Add text searching

GMOD · Dec 16, 2022 · 20da5a8 · 20da5a8
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diff --git a/embedded_demos/README.md b/embedded_demos/README.md
@@ -0,0 +1,22 @@
+# JBrowse 2 embedded demos
+
+## Linear genome view demo
+
+This demo shows a variety of tracks on hg38
+
+The text searching index created by running `jbrowse text-index` on the specific
+gene track file. This uses the --fileId to say what the trackId is of the file
+we are indexing with --file
+
+```bash
+## create index
+jbrowse text-index --file https://s3.amazonaws.com/jbrowse.org/genomes/GRCh38/ncbi_refseq/GCA_000001405.15_GRCh38_full_analysis_set.refseq_annotation.sorted.gff.gz --fileId genes
+
+## upload to aws
+aws s3 sync trix s3://jbrowse.org/genomes/GRCh38/ncbi_refseq/trix --delete
+
+```
+
+## Circular genome view demo
+
+This demo shows translocations SVs
diff --git a/embedded_demos/base/linear/assembly.ts b/embedded_demos/base/linear/assembly.ts
@@ -16,16 +16,6 @@ const assembly = {
         uri: 'https://jbrowse.org/genomes/GRCh38/fasta/hg38.prefix.fa.gz.gzi',
       },
     },
-    displays: [
-      {
-        type: 'LinearReferenceSequenceDisplay',
-        displayId:
-          'GRCh38-ReferenceSequenceTrack-LinearReferenceSequenceDisplay',
-        renderer: {
-          type: 'DivSequenceRenderer',
-        },
-      },
-    ],
   },
   refNameAliases: {
     adapter: {

diff --git a/embedded_demos/base/linear/tracks.ts b/embedded_demos/base/linear/tracks.ts
@@ -1,8 +1,7 @@
 const tracks = [
   {
     type: 'FeatureTrack',
-    trackId:
-      'GCA_000001405.15_GRCh38_full_analysis_set.refseq_annotation.sorted.gff',
+    trackId: 'genes',
     name: 'NCBI RefSeq Genes',
     assemblyNames: ['GRCh38'],
     category: ['Genes'],
@@ -17,6 +16,22 @@ const tracks = [
         },
       },
     },
+    textSearching: {
+      textSearchAdapter: {
+        type: 'TrixTextSearchAdapter',
+        textSearchAdapterId: 'gff3tabix_genes-index',
+        ixFilePath: {
+          uri: 'https://jbrowse.org/genomes/GRCh38/ncbi_refseq/trix/GCA_000001405.15_GRCh38_full_analysis_set.refseq_annotation.sorted.gff.gz.ix',
+        },
+        ixxFilePath: {
+          uri: 'https://jbrowse.org/genomes/GRCh38/ncbi_refseq/trix/GCA_000001405.15_GRCh38_full_analysis_set.refseq_annotation.sorted.gff.gz.ixx',
+        },
+        metaFilePath: {
+          uri: 'https://jbrowse.org/genomes/GRCh38/ncbi_refseq/trix/GCA_000001405.15_GRCh38_full_analysis_set.refseq_annotation.sorted.gff.gz_meta.json',
+        },
+        assemblyNames: ['GRCh38'],
+      },
+    },
   },
   {
     type: 'FeatureTrack',

diff --git a/embedded_demos/build_demos.sh b/embedded_demos/build_demos.sh
@@ -0,0 +1,2 @@
+#!/bin/bash
+for i in jbrowse*; do cd $i; yarn; yarn build; cd -; done;
diff --git a/embedded_demos/jbrowse-react-linear-genome-view-cra5/src/assembly.ts b/embedded_demos/jbrowse-react-linear-genome-view-cra5/src/assembly.ts
@@ -16,16 +16,6 @@ const assembly = {
         uri: 'https://jbrowse.org/genomes/GRCh38/fasta/hg38.prefix.fa.gz.gzi',
       },
     },
-    displays: [
-      {
-        type: 'LinearReferenceSequenceDisplay',
-        displayId:
-          'GRCh38-ReferenceSequenceTrack-LinearReferenceSequenceDisplay',
-        renderer: {
-          type: 'DivSequenceRenderer',
-        },
-      },
-    ],
   },
   refNameAliases: {
     adapter: {

