@jbrowse/core 1.7.11 → 2.1.0

package/configuration/util.js

@@ -1,26 +1,8 @@
 "use strict";
-
-var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
-
-Object.defineProperty(exports, "__esModule", {
-  value: true
-});
-exports.getConf = getConf;
-exports.getTypeNamesFromExplicitlyTypedUnion = getTypeNamesFromExplicitlyTypedUnion;
-exports.isBareConfigurationSchemaType = isBareConfigurationSchemaType;
-exports.isConfigurationModel = isConfigurationModel;
-exports.isConfigurationSchemaType = isConfigurationSchemaType;
-exports.isConfigurationSlotType = isConfigurationSlotType;
-exports.readConfObject = readConfObject;
-
-var _typeof2 = _interopRequireDefault(require("@babel/runtime/helpers/typeof"));
-
-var _toConsumableArray2 = _interopRequireDefault(require("@babel/runtime/helpers/toConsumableArray"));
-
-var _mobxStateTree = require("mobx-state-tree");
-
-var _mstReflection = require("../util/mst-reflection");
-
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.isConfigurationSlotType = exports.isConfigurationModel = exports.isConfigurationSchemaType = exports.isBareConfigurationSchemaType = exports.getTypeNamesFromExplicitlyTypedUnion = exports.getConf = exports.readConfObject = void 0;
+const mobx_state_tree_1 = require("mobx-state-tree");
+const mst_reflection_1 = require("../util/mst-reflection");
 /**
  * given a configuration model (an instance of a ConfigurationSchema),
  * read the configuration variable at the given path
@@ -30,70 +12,63 @@ var _mstReflection = require("../util/mst-reflection");
  * @param args - extra arguments e.g. for a feature callback,
  *  will be sent to each of the slotNames
  */
-function readConfObject(confObject) {
-  var slotPath = arguments.length > 1 && arguments[1] !== undefined ? arguments[1] : undefined;
-  var args = arguments.length > 2 && arguments[2] !== undefined ? arguments[2] : {};
-
-  if (!confObject) {
-    throw new TypeError('must provide conf object to read');
-  }
-
-  if (!slotPath) {
-    return JSON.parse(JSON.stringify((0, _mobxStateTree.getSnapshot)(confObject)));
-  }
-
-  if (typeof slotPath === 'string') {
-    var slot = confObject[slotPath]; // check for the subconf being a map if we don't find it immediately
-
-    if (!slot && (0, _mobxStateTree.isStateTreeNode)(confObject) && (0, _mobxStateTree.isMapType)((0, _mobxStateTree.getType)(confObject))) {
-      slot = confObject.get(slotPath);
+function readConfObject(confObject, slotPath = undefined, 
+// eslint-disable-next-line @typescript-eslint/no-explicit-any
+args = {}) {
+    if (!confObject) {
+        throw new TypeError('must provide conf object to read');
     }
-
-    if (!slot) {
-      return undefined; // if we want to be very strict about config slots, we could uncomment the below
-      // instead of returning undefine
-      //
-      // const modelType = getType(model)
-      // const schemaType = model.configuration && getType(model.configuration)
-      // throw new Error(
-      //   `no slot "${slotName}" found in ${modelType.name} configuration (${
-      //     schemaType.name
-      //   })`,
-      // )
+    if (!slotPath) {
+        return JSON.parse(JSON.stringify((0, mobx_state_tree_1.getSnapshot)(confObject)));
     }
-
-    if (slot.expr) {
-      var appliedFunc = slot.expr.evalSync(args);
-
-      if ((0, _mobxStateTree.isStateTreeNode)(appliedFunc)) {
-        return JSON.parse(JSON.stringify((0, _mobxStateTree.getSnapshot)(appliedFunc)));
-      }
-
-      return appliedFunc;
-    }
-
-    if ((0, _mobxStateTree.isStateTreeNode)(slot)) {
-      return JSON.parse(JSON.stringify((0, _mobxStateTree.getSnapshot)(slot)));
+    if (typeof slotPath === 'string') {
+        let slot = confObject[slotPath];
