@jbrowse/plugin-config 5.0.0-beta.13 → 5.0.0-beta.14

package/README.md

@@ -0,0 +1,25 @@
+# @jbrowse/plugin-config
+
+JBrowse 2 config utilities
+
+<!-- API_DOCS_START -->
+
+## API
+
+Auto-generated from `#api` JSDoc tags in this package. Do not edit by hand.
+
+### registerConfigAdapters
+
+Registers `FromConfigAdapter`, whose features a track config writes inline, and
+the alias adapters an assembly's `refNameAliases` reads through, on a plugin
+manager that wants them without the configuration editor, as a headless host
+does.
+
+```js
+// type signature
+(pluginManager: PluginManager) => void
+```
+
+[Source code](https://github.com/GMOD/jbrowse-components/blob/main/plugins/config/src/adapters.ts)
+
+<!-- API_DOCS_END -->

package/esm/ConfigurationEditorWidget/components/AddNewField.d.ts

@@ -1,6 +1,7 @@
 import type { ReactNode } from 'react';
-export default function AddNewField({ onAdd, testid, startAdornment, }: {
+declare const AddNewField: ({ onAdd, testid, startAdornment, }: {
     onAdd: (value: string) => void;
     testid?: string;
     startAdornment?: ReactNode;
-}): import("react").JSX.Element;
+}) => import("react").JSX.Element;
+export default AddNewField;

package/esm/ConfigurationEditorWidget/components/AddNewField.js

@@ -2,9 +2,10 @@ import { jsx as _jsx } from "react/jsx-runtime";
 import { useState } from 'react';
 import AddIcon from '@mui/icons-material/Add';
 import { IconButton, InputAdornment, TextField } from '@mui/material';
+import { observer } from 'mobx-react';
 // shared "add new" entry field used by the string-array and map slot editors:
 // a text box that commits its contents via onAdd and clears itself
-export default function AddNewField({ onAdd, testid, startAdornment, }) {
+const AddNewField = observer(function AddNewField({ onAdd, testid, startAdornment, }) {
     const [value, setValue] = useState('');
     function commit() {
         if (value !== '') {
@@ -26,4 +27,5 @@ export default function AddNewField({ onAdd, testid, startAdornment, }) {
                         }, children: _jsx(AddIcon, {}) }) })),
             },
         } }));
-}
+});
+export default AddNewField;

package/esm/ConfigurationEditorWidget/components/ColorEditor.js

@@ -24,7 +24,7 @@ const useStyles = makeStyles()({
 // in the field and reaches the slot once it does; leaving the field drops an
 // unparsed draft. "Unset" is reachable through the slot's reset button, which
 // is where every other slot type puts it. Only a slot declaring a
-// `contextVariable` takes a `jexl:` callback, which an entry of a colour list
+// `contextVariable` takes a `jexl:` callback, which an entry of a color list
 // never does.
 /** #slotEditor text field beside a swatch that opens a color picker */
 const ColorEditor = observer(function ColorEditor({ slot, }) {

package/esm/ConfigurationEditorWidget/components/ConfigurationTextField.d.ts

@@ -1,4 +1,5 @@
 import type { TextFieldProps } from '@mui/material';
-export default function ConfigurationTextField(props: {
+declare const ConfigurationTextField: (props: {
     helperText?: string;
-} & TextFieldProps): import("react").JSX.Element;
+} & TextFieldProps) => import("react").JSX.Element;
+export default ConfigurationTextField;