diff --git a/embedded_demos/jbrowse-react-linear-genome-view-cra5/src/tracks.ts b/embedded_demos/jbrowse-react-linear-genome-view-cra5/src/tracks.ts
@@ -1,8 +1,7 @@
 const tracks = [
   {
     type: 'FeatureTrack',
-    trackId:
-      'GCA_000001405.15_GRCh38_full_analysis_set.refseq_annotation.sorted.gff',
+    trackId: 'genes',
     name: 'NCBI RefSeq Genes',
     assemblyNames: ['GRCh38'],
     category: ['Genes'],
@@ -17,6 +16,21 @@ const tracks = [
         },
       },
     },
+    textSearching: {
+      textSearchAdapter: {
+        type: 'TrixTextSearchAdapter',
+        textSearchAdapterId: 'gff3tabix_genes-index',
+        ixFilePath: {
+          uri: 'https://jbrowse.org/genomes/GRCh38/ncbi_refseq/trix/GCA_000001405.15_GRCh38_full_analysis_set.refseq_annotation.sorted.gff.gz.ix',
+        },
+        ixxFilePath: {
+          uri: 'https://jbrowse.org/genomes/GRCh38/ncbi_refseq/trix/GCA_000001405.15_GRCh38_full_analysis_set.refseq_annotation.sorted.gff.gz.ixx',
+        },
+        metaFilePath: {
+          uri: 'https://jbrowse.org/genomes/GRCh38/ncbi_refseq/trix/GCA_000001405.15_GRCh38_full_analysis_set.refseq_annotation.sorted.gff.gz_meta.json',
+        },
+      },
+    },
   },
   {
     type: 'FeatureTrack',

diff --git a/embedded_demos/jbrowse-react-linear-genome-view-nextjs/utils/assembly.ts b/embedded_demos/jbrowse-react-linear-genome-view-nextjs/utils/assembly.ts
@@ -16,16 +16,6 @@ const assembly = {
         uri: 'https://jbrowse.org/genomes/GRCh38/fasta/hg38.prefix.fa.gz.gzi',
       },
     },
-    displays: [
-      {
-        type: 'LinearReferenceSequenceDisplay',
-        displayId:
-          'GRCh38-ReferenceSequenceTrack-LinearReferenceSequenceDisplay',
-        renderer: {
-          type: 'DivSequenceRenderer',
-        },
-      },
-    ],
   },
   refNameAliases: {
     adapter: {

diff --git a/embedded_demos/jbrowse-react-linear-genome-view-nextjs/utils/tracks.ts b/embedded_demos/jbrowse-react-linear-genome-view-nextjs/utils/tracks.ts
@@ -1,8 +1,7 @@
 const tracks = [
   {
     type: 'FeatureTrack',
-    trackId:
-      'GCA_000001405.15_GRCh38_full_analysis_set.refseq_annotation.sorted.gff',
+    trackId: 'genes',
     name: 'NCBI RefSeq Genes',
     assemblyNames: ['GRCh38'],
     category: ['Genes'],
@@ -17,6 +16,21 @@ const tracks = [
         },
       },
     },
+    textSearching: {
+      textSearchAdapter: {
+        type: 'TrixTextSearchAdapter',
+        textSearchAdapterId: 'gff3tabix_genes-index',
+        ixFilePath: {
+          uri: 'https://jbrowse.org/genomes/GRCh38/ncbi_refseq/trix/GCA_000001405.15_GRCh38_full_analysis_set.refseq_annotation.sorted.gff.gz.ix',
+        },
+        ixxFilePath: {
+          uri: 'https://jbrowse.org/genomes/GRCh38/ncbi_refseq/trix/GCA_000001405.15_GRCh38_full_analysis_set.refseq_annotation.sorted.gff.gz.ixx',
+        },
+        metaFilePath: {
+          uri: 'https://jbrowse.org/genomes/GRCh38/ncbi_refseq/trix/GCA_000001405.15_GRCh38_full_analysis_set.refseq_annotation.sorted.gff.gz_meta.json',
+        },
+      },
+    },
   },
   {
     type: 'FeatureTrack',