+        // check for the subconf being a map if we don't find it immediately
+        if (!slot &&
+            (0, mobx_state_tree_1.isStateTreeNode)(confObject) &&
+            (0, mobx_state_tree_1.isMapType)((0, mobx_state_tree_1.getType)(confObject))) {
+            slot = confObject.get(slotPath);
+        }
+        if (!slot) {
+            return undefined;
+            // if we want to be very strict about config slots, we could uncomment the below
+            // instead of returning undefine
+            //
+            // const modelType = getType(model)
+            // const schemaType = model.configuration && getType(model.configuration)
+            // throw new Error(
+            //   `no slot "${slotName}" found in ${modelType.name} configuration (${
+            //     schemaType.name
+            //   })`,
+            // )
+        }
+        if (slot.expr) {
+            const appliedFunc = slot.expr.evalSync(args);
+            if ((0, mobx_state_tree_1.isStateTreeNode)(appliedFunc)) {
+                return JSON.parse(JSON.stringify((0, mobx_state_tree_1.getSnapshot)(appliedFunc)));
+            }
+            return appliedFunc;
+        }
+        if ((0, mobx_state_tree_1.isStateTreeNode)(slot)) {
+            return JSON.parse(JSON.stringify((0, mobx_state_tree_1.getSnapshot)(slot)));
+        }
+        return slot;
     }
-
-    return slot;
-  }
-
-  var slotName = slotPath[0];
-
-  if (slotPath.length > 1) {
-    var newPath = slotPath.slice(1);
-    var subConf = confObject[slotName]; // check for the subconf being a map if we don't find it immediately
-
-    if (!subConf && (0, _mobxStateTree.isStateTreeNode)(confObject) && (0, _mobxStateTree.isMapType)((0, _mobxStateTree.getType)(confObject))) {
-      subConf = confObject.get(slotName);
+    const slotName = slotPath[0];
+    if (slotPath.length > 1) {
+        const newPath = slotPath.slice(1);
+        let subConf = confObject[slotName];
+        // check for the subconf being a map if we don't find it immediately
+        if (!subConf &&
+            (0, mobx_state_tree_1.isStateTreeNode)(confObject) &&
+            (0, mobx_state_tree_1.isMapType)((0, mobx_state_tree_1.getType)(confObject))) {
+            subConf = confObject.get(slotName);
+        }
+        return subConf ? readConfObject(subConf, newPath, args) : undefined;
     }
-
-    return subConf ? readConfObject(subConf, newPath, args) : undefined;
-  }
-
-  return readConfObject(confObject, slotName, args);
+    return readConfObject(confObject, slotName, args);
 }
+exports.readConfObject = readConfObject;
 /**
  * helper method for readConfObject, reads the config from a mst model
  *
@@ -102,25 +77,19 @@ function readConfObject(confObject) {
  * @param args - extra arguments e.g. for a feature callback,
  *   will be sent to each of the slotNames
  */
-
-
-function getConf(model) {
-  var slotPath = arguments.length > 1 && arguments[1] !== undefined ? arguments[1] : undefined;
-  var args = arguments.length > 2 && arguments[2] !== undefined ? arguments[2] : {};
-
-  if (!model) {
-    throw new TypeError('must provide a model object');
-  }
-
-  var _ref = model,
-      configuration = _ref.configuration;
-
-  if (isConfigurationModel(configuration)) {
-    return readConfObject(configuration, slotPath, args);
-  }
-
-  throw new TypeError('cannot getConf on this model, it has no configuration');
+function getConf(model, slotPath = undefined, 
+// eslint-disable-next-line @typescript-eslint/no-explicit-any
+args = {}) {
+    if (!model) {
+        throw new TypeError('must provide a model object');
+    }
+    const { configuration } = model;
+    if (isConfigurationModel(configuration)) {
