowse-web/build/config.json
+          aws s3 sync --delete products/jbrowse-web/build s3://jbrowse.org/code/jb2/$(echo ${{github.ref}} | cut -d "/" -f3-)
diff --git a/.travis.yml b/.travis.yml
diff --git a/README.md b/README.md
@@ -1,4 +1,4 @@
-[![Build Status](https://img.shields.io/travis/com/GMOD/jbrowse-components/master.svg?logo=travis&style=for-the-badge)](https://travis-ci.com/GMOD/jbrowse-components)
+[![Build Status](https://img.shields.io/github/workflow/status/GMOD/jbrowse-components/Push/master?logo=github&style=for-the-badge)](https://github.com/GMOD/jbrowse-components/actions?query=branch%3Amaster+workflow%3APush+)
 [![Coverage Status](https://img.shields.io/codecov/c/github/GMOD/jbrowse-components/master.svg?logo=codecov&style=for-the-badge)](https://codecov.io/gh/GMOD/jbrowse-components/branch/master)
 [![Contributor Covenant](https://img.shields.io/badge/Contributor%20Covenant-v1.4%20adopted-ff69b4.svg?style=for-the-badge&logo=data:image/svg+xml;base64,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)](CODE_OF_CONDUCT.md)
 

diff --git a/lerna.json b/lerna.json
@@ -1,6 +1,5 @@
 {
-  "version": "independent",
+  "version": "1.0.1",
   "npmClient": "yarn",
-  "useWorkspaces": true,
-  "independent": true
+  "useWorkspaces": true
 }
diff --git a/package.json b/package.json
@@ -1,13 +1,15 @@
 {
   "name": "root",
   "private": true,
+  "repository": "https://github.com/GMOD/jbrowse-components",
   "workspaces": [
     "packages/*",
     "products/*",
     "plugins/*"
   ],
   "scripts": {
     "build": "yarn useDist && node scripts/build.js && yarn useSrc",
+    "changelog": "lerna-changelog",
     "useDist": "lerna run useDist --scope \"@jbrowse/plugin*\"",
     "useSrc": "lerna run useSrc --scope \"@jbrowse/plugin*\"",
     "lerna-publish": "lerna publish --no-push",
@@ -37,6 +39,12 @@
     "@oclif/dev-cli": "^1",
     "@oclif/test": "^1.2.7",
     "@rescripts/cli": "^0.0.14",
+    "@storybook/addon-actions": "^6.0.28",
+    "@storybook/addon-docs": "^6.0.28",
+    "@storybook/addon-links": "^6.0.28",
+    "@storybook/addons": "^6.0.28",
+    "@storybook/preset-create-react-app": "^3.1.5",
+    "@storybook/react": "^6.0.28",
     "@testing-library/jest-dom": "^5.5.0",
     "@testing-library/react": "^9.0.0",
     "@types/base64-js": "^1.2.5",
@@ -75,6 +83,7 @@
     "@types/string-template": "^1.0.2",
     "@types/unzipper": "^0.10.3",
     "babel-loader": "^8.1.0",
+    "babel-plugin-inline-import-data-uri": "^1.0.1",
     "babel-preset-mobx": "^2.0.0",
     "babel-preset-react-app": "9.1.2",
     "babel-preset-typescript": "^7.0.0-alpha.19",
@@ -104,6 +113,7 @@
     "jest-localstorage-mock": "^2.4.3",
     "jest-pnp-resolver": "^1.2.0",
     "lerna": "^3.4.1",
+    "lerna-changelog": "^1.0.1",
     "mobx": "^5.0.0",
     "mobx-react": "^6.0.0",
     "mobx-state-tree": "3.14.1",
@@ -117,12 +127,15 @@
     "prop-types": "^15.0.0",
     "range-parser": "^1.2.1",
     "react": "^16.8.0",
+    "react-docgen-typescript-loader": "^3.7.2",
     "react-dom": "^16.8.0",
+    "react-is": "^16.13.1",
     "react-scripts": "^3.3.0",
     "requestidlecallback-polyfill": "^1.0.2",
     "rimraf": "^3.0.2",
     "rxjs": "^6.0.0",
     "standard-changelog": "^2.0.7",
+    "ts-loader": "^7.0.5",
     "ts-node": "^8",
     "tsdx": "^0.14.0",
     "tslib": "^2.0.1",

