Merge pull request #15 from GMOD/2.0.1-lgv-update

2.0.1 lgv update

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: JBrowseR
 Title: An R Interface to the JBrowse 2 Genome Browser
-Version: 0.9.0.9000
+Version: 0.9.1
 Authors@R: 
     c(person(given = "Elliot",
              family = "Hershberg",

NAMESPACE

@@ -8,6 +8,7 @@ export(default_session)
 export(json_config)
 export(renderJBrowseR)
 export(serve_data)
+export(text_index)
 export(theme)
 export(track_alignments)
 export(track_data_frame)

NEWS.md

@@ -1,3 +1,8 @@
+# JBrowse 0.9.1
+
+- Updated `@jbrowse/react-linear-genome-view` to latest release (2.0.1). Check out the [JB2 release notes](https://jbrowse.org/jb2/blog/2022/07/13/v2.0.1-release/) to learn about all of the features!
+- Added a new function `text_index()` to provide support for text search.
+
 # JBrowseR 0.9.0
 
 - Updated `@jbrowse/react-linear-genome-view` to latest release (1.4.4). Check out the [JB2 release notes](https://jbrowse.org/jb2/blog/2021/09/14/v1.4.4-release/) to learn about all of the features!

R/text-index.R

@@ -0,0 +1,51 @@
+#' Create configuration for a JBrowse 2 text index
+#'
+#' Creates the necessary configuration string for an adapter to a text index for
+#' gene name search in the browser.
+#'
+#' Note: this function currently only supports aggregate indeces.
+#'
+#' For more information on JBrowse 2 text indeces, visit:
+#' \url{https://jbrowse.org/jb2/docs/config_guide/#text-searching}
+#'
+#' @param ix_uri the URI for the ix file
+#' @param ixx_uri the URI for the ixx file
+#' @param meta_uri the URI for the JSON metadata file
+#' @param assembly the assembly associated with the text index
+#'
+#' @return a character vector with the JSON text index adapter.
+#'
+#' @export
+#'
+#' @examples
+#' text_index(
+#' "https://jbrowse.org/genomes/hg19/trix/hg19.ix",
+#' "https://jbrowse.org/genomes/hg19/trix/hg19.ixx",
+#' "https://jbrowse.org/genomes/hg19/trix/meta.json",
+#' "hg19"
+#' )
+text_index <- function(ix_uri, ixx_uri, meta_uri, assembly) {
+  id <- paste0(assembly, "-index")
+
+  as.character(
+    stringr::str_glue(
+      "{{",
+      '"type": "TrixTextSearchAdapter", ',
+      '"textSearchAdapterId": "{id}", ',
+      '"ixFilePath": {{',
+      '"uri": "{ix_uri}", ',
+      '"locationType": "UriLocation"',
+      "}}, ",
+      '"ixxFilePath": {{',
+      '"uri": "{ixx_uri}", ',
+      '"locationType": "UriLocation"',
+      "}}, ",
+      '"metaFilePath": {{',
+      '"uri": "{meta_uri}", ',
+      '"locationType": "UriLocation"',
+      "}}, ",
+      '"assemblyNames": ["{assembly}"]',
+      "}}"
+    )
+  )
+}

_pkgdown.yml

@@ -27,6 +27,7 @@ reference:
 - contents:
   - theme
   - json_config
+  - text_index
 - title: "Utilities"
 - contents:
   - serve_data

example_apps/custom_app.R

@@ -2,6 +2,11 @@ library(shiny)
 library(JBrowseR)
 
 ui <- fluidPage(
+  tags$head(
+    tags$style(HTML(
+      "html { font-size: 14px }"
+    ))
+  ),
   titlePanel("JBrowseR Example"),
   JBrowseROutput("widgetOutput")
 )