+        return readConfObject(configuration, slotPath, args);
+    }
+    throw new TypeError('cannot getConf on this model, it has no configuration');
 }
+exports.getConf = getConf;
 /**
  * given a union of explicitly typed configuration schema types,
  * extract an array of the type names contained in the union
@@ -128,90 +97,79 @@ function getConf(model) {
  * @param unionType -
  * @returns Array of type names contained in the union
  */
-
-
 function getTypeNamesFromExplicitlyTypedUnion(maybeUnionType) {
-  if ((0, _mobxStateTree.isType)(maybeUnionType)) {
-    maybeUnionType = (0, _mstReflection.resolveLateType)(maybeUnionType); // @ts-ignore
-
-    if ((0, _mobxStateTree.isUnionType)(maybeUnionType)) {
-      var typeNames = [];
-      (0, _mstReflection.getUnionSubTypes)(maybeUnionType).forEach(function (type) {
-        type = (0, _mstReflection.resolveLateType)(type);
-        var typeName = getTypeNamesFromExplicitlyTypedUnion(type);
-
-        if (!typeName.length) {
-          var def = (0, _mstReflection.getDefaultValue)(type);
-          typeName = [def.type];
+    if ((0, mobx_state_tree_1.isType)(maybeUnionType)) {
+        maybeUnionType = (0, mst_reflection_1.resolveLateType)(maybeUnionType);
+        // @ts-ignore
+        if ((0, mobx_state_tree_1.isUnionType)(maybeUnionType)) {
+            const typeNames = [];
+            (0, mst_reflection_1.getUnionSubTypes)(maybeUnionType).forEach(type => {
+                type = (0, mst_reflection_1.resolveLateType)(type);
+                let typeName = getTypeNamesFromExplicitlyTypedUnion(type);
+                if (!typeName.length) {
+                    const def = (0, mst_reflection_1.getDefaultValue)(type);
+                    typeName = [def.type];
+                }
+                if (!typeName[0]) {
+                    // debugger
+                    throw new Error(`invalid config schema type ${type}`);
+                }
+                typeNames.push(...typeName);
+            });
+            return typeNames;
         }
-
-        if (!typeName[0]) {
-          // debugger
-          throw new Error("invalid config schema type ".concat(type));
-        }
-
-        typeNames.push.apply(typeNames, (0, _toConsumableArray2.default)(typeName));
-      });
-      return typeNames;
     }
-  }
-
-  return [];
+    return [];
 }
-
+exports.getTypeNamesFromExplicitlyTypedUnion = getTypeNamesFromExplicitlyTypedUnion;
 function isBareConfigurationSchemaType(thing) {
-  if ((0, _mobxStateTree.isType)(thing)) {
-    if ((0, _mobxStateTree.isModelType)(thing) && ('isJBrowseConfigurationSchema' in thing || thing.name.includes('ConfigurationSchema'))) {
-      return true;
-    } // if it's a late type, assume its a config schema
-
-
-    if ((0, _mobxStateTree.isLateType)(thing)) {
-      return true;
+    if ((0, mobx_state_tree_1.isType)(thing)) {
+        if ((0, mobx_state_tree_1.isModelType)(thing) &&
+            ('isJBrowseConfigurationSchema' in thing ||
+                thing.name.includes('ConfigurationSchema'))) {
+            return true;
+        }
+        // if it's a late type, assume its a config schema
+        if ((0, mobx_state_tree_1.isLateType)(thing)) {
+            return true;
+        }
     }
-  }
-
-  return false;
+    return false;
 }
-
+exports.isBareConfigurationSchemaType = isBareConfigurationSchemaType;
 function isConfigurationSchemaType(thing) {
-  if (!(0, _mobxStateTree.isType)(thing)) {
+    if (!(0, mobx_state_tree_1.isType)(thing)) {
+        return false;
+    }
+    // written as a series of if-statements instead of a big logical OR
+    // because this construction gives much better debugging backtraces.