package/esm/ConfigurationEditorWidget/components/ConfigurationTextField.js

@@ -1,9 +1,10 @@
 import { jsx as _jsx } from "react/jsx-runtime";
 import { SanitizedHTML } from '@jbrowse/core/ui';
 import { TextField } from '@mui/material';
+import { observer } from 'mobx-react';
 // adds ability to have html in helperText. note that FormHelperTextProps is
 // div because the default is p which does not like div children
-export default function ConfigurationTextField(props) {
+const ConfigurationTextField = observer(function ConfigurationTextField(props) {
     const { helperText, slotProps, ...rest } = props;
     return (_jsx(TextField, { ...rest, helperText: _jsx(SanitizedHTML, { html: helperText || '' }), fullWidth: true, 
         // merged, not replaced: this component owns `formHelperText` (the div
@@ -16,4 +17,5 @@ export default function ConfigurationTextField(props) {
                 component: 'div',
             },
         } }));
-}
+});
+export default ConfigurationTextField;

package/esm/ConfigurationEditorWidget/components/MapEntryCard.d.ts

@@ -1,8 +1,9 @@
-export default function MapEntryCard({ title, onDelete, children, }: {
+declare const MapEntryCard: ({ title, onDelete, children, }: {
     title: string;
     onDelete: () => void;
     children: React.ReactNode;
-}): import("react").JSX.Element;
-export declare function MapAddCard({ onAdd }: {
+}) => import("react").JSX.Element;
+export default MapEntryCard;
+export declare const MapAddCard: ({ onAdd, }: {
     onAdd: (key: string) => void;
-}): import("react").JSX.Element;
+}) => import("react").JSX.Element;

package/esm/ConfigurationEditorWidget/components/MapEntryCard.js

@@ -2,6 +2,7 @@ import { jsx as _jsx, jsxs as _jsxs } from "react/jsx-runtime";
 import { makeStyles } from '@jbrowse/core/util/tss-react';
 import DeleteIcon from '@mui/icons-material/Delete';
 import { Card, CardContent, CardHeader, IconButton } from '@mui/material';
+import { observer } from 'mobx-react';
 import AddNewField from './AddNewField.js';
 const useStyles = makeStyles()(theme => ({
     card: {
@@ -10,14 +11,15 @@ const useStyles = makeStyles()(theme => ({
 }));
 // shared card for a single key in a map slot editor: a titled card with a
 // delete button wrapping the per-value editor passed as children
-export default function MapEntryCard({ title, onDelete, children, }) {
+const MapEntryCard = observer(function MapEntryCard({ title, onDelete, children, }) {
     const { classes } = useStyles();
     return (_jsxs(Card, { raised: true, className: classes.card, children: [_jsx(CardHeader, { title: title, action: _jsx(IconButton, { onClick: () => {
                         onDelete();
                     }, children: _jsx(DeleteIcon, {}) }) }), _jsx(CardContent, { children: children })] }));
-}
+});
+export default MapEntryCard;
 // trailing card in a map slot editor holding the "add new key" field
-export function MapAddCard({ onAdd }) {
+export const MapAddCard = observer(function MapAddCard({ onAdd, }) {
     const { classes } = useStyles();
     return (_jsx(Card, { raised: true, className: classes.card, children: _jsx(CardHeader, { disableTypography: true, title: _jsx(AddNewField, { onAdd: onAdd }) }) }));
-}
+});

package/esm/ConfigurationEditorWidget/components/MapSlotEditor.d.ts

@@ -1,8 +1,9 @@
-export default function MapSlotEditor<V>({ name, description, entries, emptyValue, setMap, renderValue, }: {
+declare const MapSlotEditor: <V>({ name, description, entries, emptyValue, setMap, renderValue, }: {
     name: string;
     description: string;
     entries: [string, V][];
     emptyValue: V;
     setMap: (val: Record<string, V>) => void;
     renderValue: (val: V, set: (val: V) => void, key: string) => React.ReactNode;
-}): import("react").JSX.Element;
+}) => import("react").JSX.Element;
+export default MapSlotEditor;

