@jbrowse/plugin-config 1.7.11 → 2.0.0

package/esm/FromConfigAdapter/FromConfigRegionsAdapter.d.ts

@@ -0,0 +1,23 @@
+import { BaseAdapter, RegionsAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
+import { ConfigurationModel } from '@jbrowse/core/configuration/configurationSchema';
+import { configSchema as FromConfigAdapterConfigSchema } from './configSchema';
+import PluginManager from '@jbrowse/core/PluginManager';
+import { getSubAdapterType } from '@jbrowse/core/data_adapters/dataAdapterCache';
+/**
+ * Adapter that just returns the features defined in its `features` configuration
+ * key, like:
+ *   `"features": [ { "refName": "ctgA", "start":1, "end":20 }, ... ]`
+ */
+export default class FromConfigRegionsAdapter extends BaseAdapter implements RegionsAdapter {
+    private features;
+    constructor(config: ConfigurationModel<typeof FromConfigAdapterConfigSchema>, getSubAdapter?: getSubAdapterType, pluginManager?: PluginManager);
+    /**
+     * Get refName, start, and end for all features after collapsing any overlaps
+     */
+    getRegions(): Promise<{
+        refName: string;
+        start: number;
+        end: number;
+    }[]>;
+    freeResources(): void;
+}

package/esm/FromConfigAdapter/FromConfigRegionsAdapter.js

@@ -0,0 +1,50 @@
+import { BaseAdapter, } from '@jbrowse/core/data_adapters/BaseAdapter';
+import { readConfObject } from '@jbrowse/core/configuration';
+import FromConfigAdapter from './FromConfigAdapter';
+/**
+ * Adapter that just returns the features defined in its `features` configuration
+ * key, like:
+ *   `"features": [ { "refName": "ctgA", "start":1, "end":20 }, ... ]`
+ */
+export default class FromConfigRegionsAdapter extends BaseAdapter {
+    constructor(config, getSubAdapter, pluginManager) {
+        super(config, getSubAdapter, pluginManager);
+        const features = readConfObject(config, 'features');
+        this.features = FromConfigAdapter.makeFeatures(features || []);
+    }
+    /**
+     * Get refName, start, and end for all features after collapsing any overlaps
+     */
+    async getRegions() {
+        const regions = [];
+        // recall: features are stored in this object sorted by start coordinate
+        for (const [refName, features] of this.features) {
+            let currentRegion;
+            for (const feature of features) {
+                if (currentRegion &&
+                    currentRegion.end >= feature.get('start') &&
+                    currentRegion.start <= feature.get('end')) {
+                    currentRegion.end = feature.get('end');
+                }
+                else {
+                    if (currentRegion) {
+                        regions.push(currentRegion);
+                    }
+                    currentRegion = {
+                        refName,
+                        start: feature.get('start'),
+                        end: feature.get('end'),
+                    };
+                }
+            }
+            if (currentRegion) {
+                regions.push(currentRegion);
+            }
+        }
+        // sort the regions by refName
+        regions.sort((a, b) => a.refName.localeCompare(b.refName));
+        return regions;
+    }
+    freeResources( /* { region } */) { }
+}
+//# sourceMappingURL=FromConfigRegionsAdapter.js.map

package/esm/FromConfigAdapter/FromConfigRegionsAdapter.js.map

@@ -0,0 +1 @@
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package/esm/FromConfigAdapter/FromConfigSequenceAdapter.d.ts

