@jbrowse/plugin-config 1.6.5 → 1.6.8

package/dist/ConfigurationEditorWidget/index.d.ts

@@ -1,3 +1,3 @@
 export { default as stateModelFactory } from "./model";
-export const configSchema: import("@jbrowse/core/configuration/configurationSchema").AnyConfigurationSchemaType;
+export const configSchema: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
 export const HeadingComponent: import("mobx-react/dist/types/IReactComponent").IReactComponent<any>;

package/dist/FromConfigAdapter/FromConfigAdapter.d.ts

@@ -16,7 +16,7 @@ export default class FromConfigAdapter extends BaseFeatureDataAdapter {
     static makeFeature(data: SimpleFeatureSerialized): SimpleFeature;
     getRefNames(): Promise<string[]>;
     getRefNameAliases(): Promise<{
-        refName: any;
+        refName: string;
         aliases: any;
     }[]>;
     getFeatures(region: NoAssemblyRegion): import("rxjs").Observable<Feature>;

package/dist/FromConfigAdapter/FromConfigRegionsAdapter.d.ts

@@ -16,8 +16,8 @@ export default class FromConfigRegionsAdapter extends BaseAdapter implements Reg
      */
     getRegions(): Promise<{
         refName: string;
-        start: any;
-        end: any;
+        start: number;
+        end: number;
     }[]>;
     freeResources(): void;
 }

package/dist/FromConfigAdapter/FromConfigSequenceAdapter.d.ts

@@ -13,8 +13,8 @@ export default class FromConfigSequenceAdapter extends FromConfigAdapter {
      */
     getRegions(): Promise<{
         refName: string;
-        start: any;
-        end: any;
+        start: number;
+        end: number;
     }[]>;
     /**
      * called to provide a hint that data tied to a certain region

package/dist/FromConfigAdapter/configSchema.d.ts

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

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

package/dist/plugin-config.cjs.development.js

@@ -25,10 +25,8 @@ var reactSyntaxHighlighter = require('react-syntax-highlighter');
 var json = _interopDefault(require('react-syntax-highlighter/dist/cjs/languages/hljs/json'));
 var a11yDark = _interopDefault(require('react-syntax-highlighter/dist/cjs/styles/hljs/a11y-dark'));
 var a11yLight = _interopDefault(require('react-syntax-highlighter/dist/cjs/styles/hljs/a11y-light'));
-var FormGroup = _interopDefault(require('@material-ui/core/FormGroup'));
-var FormLabel = _interopDefault(require('@material-ui/core/FormLabel'));
-var styles = require('@material-ui/core/styles');
 var pluralize = require('pluralize');
+var ExpandMoreIcon = _interopDefault(require('@material-ui/icons/ExpandMore'));
 var ui = require('@jbrowse/core/ui');
 var mstReflection = require('@jbrowse/core/util/mst-reflection');
 var DeleteIcon = _interopDefault(require('@material-ui/icons/Delete'));
@@ -40,6 +38,7 @@ var ReactPropTypes = _interopDefault(require('prop-types'));
 var TextField = _interopDefault(require('@material-ui/core/TextField'));
 var MenuItem = _interopDefault(require('@material-ui/core/MenuItem'));
 var Paper = _interopDefault(require('@material-ui/core/Paper'));
+var styles = require('@material-ui/core/styles');
 var reactColor = require('react-color');
 
 function ownKeys(object, enumerableOnly) {
@@ -280,10 +279,6 @@ function _slicedToArray(arr, i) {
   return _arrayWithHoles(arr) || _iterableToArrayLimit(arr, i) || _unsupportedIterableToArray(arr, i) || _nonIterableRest();
 }
 
-function _toArray(arr) {
-  return _arrayWithHoles(arr) || _iterableToArray(arr) || _unsupportedIterableToArray(arr) || _nonIterableRest();
-}
-
 function _toConsumableArray(arr) {
   return _arrayWithoutHoles(arr) || _iterableToArray(arr) || _unsupportedIterableToArray(arr) || _nonIterableSpread();
 }
@@ -1664,7 +1659,7 @@ var RefNameAliasAdapter = /*#__PURE__*/function (_BaseAdapter) {
     key: "getRefNameAliases",
     value: function () {
       var _getRefNameAliases = /*#__PURE__*/_asyncToGenerator( /*#__PURE__*/runtime_1.mark(function _callee() {
-        var loc, results;
+        var loc, results, refColumn;
         return runtime_1.wrap(function _callee$(_context) {
           while (1) {
             switch (_context.prev = _context.next) {
@@ -1684,13 +1679,15 @@ var RefNameAliasAdapter = /*#__PURE__*/function (_BaseAdapter) {
 
               case 5:
                 results = _context.sent;
+                refColumn = configuration.readConfObject(this.config, 'refNameColumn');
                 return _context.abrupt("return", results.trim().split('\n').filter(function (f) {
                   return !!f && !f.startsWith('#');
                 }).map(function (row) {
-                  var _row$split = row.split('\t'),
-                      _row$split2 = _toArray(_row$split),
-                      refName = _row$split2[0],
-                      aliases = _row$split2.slice(1);
+                  var aliases = row.split('\t');
+
+                  var _aliases$splice = aliases.splice(refColumn, 1),
+                      _aliases$splice2 = _slicedToArray(_aliases$splice, 1),
+                      refName = _aliases$splice2[0];
 
                   return {
                     refName: refName,
@@ -1698,7 +1695,7 @@ var RefNameAliasAdapter = /*#__PURE__*/function (_BaseAdapter) {
                   };
                 }));
 