package/esm/ConfigurationEditorWidget/components/MapSlotEditor.js

@@ -1,11 +1,12 @@
 import { Fragment as _Fragment, jsx as _jsx, jsxs as _jsxs } from "react/jsx-runtime";
 import { FormHelperText, InputLabel } from '@mui/material';
+import { observer } from 'mobx-react';
 import MapEntryCard, { MapAddCard } from './MapEntryCard.js';
 // shared shell for map slot editors (numberMap, stringArrayMap): a labelled
 // list of per-key cards plus an "add key" card. The owning wrapper stays the
 // observer and passes plain entries in, so this stays a non-observer generic
 // (which keeps JSX type args working at the call sites).
-export default function MapSlotEditor({ name, description, entries, emptyValue, setMap, renderValue, }) {
+const MapSlotEditor = observer(function MapSlotEditor({ name, description, entries, emptyValue, setMap, renderValue, }) {
     const obj = Object.fromEntries(entries);
     return (_jsxs(_Fragment, { children: [_jsx(InputLabel, { children: name }), entries.map(([key, val]) => (_jsx(MapEntryCard, { title: key, onDelete: () => {
                     const { [key]: _omit, ...rest } = obj;
@@ -15,4 +16,5 @@ export default function MapSlotEditor({ name, description, entries, emptyValue,
                 }, key) }, key))), _jsx(MapAddCard, { onAdd: key => {
                     setMap({ ...obj, [key]: emptyValue });
                 } }), _jsx(FormHelperText, { children: description })] }));
-}
+});
+export default MapSlotEditor;

package/esm/FromConfigAdapter/configSchema.d.ts

@@ -2,8 +2,8 @@
  * #config FromConfigAdapter
  * #trackType FeatureTrack
  * #fileFormat inline | Inline features | Features written straight into config.json
- * supplies features inline in the config instead of reading a file, useful for
- * small feature sets added via a URL or session spec
+ * Supplies features written inline in the config, for a small feature set
+ * added through a URL or session spec.
  *
  * #example
  * ```js

package/esm/FromConfigAdapter/configSchema.js

@@ -3,8 +3,8 @@ import { ConfigurationSchema } from '@jbrowse/core/configuration';
  * #config FromConfigAdapter
  * #trackType FeatureTrack
  * #fileFormat inline | Inline features | Features written straight into config.json
- * supplies features inline in the config instead of reading a file, useful for
- * small feature sets added via a URL or session spec
+ * Supplies features written inline in the config, for a small feature set
+ * added through a URL or session spec.
  *
  * #example
  * ```js
@@ -37,5 +37,11 @@ const configSchema = ConfigurationSchema('FromConfigAdapter', {
         type: 'frozen',
         defaultValue: [],
     },
-}, { explicitlyTyped: true });
+}, 
+// v1 named the feature class the adapter built
+{
+    explicitlyTyped: true,
+    closed: true,
+    retired: { featureClass: () => ({}) },
+});
 export default configSchema;

package/esm/FromConfigRegionsAdapter/configSchema.d.ts

@@ -2,7 +2,8 @@
  * #config FromConfigRegionsAdapter
  * #trackType ReferenceSequenceTrack
  * #fileFormat inline | Inline regions | refNames and sizes only, no sequence
- * used for specifying refNames+sizes of an assembly
+ * Supplies an assembly's reference names and sizes inline in the config, with
+ * no sequence.
  *
  * #example
  * Supplies refNames+sizes with no sequence, as the adapter of an assembly's

package/esm/FromConfigRegionsAdapter/configSchema.js

@@ -3,7 +3,8 @@ import { ConfigurationSchema } from '@jbrowse/core/configuration';
  * #config FromConfigRegionsAdapter
  * #trackType ReferenceSequenceTrack
  * #fileFormat inline | Inline regions | refNames and sizes only, no sequence
- * used for specifying refNames+sizes of an assembly
+ * Supplies an assembly's reference names and sizes inline in the config, with
+ * no sequence.
  *
  * #example
  * Supplies refNames+sizes with no sequence, as the adapter of an assembly's
@@ -45,5 +46,7 @@ const regionsConfigSchema = ConfigurationSchema('FromConfigRegionsAdapter', {
     },
 }, {
     explicitlyTyped: true,
+    closed: true,
+    retired: { featureClass: () => ({}) },
 });
 export default regionsConfigSchema;