diff --git a/packages/core/BaseFeatureWidget/BaseFeatureDetail.tsx b/packages/core/BaseFeatureWidget/BaseFeatureDetail.tsx
@@ -61,7 +61,7 @@ const coreRenderedDetails = [
 ]
 
 interface BaseCardProps {
-  title: string
+  title?: string
 }
 
 export const BaseCard: FunctionComponent<BaseCardProps> = props => {
@@ -107,7 +107,7 @@ export const BaseCoreDetails = (props: BaseProps) => {
       {coreRenderedDetails.map(key => {
         const value = displayedDetails[key.toLowerCase()]
         const strValue = String(value)
-        return value ? (
+        return value !== null && value !== undefined ? (
           <div className={classes.field} key={key}>
             <div className={classes.fieldName}>{key}</div>
             <div className={classes.fieldValue}>
@@ -156,7 +156,7 @@ export const Attributes: FunctionComponent<AttributeProps> = props => {
 
   const SimpleValue = ({ name, value }: { name: string; value: any }) => {
     const description = descriptions && descriptions[name]
-    return (
+    return value ? (
       <div style={{ display: 'flex' }}>
         {description ? (
           <Tooltip title={description} placement="left">
@@ -167,7 +167,7 @@ export const Attributes: FunctionComponent<AttributeProps> = props => {
         )}
         <div className={classes.fieldValue}>{formatter(value)}</div>
       </div>
-    )
+    ) : null
   }
   const ArrayValue = ({ name, value }: { name: string; value: any[] }) => {
     const description = descriptions && descriptions[name]

diff --git a/packages/core/CHANGELOG.md b/packages/core/CHANGELOG.md
@@ -1,3 +1,13 @@
+## [1.0.1](https://github.com/GMOD/jbrowse-components/compare/v0.0.1-beta.11...v1.0.1) (2020-11-25)
+
+### Reverts
+
+- Revert "make rootModel setSession check and attempt to remove undefined MST references" ([c2c06d6](https://github.com/GMOD/jbrowse-components/commit/c2c06d6e18c60a09a4cdda15f53de1c3da7bc520))
+- Revert "Bump @docusaurus alpha version" ([32b604a](https://github.com/GMOD/jbrowse-components/commit/32b604a1ef829f2d2e17fa3822184577ea951e69))
+- Revert "Remove checkLocation from CLI base class" ([d399135](https://github.com/GMOD/jbrowse-components/commit/d399135e364d3553130c919bdfccbf17e14d6a9b))
+- Revert "Allow touchscreen using pointer events (#1112)" the pointer ([404546e](https://github.com/GMOD/jbrowse-components/commit/404546e5a1c71510a90a777957d32cd2c8f71ed1)), closes [#1112](https://github.com/GMOD/jbrowse-components/issues/1112)
+- Revert "Simplify command unzip (#1075)" ([9c0b975](https://github.com/GMOD/jbrowse-components/commit/9c0b97504b7a423a9c356ac3ffffc2754224c65a)), closes [#1075](https://github.com/GMOD/jbrowse-components/issues/1075)
+
 # [1.0.0](https://github.com/GMOD/jbrowse-components/compare/v0.0.1-beta.11...v1.0.0) (2020-11-06)
 
