Merge branch 'main' into 2020_desktop_builds

GMOD · Aug 6, 2021 · e63577f · e63577f
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -1,3 +1,74 @@
+## 1.3.3 (2021-08-02)
+
+<details><summary>Packages in this release</summary>
+<p>
+
+| Package                                 | Download                                                         |
+| --------------------------------------- | ---------------------------------------------------------------- |
+| @jbrowse/core                           | https://www.npmjs.com/package/@jbrowse/core                      |
+| @jbrowse/plugin-alignments              | https://www.npmjs.com/package/@jbrowse/plugin-alignments         |
+| @jbrowse/plugin-breakpoint-split-view   |                                                                  |
+| @jbrowse/plugin-circular-view           | https://www.npmjs.com/package/@jbrowse/plugin-circular-view      |
+| @jbrowse/plugin-config                  | https://www.npmjs.com/package/@jbrowse/plugin-config             |
+| @jbrowse/plugin-data-management         | https://www.npmjs.com/package/@jbrowse/plugin-data-management    |
+| @jbrowse/plugin-dotplot-view            |                                                                  |
+| @jbrowse/plugin-filtering               |                                                                  |
+| @jbrowse/plugin-gff3                    | https://www.npmjs.com/package/@jbrowse/plugin-gff3               |
+| @jbrowse/plugin-hic                     |                                                                  |
+| @jbrowse/plugin-legacy-jbrowse          | https://www.npmjs.com/package/@jbrowse/plugin-legacy-jbrowse     |
+| @jbrowse/plugin-linear-comparative-view |                                                                  |
+| @jbrowse/plugin-linear-genome-view      | https://www.npmjs.com/package/@jbrowse/plugin-linear-genome-view |
+| @jbrowse/plugin-lollipop                |                                                                  |
+| @jbrowse/plugin-menus                   |                                                                  |
+| @jbrowse/plugin-sequence                | https://www.npmjs.com/package/@jbrowse/plugin-sequence           |
+| @jbrowse/plugin-spreadsheet-view        |                                                                  |
+| @jbrowse/plugin-sv-inspector            |                                                                  |
+| @jbrowse/plugin-svg                     | https://www.npmjs.com/package/@jbrowse/plugin-svg                |
+| @jbrowse/plugin-trackhub-registry       |                                                                  |
+| @jbrowse/plugin-variants                | https://www.npmjs.com/package/@jbrowse/plugin-variants           |
+| @jbrowse/plugin-wiggle                  | https://www.npmjs.com/package/@jbrowse/plugin-wiggle             |
+| @jbrowse/cli                            | https://www.npmjs.com/package/@jbrowse/cli                       |
+| @jbrowse/desktop                        |                                                                  |
+| @jbrowse/react-linear-genome-view       | https://www.npmjs.com/package/@jbrowse/react-linear-genome-view  |
+| @jbrowse/web                            |                                                                  |
+
+</p>
+</details>
+
+#### :rocket: Enhancement
+
+- Other
+  - [#2127](https://github.com/GMOD/jbrowse-components/pull/2127) Add example dataset for COLO829 ([@cmdcolin](https://github.com/cmdcolin))
+- `core`
+  - [#2141](https://github.com/GMOD/jbrowse-components/pull/2141) Update to @material-ui/core@4.12.2 ([@cmdcolin](https://github.com/cmdcolin))
+  - [#2126](https://github.com/GMOD/jbrowse-components/pull/2126) Allow opening plaintext .vcf files from the "Add track" workflow ([@cmdcolin](https://github.com/cmdcolin))
+
+#### :bug: Bug Fix
+
+- Other
+  - [#2159](https://github.com/GMOD/jbrowse-components/pull/2159) Stop local storage quota-exceeded errors preventing the app from starting ([@cmdcolin](https://github.com/cmdcolin))
+  - [#2161](https://github.com/GMOD/jbrowse-components/pull/2161) Remove outline from clicking on SVG chord tracks ([@cmdcolin](https://github.com/cmdcolin))
+  - [#2157](https://github.com/GMOD/jbrowse-components/pull/2157) Fix rendering of negative strand alignment modifications/methylation ([@cmdcolin](https://github.com/cmdcolin))
+  - [#2131](https://github.com/GMOD/jbrowse-components/pull/2131) Fix mouseovers/click handlers after "force load" button pressed ([@cmdcolin](https://github.com/cmdcolin))
+  - [#2128](https://github.com/GMOD/jbrowse-components/pull/2128) Fix using the "Color by modifications" setting on files that need ref renaming ([@cmdcolin](https://github.com/cmdcolin))
+  - [#2115](https://github.com/GMOD/jbrowse-components/pull/2115) Fix bug where sometimes plugin could not be removed from UI ([@garrettjstevens](https://github.com/garrettjstevens))
+  - [#2119](https://github.com/GMOD/jbrowse-components/pull/2119) Fix loading indicator on the reference sequence selector getting stuck ([@cmdcolin](https://github.com/cmdcolin))
+- `core`
+  - [#2101](https://github.com/GMOD/jbrowse-components/pull/2101) Fix behavior of the end-of-list indicator in refNameAutocomplete to always display as a disabled item ([@teresam856](https://github.com/teresam856))
+
+#### :house: Internal
+
+- Other
+  - [#2152](https://github.com/GMOD/jbrowse-components/pull/2152) Remove storybook symlink workaround ([@garrettjstevens](https://github.com/garrettjstevens))
+- `core`
+  - [#2099](https://github.com/GMOD/jbrowse-components/pull/2099) Use rbush data structure for layout of feature tracks ([@cmdcolin](https://github.com/cmdcolin))
+
+#### Committers: 3
+
+- Colin Diesh ([@cmdcolin](https://github.com/cmdcolin))
+- Garrett Stevens ([@garrettjstevens](https://github.com/garrettjstevens))
+- Teresa Martinez ([@teresam856](https://github.com/teresam856))
+
 ## 1.3.2 (2021-07-07)
 
