Colors from csv

plugins/data-management/src/UCSCTrackHub/ucscTrackHub.ts

@@ -3,7 +3,7 @@ import { generateUnknownTrackConf } from '@jbrowse/core/util/tracks'
 
 import { makeLoc2, makeLoc, makeLocAlt } from './util'
 
-import type { RaStanza, TrackDbFile  } from '@gmod/ucsc-hub'
+import type { RaStanza, TrackDbFile } from '@gmod/ucsc-hub'
 import type { FileLocation } from '@jbrowse/core/util'
 
 export function generateTracks({

plugins/variants/src/MultiLinearVariantDisplay/components/VariantDisplayComponent.tsx

@@ -70,7 +70,7 @@ const MultiLinearVariantDisplayComponent = observer(function (props: {
               )
                 .filter(([key]) => key !== 'color')
                 .map(([key, value]) => `${key}:${value}`)
-                .join('\n')}
+                .join('<br/>')}
             />
           </BaseTooltip>
         </div>

plugins/variants/src/MultiLinearVariantDisplay/model.ts

@@ -1,14 +1,11 @@
 import { lazy } from 'react'
 
-import { set1 } from '@jbrowse/core/ui/colors'
 import { getSession } from '@jbrowse/core/util'
 import { stopStopToken } from '@jbrowse/core/util/stopToken'
 import { linearBareDisplayStateModelFactory } from '@jbrowse/plugin-linear-genome-view'
 import deepEqual from 'fast-deep-equal'
 import { isAlive, types } from 'mobx-state-tree'
 
-import { randomColor } from '../util'
-
 import type { Source } from '../types'
 import type PluginManager from '@jbrowse/core/PluginManager'
 import type { AnyConfigurationSchemaType } from '@jbrowse/core/configuration'
@@ -24,7 +21,7 @@ const ClusterDialog = lazy(() => import('../shared/ClusterDialog'))
 /**
  * #stateModel MultiLinearVariantDisplay
  * extends
- * - [SharedVariantMixin](../sharedvariantmixin)
+ * - [LinearBareDisplay](../linearbaredisplay)
  */
 export function stateModelFactory(
   pluginManager: PluginManager,
@@ -160,15 +157,10 @@ export function stateModelFactory(
           self.sourcesVolatile?.map(s => [s.name, s]) || [],
         )
         const iter = self.layout.length ? self.layout : self.sourcesVolatile
-        return iter
-          ?.map(s => ({
-            ...sources[s.name],
-            ...s,
-          }))
-          .map((s, i) => ({
-            ...s,
-            color: s.color || set1[i] || randomColor(s.name),
-          }))
+        return iter?.map(s => ({
+          ...sources[s.name],
+          ...s,
+        }))
       },
     }))
 

plugins/variants/src/MultiLinearVariantMatrixDisplay/components/VariantDisplayComponent.tsx

@@ -70,7 +70,7 @@ const MultiLinearVariantMatrixDisplayComponent = observer(function (props: {
               )
                 .filter(([key]) => key !== 'color')
                 .map(([key, value]) => `${key}:${value}`)
-                .join('\n')}
+                .join('<br/>')}
             />
           </BaseTooltip>
         </>

plugins/variants/src/MultiLinearVariantMatrixDisplay/model.ts

@@ -1,15 +1,12 @@
 import { lazy } from 'react'
 
 import { ConfigurationReference } from '@jbrowse/core/configuration'
-import { set1 } from '@jbrowse/core/ui/colors'
 import { getSession } from '@jbrowse/core/util'
 import { stopStopToken } from '@jbrowse/core/util/stopToken'
 import { linearBareDisplayStateModelFactory } from '@jbrowse/plugin-linear-genome-view'
 import deepEqual from 'fast-deep-equal'
 import { isAlive, types } from 'mobx-state-tree'
 
-import { randomColor } from '../util'
-
 import type { Source } from '../types'
 import type { AnyConfigurationSchemaType } from '@jbrowse/core/configuration'
 import type { Feature } from '@jbrowse/core/util'
@@ -24,7 +21,7 @@ const ClusterDialog = lazy(() => import('../shared/ClusterDialog'))
 /**
  * #stateModel LinearVariantMatrixDisplay
  * extends
- * - [LinearBasicDisplay](../linearbasicdisplay)
+ * - [LinearBareDisplay](../linearbaredisplay)
  */
 export default function stateModelFactory(
   configSchema: AnyConfigurationSchemaType,
@@ -142,15 +139,10 @@ export default function stateModelFactory(
         const sources = Object.fromEntries(
           self.sourcesVolatile?.map(s => [s.name, s]) || [],
         )
-        return this.preSources
-          ?.map(s => ({
-            ...sources[s.name],
-            ...s,
-          }))
-          .map((s, i) => ({
-            ...s,
-            color: s.color || set1[i] || randomColor(s.name),
-          }))
+        return this.preSources?.map(s => ({
+          ...sources[s.name],
+          ...s,
+        }))
       },
     }))
     .views(self => {

plugins/variants/src/StructuralVariantChordRenderer/Chord.tsx

@@ -5,9 +5,9 @@ import { readConfObject } from '@jbrowse/core/configuration'
 import { getStrokeProps, polarToCartesian } from '@jbrowse/core/util'
 import { observer } from 'mobx-react'
 