+    // also, note that the order of these statements matters, because
+    // for example some union types are also optional types
+    if (isBareConfigurationSchemaType(thing)) {
+        return true;
+    }
+    if ((0, mobx_state_tree_1.isUnionType)(thing)) {
+        return (0, mst_reflection_1.getUnionSubTypes)(thing).every(t => isConfigurationSchemaType(t) || t.name === 'undefined');
+    }
+    if ((0, mobx_state_tree_1.isOptionalType)(thing) && isConfigurationSchemaType((0, mst_reflection_1.getSubType)(thing))) {
+        return true;
+    }
+    if ((0, mobx_state_tree_1.isArrayType)(thing) && isConfigurationSchemaType((0, mst_reflection_1.getSubType)(thing))) {
+        return true;
+    }
+    if ((0, mobx_state_tree_1.isMapType)(thing) && isConfigurationSchemaType((0, mst_reflection_1.getSubType)(thing))) {
+        return true;
+    }
     return false;
-  } // written as a series of if-statements instead of a big logical OR
-  // because this construction gives much better debugging backtraces.
-  // also, note that the order of these statements matters, because
-  // for example some union types are also optional types
-
-
-  if (isBareConfigurationSchemaType(thing)) {
-    return true;
-  }
-
-  if ((0, _mobxStateTree.isUnionType)(thing)) {
-    return (0, _mstReflection.getUnionSubTypes)(thing).every(function (t) {
-      return isConfigurationSchemaType(t) || t.name === 'undefined';
-    });
-  }
-
-  if ((0, _mobxStateTree.isOptionalType)(thing) && isConfigurationSchemaType((0, _mstReflection.getSubType)(thing))) {
-    return true;
-  }
-
-  if ((0, _mobxStateTree.isArrayType)(thing) && isConfigurationSchemaType((0, _mstReflection.getSubType)(thing))) {
-    return true;
-  }
-
-  if ((0, _mobxStateTree.isMapType)(thing) && isConfigurationSchemaType((0, _mstReflection.getSubType)(thing))) {
-    return true;
-  }
-
-  return false;
 }
-
+exports.isConfigurationSchemaType = isConfigurationSchemaType;
 function isConfigurationModel(thing) {
-  return (0, _mobxStateTree.isStateTreeNode)(thing) && isConfigurationSchemaType((0, _mobxStateTree.getType)(thing));
+    return (0, mobx_state_tree_1.isStateTreeNode)(thing) && isConfigurationSchemaType((0, mobx_state_tree_1.getType)(thing));
 }
-
+exports.isConfigurationModel = isConfigurationModel;
 function isConfigurationSlotType(thing) {
-  return (0, _typeof2.default)(thing) === 'object' && thing !== null && 'isJBrowseConfigurationSlot' in thing;
-}
+    return (typeof thing === 'object' &&
+        thing !== null &&
+        'isJBrowseConfigurationSlot' in thing);
+}
+exports.isConfigurationSlotType = isConfigurationSlotType;

package/data_adapters/BaseAdapter.d.ts

@@ -34,6 +34,7 @@ export declare abstract class BaseAdapter {
     id: string;
     static capabilities: string[];
     constructor(config?: AnyConfigurationModel, getSubAdapter?: getSubAdapterType | undefined, pluginManager?: PluginManager | undefined);
+    getConf(arg: string | string[]): any;
     /**
      * 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
@@ -59,11 +60,10 @@ export declare abstract class BaseFeatureDataAdapter extends BaseAdapter {
      * @param opts - Feature adapter options
      */
     abstract getRefNames(opts?: BaseOptions): Promise<string[]>;
-    getConf(arg: string | string[]): any;
     /**
      * Get features from the data source that overlap a region
      * @param region - Region
-     * @param options - Feature adapter options
+     * @param opts - Feature adapter options
      * @returns Observable of Feature objects in the region
      */
     abstract getFeatures(region: Region, opts?: BaseOptions): Observable<Feature>;