Merge pull request #157 from BimberLab/22.3_fb_merge

Merge discvr-21.11 to discvr-22.3

Author: bbimber

jbrowse/package-lock.json

@@ -12,25 +12,31 @@
     "clean": "rimraf resources/web/gen && rimraf resources/web/jbrowse/gen && rimraf resources/views/gen && rimraf resources/views/browser*",
     "test": "cross-env NODE_ENV=test jest",
     "jb-pkg": "pkg ./node_modules/@jbrowse/cli --out-path ./resources/external/jb-cli"
+  },
+  "peerDependencies": {
+
   },
   "dependencies": {
-    "@jbrowse/cli": "1.5.1",
-    "@jbrowse/react-linear-genome-view": "^1.5.1",
-    "@labkey/components": "^2.102.0",
-    "@material-ui/core": "^4.12.3",
+    "@jbrowse/cli": "^1.7.4",
+    "@jbrowse/core": "^1.7.4",
+    "@jbrowse/plugin-variants": "^1.7.4",
+    "@jbrowse/plugin-svg": "^1.7.4",
+    "@jbrowse/plugin-linear-genome-view": "^1.7.4",
+    "@jbrowse/react-linear-genome-view": "^1.7.4",
+    "@labkey/api": "^1.10.0",
+    "@labkey/components": "2.157.0",
+    "@gmod/vcf": "^5.0.6",
+    "react": "^16.14.0",
     "assert": "^2.0.0",
     "browserify-zlib": "^0.2.0",
     "buffer": "^6.0.3",
     "jquery": "^3.6.0",
     "jspdf": "^2.5.1",
     "jspdf-autotable": "^3.5.23",
-    "mobx": "^5.0.0",
-    "mobx-react": "^6.0.0",
-    "mobx-state-tree": "3.14.1",
-    "node-polyfill-webpack-plugin": "1.1.0",
+    "node-polyfill-webpack-plugin": "1.1.4",
     "path-browserify": "^1.0.1",
     "pkg": "^5.3.2",
-    "react-data-grid": "^7.0.0-beta.11",
+    "react-data-grid": "^7.0.0-beta.12",
     "react-google-charts": "^3.0.15",
     "react-hot-loader": "^4.13.0",
     "regenerator-runtime": "^0.13.9",
@@ -41,19 +47,19 @@
     "xlsx": "^0.18.3"
   },
   "devDependencies": {
-    "@labkey/build": "^5.0.0",
-    "@types/enzyme": "^3.10.9",
-    "@types/jest": "^27.4.0",
-    "@types/react": "^17.0.38",
-    "@types/react-dom": "^17.0.11",
+    "@labkey/build": "^6.0.0",
+    "@types/enzyme": "^3.10.12",
+    "@types/jest": "^27.4.1",
+    "@types/jquery": "^3.5.14",
+    "@types/jexl": "^2.3.0",
     "enzyme": "^3.11.0",
     "enzyme-adapter-react-16": "^1.15.6",
     "enzyme-to-json": "^3.6.2",
     "jest": "^27.4.7",
     "jest-cli": "^27.4.7",
     "jest-teamcity-reporter": "^0.9.0",
     "react-test-renderer": "^17.0.2",
-    "rimraf": "~3.0.2",
+    "rimraf": "^3.0.2",
     "ts-jest": "^27.0.5"
   },
   "browser": {

jbrowse/package.json

@@ -6,8 +6,6 @@ import { Feature } from '@jbrowse/core/util/simpleFeature';
 import ExtendedVcfFeature from './ExtendedVcfFeature';
 import { default as VcfTabixAdapter } from '@jbrowse/plugin-variants/src/VcfTabixAdapter/VcfTabixAdapter';
 import { VcfFeature } from '@jbrowse/plugin-variants';
-import { Instance } from 'mobx-state-tree';
-import MyConfigSchema from './configSchema';
 
 export default class extends VcfTabixAdapter {
     protected featureCache = new QuickLRU({ maxSize: 20 })

jbrowse/src/client/JBrowse/Browser/plugins/ExtendedVariantPlugin/ExtendedVariantAdapter/ExtendedVariantAdapter.ts