@@ -0,0 +1,25 @@
+import { Feature } from '@jbrowse/core/util/simpleFeature';
+import { NoAssemblyRegion } from '@jbrowse/core/util/types';
+import FromConfigAdapter from './FromConfigAdapter';
+export default class FromConfigSequenceAdapter extends FromConfigAdapter {
+    /**
+     * Fetch features for a certain region
+     * @param region - Region
+     * @returns Observable of Feature objects in the region
+     */
+    getFeatures(region: NoAssemblyRegion): import("rxjs").Observable<Feature>;
+    /**
+     * Get refName, start, and end for all features after collapsing any overlaps
+     */
+    getRegions(): Promise<{
+        refName: string;
+        start: number;
+        end: number;
+    }[]>;
+    /**
+     * called to provide a hint that data tied to a certain region
+     * will not be needed for the forseeable future and can be purged
+     * from caches, etc
+     */
+    freeResources(): void;
+}

package/esm/FromConfigAdapter/FromConfigSequenceAdapter.js

@@ -0,0 +1,73 @@
+import SimpleFeature from '@jbrowse/core/util/simpleFeature';
+import { ObservableCreate } from '@jbrowse/core/util/rxjs';
+import { toArray } from 'rxjs/operators';
+import FromConfigAdapter from './FromConfigAdapter';
+export default class FromConfigSequenceAdapter extends FromConfigAdapter {
+    /**
+     * Fetch features for a certain region
+     * @param region - Region
+     * @returns Observable of Feature objects in the region
+     */
+    getFeatures(region) {
+        // TODO: restore commented version below once TSDX supports Rollup v2
+        // xref: https://github.com/rollup/rollup/blob/master/CHANGELOG.md#bug-fixes-45
+        // return ObservableCreate<Feature>(async observer => {
+        //   const feats = await super.getFeatures(region).pipe(toArray()).toPromise()
+        const superGetFeatures = super.getFeatures;
+        return ObservableCreate(async (observer) => {
+            const feats = await superGetFeatures
+                .call(this, region)
+                .pipe(toArray())
+                .toPromise();
+            const feat = feats[0];
+            observer.next(new SimpleFeature({
+                ...feat.toJSON(),
+                uniqueId: `${feat.id()}:${region.start}-${region.end}`,
+                end: region.end,
+                start: region.start,
+                seq: feat
+                    .get('seq')
+                    .slice(Math.max(region.start - feat.get('start'), 0), Math.max(region.end - feat.get('start'), 0)),
+            }));
+            observer.complete();
+        });
+    }
+    /**
+     * Get refName, start, and end for all features after collapsing any overlaps
+     */
+    async getRegions() {
+        const regions = [];
+        // recall: features are stored in this object sorted by start coordinate
+        for (const [refName, features] of this.features) {
+            let currentRegion;
+            for (const feature of features) {
+                if (currentRegion &&
+                    currentRegion.end >= feature.get('start') &&
+                    currentRegion.start <= feature.get('end')) {
+                    currentRegion.end = feature.get('end');
+                }
+                else {
+                    if (currentRegion) {
+                        regions.push(currentRegion);
+                    }
+                    currentRegion = {
+                        refName,
+                        start: feature.get('start'),
+                        end: feature.get('end'),
+                    };
+                }
+            }
+            if (currentRegion) {
+                regions.push(currentRegion);
+            }
+        }
+        return regions;
+    }
+    /**
+     * called to provide a hint that data tied to a certain region
+     * will not be needed for the forseeable future and can be purged
+     * from caches, etc
+     */
+    freeResources( /* { region } */) { }
+}
+//# sourceMappingURL=FromConfigSequenceAdapter.js.map

package/esm/FromConfigAdapter/FromConfigSequenceAdapter.js.map

@@ -0,0 +1 @@
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package/esm/FromConfigAdapter/configSchema.d.ts

@@ -0,0 +1,3 @@
+export declare const configSchema: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
+export declare const regionsConfigSchema: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
+export declare const sequenceConfigSchema: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;