-              case 7:
+              case 8:
               case "end":
                 return _context.stop();
             }
@@ -1745,6 +1742,10 @@ var refNameAliasAdapterConfigSchema = /*#__PURE__*/configuration.ConfigurationSc
       uri: '/path/to/my/aliases.txt',
       locationType: 'UriLocation'
     }
+  },
+  refNameColumn: {
+    type: 'number',
+    defaultValue: 0
   }
 }, {
   explicitlyTyped: true
@@ -1982,10 +1983,12 @@ function CallbackEditor(_ref) {
 
       var jexlDebouncedCode = debouncedCode.startsWith('jexl:') ? debouncedCode : "jexl:".concat(debouncedCode);
       jexlStrings.stringToJexlExpression(jexlDebouncedCode, (_getEnv$pluginManager = mobxStateTree.getEnv(slot).pluginManager) === null || _getEnv$pluginManager === void 0 ? void 0 : _getEnv$pluginManager.jexl);
-      slot.set(jexlDebouncedCode); // slot.set `jexl:${debouncedCode}`
-
+      slot.set(jexlDebouncedCode);
       setCodeError(null);
     } catch (e) {
+      console.error({
+        e: e
+      });
       setCodeError(e);
     }
   }, [debouncedCode, slot]); // if default value is a callback, will have to remove jexl:
@@ -1998,7 +2001,7 @@ function CallbackEditor(_ref) {
     className: classes.callbackEditor,
     value: code.startsWith('jexl:') ? code.split('jexl:')[1] : code,
     onValueChange: function onValueChange(newCode) {
-      setCode(newCode);
+      return setCode(newCode);
     },
     highlight: function highlight(newCode) {
       return newCode;
@@ -2007,7 +2010,11 @@ function CallbackEditor(_ref) {
     style: {
       background: error ? '#fdd' : undefined
     }
-  }), /*#__PURE__*/React__default.createElement(core.FormHelperText, null, slot.description)), /*#__PURE__*/React__default.createElement(core.Tooltip, {
+  }), error ? /*#__PURE__*/React__default.createElement(core.FormHelperText, {
+    style: {
+      color: '#f00'
+    }
+  }, "".concat(error)) : null, /*#__PURE__*/React__default.createElement(core.FormHelperText, null, slot.description)), /*#__PURE__*/React__default.createElement(core.Tooltip, {
     title: /*#__PURE__*/React__default.createElement("div", null, "Callbacks are written in Jexl format. Click to learn more.", /*#__PURE__*/React__default.createElement("br", null), " Names of available context items: ", slot.contextVariable),
     arrow: true
   }, /*#__PURE__*/React__default.createElement(core.IconButton, {
@@ -2462,13 +2469,10 @@ var useSlotEditorStyles = /*#__PURE__*/core.makeStyles(function (theme) {
     paper: {
       display: 'flex',
       marginBottom: theme.spacing(2),
-      position: 'relative',
-      overflow: 'visible'
+      position: 'relative'
     },
     paperContent: {
-      flex: 'auto',
-      padding: theme.spacing(1),
-      overflow: 'auto'
+      width: '100%'
     },
     slotModeSwitch: {
       width: 24,
@@ -2540,18 +2544,20 @@ var TypeSelector = /*#__PURE__*/mobxReact.observer(function (_ref) {
   }))));
 });
 
-var useStyles$3 = /*#__PURE__*/styles.makeStyles(function (theme) {
+var useStyles$3 = /*#__PURE__*/core.makeStyles(function (theme) {
   return {
-    subSchemaContainer: {
-      marginLeft: theme.spacing(1),
-      borderLeft: "1px solid ".concat(theme.palette.secondary.main),
-      paddingLeft: theme.spacing(1),
-      marginBottom: theme.spacing(1)
+    expandIcon: {
+      color: '#fff'
     },
     root: {
-      padding: theme.spacing(1, 3, 1, 1),
-      background: theme.palette.background["default"],
-      overflowX: 'hidden'
+      padding: theme.spacing(1, 3, 1, 1)
+    },
+    expansionPanelDetails: {
+      display: 'block',
+      padding: theme.spacing(1)
+    },
+    accordion: {
+      border: "1px solid ".concat(theme.palette.text.primary)
     }
   };
 });
@@ -2561,19 +2567,21 @@ var Member = /*#__PURE__*/mobxReact.observer(function (props) {
       slotSchema = props.slotSchema,
       schema = props.schema,
       _props$slot = props.slot,
-      slot = _props$slot === void 0 ? schema[slotName] : _props$slot;
+      slot = _props$slot === void 0 ? schema[slotName] : _props$slot,
+      _props$path = props.path,
+      path = _props$path === void 0 ? [] : _props$path;
   var typeSelector;
 