package/esm/FromConfigSequenceAdapter/configSchema.d.ts

@@ -2,8 +2,8 @@
  * #config FromConfigSequenceAdapter
  * #trackType ReferenceSequenceTrack
  * #fileFormat inline | Inline sequence | Each feature's `seq` holds the bases for its region
- * supplies reference sequence inline in the config; each feature's `seq` holds
- * the bases for its region
+ * Supplies a reference sequence inline in the config, as features whose `seq`
+ * holds the bases for each region.
  *
  * #example
  * Used as the adapter of an assembly's `sequence` (a `ReferenceSequenceTrack`):

package/esm/FromConfigSequenceAdapter/configSchema.js

@@ -3,8 +3,8 @@ import { ConfigurationSchema } from '@jbrowse/core/configuration';
  * #config FromConfigSequenceAdapter
  * #trackType ReferenceSequenceTrack
  * #fileFormat inline | Inline sequence | Each feature's `seq` holds the bases for its region
- * supplies reference sequence inline in the config; each feature's `seq` holds
- * the bases for its region
+ * Supplies a reference sequence inline in the config, as features whose `seq`
+ * holds the bases for each region.
  *
  * #example
  * Used as the adapter of an assembly's `sequence` (a `ReferenceSequenceTrack`):
@@ -44,5 +44,7 @@ const sequenceConfigSchema = ConfigurationSchema('FromConfigSequenceAdapter', {
     },
 }, {
     explicitlyTyped: true,
+    closed: true,
+    retired: { featureClass: () => ({}) },
 });
 export default sequenceConfigSchema;

package/esm/NcbiSequenceReportAliasAdapter/configSchema.d.ts

@@ -2,7 +2,8 @@ import type { Instance } from '@jbrowse/mobx-state-tree';
 export declare function normalizeSnapshot(snap: Record<string, unknown>): Record<string, unknown>;
 /**
  * #config NcbiSequenceReportAliasAdapter
- * can read "sequence_report.tsv" type files from NCBI
+ * Reads refName aliases for an assembly from an NCBI `sequence_report.tsv`
+ * file.
  *
  * #example
  * Goes on an ASSEMBLY, under `refNameAliases` — not on a track. The file ships

package/esm/NcbiSequenceReportAliasAdapter/configSchema.js

@@ -4,7 +4,8 @@ export function normalizeSnapshot(snap) {
 }
 /**
  * #config NcbiSequenceReportAliasAdapter
- * can read "sequence_report.tsv" type files from NCBI
+ * Reads refName aliases for an assembly from an NCBI `sequence_report.tsv`
+ * file.
  *
  * #example
  * Goes on an ASSEMBLY, under `refNameAliases` — not on a track. The file ships
@@ -77,6 +78,11 @@ const NcbiSequenceReportAliasAdapterConfigSchema = ConfigurationSchema('NcbiSequ
     },
 }, {
     explicitlyTyped: true,
+    closed: true,
+    retired: {
+        // eslint-disable-next-line @eslint-react/no-unnecessary-use-prefix -- the retired slot's own name
+        useUcscNameOverride: useNameOverride => ({ useNameOverride }),
+    },
     /**
      * #preProcessSnapshot
      *

package/esm/RefNameAliasAdapter/configSchema.d.ts

@@ -2,8 +2,8 @@ import type { Instance } from '@jbrowse/mobx-state-tree';
 export declare function normalizeSnapshot(snap: Record<string, unknown>): Record<string, unknown>;
 /**
  * #config RefNameAliasAdapter
- * can read "chromAliases" type files from UCSC or any tab separated file of
- * refName aliases
+ * Reads refName aliases for an assembly from a UCSC `chromAlias` file or any
+ * other tab-separated table of aliases.
  *
  * #example
  * Goes on an ASSEMBLY, under `refNameAliases` — not on a track. Writing

