Merge remote-tracking branch 'origin/main' into add_canvas_feature_re…

…nderer
GMOD · Nov 17, 2024 · 7a89844 · 7a89844
2 parents def3bf9 + 2d52a06
commit 7a89844
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Showing 223 changed files with 7,238 additions and 4,957 deletions.
diff --git a/eslint.config.mjs b/eslint.config.mjs
@@ -79,7 +79,7 @@ export default tseslint.config(
           markers: ['/'],
         },
       ],
-
+      'one-var': ['error', 'never'],
       'react-refresh/only-export-components': 'warn',
       'react/no-unescaped-entities': 'off',
       'react/no-is-mounted': 'off',

diff --git a/package.json b/package.json
@@ -101,7 +101,7 @@
     "dependency-graph": "^1.0.0",
     "dotenv": "^16.3.1",
     "dotenv-expand": "^11.0.3",
-    "electron": "33.0.2",
+    "electron": "33.2.0",
     "electron-builder": "^25.1.6",
     "electron-mock-ipc": "^0.3.8",
     "eslint": "^9.0.0",

diff --git a/packages/core/BaseFeatureWidget/SequenceFeatureDetails/model.ts b/packages/core/BaseFeatureWidget/SequenceFeatureDetails/model.ts
@@ -12,22 +12,54 @@ function localStorageGetNumber(key: string, defaultVal: number) {
   return +(localStorageGetItem(key) ?? defaultVal)
 }
 
+function localStorageGetBoolean(key: string, defaultVal: boolean) {
+  return Boolean(
+    JSON.parse(localStorageGetItem(key) || JSON.stringify(defaultVal)),
+  )
+}
+
+function localStorageSetNumber(key: string, value: number) {
+  localStorageSetItem(key, JSON.stringify(value))
+}
+
+function localStorageSetBoolean(key: string, value: boolean) {
+  localStorageSetItem(key, JSON.stringify(value))
+}
+
+const p = 'sequenceFeatureDetails'
+
 export function SequenceFeatureDetailsF() {
   return types
     .model('SequenceFeatureDetails')
     .volatile(() => ({
+      /**
+       * #volatile
+       */
       showCoordinatesSetting:
-        localStorageGetItem('sequenceFeatureDetails-showCoordinatesSetting') ||
-        'none',
-      intronBp: localStorageGetNumber('sequenceFeatureDetails-intronBp', 10),
-      upDownBp: localStorageGetNumber('sequenceFeatureDetails-upDownBp', 100),
-      upperCaseCDS: Boolean(
-        JSON.parse(
-          localStorageGetItem('sequenceFeatureDetails-upperCaseCDS') || 'true',
-        ),
-      ),
+        localStorageGetItem(`${p}-showCoordinatesSetting`) || 'none',
+      /**
+       * #volatile
+       */
+      intronBp: localStorageGetNumber(`${p}-intronBp`, 10),
+      /**
+       * #volatile
+       */
+      upDownBp: localStorageGetNumber(`${p}-upDownBp`, 100),
+      /**
+       * #volatile
+       */
+      upperCaseCDS: localStorageGetBoolean(`${p}-upperCaseCDS`, true),
+      /**
+       * #volatile
+       */
       charactersPerRow: 100,
+      /**
+       * #volatile
+       */
       feature: undefined as SimpleFeatureSerialized | undefined,
+      /**
+       * #volatile
+       */
       mode: '',
     }))
     .actions(self => ({
@@ -110,20 +142,11 @@ export function SequenceFeatureDetailsF() {
         addDisposer(
           self,
           autorun(() => {
+            localStorageSetNumber(`${p}-upDownBp`, self.upDownBp)
+            localStorageSetNumber(`${p}-intronBp`, self.intronBp)
+            localStorageSetBoolean(`${p}-upperCaseCDS`, self.upperCaseCDS)
             localStorageSetItem(
-              'sequenceFeatureDetails-upDownBp',
-              JSON.stringify(self.upDownBp),
-            )
-            localStorageSetItem(
-              'sequenceFeatureDetails-intronBp',
-              JSON.stringify(self.intronBp),
-            )
-            localStorageSetItem(
-              'sequenceFeatureDetails-upperCaseCDS',
-              JSON.stringify(self.upperCaseCDS),
-            )
-            localStorageSetItem(
-              'sequenceFeatureDetails-showCoordinatesSetting',
+              `${p}-showCoordinatesSetting`,
               self.showCoordinatesSetting,
             )
           }),