package/esm/FromConfigAdapter/configSchema.js

@@ -0,0 +1,32 @@
+import { ConfigurationSchema } from '@jbrowse/core/configuration';
+export const configSchema = ConfigurationSchema('FromConfigAdapter', {
+    features: {
+        type: 'frozen',
+        defaultValue: [],
+    },
+    featureClass: {
+        type: 'string',
+        defaultValue: 'SimpleFeature',
+    },
+}, { explicitlyTyped: true, implicitIdentifier: 'adapterId' });
+export const regionsConfigSchema = ConfigurationSchema('FromConfigRegionsAdapter', {
+    features: {
+        type: 'frozen',
+        defaultValue: [],
+    },
+    featureClass: {
+        type: 'string',
+        defaultValue: 'SimpleFeature',
+    },
+}, { explicitlyTyped: true, implicitIdentifier: 'adapterId' });
+export const sequenceConfigSchema = ConfigurationSchema('FromConfigSequenceAdapter', {
+    features: {
+        type: 'frozen',
+        defaultValue: [],
+    },
+    featureClass: {
+        type: 'string',
+        defaultValue: 'SimpleFeature',
+    },
+}, { explicitlyTyped: true, implicitIdentifier: 'adapterId' });
+//# sourceMappingURL=configSchema.js.map

package/esm/FromConfigAdapter/configSchema.js.map

@@ -0,0 +1 @@
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package/esm/FromConfigAdapter/index.d.ts

@@ -0,0 +1,4 @@
+export { default as AdapterClass } from './FromConfigAdapter';
+export { default as RegionsAdapterClass } from './FromConfigRegionsAdapter';
+export { default as SequenceAdapterClass } from './FromConfigSequenceAdapter';
+export { configSchema, regionsConfigSchema, sequenceConfigSchema, } from './configSchema';

package/esm/FromConfigAdapter/index.js

@@ -0,0 +1,5 @@
+export { default as AdapterClass } from './FromConfigAdapter';
+export { default as RegionsAdapterClass } from './FromConfigRegionsAdapter';
+export { default as SequenceAdapterClass } from './FromConfigSequenceAdapter';
+export { configSchema, regionsConfigSchema, sequenceConfigSchema, } from './configSchema';
+//# sourceMappingURL=index.js.map

package/esm/FromConfigAdapter/index.js.map

@@ -0,0 +1 @@
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package/esm/RefNameAliasAdapter/RefNameAliasAdapter.d.ts

@@ -0,0 +1,8 @@
+import { BaseRefNameAliasAdapter, BaseAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
+export default class RefNameAliasAdapter extends BaseAdapter implements BaseRefNameAliasAdapter {
+    getRefNameAliases(): Promise<{
+        refName: string;
+        aliases: string[];
+    }[]>;
+    freeResources(): Promise<void>;
+}

package/esm/RefNameAliasAdapter/RefNameAliasAdapter.js

@@ -0,0 +1,24 @@
+import { BaseAdapter, } from '@jbrowse/core/data_adapters/BaseAdapter';
+import { openLocation } from '@jbrowse/core/util/io';
+import { readConfObject } from '@jbrowse/core/configuration';
+export default class RefNameAliasAdapter extends BaseAdapter {
+    async getRefNameAliases() {
+        const loc = readConfObject(this.config, 'location');
+        if (loc.uri === '' || loc.uri === '/path/to/my/aliases.txt') {
+            return [];
+        }
+        const results = await openLocation(loc).readFile('utf8');
+        const refColumn = readConfObject(this.config, 'refNameColumn');
+        return results
+            .trim()
+            .split('\n')
+            .filter(f => !!f && !f.startsWith('#'))
+            .map(row => {
+            const aliases = row.split('\t');
+            const [refName] = aliases.splice(refColumn, 1);
+            return { refName, aliases: aliases.filter(f => !!f.trim()) };
+        });
+    }
+    async freeResources() { }
+}
+//# sourceMappingURL=RefNameAliasAdapter.js.map

package/esm/RefNameAliasAdapter/RefNameAliasAdapter.js.map

@@ -0,0 +1 @@
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package/esm/RefNameAliasAdapter/configSchema.d.ts