+import type { AnyRegion, Block } from './types'
 import type { AnyConfigurationModel } from '@jbrowse/core/configuration'
 import type { Feature } from '@jbrowse/core/util'
-import type { AnyRegion, Block } from './types'
 
 function bpToRadians(block: Block, pos: number) {
   const blockStart = block.region.elided ? 0 : block.region.start

plugins/variants/src/VcfAdapter/VcfAdapter.ts

@@ -1,11 +1,10 @@
 import IntervalTree from '@flatten-js/interval-tree'
-import VCF from '@gmod/vcf'
+import VcfParser from '@gmod/vcf'
 import { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter'
 import { fetchAndMaybeUnzip } from '@jbrowse/core/util'
 import { openLocation } from '@jbrowse/core/util/io'
 import { ObservableCreate } from '@jbrowse/core/util/rxjs'
 
-// local
 import VcfFeature from '../VcfFeature'
 
 import type { BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter'
@@ -18,6 +17,7 @@ export default class VcfAdapter extends BaseFeatureDataAdapter {
 
   vcfFeatures?: Promise<{
     header: string
+    parser: VcfParser
     intervalTreeMap: Record<string, (sc?: StatusCallback) => IntervalTree>
   }>
 
@@ -29,8 +29,7 @@ export default class VcfAdapter extends BaseFeatureDataAdapter {
   }
 
   async getMetadata() {
-    const { header } = await this.setup()
-    const parser = new VCF({ header })
+    const { parser } = await this.setup()
     return parser.getMetadata()
   }
 
@@ -72,7 +71,7 @@ export default class VcfAdapter extends BaseFeatureDataAdapter {
     }
 
     const header = headerLines.join('\n')
-    const parser = new VCF({ header })
+    const parser = new VcfParser({ header })
 
     const intervalTreeMap = Object.fromEntries(
       Object.entries(featureMap).map(([refName, lines]) => [
@@ -99,6 +98,7 @@ export default class VcfAdapter extends BaseFeatureDataAdapter {
 
     return {
       header,
+      parser,
       intervalTreeMap,
     }
   }
@@ -135,5 +135,26 @@ export default class VcfAdapter extends BaseFeatureDataAdapter {
     }, opts.stopToken)
   }
 
+  async getSources() {
+    const conf = this.getConf('samplesTsvLocation')
+    if (conf.uri === '' || conf.uri === '/path/to/samples.tsv') {
+      const { parser } = await this.setup()
+      return parser.samples.map(name => ({
+        name,
+      }))
+    } else {
+      const txt = await openLocation(conf).readFile('utf8')
+      const lines = txt.split(/\n|\r\n|\r/)
+      const header = lines[0]!.split('\t')
+      return lines.slice(1).map(line =>
+        Object.fromEntries(
+          line
+            .split('\t')
+            // force col 0 to be called name
+            .map((c, idx) => [idx === 0 ? 'name' : header[idx], c]),
+        ),
+      )
+    }
+  }
   public freeResources(): void {}
 }

plugins/variants/src/VcfAdapter/configSchema.ts

@@ -21,9 +21,14 @@ const VcfAdapter = ConfigurationSchema(
     /**
      * #slot
      */
-    samples: {
-      type: 'frozen',
-      defaultValue: [],
+    samplesTsvLocation: {
+      type: 'fileLocation',
+      defaultValue: {
+        uri: '/path/to/samples.tsv',
+        description:
+          'tsv with header like name\tpopulation\tetc. where the first column is required, and is the sample names',
+        locationType: 'UriLocation',
+      },
     },
   },
   { explicitlyTyped: true },

plugins/variants/src/VcfTabixAdapter/VcfTabixAdapter.ts

@@ -83,12 +83,26 @@ export default class VcfTabixAdapter extends BaseFeatureDataAdapter {
       observer.complete()
     }, opts.stopToken)
   }
-
   async getSources() {
-    const { parser } = await this.configure()
-    return parser.samples.map(name => ({
-      name,
-    }))
+    const conf = this.getConf('samplesTsvLocation')
+    if (conf.uri === '' || conf.uri === '/path/to/samples.tsv') {
+      const { parser } = await this.configure()
+      return parser.samples.map(name => ({
+        name,
+      }))
+    } else {
+      const txt = await openLocation(conf).readFile('utf8')
+      const lines = txt.split(/\n|\r\n|\r/)
+      const header = lines[0]!.split('\t')
+      return lines.slice(1).map(line =>
+        Object.fromEntries(
+          line
+            .split('\t')
+            // force col 0 to be called name
+            .map((c, idx) => [idx === 0 ? 'name' : header[idx], c]),
+        ),
+      )
+    }
   }
 
   public freeResources(/* { region } */): void {}

plugins/variants/src/VcfTabixAdapter/configSchema.ts

@@ -39,9 +39,14 @@ const VcfTabixAdapter = ConfigurationSchema(
     /**
      * #slot
      */
-    samples: {
-      type: 'frozen',
-      defaultValue: [],
+    samplesTsvLocation: {
+      type: 'fileLocation',
+      defaultValue: {
+        uri: '/path/to/samples.tsv',
+        description:
+          'tsv with header like name\tpopulation\tetc. where the first column is required, and is the sample names',
+        locationType: 'UriLocation',
+      },
     },
   },
   { explicitlyTyped: true },

plugins/variants/src/getMultiVariantFeaturesAutorun.ts

@@ -17,7 +17,7 @@ export interface Source {
   name: string
   color?: string
   group?: string
-  [key: string]: string | undefined
+  [key: string]: unknown
 }
 
 export function getMultiVariantFeaturesAutorun(self: {