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Merge pull request #37 from jctrotter/discvr-21.3-jbrowse2
Discvr 21.3 jbrowse2 react linear genome view
2 parents 4c528d3 + fc5a6f9 commit 0c0076c

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‎.gitignore‎

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@@ -8,3 +8,9 @@
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/jbrowse/jb_run.js
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/jbrowse/jb_setup.js
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/jbrowse/.gradle
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# Ignore labkey-npm build artifacts
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**/gen/**
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# Ignore MacOS .DS_Store artifacts
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**/.DS_Store

‎SequenceAnalysis/src/org/labkey/sequenceanalysis/query/SequenceAnalysisCustomizer.java‎

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@@ -161,7 +161,7 @@ public void customizeColumn(BaseColumnInfo col, AbstractTableInfo ti)
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COL_ENUM(Class dataType, @Nullable Collection<String> alternateNames){
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this.dataType = dataType;
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if (alternateNames != null)
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this.alternateNames.addAll(alternateNames);
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this.alternateNames.addAll(alternateNames);
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}
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public Collection<String> getAlternateNames()
@@ -181,8 +181,8 @@ private static void addFk(Container c, User u, BaseColumnInfo col, String schema
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if (col.getFk() == null)
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{
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col.setFk(QueryForeignKey.from(DefaultSchema.get(u,c),null)
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.schema(schema, c)
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.to(query, pkCol, displayCol));
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.schema(schema, c)
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.to(query, pkCol, displayCol));
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}
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}
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@@ -269,4 +269,4 @@ public void renderGridCellContents(RenderContext ctx, Writer out) throws IOExcep
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};
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}
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}
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}
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}

‎jbrowse/.npmrc‎

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# Set registry for @labkey scopes
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@labkey:registry=https://artifactory.labkey.com/artifactory/api/npm/libs-client/

‎jbrowse/README.md‎

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Page is visible at http://localhost:8080/labkey/home/jbrowse-jbrowse.view?