@@ -0,0 +1,2 @@
+declare const _default: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
+export default _default;

package/esm/RefNameAliasAdapter/configSchema.js

@@ -0,0 +1,15 @@
+import { ConfigurationSchema } from '@jbrowse/core/configuration';
+export default ConfigurationSchema('RefNameAliasAdapter', {
+    location: {
+        type: 'fileLocation',
+        defaultValue: {
+            uri: '/path/to/my/aliases.txt',
+            locationType: 'UriLocation',
+        },
+    },
+    refNameColumn: {
+        type: 'number',
+        defaultValue: 0,
+    },
+}, { explicitlyTyped: true });
+//# sourceMappingURL=configSchema.js.map

package/esm/RefNameAliasAdapter/configSchema.js.map

@@ -0,0 +1 @@
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package/esm/RefNameAliasAdapter/index.d.ts

@@ -0,0 +1,2 @@
+export { default as AdapterClass } from './RefNameAliasAdapter';
+export { default as configSchema } from './configSchema';

package/esm/RefNameAliasAdapter/index.js

@@ -0,0 +1,3 @@
+export { default as AdapterClass } from './RefNameAliasAdapter';
+export { default as configSchema } from './configSchema';
+//# sourceMappingURL=index.js.map

package/esm/RefNameAliasAdapter/index.js.map

@@ -0,0 +1 @@
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package/esm/index.d.ts

@@ -0,0 +1,18 @@
+/// <reference types="react" />
+import Plugin from '@jbrowse/core/Plugin';
+import PluginManager from '@jbrowse/core/PluginManager';
+declare const LazyConfigurationEditorComponent: import("react").LazyExoticComponent<({ model }: {
+    model: {
+        target: {
+            [x: string]: any;
+        } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
+            setSubschema(slotName: string, data: unknown): any;
+        } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>;
+    };
+}) => JSX.Element>;
+export default class extends Plugin {
+    name: string;
+    install(pluginManager: PluginManager): void;
+}
+export { default as JsonEditor } from './ConfigurationEditorWidget/components/JsonEditor';
+export { LazyConfigurationEditorComponent as ConfigurationEditor };

package/esm/index.js

@@ -0,0 +1,72 @@
+import { lazy } from 'react';
+import AdapterType from '@jbrowse/core/pluggableElementTypes/AdapterType';
+import WidgetType from '@jbrowse/core/pluggableElementTypes/WidgetType';
+import Plugin from '@jbrowse/core/Plugin';
+import { configSchema as ConfigurationEditorConfigSchema, HeadingComponent as ConfigurationEditorHeadingComponent, stateModelFactory as ConfigurationEditorStateModelFactory, } from './ConfigurationEditorWidget';
+import { configSchema as fromConfigAdapterConfigSchema, regionsConfigSchema as fromConfigRegionsAdapterConfigSchema, sequenceConfigSchema as fromConfigSequenceAdapterConfigSchema, } from './FromConfigAdapter';
+import { configSchema as refNameAliasAdapterConfigSchema } from './RefNameAliasAdapter';
+const LazyConfigurationEditorComponent = lazy(() => import('./ConfigurationEditorWidget/components/ConfigurationEditor'));
+export default class extends Plugin {
+    constructor() {
+        super(...arguments);
+        this.name = 'ConfigurationPlugin';
+    }
+    install(pluginManager) {
+        pluginManager.addAdapterType(() => new AdapterType({
+            name: 'FromConfigAdapter',
+            configSchema: fromConfigAdapterConfigSchema,
+            getAdapterClass: () => import('./FromConfigAdapter/FromConfigAdapter').then(r => r.default),
+            adapterMetadata: {
+                category: null,
+                hiddenFromGUI: true,
+                displayName: null,
+                description: null,
+            },
+        }));
+        pluginManager.addAdapterType(() => new AdapterType({
+            name: 'FromConfigRegionsAdapter',
+            configSchema: fromConfigRegionsAdapterConfigSchema,
+            getAdapterClass: () => import('./FromConfigAdapter/FromConfigRegionsAdapter').then(r => r.default),
+            adapterMetadata: {
+                category: null,
+                hiddenFromGUI: true,
+                displayName: null,
+                description: null,
+            },
+        }));
+        pluginManager.addAdapterType(() => new AdapterType({
+            name: 'FromConfigSequenceAdapter',
+            configSchema: fromConfigSequenceAdapterConfigSchema,
+            getAdapterClass: () => import('./FromConfigAdapter/FromConfigSequenceAdapter').then(r => r.default),
+            adapterMetadata: {
+                category: null,
+                hiddenFromGUI: true,
+                displayName: null,
+                description: null,
+            },
+        }));
+        pluginManager.addAdapterType(() => new AdapterType({
+            name: 'RefNameAliasAdapter',
+            configSchema: refNameAliasAdapterConfigSchema,
+            getAdapterClass: () => import('./RefNameAliasAdapter/RefNameAliasAdapter').then(r => r.default),
+            adapterMetadata: {
+                category: null,
+                hiddenFromGUI: true,
+                displayName: null,
+                description: null,
+            },
+        }));
+        pluginManager.addWidgetType(() => {
+            return new WidgetType({
+                name: 'ConfigurationEditorWidget',
+                HeadingComponent: ConfigurationEditorHeadingComponent,
+                configSchema: ConfigurationEditorConfigSchema,
+                stateModel: ConfigurationEditorStateModelFactory(pluginManager),
+                ReactComponent: LazyConfigurationEditorComponent,
+            });
+        });
+    }
+}
+export { default as JsonEditor } from './ConfigurationEditorWidget/components/JsonEditor';
+export { LazyConfigurationEditorComponent as ConfigurationEditor };
+//# sourceMappingURL=index.js.map

