Add diamond support to multi-blast, and enable on ortho-site (#1197)

* Attempt to get local dev working for multi-blast

* Upgrade recoil to work with React 18 types

* Wire multi-blast in ortho-site

* Make blastOntologyDatabase optional, and add magic string to indicate
all algorithm options are available.

* Update search name

* Handle optional blastOntologyDatabase property

* Add options for custom workspace header, and remove hardcoded path.

* Add new route for map-proteins

* add multi-blast vars to sample file

* Handle empty advanced params, allow file-only sequence param, and use file-based request if a file is provided.

* Add diamond config types and mappings with wdk search parameter values

* eValue should be a number for diamond

* Only assign parameter values when the config value is defined

* Update link in header

* Update workspace heading

* Make link relative

* Add generic method to fetch a specific report file

* Add support for customizing verbiage

* Reduce margin

* Add method to get download url for a file

* Relativize links

target can be null

* target can be null

* Add result view for diamond jobs

* go to new form for map-proteins

* fix issues with multi-blast local dev site

* Make help tab configurable

* Request headers and use for preview and download

* Make paths relative to workspace root

* Update comment

* Map stitle to new columns

* Add support for AbortSignal to usePromise

* Handle AbortSignal

packages/libs/multi-blast/config-overrides.js

@@ -1,4 +1,4 @@
-const path = require('path');
+const webpack = require('webpack');
 
 /*
  * The following gives preference to the project's root node_modules directory when loading modules and loaders.
@@ -10,18 +10,37 @@ module.exports = function override(config, env) {
     ...config,
     resolve: {
       ...config.resolve,
-      modules: [
-        path.join(__dirname, 'node_modules'),
-        ...(config.resolve.modules || ['node_modules']),
-      ],
+      fallback: {
+        path: 'path-browserify',
+        stream: 'stream-browserify',
+        querystring: 'querystring-es3',
+        assert: 'assert',
+        buffer: 'buffer',
+        fs: false,
+      },
     },
-    resolveLoader: {
-      ...config.resolveLoader,
-      modules: [
-        path.join(__dirname, 'node_modules'),
-        ...(config.resolveLoader.modules || ['node_modules']),
+    plugins: [
+      ...config.plugins,
+      new webpack.ProvidePlugin({
+        // This is needed by shape2geohash, used by MapVEuMap
+        process: 'process/browser',
+      }),
+    ],
+    externals: [{ jquery: 'jQuery' }],
+    module: {
+      ...config.module,
+      rules: [
+        ...config.module.rules,
+        {
+          test: /\.(js|jsx|ts|tsx)$/,
+          exclude: /node_modules\/(?!(@veupathdb))/,
+          enforce: 'pre',
+          use: 'source-map-loader',
+        },
       ],
     },
-    externals: [{ jquery: 'jQuery' }],
+    snapshot: {
+      managedPaths: [],
+    },
   };
 };

packages/libs/multi-blast/package.json

@@ -12,7 +12,8 @@
     "src/lib"
   ],
   "sideEffects": [
-    "*.scss"
+    "*.scss",
+    "src/globals.js"
   ],
   "dependencies": {
     "@veupathdb/coreui": "workspace:^",
@@ -99,9 +100,9 @@
     "react-redux": "^7.2.6",
     "react-router": "^5.2.0",
     "react-router-dom": "^5.2.0",
-    "react-scripts": "4.0.1",
+    "react-scripts": "5.0.1",
     "read": "^1.0.7",
-    "recoil": "^0.2.0",
+    "recoil": "^0.7.7",
     "redux": "^4.0.0",
     "sass": "^1.56.2",
     "script-loader": "^0.7.2",

packages/libs/multi-blast/src/index.tsx

@@ -1,15 +1,22 @@
 import './globals';
+
+// eslint-disable-next-line import/no-webpack-loader-syntax
+import '!!script-loader!@veupathdb/wdk-client/vendored/jquery';
+// eslint-disable-next-line import/no-webpack-loader-syntax
+import '!!script-loader!@veupathdb/wdk-client/vendored/jquery-migrate-1.2.1';
+// eslint-disable-next-line import/no-webpack-loader-syntax
+import '!!script-loader!@veupathdb/wdk-client/vendored/jquery-ui';
+// eslint-disable-next-line import/no-webpack-loader-syntax
+import '!!script-loader!@veupathdb/wdk-client/vendored/jquery.qtip.min';
+
 import React, { Suspense } from 'react';
 import { Redirect, RouteComponentProps } from 'react-router';
 import { RecoilRoot } from 'recoil';
-import { initialize } from '@veupathdb/web-common/lib/bootstrap';
-import {
-  BlastSummaryViewPlugin,
-  GenomeSummaryViewPlugin,
-  ResultTableSummaryViewPlugin,
-} from '@veupathdb/wdk-client/lib/Plugins';
+import { initialize } from '@veupathdb/wdk-client';
+import { ResultTableSummaryViewPlugin } from '@veupathdb/wdk-client/lib/Plugins';
 import { RouteEntry } from '@veupathdb/wdk-client/lib/Core/RouteEntry';
 import { ClientPluginRegistryEntry } from '@veupathdb/wdk-client/lib/Utils/ClientPlugin';
+import BlastSummaryViewPlugin from '@veupathdb/blast-summary-view/lib/Controllers/BlastSummaryViewController';
 
 import {
   OrganismParam,
@@ -28,9 +35,6 @@ import { BlastWorkspaceRouter } from './lib/controllers/BlastWorkspaceRouter';
 import { isMultiBlastQuestion } from './lib/utils/pluginConfig';
 import { wrapWdkService } from './lib/utils/wdkServiceIntegration';
 
-import '@veupathdb/wdk-client/lib/Core/Style/index.scss';
-import '@veupathdb/web-common/lib/styles/client.scss';
-
 import './index.css';
 
 initialize({
@@ -93,11 +97,6 @@ initialize({
       name: '_default',
       component: ResultTableSummaryViewPlugin,
     },
-    {
-      type: 'summaryView',
-      name: 'genomic-view',
-      component: GenomeSummaryViewPlugin,
-    },
     {
       type: 'summaryView',
       name: 'blast-view',

packages/libs/multi-blast/src/lib/components/BlastForm.scss

@@ -1,12 +1,16 @@
 .wdk-QuestionForm {
   &MultiBlast {
+    > * + * {
+      margin-block-start: 1em;
+    }
+
     .SequenceParam {
       display: inline-flex;
       flex-direction: column;
       gap: 1em;
 
       &Instructions {
-        font-size: 1.2em;
+        font-size: 1.1em;
       }
 
       textarea {