 <details><summary>Packages in this release</summary>

diff --git a/lerna.json b/lerna.json
@@ -1,5 +1,5 @@
 {
-  "version": "1.3.2",
+  "version": "1.3.3",
   "npmClient": "yarn",
   "useWorkspaces": true
 }
diff --git a/packages/core/PluginManager.ts b/packages/core/PluginManager.ts
@@ -195,6 +195,8 @@ export default class PluginManager {
 
   rootModel?: AbstractRootModel
 
+  extensionPoints: Map<string, Function[]> = new Map()
+
   constructor(initialPlugins: (Plugin | PluginLoadRecord)[] = []) {
     // add the core plugin
     this.addPlugin({ plugin: new CorePlugin(), metadata: { isCore: true } })
@@ -308,7 +310,7 @@ export default class PluginManager {
     const typeRecord = this.getElementTypeRecord(groupName)
 
     this.elementCreationSchedule.add(groupName, () => {
-      const newElement = creationCallback(this)
+      let newElement = creationCallback(this)
       if (!newElement.name) {
         throw new Error(`cannot add a ${groupName} with no name`)
       }
@@ -319,6 +321,11 @@ export default class PluginManager {
         )
       }
 
+      newElement = this.evaluateExtensionPoint(
+        'Core-extendPluggableElement',
+        newElement,
+      ) as PluggableElementType
+
       typeRecord.add(newElement.name, newElement)
     })
 
@@ -551,4 +558,31 @@ export default class PluginManager {
   ): this {
     return this.addElementType('rpc method', creationCallback)
   }
+
+  addToExtensionPoint<T>(
+    extensionPointName: string,
+    callback: (extendee: T) => T,
+  ) {
+    let callbacks = this.extensionPoints.get(extensionPointName)
+    if (!callbacks) {
+      callbacks = []
+      this.extensionPoints.set(extensionPointName, callbacks)
+    }
+    callbacks.push(callback)
+  }
+
+  evaluateExtensionPoint(extensionPointName: string, extendee: unknown) {
+    const callbacks = this.extensionPoints.get(extensionPointName)
+    let accumulator = extendee
+    if (callbacks) {
+      for (const callback of callbacks) {
+        try {
+          accumulator = callback(accumulator)
+        } catch (error) {
+          console.error(error)
+        }
+      }
+    }
+    return accumulator
+  }
 }
diff --git a/packages/core/package.json b/packages/core/package.json
@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/core",
-  "version": "1.3.2",
+  "version": "1.3.3",
   "description": "JBrowse 2 core libraries used by plugins",
   "keywords": [
     "jbrowse",