diff --git a/packages/core/data_adapters/CytobandAdapter/CytobandAdapter.ts b/packages/core/data_adapters/CytobandAdapter/CytobandAdapter.ts
@@ -1,20 +1,20 @@
-import { unzip } from '@gmod/bgzf-filehandle'
-
 // locals
-import { isGzip, SimpleFeature } from '../../util'
+import { fetchAndMaybeUnzip, SimpleFeature } from '../../util'
 import { openLocation } from '../../util/io'
 import { BaseAdapter } from '../BaseAdapter'
+import { BaseOptions } from '../BaseAdapter/BaseOptions'
 
 export default class CytobandAdapter extends BaseAdapter {
-  async getData() {
-    const pm = this.pluginManager
-    const loc = this.getConf('cytobandLocation')
-    if (loc.uri === '' || loc.uri === '/path/to/cytoband.txt.gz') {
+  async getData(opts?: BaseOptions) {
+    const conf = this.getConf('cytobandLocation')
+    if (conf.uri === '' || conf.uri === '/path/to/cytoband.txt.gz') {
       return []
     }
-    const buffer = await openLocation(loc, pm).readFile()
-    const buf = isGzip(buffer) ? await unzip(buffer) : buffer
-    const text = new TextDecoder('utf8', { fatal: true }).decode(buf)
+
+    const pm = this.pluginManager
+    const buf = await fetchAndMaybeUnzip(openLocation(conf, pm), opts)
+    const decoder = new TextDecoder('utf8', { fatal: true })
+    const text = decoder.decode(buf)
     return text
       .split(/\n|\r\n|\r/)
       .filter(f => !!f.trim())
@@ -25,8 +25,9 @@ export default class CytobandAdapter extends BaseAdapter {
           refName: refName!,
           start: +start!,
           end: +end!,
-          name: name!,
-          type: type!,
+          name,
+          type,
+          gieStain: type || name,
         })
       })
   }

diff --git a/packages/core/package.json b/packages/core/package.json
@@ -44,7 +44,7 @@
     "copy-to-clipboard": "^3.3.1",
     "deepmerge": "^4.2.2",
     "detect-node": "^2.1.0",
-    "dompurify": "^3.0.0",
+    "dompurify": "^3.2.0",
     "escape-html": "^1.0.3",
     "fast-deep-equal": "^3.1.3",
     "generic-filehandle": "^3.0.0",

diff --git a/packages/core/ui/AssemblySelector.tsx b/packages/core/ui/AssemblySelector.tsx
@@ -71,15 +71,17 @@ const AssemblySelector = observer(function ({
       variant="outlined"
       helperText={error || helperText}
       value={selection || ''}
-      inputProps={{ 'data-testid': 'assembly-selector' }}
       onChange={event => {
         setLastSelected(event.target.value)
       }}
       error={!!error}
-      InputProps={InputProps}
       disabled={!!error}
       className={classes.importFormEntry}
       {...TextFieldProps}
+      slotProps={{
+        input: InputProps,
+        htmlInput: { 'data-testid': 'assembly-selector' },
+      }}
     >
       {assemblyNames.map(name => {
         const assembly = assemblyManager.get(name)

diff --git a/packages/core/ui/FileSelector/UrlChooser.tsx b/packages/core/ui/FileSelector/UrlChooser.tsx
@@ -16,7 +16,6 @@ const UrlChooser = observer(function ({
     <TextField
       fullWidth
       variant="outlined"
-      inputProps={{ 'data-testid': 'urlInput' }}
       defaultValue={location && isUriLocation(location) ? location.uri : ''}
       label={label || 'Enter URL'}
       onChange={event => {
@@ -25,6 +24,9 @@ const UrlChooser = observer(function ({
           locationType: 'UriLocation',
         })
       }}
+      slotProps={{
+        htmlInput: { 'data-testid': 'urlInput' },
+      }}
     />
   )
 })