diff --git a/embedded_demos/jbrowse-react-linear-genome-view-vanillajs/assembly.js b/embedded_demos/jbrowse-react-linear-genome-view-vanillajs/assembly.js
@@ -16,16 +16,6 @@ const assembly = {
         uri: 'https://jbrowse.org/genomes/GRCh38/fasta/hg38.prefix.fa.gz.gzi',
       },
     },
-    displays: [
-      {
-        type: 'LinearReferenceSequenceDisplay',
-        displayId:
-          'GRCh38-ReferenceSequenceTrack-LinearReferenceSequenceDisplay',
-        renderer: {
-          type: 'DivSequenceRenderer',
-        },
-      },
-    ],
   },
   refNameAliases: {
     adapter: {

diff --git a/embedded_demos/jbrowse-react-linear-genome-view-vanillajs/tracks.js b/embedded_demos/jbrowse-react-linear-genome-view-vanillajs/tracks.js
@@ -1,8 +1,7 @@
 const tracks = [
   {
     type: 'FeatureTrack',
-    trackId:
-      'GCA_000001405.15_GRCh38_full_analysis_set.refseq_annotation.sorted.gff',
+    trackId: 'genes',
     name: 'NCBI RefSeq Genes',
     assemblyNames: ['GRCh38'],
     category: ['Genes'],
@@ -17,6 +16,21 @@ const tracks = [
         },
       },
     },
+    textSearching: {
+      textSearchAdapter: {
+        type: 'TrixTextSearchAdapter',
+        textSearchAdapterId: 'gff3tabix_genes-index',
+        ixFilePath: {
+          uri: 'https://jbrowse.org/genomes/GRCh38/ncbi_refseq/trix/GCA_000001405.15_GRCh38_full_analysis_set.refseq_annotation.sorted.gff.gz.ix',
+        },
+        ixxFilePath: {
+          uri: 'https://jbrowse.org/genomes/GRCh38/ncbi_refseq/trix/GCA_000001405.15_GRCh38_full_analysis_set.refseq_annotation.sorted.gff.gz.ixx',
+        },
+        metaFilePath: {
+          uri: 'https://jbrowse.org/genomes/GRCh38/ncbi_refseq/trix/GCA_000001405.15_GRCh38_full_analysis_set.refseq_annotation.sorted.gff.gz_meta.json',
+        },
+      },
+    },
   },
   {
     type: 'FeatureTrack',

diff --git a/embedded_demos/jbrowse-react-linear-genome-view-vite/src/App.tsx b/embedded_demos/jbrowse-react-linear-genome-view-vite/src/App.tsx
@@ -8,64 +8,6 @@ import {
 import assembly from './assembly'
 import tracks from './tracks'
 
-const defaultSession = {
-  name: 'this session',
-  view: {
-    id: 'linearGenomeView',
-    type: 'LinearGenomeView',
-    tracks: [
-      {
-        id: '7PWx6ki1_',
-        type: 'ReferenceSequenceTrack',
-        configuration: 'GRCh38-ReferenceSequenceTrack',
-        displays: [
-          {
-            id: 'pa_7lx6FDh',
-            type: 'LinearReferenceSequenceDisplay',
-            height: 210,
-            configuration:
-              'GRCh38-ReferenceSequenceTrack-LinearReferenceSequenceDisplay',
-          },
-        ],
-      },
-      {
-        id: 'KHwe41KXk',
-        type: 'AlignmentsTrack',
-        configuration: 'NA12878.alt_bwamem_GRCh38DH.20150826.CEU.exome',
-        displays: [
-          {
-            id: '_-kwYVczT8',
-            type: 'LinearAlignmentsDisplay',
-            PileupDisplay: {
-              id: '1HTk32IDZJ',
-              type: 'LinearPileupDisplay',
-              height: 100,
-              configuration: {
-                type: 'LinearPileupDisplay',
-                displayId:
-                  'NA12878.alt_bwamem_GRCh38DH.20150826.CEU.exome-LinearAlignmentsDisplay_pileup_xyz',
-              },
-            },
-            SNPCoverageDisplay: {
-              id: 'ZBXRXmuDrc',
-              type: 'LinearSNPCoverageDisplay',
-              height: 45,
-              configuration: {
-                type: 'LinearSNPCoverageDisplay',
-                displayId:
-                  'NA12878.alt_bwamem_GRCh38DH.20150826.CEU.exome-LinearAlignmentsDisplay_snpcoverage_xyz',
-              },
-            },
-            configuration:
-              'NA12878.alt_bwamem_GRCh38DH.20150826.CEU.exome-LinearAlignmentsDisplay',
-            height: 250,
-          },
-        ],
-      },
-    ],
-  },
-}
-
 function View() {
   const [viewState, setViewState] =
     useState<ReturnType<typeof createViewState>>()
@@ -80,8 +22,12 @@ function View() {
       onChange: patch => {
         setPatches(previous => previous + JSON.stringify(patch) + '\n')
       },
-      defaultSession,
     })
+    state.session.view.showTrack('GRCh38-ReferenceSequenceTrack')
+    state.session.view.showTrack('genes')
+    state.session.view.showTrack(
+      'NA12878.alt_bwamem_GRCh38DH.20150826.CEU.exome',
+    )
     setViewState(state)
   }, [])
 