package/esm/index.js.map

@@ -0,0 +1 @@
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package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-config",
-  "version": "1.7.11",
+  "version": "2.0.0",
   "description": "JBrowse 2 config utilities",
   "keywords": [
     "jbrowse",
@@ -20,38 +20,45 @@
   "main": "dist/index.js",
   "files": [
     "dist",
-    "src"
+    "src",
+    "esm"
   ],
   "scripts": {
-    "build": "babel src --root-mode upward --out-dir dist --extensions .ts,.js,.tsx,.jsx",
+    "build": "npm-run-all build:*",
     "test": "cd ../..; jest plugins/config",
     "prepublishOnly": "yarn test",
     "prepack": "yarn build; yarn useDist",
     "postpack": "yarn useSrc",
     "useDist": "node ../../scripts/useDist.js",
     "useSrc": "node ../../scripts/useSrc.js",
-    "postbuild": "tsc --build tsconfig.build.json"
+    "prebuild": "npm run clean",
+    "build:esm": "tsc --build tsconfig.build.esm.json",
+    "build:es5": "tsc --build tsconfig.build.es5.json",
+    "clean": "rimraf dist esm *.tsbuildinfo"
   },
   "dependencies": {
     "@babel/runtime": "^7.17.9",
-    "@material-ui/icons": "^4.9.1",
+    "@mui/icons-material": "^5.0.1",
     "pluralize": "^8.0.0",
-    "react-color": "^2.19.3",
-    "react-simple-code-editor": "0.9.3",
-    "react-syntax-highlighter": "^14.0.0"
+    "react-color": "^2.19.3"
   },
   "peerDependencies": {
     "@jbrowse/core": "^1.0.0",
-    "@material-ui/core": "^4.12.2",
-    "mobx-react": "^6.0.0",
-    "mobx-state-tree": "3.14.1",
+    "@mui/material": "^5.0.0",
+    "mobx": "^6.0.0",
+    "mobx-react": "^7.0.0",
+    "mobx-state-tree": "^5.0.0",
     "prop-types": "^15.0.0",
     "react": ">=16.8.0",
     "react-dom": ">=16.8.0",
-    "rxjs": "^6.0.0"
+    "rxjs": "^6.0.0",
+    "tss-react": "^3.0.0"
   },
   "publishConfig": {
     "access": "public"
   },
-  "gitHead": "5c21beb48a21f08b0091d293f09ac99174c48f77"
+  "distModule": "esm/index.js",
+  "srcModule": "src/index.ts",
+  "module": "esm/index.js",
+  "gitHead": "ecc7f5d47351a5ea04bc00f3a6eb6dfb607342e6"
 }

package/src/ConfigurationEditorWidget/components/{CallbackEditor.js → CallbackEditor.tsx}

