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Remove src imports from JBrowse (#215)
* Update to latest version of JBrowse * Refactor VariantTable to let columns be driven by the VCF
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‎SequenceAnalysis/test/sampledata/sequenceAnalysis/genomeAnnotations/fakeData.gff‎

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@@ -1,5 +1,5 @@
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SIVmac239 SS_probe probe 2691 2805 . + . gene_id=Gag; transcript_id=Gag; Identity=94.6
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SIVmac239 SS_probe probe 4165 4237 . + . gene_id=Gag; transcript_id=Gag; Identity=93
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SIVmac239 SS_probe probe 5251 5370 . + . gene_id=Gag; transcript_id=Gag; Identity=92.4
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SIVmac239 SS_probe probe 8510 8630 . + . gene_id=Gag; transcript_id=Gag; Identity=95
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SIVmac239 SS_probe probe 10373 10493 . + . gene_id=Gag; transcript_id=Gag; Identity=95
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SIVmac239 SS_probe probe 2691 2805 . + . gene_id=Gene0; transcript_id=Gene0; Identity=94.6
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SIVmac239 SS_probe probe 4165 4237 . + . gene_id=Gene1; transcript_id=Gene1; Identity=93
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SIVmac239 SS_probe probe 5251 5370 . + . gene_id=Gene1; transcript_id=Gene1; Identity=92.4
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SIVmac239 SS_probe probe 8510 8630 . + . gene_id=Gene3; transcript_id=Gene3; Identity=95
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SIVmac239 SS_probe probe 10373 10493 . + . gene_id=Gene4; transcript_id=Gene4; Identity=95

‎jbrowse/api-src/org/labkey/api/jbrowse/JBrowseFieldDescriptor.java‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -180,7 +180,7 @@ public JSONObject toJSON() {
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fieldDescriptorJSON.put("name", _fieldName);
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fieldDescriptorJSON.put("label", _label == null ? _fieldName : _label);
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fieldDescriptorJSON.put("description", _description);
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fieldDescriptorJSON.put("type", _type.toString());
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fieldDescriptorJSON.put("type", _type == null ? null : _type.toString());
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fieldDescriptorJSON.put("isInDefaultColumns", _isInDefaultColumns);
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fieldDescriptorJSON.put("isIndexed", _isIndexed);
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fieldDescriptorJSON.put("isMultiValued", _isMultiValued);

‎jbrowse/build.gradle‎

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Original file line numberDiff line numberDiff line change
@@ -37,7 +37,6 @@ def jbPkgTask = project.tasks.named("npm_run_jb-pkg")
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jbPkgTask.configure {
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outputs.cacheIf {false}
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inputs.dir(project.file("./node_modules/@jbrowse/cli")).withPathSensitivity(PathSensitivity.RELATIVE)
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outputs.dir(project.file("./resources/external/jb-cli"))
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}
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‎jbrowse/config/dev.config.js‎

Lines changed: 3 additions & 24 deletions
Original file line numberDiff line numberDiff line change
@@ -12,35 +12,14 @@ const NodePolyfillPlugin = require("node-polyfill-webpack-plugin")
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const clientConfig = devConfig
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// See: https://stackoverflow.com/questions/68707553/uncaught-referenceerror-buffer-is-not-defined
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clientConfig.resolve.fallback =
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{
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"buffer": require.resolve("buffer"),
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"path": require.resolve("path-browserify"),
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"stream": require.resolve("stream-browserify"),
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"zlib": require.resolve("browserify-zlib"),
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"vm": require.resolve("vm-browserify"),
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"fs": false
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"buffer": require.resolve("buffer")
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}
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clientConfig.resolve.alias["react/jsx-dev-runtime"] = "react/jsx-dev-runtime.js"
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clientConfig.resolve.alias["react/jsx-runtime"] = "react/jsx-runtime.js"
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clientConfig.resolve.alias["process/browser"] = "process/browser.js"
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clientConfig.plugins = [new NodePolyfillPlugin()].concat(constants.processPlugins(entryPoints))
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clientConfig.module.rules = clientConfig.module.rules.concat(
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{
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test: /\.m?js$/,
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exclude: /node_modules/,
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use: {
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loader: 'babel-loader',
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options: {
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presets: [
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['@babel/preset-env', { targets: "defaults" }],
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['@babel/preset-react']
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]
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}
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}
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})
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clientConfig.output.publicPath = 'auto'
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module.exports = [clientConfig]

‎jbrowse/config/prod.config.js‎

Lines changed: 7 additions & 23 deletions
Original file line numberDiff line numberDiff line change
@@ -12,35 +12,19 @@ const NodePolyfillPlugin = require("node-polyfill-webpack-plugin")
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const clientConfig = prodConfig
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// See: https://stackoverflow.com/questions/68707553/uncaught-referenceerror-buffer-is-not-defined
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clientConfig.resolve.fallback =
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{
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"buffer": require.resolve("buffer"),
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"path": require.resolve("path-browserify"),
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"stream": require.resolve("stream-browserify"),
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"zlib": require.resolve("browserify-zlib"),
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"vm": require.resolve("vm-browserify"),
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"fs": false
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"buffer": require.resolve("buffer")
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}
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clientConfig.resolve.alias["react/jsx-dev-runtime"] = "react/jsx-dev-runtime.js"
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clientConfig.resolve.alias["react/jsx-runtime"] = "react/jsx-runtime.js"
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clientConfig.resolve.alias["process/browser"] = "process/browser.js"
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clientConfig.resolve.fallback =
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{
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"buffer": require.resolve("buffer")
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}
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clientConfig.plugins = [new NodePolyfillPlugin()].concat(constants.processPlugins(entryPoints))
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clientConfig.module.rules = clientConfig.module.rules.concat(
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{
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test: /\.m?js$/,
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exclude: /node_modules/,
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use: {
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loader: 'babel-loader',
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options: {
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presets: [
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['@babel/preset-env', { targets: "defaults" }],
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['@babel/preset-react']
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]
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}
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}
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})
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clientConfig.output.publicPath = 'auto'
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module.exports = [clientConfig]

‎jbrowse/config/watch.config.js‎

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Original file line numberDiff line numberDiff line change
@@ -15,32 +15,10 @@ const clientConfig = watchConfig
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clientConfig.resolve.fallback =
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{
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"buffer": require.resolve("buffer"),
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"path": require.resolve("path-browserify"),
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"stream": require.resolve("stream-browserify"),
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"zlib": require.resolve("browserify-zlib"),
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"vm": require.resolve("vm-browserify"),
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"fs": false
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}
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clientConfig.resolve.alias["react/jsx-dev-runtime"] = "react/jsx-dev-runtime.js"
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clientConfig.resolve.alias["react/jsx-runtime"] = "react/jsx-runtime.js"
27-
clientConfig.resolve.alias["process/browser"] = "process/browser.js"
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clientConfig.plugins = [new NodePolyfillPlugin()].concat(constants.processPlugins(entryPoints))
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31-
clientConfig.module.rules = clientConfig.module.rules.concat(
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{
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test: /\.m?js$/,
34-
exclude: /node_modules/,
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use: {
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loader: 'babel-loader',
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options: {
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presets: [
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['@babel/preset-env', { targets: "defaults" }],
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['@babel/preset-react']
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]
42-
}
43-
}
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})
22+
clientConfig.output.publicPath = 'auto'
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module.exports = [clientConfig]

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