@jbrowse/plugin-config 1.6.7 → 1.7.0

package/dist/FromConfigAdapter/FromConfigRegionsAdapter.test.js

@@ -0,0 +1,200 @@
+"use strict";
+
+var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
+
+var _regenerator = _interopRequireDefault(require("@babel/runtime/regenerator"));
+
+var _asyncToGenerator2 = _interopRequireDefault(require("@babel/runtime/helpers/asyncToGenerator"));
+
+var _FromConfigRegionsAdapter = _interopRequireDefault(require("./FromConfigRegionsAdapter"));
+
+var _configSchema = require("./configSchema");
+
+test('adapter can fetch regions 1', /*#__PURE__*/(0, _asyncToGenerator2["default"])( /*#__PURE__*/_regenerator["default"].mark(function _callee() {
+  var features, adapter, result;
+  return _regenerator["default"].wrap(function _callee$(_context) {
+    while (1) {
+      switch (_context.prev = _context.next) {
+        case 0:
+          features = [{
+            uniqueId: 'one',
+            refName: 'ctgA',
+            start: 250,
+            end: 400
+          }, {
+            uniqueId: 'two',
+            refName: 'ctgA',
+            start: 150,
+            end: 300
+          }, {
+            uniqueId: 'three',
+            refName: 'ctgB',
+            start: 50,
+            end: 60
+          }];
+          adapter = new _FromConfigRegionsAdapter["default"](_configSchema.regionsConfigSchema.create({
+            features: features
+          }));
+          _context.next = 4;
+          return adapter.getRegions();
+
+        case 4:
+          result = _context.sent;
+          expect(result).toEqual([{
+            refName: 'ctgA',
+            start: 150,
+            end: 400
+          }, {
+            refName: 'ctgB',
+            start: 50,
+            end: 60
+          }]);
+
+        case 6:
+        case "end":
+          return _context.stop();
+      }
+    }
+  }, _callee);
+})));
+test('adapter can fetch regions 2', /*#__PURE__*/(0, _asyncToGenerator2["default"])( /*#__PURE__*/_regenerator["default"].mark(function _callee2() {
+  var features, adapter, result;
+  return _regenerator["default"].wrap(function _callee2$(_context2) {
+    while (1) {
+      switch (_context2.prev = _context2.next) {
+        case 0:
+          features = [{
+            uniqueId: 'three',
+            refName: 'ctgB',
+            start: 50,
+            end: 60
+          }, {
+            uniqueId: 'two',
+            refName: 'ctgA',
+            start: 150,
+            end: 300
+          }, {
+            uniqueId: 'one',
+            refName: 'ctgA',
+            start: 250,
+            end: 400
+          }];
+          adapter = new _FromConfigRegionsAdapter["default"](_configSchema.regionsConfigSchema.create({
+            features: features
+          }));
+          _context2.next = 4;
+          return adapter.getRegions();
+
+        case 4:
+          result = _context2.sent;
+          expect(result).toEqual([{
+            refName: 'ctgA',
+            start: 150,
+            end: 400
+          }, {
+            refName: 'ctgB',
+            start: 50,
+            end: 60
+          }]);
+
+        case 6:
+        case "end":
+          return _context2.stop();
+      }
+    }
+  }, _callee2);
+})));
+test('adapter can fetch regions 3', /*#__PURE__*/(0, _asyncToGenerator2["default"])( /*#__PURE__*/_regenerator["default"].mark(function _callee3() {
+  var features, adapter, result;
+  return _regenerator["default"].wrap(function _callee3$(_context3) {
+    while (1) {
+      switch (_context3.prev = _context3.next) {
+        case 0:
+          features = [{
+            uniqueId: 'two',
+            refName: 'ctgA',
+            start: 150,
+            end: 300
+          }, {
+            uniqueId: 'one',
+            refName: 'ctgA',
+            start: 250,
+            end: 400
+          }, {
+            uniqueId: 'three',
+            refName: 'ctgB',
+            start: 50,
+            end: 60
+          }];
+          adapter = new _FromConfigRegionsAdapter["default"](_configSchema.regionsConfigSchema.create({
+            features: features
+          }));
+          _context3.next = 4;
+          return adapter.getRegions();
+
+        case 4:
+          result = _context3.sent;
+          expect(result).toEqual([{
+            refName: 'ctgA',
+            start: 150,
+            end: 400
+          }, {
+            refName: 'ctgB',
+            start: 50,
+            end: 60
+          }]);
+
+        case 6:
+        case "end":
+          return _context3.stop();
+      }
+    }
+  }, _callee3);
+})));
+test('adapter can fetch regions 4', /*#__PURE__*/(0, _asyncToGenerator2["default"])( /*#__PURE__*/_regenerator["default"].mark(function _callee4() {
+  var features, adapter, result;
+  return _regenerator["default"].wrap(function _callee4$(_context4) {
+    while (1) {
+      switch (_context4.prev = _context4.next) {
+        case 0:
+          features = [{
+            uniqueId: 'two',
+            refName: 'ctgA',
+            start: 150,
+            end: 300
+          }, {
+            uniqueId: 'onePrime',
+            refName: 'ctgA',
+            start: 300,
+            end: 400
+          }, {
+            uniqueId: 'three',
+            refName: 'ctgB',
+            start: 50,
+            end: 60
+          }];
+          adapter = new _FromConfigRegionsAdapter["default"](_configSchema.regionsConfigSchema.create({
+            features: features
+          }));
+          _context4.next = 4;
+          return adapter.getRegions();
+
+        case 4:
+          result = _context4.sent;
+          expect(result).toEqual([{
+            refName: 'ctgA',
+            start: 150,
+            end: 400
+          }, {
+            refName: 'ctgB',
+            start: 50,
+            end: 60
+          }]);
+
+        case 6:
+        case "end":
+          return _context4.stop();
+      }
+    }
+  }, _callee4);
+})));

