jbrowse2 initial implementation

Author: jctrotter

jbrowse/.DS_Store

@@ -0,0 +1,2 @@
+# Set registry for @labkey scopes
+@labkey:registry=https://artifactory.labkey.com/artifactory/api/npm/libs-client/

jbrowse/.npmrc

@@ -18,87 +18,4 @@ dependencies {
     BuildUtils.addLabKeyDependency(project: project, config: "modules", depProjectPath: ":server:modules:LabDevKitModules:LDK", depProjectConfig: "published", depExtension: "module")
     BuildUtils.addLabKeyDependency(project: project, config: "modules", depProjectPath: ":server:modules:DiscvrLabKeyModules:SequenceAnalysis", depProjectConfig: "published", depExtension: "module")
     BuildUtils.addLabKeyDependency(project: project, config: "modules", depProjectPath: BuildUtils.getPlatformModuleProjectPath(project.gradle, "pipeline"), depProjectConfig: "published", depExtension: "module")
-}
-
-ConfigurableFileTree copyDestination = fileTree("./resources/web/jbrowseApp/");
-project.task("copyJBrowse",
-        type: Copy,
-        group: "Build",
-        description: "Copy jbrowse app into webapp directory",
-        { CopySpec copy ->
-            copy.from fileTree("./node_modules/@gmod/jbrowse").exclude('css/main.css')
-            copy.into copyDestination.getDir()
-        }
-).doFirst({
-    File f = project.file('./node_modules/@gmod/jbrowse');
-    if (!f.exists()){
-        throw new GradleException("Input source for copyJBrowse doesn't exist: " + f.getAbsolutePath())
-    }
-}).onlyIf({
-    //this is a very expensive step and the input should rarely change
-    if (copyDestination.getDir().exists()) {
-        List<File> copiedFiles = copyDestination.exclude("./resources/web/jbrowseApp/css/").sort {it.lastModified()};
-        if (copiedFiles.isEmpty()) {
-            return true;
-        }
-        
-        File firstModifiedCopiedFile = copiedFiles.first()
-        File lastModifiedSourceFile = fileTree('./node_modules/@gmod/jbrowse').exclude('package.json').sort {it.lastModified()}.last()
-        if (firstModifiedCopiedFile.lastModified() < lastModifiedSourceFile.lastModified()) {
-            println("Source has been modified, need to copy again")
-            println("Copy last copied: " + new Date(firstModifiedCopiedFile.lastModified()))
-            println("First modified file: " + firstModifiedCopiedFile.getPath())
-
-            println("Source last modified: " + new Date(lastModifiedSourceFile.lastModified()))
-            println("Last modified file: " + lastModifiedSourceFile.getPath())
-
-            return true;
-        }
-        else {
-            println("Up to date, no need to copy")
-            return false;
-        }
-    }
-
-    return true;
-})
-
-project.task("copyJBrowseCss",
-        type: Copy,
-        group: "Build",
-        description: "Copy jbrowse main.css into webapp directory",
-        { CopySpec copy ->
-            copy.from new File("./webpack/main.css")
-            copy.into new File("./resources/web/jbrowseApp/css/")
-        }
-).doFirst({
-    File f = project.file('./resources/web/jbrowseApp/index.html');
-    if (!f.exists())
-    {
-        throw new GradleException("copyJBrowse was not successful.  missing: " + f.getAbsolutePath())
-    }
-
-    File f2 = project.file('./resources/web/jbrowseApp/src/dijit/themes/dijit.css');
-    if (!f2.exists())
-    {
-        throw new GradleException("copyJBrowse was not successful.  missing jbrowse dependencies: " + f2.getAbsolutePath())
-    }
-
-    // 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.
-    // There's a jbrowse PR around this as well.
-    File f3 = project.file('./resources/web/jbrowseApp/src/jszlib');
-    if (!f3.exists())
-    {
-        throw new GradleException("copyJBrowse was not successful.  missing jbrowse dependencies: " + f3.getAbsolutePath())
-    }
-})
-
-
-project.tasks.copyJBrowse.dependsOn(project.tasks.npmInstall)
-
-project.tasks.copyJBrowse.mustRunAfter("npmRunBuild")
-project.tasks.copyJBrowse.mustRunAfter("npmRunBuildProd")
-
-project.tasks.copyJBrowseCss.dependsOn(project.tasks.copyJBrowse)
-project.tasks.processModuleResources.dependsOn(project.tasks.copyJBrowse)
-project.tasks.processModuleResources.dependsOn(project.tasks.copyJBrowseCss)
+}

jbrowse/build.gradle

@@ -0,0 +1,46 @@
+/*
+ * Copyright (c) 2019 LabKey Corporation
+ *
+ * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0
+ */
+
+ // COPY THIS FILE TO node_modules/@labkey/build/webpack/dev.config.js
+const lkModule = process.env.LK_MODULE;
+const entryPoints = require('../../../../src/client/entryPoints');
+const constants = require('./constants');
+const webpack = require('webpack');
+
+// set based on the lk module calling this config
+__dirname = lkModule;
+
+module.exports = {
+    context: constants.context(__dirname),
+
+    mode: 'development',
+
+    devtool: 'eval',
+
+    entry: constants.processEntries(entryPoints),
+
+    output: {
+        path: constants.outputPath(__dirname),
+        publicPath: './', // allows context path to resolve in both js/css
+        filename: '[name].js'
+    },
+
+    module: {
+        rules: constants.loaders.TYPESCRIPT_LOADERS.concat(constants.loaders.STYLE_LOADERS)
+    },
+
+    resolve: {
+        extensions: constants.extensions.TYPESCRIPT
+    },
+
+    plugins: [new webpack.ProvidePlugin({
+        regeneratorRuntime: 'regenerator-runtime',
+    })],
+
+    node: {
+        fs: "empty"
+    },
+};