diff --git a/packages/core/ui/SanitizedHTML.tsx b/packages/core/ui/SanitizedHTML.tsx
@@ -72,18 +72,15 @@ export default function SanitizedHTML({
     // see https://github.com/cure53/DOMPurify/issues/317
     // only have to add this once, and can't do it globally because dompurify
     // not yet initialized at global scope
-    dompurify.addHook(
-      'afterSanitizeAttributes',
-      (node: {
-        tagName: string
-        setAttribute: (arg0: string, arg1: string) => void
-      }) => {
-        if (node.tagName === 'A') {
-          node.setAttribute('rel', 'noopener noreferrer')
-          node.setAttribute('target', '_blank')
-        }
-      },
-    )
+    dompurify.addHook('afterSanitizeAttributes', node => {
+      // @ts-expect-error
+      if (node.tagName === 'A') {
+        // @ts-expect-error
+        node.setAttribute('rel', 'noopener noreferrer')
+        // @ts-expect-error
+        node.setAttribute('target', '_blank')
+      }
+    })
   }
 
   return (

diff --git a/packages/core/ui/theme.ts b/packages/core/ui/theme.ts
@@ -86,6 +86,7 @@ const midnight = '#0D233F'
 const grape = '#721E63'
 const forest = refTheme.palette.augmentColor({ color: { main: '#135560' } })
 const mandarin = refTheme.palette.augmentColor({ color: { main: '#FFB11D' } })
+const lightgrey = refTheme.palette.augmentColor({ color: { main: '#aaa' } })
 const bases = {
   A: refTheme.palette.augmentColor({ color: green }),
   C: refTheme.palette.augmentColor({ color: blue }),
@@ -468,66 +469,43 @@ export function createJBrowseTheme(
   return createTheme(
     createJBrowseBaseTheme(
       themeName === 'default'
-        ? deepmerge(themes.default!, augmentTheme(configTheme), {
+        ? deepmerge(themes.default!, augmentThemeColors(configTheme), {
             arrayMerge: overwriteArrayMerge,
           })
-        : augmentThemePlus(themes[themeName]),
+        : addMissingColors(themes[themeName]),
     ),
   )
 }
 
-function augmentTheme(theme: ThemeOptions = {}) {
-  if (theme.palette?.tertiary) {
-    theme = deepmerge(theme, {
-      palette: {
-        tertiary: refTheme.palette.augmentColor(
-          'color' in theme.palette.tertiary
-            ? (theme.palette.tertiary as PaletteAugmentColorOptions)
-            : { color: theme.palette.tertiary },
-        ),
-      },
-    })
-  }
-
-  if (theme.palette?.quaternary) {
-    theme = deepmerge(theme, {
-      palette: {
-        quaternary: refTheme.palette.augmentColor(
-          'color' in theme.palette.quaternary
-            ? (theme.palette.quaternary as PaletteAugmentColorOptions)
-            : { color: theme.palette.quaternary },
-        ),
-      },
-    })
+// MUI by default allows strings like '#f00' for primary and secondary and
+// augments them to have light and dark variants but not for anything else, so
+// we augment them here
+function augmentThemeColors(theme: ThemeOptions = {}) {
+  for (const entry of ['tertiary', 'quaternary', 'highlight'] as const) {
+    if (theme.palette?.[entry]) {
+      theme = deepmerge(theme, {
+        palette: {
+          [entry]: refTheme.palette.augmentColor(
+            'color' in theme.palette[entry]
+              ? (theme.palette[entry] as PaletteAugmentColorOptions)
+              : { color: theme.palette[entry] },
+          ),
+        },
+      })
+    }
   }
-
   return theme
 }
 
-// creates some blank quaternary/tertiary colors if unsupplied by a user theme
-function augmentThemePlus(theme: ThemeOptions = {}) {
-  theme = augmentTheme(theme)
-  if (!theme.palette?.quaternary) {
-    theme = deepmerge(theme, {
+// adds missing colors to users theme
+function addMissingColors(theme: ThemeOptions = {}) {
+  return augmentThemeColors(
+    deepmerge(theme, {
       palette: {
-        quaternary: refTheme.palette.augmentColor({
-          color: {
-            main: '#aaa',
-          },
-        }),
-      },
-    })
-  }
-  if (!theme.palette?.tertiary) {
-    theme = deepmerge(theme, {
-      palette: {
-        tertiary: refTheme.palette.augmentColor({
-          color: {
-            main: '#aaa',
-          },
-        }),
+        quaternary: theme.palette?.quaternary || lightgrey,
+        tertiary: theme.palette?.tertiary || lightgrey,
+        highlight: theme.palette?.highlight || mandarin,
       },
-    })
-  }
-  return theme
+    }),
+  )
 }