‎jbrowse/build.gradle‎

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@@ -22,75 +22,75 @@ dependencies {
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ConfigurableFileTree copyDestination = fileTree("./resources/web/jbrowseApp/");
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project.task("copyJBrowse",
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type: Copy,
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group: "Build",
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description: "Copy jbrowse app into webapp directory",
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{ CopySpec copy ->
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copy.from fileTree("./node_modules/@gmod/jbrowse").exclude('css/main.css')
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copy.into copyDestination.getDir()
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}
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type: Copy,
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group: "Build",
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description: "Copy jbrowse app into webapp directory",
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{ CopySpec copy ->
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copy.from fileTree("./node_modules/@gmod/jbrowse").exclude('css/main.css')
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copy.into copyDestination.getDir()
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}
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).doFirst({
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File f = project.file('./node_modules/@gmod/jbrowse');
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if (!f.exists()){
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throw new GradleException("Input source for copyJBrowse doesn't exist: " + f.getAbsolutePath())
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}
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File f = project.file('./node_modules/@gmod/jbrowse');
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if (!f.exists()){
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throw new GradleException("Input source for copyJBrowse doesn't exist: " + f.getAbsolutePath())
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}
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}).onlyIf({
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//this is a very expensive step and the input should rarely change
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if (copyDestination.getDir().exists()) {
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List<File> copiedFiles = copyDestination.exclude("./resources/web/jbrowseApp/css/").sort {it.lastModified()};
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if (copiedFiles.isEmpty()) {
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return true;
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}
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File firstModifiedCopiedFile = copiedFiles.first()
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File lastModifiedSourceFile = fileTree('./node_modules/@gmod/jbrowse').exclude('package.json').sort {it.lastModified()}.last()
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if (firstModifiedCopiedFile.lastModified() < lastModifiedSourceFile.lastModified()) {
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println("Source has been modified, need to copy again")
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println("Copy last copied: " + new Date(firstModifiedCopiedFile.lastModified()))
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println("First modified file: " + firstModifiedCopiedFile.getPath())
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//this is a very expensive step and the input should rarely change
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if (copyDestination.getDir().exists()) {
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List<File> copiedFiles = copyDestination.exclude("./resources/web/jbrowseApp/css/").sort {it.lastModified()};
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if (copiedFiles.isEmpty()) {
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return true;
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}
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File firstModifiedCopiedFile = copiedFiles.first()
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File lastModifiedSourceFile = fileTree('./node_modules/@gmod/jbrowse').exclude('package.json').sort {it.lastModified()}.last()
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if (firstModifiedCopiedFile.lastModified() < lastModifiedSourceFile.lastModified()) {
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println("Source has been modified, need to copy again")
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println("Copy last copied: " + new Date(firstModifiedCopiedFile.lastModified()))
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println("First modified file: " + firstModifiedCopiedFile.getPath())
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52-
println("Source last modified: " + new Date(lastModifiedSourceFile.lastModified()))
53-
println("Last modified file: " + lastModifiedSourceFile.getPath())
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println("Source last modified: " + new Date(lastModifiedSourceFile.lastModified()))
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println("Last modified file: " + lastModifiedSourceFile.getPath())
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55-
return true;
56-
}
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else {
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println("Up to date, no need to copy")
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return false;
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}
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}
55+
return true;
56+
}
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else {
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println("Up to date, no need to copy")
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return false;
60+
}
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}
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63-
return true;
63+
return true;
6464
})
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6666
project.task("copyJBrowseCss",
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type: Copy,
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group: "Build",
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description: "Copy jbrowse main.css into webapp directory",
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{ CopySpec copy ->
71-
copy.from new File("./webpack/main.css")
72-
copy.into new File("./resources/web/jbrowseApp/css/")
73-
}
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type: Copy,
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group: "Build",
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description: "Copy jbrowse main.css into webapp directory",
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{ CopySpec copy ->
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copy.from new File("./webpack/main.css")
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copy.into new File("./resources/web/jbrowseApp/css/")
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}
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).doFirst({
75-
File f = project.file('./resources/web/jbrowseApp/index.html');
76-
if (!f.exists())
77-
{
78-
throw new GradleException("copyJBrowse was not successful. missing: " + f.getAbsolutePath())
79-
}
75+
File f = project.file('./resources/web/jbrowseApp/index.html');
76+
if (!f.exists())
77+
{
78+
throw new GradleException("copyJBrowse was not successful. missing: " + f.getAbsolutePath())
79+
}
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81-
File f2 = project.file('./resources/web/jbrowseApp/src/dijit/themes/dijit.css');
82-
if (!f2.exists())
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{
84-
throw new GradleException("copyJBrowse was not successful. missing jbrowse dependencies: " + f2.getAbsolutePath())
85-
}
81+
File f2 = project.file('./resources/web/jbrowseApp/src/dijit/themes/dijit.css');
82+
if (!f2.exists())
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{
84+
throw new GradleException("copyJBrowse was not successful. missing jbrowse dependencies: " + f2.getAbsolutePath())
85+
}
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87-
// NOTE: due to bug/inconsistency in how the jbrowse postinstall script is run, several modules may not be copied to /src. This is a check against this.
88-
// There's a jbrowse PR around this as well.
89-
File f3 = project.file('./resources/web/jbrowseApp/src/jszlib');
90-
if (!f3.exists())
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{
92-
throw new GradleException("copyJBrowse was not successful. missing jbrowse dependencies: " + f3.getAbsolutePath())
93-
}
87+
// NOTE: due to bug/inconsistency in how the jbrowse postinstall script is run, several modules may not be copied to /src. This is a check against this.
88+
// There's a jbrowse PR around this as well.
89+
File f3 = project.file('./resources/web/jbrowseApp/src/jszlib');
90+
if (!f3.exists())
91+
{
92+
throw new GradleException("copyJBrowse was not successful. missing jbrowse dependencies: " + f3.getAbsolutePath())
93+
}
9494
})
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9696