example_apps/hg38_index_app.R

@@ -0,0 +1,30 @@
+library(shiny)
+library(JBrowseR)
+
+ui <- fluidPage(titlePanel("JBrowseR Example"),
+                JBrowseROutput("widgetOutput"))
+
+server <- function(input, output, session) {
+  hg38 <- assembly(
+    "https://jbrowse.org/genomes/GRCh38/fasta/hg38.prefix.fa.gz",
+    bgzip = TRUE,
+    aliases = c("GRCh38"),
+    refname_aliases = "https://s3.amazonaws.com/jbrowse.org/genomes/GRCh38/hg38_aliases.txt"
+  )
+
+
+  output$widgetOutput <- renderJBrowseR(JBrowseR(
+    "View",
+    location = "10:29,838,737..29,838,819",
+    assembly = hg38,
+    text_index = text_index(
+      "https://jbrowse.org/genomes/GRCh38/trix/hg38.ix",
+      "https://jbrowse.org/genomes/GRCh38/trix/hg38.ixx",
+      "https://jbrowse.org/genomes/GRCh38/trix/meta.json",
+      "hg38"
+    )
+  ))
+
+}
+
+shinyApp(ui, server)

package.json

@@ -1,7 +1,7 @@
 {
   "private": true,
   "dependencies": {
-    "@jbrowse/react-linear-genome-view": "^1.4.4",
+    "@jbrowse/react-linear-genome-view": "^2.0.1",
     "react": "^17.0.1",
     "react-dom": "^17.0.1"
   },

srcjs/components/JsonView.jsx

@@ -7,7 +7,7 @@ import { messageShiny } from "../utils";
 
 export default function View(props) {
   const configObject = JSON.parse(props.config);
-  const { assembly, tracks, defaultSession, theme } = configObject;
+  const { assembly, tracks, defaultSession, theme, text_index } = configObject;
   const location = props.location;
   const state = createViewState({
     assembly,
@@ -16,9 +16,8 @@ export default function View(props) {
     location,
     onChange: messageShiny,
     configuration: { theme },
+    aggregateTextSearchAdapters: [text_index],
   });
 
-  return (
-    <JBrowseLinearGenomeView viewState={state} />
-  );
+  return <JBrowseLinearGenomeView viewState={state} />;
 }

srcjs/components/View.jsx

@@ -14,6 +14,8 @@ export default function View(props) {
     if (key === "theme") {
       theme = JSON.parse(value);
       stateOpts["configuration"] = { theme };
+    } else if (key == "text_index") {
+      stateOpts["aggregateTextSearchAdapters"] = [JSON.parse(value)];
     } else {
       // parse the string of JSON config
       key === "location"
@@ -25,7 +27,5 @@ export default function View(props) {
 
   const state = createViewState(stateOpts);
 
-  return (
-    <JBrowseLinearGenomeView viewState={state} />
-  );
+  return <JBrowseLinearGenomeView viewState={state} />;
 }

tests/testthat/test-text-index.R

@@ -0,0 +1,11 @@
+test_that("creating a text index returns valid configuration", {
+  expect_equal(
+    text_index(
+      "https://jbrowse.org/genomes/GRCh38/trix/hg38.ix",
+      "https://jbrowse.org/genomes/GRCh38/trix/hg38.ixx",
+      "https://jbrowse.org/genomes/GRCh38/trix/meta.json",
+      "hg38"
+    ),
+    "{\"type\": \"TrixTextSearchAdapter\", \"textSearchAdapterId\": \"hg38-index\", \"ixFilePath\": {\"uri\": \"https://jbrowse.org/genomes/GRCh38/trix/hg38.ix\", \"locationType\": \"UriLocation\"}, \"ixxFilePath\": {\"uri\": \"https://jbrowse.org/genomes/GRCh38/trix/hg38.ixx\", \"locationType\": \"UriLocation\"}, \"metaFilePath\": {\"uri\": \"https://jbrowse.org/genomes/GRCh38/trix/meta.json\", \"locationType\": \"UriLocation\"}, \"assemblyNames\": [\"hg38\"]}"
+  )
+})

webpack.config.js

@@ -1,5 +1,6 @@
 var path = require('path');
 var CompressionPlugin = require("compression-webpack-plugin");
+var webpack = require('webpack')
 
 module.exports = {
     mode: 'production',
@@ -33,6 +34,11 @@ module.exports = {
     stats: {
         colors: true
     },
+    plugins: [
+      new webpack.optimize.LimitChunkCountPlugin({
+        maxChunks: 1,
+      }),
+    ],
     // can toggle source map back on during development
     // devtool: 'source-map'
     devtool: '',