 ### Reverts

diff --git a/packages/core/assemblyManager/assembly.ts b/packages/core/assemblyManager/assembly.ts
@@ -2,6 +2,11 @@ import jsonStableStringify from 'json-stable-stringify'
 import { cast, getParent, IAnyType, types, Instance } from 'mobx-state-tree'
 import AbortablePromiseCache from 'abortable-promise-cache'
 import { readConfObject } from '../configuration'
+import {
+  BaseRefNameAliasAdapter,
+  RegionsAdapter,
+} from '../data_adapters/BaseAdapter'
+import PluginManager from '../PluginManager'
 import { Region } from '../util/types'
 import { Region as MSTRegion } from '../util/types/mst'
 import { makeAbortableReaction, when } from '../util'
@@ -62,7 +67,6 @@ async function loadRefNameMap(
     },
     { timeout: 1000000 },
   )
-
   const refNameMap: Record<string, string> = {}
   const { refNameAliases } = assembly
   if (!refNameAliases) {
@@ -117,7 +121,10 @@ interface CacheData {
   sessionId: string
   options: BaseOptions
 }
-export default function assemblyFactory(assemblyConfigType: IAnyType) {
+export default function assemblyFactory(
+  assemblyConfigType: IAnyType,
+  pluginManager: PluginManager,
+) {
   const adapterLoads = new AbortablePromiseCache({
     cache: new QuickLRU({ maxSize: 1000 }),
     async fill(
@@ -226,7 +233,7 @@ export default function assemblyFactory(assemblyConfigType: IAnyType) {
           // eslint-disable-next-line @typescript-eslint/no-explicit-any
           self as any,
           // @ts-ignore
-          loadAssemblyData,
+          makeLoadAssemblyData(pluginManager),
           loadAssemblyReaction,
           { name: `${self.name} assembly loading`, fireImmediately: true },
           this.setLoading,
@@ -277,29 +284,28 @@ export default function assemblyFactory(assemblyConfigType: IAnyType) {
       },
     }))
 }
-function loadAssemblyData(self: Assembly) {
-  if (self.configuration) {
-    const sequenceAdapterConfig = readConfObject(self.configuration, [
-      'sequence',
-      'adapter',
-    ])
-    const adapterConfigId = getAdapterId(sequenceAdapterConfig)
-    const { rpcManager } = getParent(self, 2)
-    const refNameAliasesAdapterConfig =
-      self.configuration.refNameAliases &&
-      readConfObject(self.configuration, ['refNameAliases', 'adapter'])
-    return {
-      sequenceAdapterConfig,
-      adapterConfigId,
-      rpcManager,
-      assemblyName: self.name,
-      refNameAliasesAdapterConfig,
+function makeLoadAssemblyData(pluginManager: PluginManager) {
+  return (self: Assembly) => {
+    if (self.configuration) {
+      const sequenceAdapterConfig = readConfObject(self.configuration, [
+        'sequence',
+        'adapter',
+      ])
+      const refNameAliasesAdapterConfig =
+        self.configuration.refNameAliases &&
+        readConfObject(self.configuration, ['refNameAliases', 'adapter'])
+      return {
+        sequenceAdapterConfig,
+        assemblyName: self.name,
+        refNameAliasesAdapterConfig,
+        pluginManager,
+      }
     }
+    return undefined
   }
-  return undefined
 }
 async function loadAssemblyReaction(
-  props: ReturnType<typeof loadAssemblyData> | undefined,
+  props: ReturnType<ReturnType<typeof makeLoadAssemblyData>> | undefined,
   signal: AbortSignal,
 ) {
   if (!props) {
@@ -308,36 +314,35 @@ async function loadAssemblyReaction(
 
   const {
     sequenceAdapterConfig,
-    rpcManager,
     assemblyName,
     refNameAliasesAdapterConfig,
+    pluginManager,
   } = props
 
-  const sessionId = `assembly-${assemblyName}`
-  const adapterRegions = (await rpcManager.call(
-    sessionId,
-    'CoreGetRegions',
-    { sessionId, adapterConfig: sequenceAdapterConfig, signal },
-    { timeout: 1000000 },
-  )) as Region[]
+  const dataAdapterType = pluginManager.getAdapterType(
+    sequenceAdapterConfig.type,
+  )
+  const adapter = new dataAdapterType.AdapterClass(
+    sequenceAdapterConfig,
+  ) as RegionsAdapter
+  const adapterRegions = (await adapter.getRegions({ signal })) as Region[]
+
   const adapterRegionsWithAssembly = adapterRegions.map(adapterRegion => {
     const { refName } = adapterRegion
     checkRefName(refName)
     return { ...adapterRegion, assemblyName }
   })
   const refNameAliases: RefNameAliases = {}
   if (refNameAliasesAdapterConfig) {
-    const refNameAliasesAborter = new AbortController()
-    const refNameAliasesList = (await rpcManager.call(
-      sessionId,
-      'CoreGetRefNameAliases',
-      {
-        sessionId,
-        adapterConfig: refNameAliasesAdapterConfig,
-        signal: refNameAliasesAborter.signal,
-      },
-      { timeout: 1000000 },
-    )) as {
+    const refAliasAdapterType = pluginManager.getAdapterType(
+      refNameAliasesAdapterConfig.type,
+    )
+    const refNameAliasAdapter = new refAliasAdapterType.AdapterClass(
+      refNameAliasesAdapterConfig,
+    ) as BaseRefNameAliasAdapter
+    const refNameAliasesList = (await refNameAliasAdapter.getRefNameAliases({
+      signal,
+    })) as {
       refName: string
       aliases: string[]
     }[]