@@ -7,8 +7,7 @@ import configSchemaF from './configSchema';
 import { getEnv, IAnyStateTreeNode, types } from 'mobx-state-tree';
 import PaletteIcon from '@material-ui/icons/Palette';
 import { default as SetMaxHeightDlg } from '@jbrowse/plugin-linear-genome-view/src/LinearBasicDisplay/components/SetMaxHeight';
-import {ActionURL} from "@labkey/api";
-import { LinearGenomeViewModel} from '@jbrowse/plugin-linear-genome-view'
+import { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view';
 import { navigateToTable } from '../../../../utils';
 
 export default jbrowse => {

…ntPlugin/ExtendedVariantDisplay/model.ts …tPlugin/ExtendedVariantDisplay/model.tsxjbrowse/src/client/JBrowse/Browser/plugins/ExtendedVariantPlugin/ExtendedVariantDisplay/model.ts renamed to jbrowse/src/client/JBrowse/Browser/plugins/ExtendedVariantPlugin/ExtendedVariantDisplay/model.tsx jbrowse/src/client/JBrowse/Browser/plugins/ExtendedVariantPlugin/ExtendedVariantDisplay/model.ts renamed to jbrowse/src/client/JBrowse/Browser/plugins/ExtendedVariantPlugin/ExtendedVariantDisplay/model.tsx

@@ -1,16 +1,13 @@
-// NEW: Diamond glyph for SNV rendering. Based off Chevron.js
-
 import { readConfObject } from '@jbrowse/core/configuration'
 import { PropTypes as CommonPropTypes } from '@jbrowse/core/util/types/mst'
 import { emphasize } from '@jbrowse/core/util/color'
 import { observer } from 'mobx-react'
 import ReactPropTypes from 'prop-types'
 import React from 'react'
-import { isUTR } from './util'
+import { isUTR } from '@jbrowse/plugin-svg/src/SvgFeatureRenderer/components/util'
 
 const utrHeightFraction = 0.65
 
-
 function Diamond(props) {
   const {
     feature,
@@ -57,11 +54,11 @@ function Diamond(props) {
           stroke={selected ? color2 : undefined}
           fill={selected ? emphasizedColor : color}
           points={[
-            [left + (width)/2, top],
-            [left + (width)/2 + (height/2), top + height / 2],
-            [left + (width)/2, top + height],
-            [left + (width)/2 - (height/2), top + height / 2],
-          ]}
+            [left + (width)/2, top].join(","),
+            [left + (width)/2 + (height/2), top + height / 2].join(","),
+            [left + (width)/2, top + height].join(","),
+            [left + (width)/2 - (height/2), top + height / 2].join(","),
+          ].join(" ")}
         />
     </>
   )

jbrowse/src/client/JBrowse/Browser/plugins/ExtendedVariantPlugin/ExtendedVariantRenderer/components/Box.js

@@ -0,0 +1,44 @@
+import jexl from 'jexl';
+import { SvgFeatureRendererReactComponent } from '@jbrowse/plugin-svg';
+import { observer } from 'mobx-react';
+import React from 'react';
+import { deserializeFilters } from '../../InfoFilterWidget/filterUtil';
+import Diamond from './Diamond';
+import { passesInfoFilters, passesSampleFilters } from '../../../../../utils';
+
+export function ExtendedVariantRendering(props) {
+    const { features, rendererConfig } = props
+    const { activeSamples, infoFilters } = rendererConfig
+
+    let expandedFilters = []
+    if (infoFilters.toJSON()) {
+        expandedFilters = deserializeFilters(infoFilters.toJSON())
+    }
+
+    const sampleFilters = activeSamples.value ? activeSamples.value.split(',') : null
+
+    function diamondValidator(feature) {
+        return feature.get('type') === "SNV";
+    }
+
+    function isFeatureDisplayed(feature) {
+        return passesInfoFilters(feature, expandedFilters) && passesSampleFilters(feature, sampleFilters)
+    }
+
+    function getDiamondValidator() {
+        return {
+            glyph: Diamond,
+            validator: diamondValidator
+        }
+    }
+
+    return (
+        <SvgFeatureRendererReactComponent
+            featureDisplayHandler={isFeatureDisplayed}
+            extraGlyphs={[getDiamondValidator()]}
+            {...props}
+        />
+    )
+}
+
+export default observer(ExtendedVariantRendering)