Merge pull request #2 from jctrotter/21.4-jbrowse2-2.1.0

merge discvr-21.4 jbrowse2 implementation to fresh 21.3 branch

Author: jctrotter

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

@@ -12,6 +12,7 @@
 import org.labkey.api.data.DisplayColumn;
 import org.labkey.api.data.DisplayColumnFactory;
 import org.labkey.api.data.JdbcType;
+import org.labkey.api.data.MutableColumnInfo;
 import org.labkey.api.data.RenderContext;
 import org.labkey.api.data.SQLFragment;
 import org.labkey.api.data.TableCustomizer;
@@ -99,21 +100,21 @@ private void customizeSharedCols(AbstractTableInfo ti)
     private enum COL_ENUM
     {
         refNtSequence(Integer.class, PageFlowUtil.set("sequenceid", "ref_nt_sequence")){
-            public void customizeColumn(BaseColumnInfo col, AbstractTableInfo ti)
+            public void customizeColumn(MutableColumnInfo col, AbstractTableInfo ti)
             {
                 col.setLabel("Ref NT Sequence");
                 addFk(ti.getUserSchema().getContainer(), ti.getUserSchema().getUser(), col, SequenceAnalysisSchema.SCHEMA_NAME, SequenceAnalysisSchema.TABLE_REF_NT_SEQUENCES, "rowid", "name");
             }
         },
         libraryId(Integer.class, PageFlowUtil.set("genomeId", "genome_id", "library_id")){
-            public void customizeColumn(BaseColumnInfo col, AbstractTableInfo ti)
+            public void customizeColumn(MutableColumnInfo col, AbstractTableInfo ti)
             {
                 col.setLabel("Reference Genome");
                 addFk(ti.getUserSchema().getContainer(), ti.getUserSchema().getUser(), col, SequenceAnalysisSchema.SCHEMA_NAME, SequenceAnalysisSchema.TABLE_REF_LIBRARIES, "rowid", "rowid");
             }
         },
         runid(Integer.class, PageFlowUtil.set("run_id")){
-            public void customizeColumn(BaseColumnInfo col, AbstractTableInfo ti)
+            public void customizeColumn(MutableColumnInfo col, AbstractTableInfo ti)
             {
                 col.setLabel("Run");
                 col.setShownInInsertView(false);
@@ -124,7 +125,7 @@ public void customizeColumn(BaseColumnInfo col, AbstractTableInfo ti)
             }
         },
         jobid(Integer.class, PageFlowUtil.set("job_id")){
-            public void customizeColumn(BaseColumnInfo col, AbstractTableInfo ti)
+            public void customizeColumn(MutableColumnInfo col, AbstractTableInfo ti)
             {
                 col.setLabel("Job Id");
                 col.setShownInInsertView(false);
@@ -134,21 +135,21 @@ public void customizeColumn(BaseColumnInfo col, AbstractTableInfo ti)
             }
         },
         dataId(Integer.class, PageFlowUtil.set("data_id")){
-            public void customizeColumn(BaseColumnInfo col, AbstractTableInfo ti)
+            public void customizeColumn(MutableColumnInfo col, AbstractTableInfo ti)
             {
                 col.setLabel("File Id");
                 addFk(ti.getUserSchema().getContainer(), ti.getUserSchema().getUser(), col, "exp", "data", "rowid", null);
             }
         },
         readset(Integer.class, PageFlowUtil.set("readsetId", "readset_id")){
-            public void customizeColumn(BaseColumnInfo col, AbstractTableInfo ti)
+            public void customizeColumn(MutableColumnInfo col, AbstractTableInfo ti)
             {
                 col.setLabel("Readset");
                 addFk(ti.getUserSchema().getContainer(), ti.getUserSchema().getUser(), col, SequenceAnalysisSchema.SCHEMA_NAME, SequenceAnalysisSchema.TABLE_READSETS, "rowid", null);
             }
         },
         analysisId(Integer.class, PageFlowUtil.set("analysis_id")){
-            public void customizeColumn(BaseColumnInfo col, AbstractTableInfo ti)
+            public void customizeColumn(MutableColumnInfo col, AbstractTableInfo ti)
             {
                 col.setLabel("Analysis Id");
                 addFk(ti.getUserSchema().getContainer(), ti.getUserSchema().getUser(), col, SequenceAnalysisSchema.SCHEMA_NAME, SequenceAnalysisSchema.TABLE_ANALYSES, "rowid", null);
@@ -176,7 +177,7 @@ private static void setNonEditable(BaseColumnInfo col)
             col.setShownInUpdateView(false);
         }
 