diff --git a/packages/core/pluggableElementTypes/models/BaseViewModel.ts b/packages/core/pluggableElementTypes/models/BaseViewModel.ts
@@ -11,7 +11,7 @@ const BaseViewModel = types
     width: 800,
   }))
   .views((/* self */) => ({
-    get menuItems(): MenuItem[] {
+    menuItems(): MenuItem[] {
       return []
     },
   }))

diff --git a/packages/core/ui/FileSelector.tsx b/packages/core/ui/FileSelector.tsx
@@ -62,9 +62,13 @@ const FileLocationEditor = observer(
               }}
               aria-label="file or url picker"
             >
-              <ToggleButton value="file" aria-label="local file">
-                File
-              </ToggleButton>
+              {new URLSearchParams(window.location.search).get(
+                'adminKey',
+              ) ? null : (
+                <ToggleButton value="file" aria-label="local file">
+                  File
+                </ToggleButton>
+              )}
               <ToggleButton value="url" aria-label="url">
                 URL
               </ToggleButton>

diff --git a/packages/core/ui/ViewContainer.tsx b/packages/core/ui/ViewContainer.tsx
@@ -87,7 +87,7 @@ const ViewMenu = observer(
   }) => {
     const [anchorEl, setAnchorEl] = useState<HTMLElement>()
 
-    if (!(model.menuItems && model.menuItems.length)) {
+    if (!model.menuItems?.().length) {
       return null
     }
 
@@ -115,7 +115,7 @@ const ViewMenu = observer(
           onClose={() => {
             setAnchorEl(undefined)
           }}
-          menuItems={model.menuItems}
+          menuItems={model.menuItems()}
         />
       </>
     )

diff --git a/packages/core/util/tracks.ts b/packages/core/util/tracks.ts
@@ -175,7 +175,7 @@ export function guessAdapter(
       type: 'VcfTabixAdapter',
       vcfGzLocation: file,
       index: {
-        location: index || makeIndex(file, 'tbi'),
+        location: index || makeIndex(file, '.tbi'),
         indexType: makeIndexType(indexName, 'CSI', 'TBI'),
       },
     }

diff --git a/packages/core/util/types/index.ts b/packages/core/util/types/index.ts
@@ -25,7 +25,10 @@ export * from './util'
 export interface AbstractViewContainer {
   views: AbstractViewModel[]
   removeView(view: AbstractViewModel): void
-  addView(typeName: string, initialState: Record<string, unknown>): void
+  addView(
+    typeName: string,
+    initialState: Record<string, unknown>,
+  ): void | AbstractViewModel
 }
 export function isViewContainer(
   thing: unknown,
@@ -119,7 +122,7 @@ export function isSessionModelWithConfigEditing(
 /** abstract interface for a session that manages widgets */
 export interface SessionWithWidgets extends AbstractSessionModel {
   visibleWidget?: { id: string }
-  widgets?: unknown[]
+  widgets: Map<string, unknown>
   addWidget(
     typeName: string,
     id: string,

diff --git a/plugins/alignments/package.json b/plugins/alignments/package.json
@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-alignments",
-  "version": "1.3.1",
+  "version": "1.3.3",
   "description": "JBrowse 2 alignments adapters, tracks, etc.",
   "keywords": [
     "jbrowse",