package/esm/RefNameAliasAdapter/configSchema.js

@@ -4,8 +4,8 @@ export function normalizeSnapshot(snap) {
 }
 /**
  * #config RefNameAliasAdapter
- * can read "chromAliases" type files from UCSC or any tab separated file of
- * refName aliases
+ * Reads refName aliases for an assembly from a UCSC `chromAlias` file or any
+ * other tab-separated table of aliases.
  *
  * #example
  * Goes on an ASSEMBLY, under `refNameAliases` — not on a track. Writing
@@ -88,6 +88,7 @@ const RefNameAliasAdapter = ConfigurationSchema('RefNameAliasAdapter', {
     },
 }, {
     explicitlyTyped: true,
+    closed: true,
     /**
      * #preProcessSnapshot
      *

package/esm/adapters.d.ts

@@ -0,0 +1,9 @@
+import type PluginManager from '@jbrowse/core/PluginManager';
+/**
+ * #api
+ * Registers `FromConfigAdapter`, whose features a track config writes inline,
+ * and the alias adapters an assembly's `refNameAliases` reads through, on a
+ * plugin manager that wants them without the configuration editor, as a
+ * headless host does.
+ */
+export declare function registerConfigAdapters(pluginManager: PluginManager): void;

package/esm/adapters.js

@@ -0,0 +1,15 @@
+import FromConfigAdapterF from './FromConfigAdapter/index.js';
+import NcbiSequenceReportAliasAdapterF from './NcbiSequenceReportAliasAdapter/index.js';
+import RefNameAliasAdapterF from './RefNameAliasAdapter/index.js';
+/**
+ * #api
+ * Registers `FromConfigAdapter`, whose features a track config writes inline,
+ * and the alias adapters an assembly's `refNameAliases` reads through, on a
+ * plugin manager that wants them without the configuration editor, as a
+ * headless host does.
+ */
+export function registerConfigAdapters(pluginManager) {
+    FromConfigAdapterF(pluginManager);
+    RefNameAliasAdapterF(pluginManager);
+    NcbiSequenceReportAliasAdapterF(pluginManager);
+}

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-config",
-  "version": "5.0.0-beta.13",
+  "version": "5.0.0-beta.14",
   "type": "module",
   "description": "JBrowse 2 config utilities",
   "keywords": [
@@ -17,17 +17,21 @@
   },
   "author": "JBrowse Team",
   "main": "esm/index.js",
+  "exports": {
+    ".": "./esm/index.js",
+    "./adapters": "./esm/adapters.js"
+  },
   "files": [
     "esm"
   ],
   "dependencies": {
-    "@jbrowse/mobx-state-tree": "^6.7.0",
-    "@mui/icons-material": "^9.4.0",
-    "@mui/material": "^9.4.0",
+    "@jbrowse/mobx-state-tree": "^6.9.0",
+    "@mui/icons-material": "^9.5.0",
+    "@mui/material": "^9.5.0",
     "mobx": "^7.0.6",
     "mobx-react": "^10.0.2",
     "rxjs": "^7.8.2",
-    "@jbrowse/core": "^5.0.0-beta.13"
+    "@jbrowse/core": "^5.0.0-beta.14"
   },
   "peerDependencies": {
     "react": ">=19.0.0",
@@ -44,8 +48,5 @@
     "build:esm": "node ../../node_modules/typescript7/bin/tsc --build tsconfig.build.esm.json",
     "clean": "rimraf esm *.tsbuildinfo"
   },
-  "types": "esm/index.d.ts",
-  "exports": {
-    ".": "./esm/index.js"
-  }
+  "types": "esm/index.d.ts"
 }