   if (configuration.isConfigurationSchemaType(slotSchema)) {
     if (slot.length) {
-      return /*#__PURE__*/React__default.createElement(React__default.Fragment, null, slot.map(function (subslot, slotIndex) {
+      return slot.map(function (subslot, slotIndex) {
         var key = "".concat(pluralize.singular(slotName), " ").concat(slotIndex + 1);
         return /*#__PURE__*/React__default.createElement(Member, _extends({}, props, {
           key: key,
           slot: subslot,
           slotName: key
         }));
-      }));
+      });
     } // if this is an explicitly typed schema, make a type-selecting dropdown
     // that can be used to change its type
 
@@ -2595,10 +2603,22 @@ var Member = /*#__PURE__*/mobxReact.observer(function (props) {
       });
     }
 
-    return /*#__PURE__*/React__default.createElement(React__default.Fragment, null, /*#__PURE__*/React__default.createElement(FormLabel, null, slotName), /*#__PURE__*/React__default.createElement("div", {
-      className: classes.subSchemaContainer
-    }, typeSelector, /*#__PURE__*/React__default.createElement(FormGroup, null, /*#__PURE__*/React__default.createElement(Schema, {
-      schema: slot
+    return /*#__PURE__*/React__default.createElement(core.Accordion, {
+      defaultExpanded: true,
+      className: classes.accordion,
+      TransitionProps: {
+        unmountOnExit: true,
+        timeout: 150
+      }
+    }, /*#__PURE__*/React__default.createElement(core.AccordionSummary, {
+      expandIcon: /*#__PURE__*/React__default.createElement(ExpandMoreIcon, {
+        className: classes.expandIcon
+      })
+    }, /*#__PURE__*/React__default.createElement(core.Typography, null, [].concat(_toConsumableArray(path), [slotName]).join('🡒'))), /*#__PURE__*/React__default.createElement(core.AccordionDetails, {
+      className: classes.expansionPanelDetails
+    }, typeSelector, /*#__PURE__*/React__default.createElement(core.FormGroup, null, /*#__PURE__*/React__default.createElement(Schema, {
+      schema: slot,
+      path: [].concat(_toConsumableArray(path), [slotName])
     }))));
   }
 
@@ -2614,8 +2634,11 @@ var Member = /*#__PURE__*/mobxReact.observer(function (props) {
   return null;
 });
 var Schema = /*#__PURE__*/mobxReact.observer(function (_ref) {
-  var schema = _ref.schema;
-  return util.iterMap(Object.entries(mobxStateTree.getMembers(schema).properties), function (_ref2) {
+  var schema = _ref.schema,
+      _ref$path = _ref.path,
+      path = _ref$path === void 0 ? [] : _ref$path;
+  var properties = mobxStateTree.getMembers(schema).properties;
+  return Object.entries(properties).map(function (_ref2) {
     var _ref3 = _slicedToArray(_ref2, 2),
         slotName = _ref3[0],
         slotSchema = _ref3[1];
@@ -2624,6 +2647,7 @@ var Schema = /*#__PURE__*/mobxReact.observer(function (_ref) {
       key: slotName,
       slotName: slotName,
       slotSchema: slotSchema,
+      path: path,
       schema: schema
     });
   });
@@ -2635,13 +2659,25 @@ var ConfigurationEditor = /*#__PURE__*/mobxReact.observer(function (_ref4) {
   // see pr #804
 
   var key = model.target && configuration.readConfObject(model.target, 'trackId');
-  return /*#__PURE__*/React__default.createElement("div", {
-    className: classes.root,
+  var name = model.target && configuration.readConfObject(model.target, 'name');
+  return /*#__PURE__*/React__default.createElement(core.Accordion, {
     key: key,
+    defaultExpanded: true,
+    className: classes.accordion,
+    TransitionProps: {
+      unmountOnExit: true,
+      timeout: 150
+    }
+  }, /*#__PURE__*/React__default.createElement(core.AccordionSummary, {
+    expandIcon: /*#__PURE__*/React__default.createElement(ExpandMoreIcon, {
+      className: classes.expandIcon
+    })
+  }, /*#__PURE__*/React__default.createElement(core.Typography, null, name ? name : 'Configuration')), /*#__PURE__*/React__default.createElement(core.AccordionDetails, {
+    className: classes.expansionPanelDetails,
     "data-testid": "configEditor"
   }, !model.target ? 'no target set' : /*#__PURE__*/React__default.createElement(Schema, {
     schema: model.target
-  }));
+  })));
 });
 
 var ConfigurationEditor$1 = {