diff --git a/plugins/alignments/src/PileupRenderer/PileupRenderer.tsx b/plugins/alignments/src/PileupRenderer/PileupRenderer.tsx
@@ -411,24 +411,41 @@ export default class PileupRenderer extends BoxRendererType {
       if (i >= 0 && i < methBins.length) {
         const l1 = regionSequence[i].toLowerCase()
         const l2 = regionSequence[i + 1].toLowerCase()
-        // color
-        if (l1 === 'c' && l2 === 'g') {
-          const s = rstart + i
-          const [leftPx, rightPx] = bpSpanPx(s, s + 1, region, bpPerPx)
-          if (methBins[i]) {
-            ctx.fillStyle = 'red'
-          } else {
-            ctx.fillStyle = 'blue'
+
+        // if we are zoomed out, display just a block over the cpg
+        if (bpPerPx > 2) {
+          if (l1 === 'c' && l2 === 'g') {
+            const s = rstart + i
+            const [leftPx, rightPx] = bpSpanPx(s, s + 2, region, bpPerPx)
+            if (methBins[i] || methBins[i + 1]) {
+              ctx.fillStyle = 'red'
+            } else {
+              ctx.fillStyle = 'blue'
+            }
+            ctx.fillRect(leftPx, topPx, rightPx - leftPx + 0.5, heightPx)
           }
-          ctx.fillRect(leftPx, topPx, rightPx - leftPx + 0.5, heightPx)
+        }
+        // if we are zoomed in, color the c inside the cpg
+        else {
+          // color
+          if (l1 === 'c' && l2 === 'g') {
+            const s = rstart + i
+            const [leftPx, rightPx] = bpSpanPx(s, s + 1, region, bpPerPx)
+            if (methBins[i]) {
+              ctx.fillStyle = 'red'
+            } else {
+              ctx.fillStyle = 'blue'
+            }
+            ctx.fillRect(leftPx, topPx, rightPx - leftPx + 0.5, heightPx)
 
-          const [leftPx2, rightPx2] = bpSpanPx(s + 1, s + 2, region, bpPerPx)
-          if (methBins[i + 1]) {
-            ctx.fillStyle = 'red'
-          } else {
-            ctx.fillStyle = 'blue'
+            const [leftPx2, rightPx2] = bpSpanPx(s + 1, s + 2, region, bpPerPx)
+            if (methBins[i + 1]) {
+              ctx.fillStyle = 'red'
+            } else {
+              ctx.fillStyle = 'blue'
+            }
+            ctx.fillRect(leftPx2, topPx, rightPx2 - leftPx2 + 0.5, heightPx)
           }
-          ctx.fillRect(leftPx2, topPx, rightPx2 - leftPx2 + 0.5, heightPx)
         }
       }
     }

diff --git a/plugins/breakpoint-split-view/package.json b/plugins/breakpoint-split-view/package.json
@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-breakpoint-split-view",
-  "version": "1.3.1",
+  "version": "1.3.3",
   "description": "JBrowse 2 breakpoint detail split view",
   "keywords": [
     "jbrowse",

diff --git a/plugins/breakpoint-split-view/src/model.ts b/plugins/breakpoint-split-view/src/model.ts
@@ -79,13 +79,13 @@ export default function stateModelFactory(pluginManager: any) {
         )
       },
 
-      get menuItems(): MenuItem[] {
+      menuItems(): MenuItem[] {
         const menuItems: MenuItem[] = []
         self.views.forEach((view, idx) => {
-          if (view.menuItems) {
+          if (view.menuItems?.()) {
             menuItems.push({
               label: `View ${idx + 1} Menu`,
-              subMenu: view.menuItems,
+              subMenu: view.menuItems(),
             })
           }
         })

diff --git a/plugins/circular-view/package.json b/plugins/circular-view/package.json
@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-circular-view",
-  "version": "1.3.2",
+  "version": "1.3.3",
   "description": "JBrowse 2 circular view",
   "keywords": [
     "jbrowse",

diff --git a/plugins/config/package.json b/plugins/config/package.json
@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-config",
-  "version": "1.3.1",
+  "version": "1.3.3",
   "description": "JBrowse 2 config utilities",
   "keywords": [
     "jbrowse",

diff --git a/plugins/data-management/package.json b/plugins/data-management/package.json
@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-data-management",
-  "version": "1.3.1",
+  "version": "1.3.3",
   "description": "JBrowse 2 linear genome view",
   "keywords": [
     "jbrowse",

diff --git a/plugins/data-management/src/PluginStoreWidget/components/InstalledPlugin.tsx b/plugins/data-management/src/PluginStoreWidget/components/InstalledPlugin.tsx
@@ -39,7 +39,7 @@ function LockedPlugin() {
   return (
     <Tooltip
       style={{ marginRight: '0.5rem' }}
-      title="This plugin was installed by an admin. It cannot be removed."
+      title="This plugin was installed by an administrator, you cannot remove it."
     >
       <LockIcon />
     </Tooltip>