diff --git a/embedded_demos/jbrowse-react-linear-genome-view-vite/src/assembly.ts b/embedded_demos/jbrowse-react-linear-genome-view-vite/src/assembly.ts
@@ -16,16 +16,6 @@ const assembly = {
         uri: 'https://jbrowse.org/genomes/GRCh38/fasta/hg38.prefix.fa.gz.gzi',
       },
     },
-    displays: [
-      {
-        type: 'LinearReferenceSequenceDisplay',
-        displayId:
-          'GRCh38-ReferenceSequenceTrack-LinearReferenceSequenceDisplay',
-        renderer: {
-          type: 'DivSequenceRenderer',
-        },
-      },
-    ],
   },
   refNameAliases: {
     adapter: {

diff --git a/embedded_demos/jbrowse-react-linear-genome-view-vite/src/tracks.ts b/embedded_demos/jbrowse-react-linear-genome-view-vite/src/tracks.ts
@@ -1,8 +1,7 @@
 const tracks = [
   {
     type: 'FeatureTrack',
-    trackId:
-      'GCA_000001405.15_GRCh38_full_analysis_set.refseq_annotation.sorted.gff',
+    trackId: 'genes',
     name: 'NCBI RefSeq Genes',
     assemblyNames: ['GRCh38'],
     category: ['Genes'],
@@ -17,6 +16,22 @@ const tracks = [
         },
       },
     },
+    textSearching: {
+      textSearchAdapter: {
+        type: 'TrixTextSearchAdapter',
+        textSearchAdapterId: 'gff3tabix_genes-index',
+        ixFilePath: {
+          uri: 'https://jbrowse.org/genomes/GRCh38/ncbi_refseq/trix/GCA_000001405.15_GRCh38_full_analysis_set.refseq_annotation.sorted.gff.gz.ix',
+        },
+        ixxFilePath: {
+          uri: 'https://jbrowse.org/genomes/GRCh38/ncbi_refseq/trix/GCA_000001405.15_GRCh38_full_analysis_set.refseq_annotation.sorted.gff.gz.ixx',
+        },
+        metaFilePath: {
+          uri: 'https://jbrowse.org/genomes/GRCh38/ncbi_refseq/trix/GCA_000001405.15_GRCh38_full_analysis_set.refseq_annotation.sorted.gff.gz_meta.json',
+        },
+        assemblyNames: ['GRCh38'],
+      },
+    },
   },
   {
     type: 'FeatureTrack',

diff --git a/embedded_demos/jbrowse-react-linear-genome-view/src/assembly.ts b/embedded_demos/jbrowse-react-linear-genome-view/src/assembly.ts
@@ -16,16 +16,6 @@ const assembly = {
         uri: 'https://jbrowse.org/genomes/GRCh38/fasta/hg38.prefix.fa.gz.gzi',
       },
     },
-    displays: [
-      {
-        type: 'LinearReferenceSequenceDisplay',
-        displayId:
-          'GRCh38-ReferenceSequenceTrack-LinearReferenceSequenceDisplay',
-        renderer: {
-          type: 'DivSequenceRenderer',
-        },
-      },
-    ],
   },
   refNameAliases: {
     adapter: {