@@ -7,35 +7,44 @@ import {
   InputLabel,
   Tooltip,
   IconButton,
-  makeStyles,
-} from '@material-ui/core'
-import HelpIcon from '@material-ui/icons/Help'
+  TextField,
+} from '@mui/material'
+import { makeStyles } from 'tss-react/mui'
+import HelpIcon from '@mui/icons-material/Help'
 import { getEnv } from 'mobx-state-tree'
-import { observer, PropTypes } from 'mobx-react'
-import Editor from 'react-simple-code-editor'
-
-// fontSize and fontFamily have to match between Editor and SyntaxHighlighter
-const fontSize = '12px'
+import { observer } from 'mobx-react'
 
 // Optimize by using system default fonts:
 // https://css-tricks.com/snippets/css/font-stacks/
 const fontFamily =
   'Consolas, "Andale Mono WT", "Andale Mono", "Lucida Console", "Lucida Sans Typewriter", "DejaVu Sans Mono", "Bitstream Vera Sans Mono", "Liberation Mono", "Nimbus Mono L", Monaco, "Courier New", Courier, monospace'
 
-const useStyles = makeStyles(theme => ({
+const useStyles = makeStyles()(theme => ({
   callbackEditor: {
     marginTop: '16px',
     borderBottom: `1px solid ${theme.palette.divider}`,
     fontFamily,
-    fontSize,
+  },
+  textAreaFont: {
+    fontFamily,
   },
 }))
 
-function CallbackEditor({ slot }) {
-  const classes = useStyles()
+function CallbackEditor({
+  slot,
+}: {
+  slot: {
+    set: (arg: string) => void
+    description: string
+    name: string
+    value: string
+    contextVariable: string
+  }
+}) {
+  const { classes } = useStyles()
 
   const [code, setCode] = useState(slot.value)
-  const [error, setCodeError] = useState()
+  const [error, setCodeError] = useState<unknown>()
   const debouncedCode = useDebounce(code, 400)
 
   useEffect(() => {
@@ -43,12 +52,16 @@ function CallbackEditor({ slot }) {
       const jexlDebouncedCode = debouncedCode.startsWith('jexl:')
         ? debouncedCode
         : `jexl:${debouncedCode}`
+
+      if (jexlDebouncedCode === 'jexl:') {
+        throw new Error('Empty jexl expression is not valid')
+      }
       stringToJexlExpression(
         jexlDebouncedCode,
         getEnv(slot).pluginManager?.jexl,
       )
       slot.set(jexlDebouncedCode)
-      setCodeError(null)
+      setCodeError(undefined)
     } catch (e) {
       console.error({ e })
       setCodeError(e)
@@ -63,13 +76,17 @@ function CallbackEditor({ slot }) {
         <InputLabel shrink htmlFor="callback-editor">
           {slot.name}
         </InputLabel>
-        <Editor
+        <TextField
+          multiline
           className={classes.callbackEditor}
           value={code.startsWith('jexl:') ? code.split('jexl:')[1] : code}
-          onValueChange={newCode => setCode(newCode)}
-          highlight={newCode => newCode}
-          padding={10}
+          onChange={event => setCode(event.target.value)}
           style={{ background: error ? '#fdd' : undefined }}
+          InputProps={{
+            classes: {
+              input: classes.textAreaFont,
+            },
+          }}
         />
         {error ? (
           <FormHelperText
@@ -106,7 +123,5 @@ function CallbackEditor({ slot }) {
     </>
   )
 }
-CallbackEditor.propTypes = {
-  slot: PropTypes.objectOrObservableObject.isRequired,
-}
+
 export default observer(CallbackEditor)