-        private static void addFk(Container c, User u, BaseColumnInfo col, String schema, String query, String pkCol, @Nullable String displayCol)
+        private static void addFk(Container c, User u, MutableColumnInfo col, String schema, String query, String pkCol, @Nullable String displayCol)
         {
             if (col.getFk() == null)
             {
@@ -186,9 +187,9 @@ private static void addFk(Container c, User u, BaseColumnInfo col, String schema
             }
         }
 
-        abstract public void customizeColumn(BaseColumnInfo col, AbstractTableInfo ti);
+        abstract public void customizeColumn(MutableColumnInfo col, AbstractTableInfo ti);
 
-        public static void processColumn(BaseColumnInfo col, AbstractTableInfo ti)
+        public static void processColumn(MutableColumnInfo col, AbstractTableInfo ti)
         {
             for (COL_ENUM colEnum : COL_ENUM.values())
             {

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

@@ -0,0 +1 @@
+Page is visible at http://localhost:8080/labkey/home/jbrowse-jbrowse.view?

jbrowse/README.md

@@ -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 +1,31 @@
+/*
+ * Copyright (c) 2019 LabKey Corporation
+ *
+ * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0
+ */
+
+const devConfig = require('../node_modules/@labkey/build/webpack/dev.config')
+
+const entryPoints = require('../src/client/entryPoints');
+const constants = require('../node_modules/@labkey/build/webpack/constants');
+const webpack = require('webpack');
+const NodePolyfillPlugin = require("node-polyfill-webpack-plugin")
+
+const clientConfig = devConfig
+
+clientConfig.resolve.fallback =
+{
+    "buffer": require.resolve("buffer"),
+    "path": require.resolve("path-browserify"),
+    "stream": require.resolve("stream-browserify"),
+    "zlib": require.resolve("browserify-zlib"),
+    "vm": require.resolve("vm-browserify"),
+    "fs": false
+}
+
+clientConfig.plugins =
+    [new webpack.ProvidePlugin({regeneratorRuntime: 'regenerator-runtime'}),
+     new NodePolyfillPlugin()].concat(constants.processPlugins(entryPoints))
+
+
+module.exports = [clientConfig]

jbrowse/config/dev.config.js

@@ -0,0 +1,31 @@
+/*
+ * Copyright (c) 2019 LabKey Corporation
+ *
+ * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0
+ */
+
+const prodConfig = require('../node_modules/@labkey/build/webpack/prod.config')
+
+const entryPoints = require('../src/client/entryPoints');
+const constants = require('../node_modules/@labkey/build/webpack/constants');
+const webpack = require('webpack');
+const NodePolyfillPlugin = require("node-polyfill-webpack-plugin")
+
+const clientConfig = prodConfig
+
+clientConfig.resolve.fallback =
+{
+    "buffer": require.resolve("buffer"),
+    "path": require.resolve("path-browserify"),
+    "stream": require.resolve("stream-browserify"),
+    "zlib": require.resolve("browserify-zlib"),
+    "vm": require.resolve("vm-browserify"),
+    "fs": false
+}
+
+clientConfig.plugins =
+    [new webpack.ProvidePlugin({regeneratorRuntime: 'regenerator-runtime'}),
+     new NodePolyfillPlugin()].concat(constants.processPlugins(entryPoints))
+
+
+module.exports = [clientConfig]

jbrowse/config/prod.config.js

@@ -0,0 +1,31 @@
+/*
+ * Copyright (c) 2019 LabKey Corporation
+ *
+ * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0
+ */
+
+const watchConfig = require('../node_modules/@labkey/build/webpack/watch.config')
+
+const entryPoints = require('../src/client/entryPoints');
+const constants = require('../node_modules/@labkey/build/webpack/constants');
+const webpack = require('webpack');
+const NodePolyfillPlugin = require("node-polyfill-webpack-plugin")
+
+const clientConfig = watchConfig
+
+clientConfig.resolve.fallback =
+{
+    "buffer": require.resolve("buffer"),
+    "path": require.resolve("path-browserify"),
+    "stream": require.resolve("stream-browserify"),
+    "zlib": require.resolve("browserify-zlib"),
+    "vm": require.resolve("vm-browserify"),
+    "fs": false
+}
+
+clientConfig.plugins =
+    [new webpack.ProvidePlugin({regeneratorRuntime: 'regenerator-runtime'}),
+     new NodePolyfillPlugin()].concat(constants.processPlugins(entryPoints))
+
+
+module.exports = [clientConfig]