@@ -101,4 +101,4 @@ project.tasks.copyJBrowse.mustRunAfter("npmRunBuildProd")
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102102
project.tasks.copyJBrowseCss.dependsOn(project.tasks.copyJBrowse)
103103
project.tasks.processModuleResources.dependsOn(project.tasks.copyJBrowse)
104-
project.tasks.processModuleResources.dependsOn(project.tasks.copyJBrowseCss)
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project.tasks.processModuleResources.dependsOn(project.tasks.copyJBrowseCss)

‎jbrowse/config/dev.config.js‎

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/*
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* Copyright (c) 2019 LabKey Corporation
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*
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* Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0
5+
*/
6+
7+
const devConfig = require('../node_modules/@labkey/build/webpack/dev.config')
8+
9+
const entryPoints = require('../src/client/entryPoints');
10+
const constants = require('../node_modules/@labkey/build/webpack/constants');
11+
const webpack = require('webpack');
12+
const NodePolyfillPlugin = require("node-polyfill-webpack-plugin")
13+
14+
const clientConfig = devConfig
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16+
clientConfig.resolve.fallback =
17+
{
18+
"buffer": require.resolve("buffer"),
19+
"path": require.resolve("path-browserify"),
20+
"stream": require.resolve("stream-browserify"),
21+
"zlib": require.resolve("browserify-zlib"),
22+
"vm": require.resolve("vm-browserify"),
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"fs": false
24+
}
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clientConfig.plugins =
27+
[new webpack.ProvidePlugin({regeneratorRuntime: 'regenerator-runtime'}),
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new NodePolyfillPlugin()].concat(constants.processPlugins(entryPoints))
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module.exports = [clientConfig]

‎jbrowse/config/prod.config.js‎

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/*
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* Copyright (c) 2019 LabKey Corporation
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*
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* Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0
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*/
6+
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const prodConfig = require('../node_modules/@labkey/build/webpack/prod.config')
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const entryPoints = require('../src/client/entryPoints');
10+
const constants = require('../node_modules/@labkey/build/webpack/constants');
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const webpack = require('webpack');
12+
const NodePolyfillPlugin = require("node-polyfill-webpack-plugin")
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const clientConfig = prodConfig
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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"),
21+
"zlib": require.resolve("browserify-zlib"),
22+
"vm": require.resolve("vm-browserify"),
23+
"fs": false
24+
}
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26+
clientConfig.plugins =
27+
[new webpack.ProvidePlugin({regeneratorRuntime: 'regenerator-runtime'}),
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new NodePolyfillPlugin()].concat(constants.processPlugins(entryPoints))
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module.exports = [clientConfig]

‎jbrowse/config/watch.config.js‎

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/*
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* Copyright (c) 2019 LabKey Corporation
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*
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* Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0
5+
*/
6+
7+
const watchConfig = require('../node_modules/@labkey/build/webpack/watch.config')
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9+
const entryPoints = require('../src/client/entryPoints');
10+
const constants = require('../node_modules/@labkey/build/webpack/constants');
11+
const webpack = require('webpack');
12+
const NodePolyfillPlugin = require("node-polyfill-webpack-plugin")
13+
14+
const clientConfig = watchConfig
15+
16+
clientConfig.resolve.fallback =
17+
{
18+
"buffer": require.resolve("buffer"),
19+
"path": require.resolve("path-browserify"),
20+
"stream": require.resolve("stream-browserify"),
21+
"zlib": require.resolve("browserify-zlib"),
22+
"vm": require.resolve("vm-browserify"),
23+
"fs": false
24+
}
25+
26+
clientConfig.plugins =
27+
[new webpack.ProvidePlugin({regeneratorRuntime: 'regenerator-runtime'}),
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new NodePolyfillPlugin()].concat(constants.processPlugins(entryPoints))
29+
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31+
module.exports = [clientConfig]

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