package/dist/FromConfigAdapter/FromConfigSequenceAdapter.js

@@ -0,0 +1,201 @@
+"use strict";
+
+var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
+
+Object.defineProperty(exports, "__esModule", {
+  value: true
+});
+exports["default"] = void 0;
+
+var _regenerator = _interopRequireDefault(require("@babel/runtime/regenerator"));
+
+var _slicedToArray2 = _interopRequireDefault(require("@babel/runtime/helpers/slicedToArray"));
+
+var _defineProperty2 = _interopRequireDefault(require("@babel/runtime/helpers/defineProperty"));
+
+var _asyncToGenerator2 = _interopRequireDefault(require("@babel/runtime/helpers/asyncToGenerator"));
+
+var _classCallCheck2 = _interopRequireDefault(require("@babel/runtime/helpers/classCallCheck"));
+
+var _createClass2 = _interopRequireDefault(require("@babel/runtime/helpers/createClass"));
+
+var _get2 = _interopRequireDefault(require("@babel/runtime/helpers/get"));
+
+var _inherits2 = _interopRequireDefault(require("@babel/runtime/helpers/inherits"));
+
+var _possibleConstructorReturn2 = _interopRequireDefault(require("@babel/runtime/helpers/possibleConstructorReturn"));
+
+var _getPrototypeOf2 = _interopRequireDefault(require("@babel/runtime/helpers/getPrototypeOf"));
+
+var _simpleFeature = _interopRequireDefault(require("@jbrowse/core/util/simpleFeature"));
+
+var _rxjs = require("@jbrowse/core/util/rxjs");
+
+var _operators = require("rxjs/operators");
+
+var _FromConfigAdapter2 = _interopRequireDefault(require("./FromConfigAdapter"));
+
+function _createForOfIteratorHelper(o, allowArrayLike) { var it = typeof Symbol !== "undefined" && o[Symbol.iterator] || o["@@iterator"]; if (!it) { if (Array.isArray(o) || (it = _unsupportedIterableToArray(o)) || allowArrayLike && o && typeof o.length === "number") { if (it) o = it; var i = 0; var F = function F() {}; return { s: F, n: function n() { if (i >= o.length) return { done: true }; return { done: false, value: o[i++] }; }, e: function e(_e) { throw _e; }, f: F }; } throw new TypeError("Invalid attempt to iterate non-iterable instance.\nIn order to be iterable, non-array objects must have a [Symbol.iterator]() method."); } var normalCompletion = true, didErr = false, err; return { s: function s() { it = it.call(o); }, n: function n() { var step = it.next(); normalCompletion = step.done; return step; }, e: function e(_e2) { didErr = true; err = _e2; }, f: function f() { try { if (!normalCompletion && it["return"] != null) it["return"](); } finally { if (didErr) throw err; } } }; }
+
+function _unsupportedIterableToArray(o, minLen) { if (!o) return; if (typeof o === "string") return _arrayLikeToArray(o, minLen); var n = Object.prototype.toString.call(o).slice(8, -1); if (n === "Object" && o.constructor) n = o.constructor.name; if (n === "Map" || n === "Set") return Array.from(o); if (n === "Arguments" || /^(?:Ui|I)nt(?:8|16|32)(?:Clamped)?Array$/.test(n)) return _arrayLikeToArray(o, minLen); }
+
+function _arrayLikeToArray(arr, len) { if (len == null || len > arr.length) len = arr.length; for (var i = 0, arr2 = new Array(len); i < len; i++) { arr2[i] = arr[i]; } return arr2; }
+
+function ownKeys(object, enumerableOnly) { var keys = Object.keys(object); if (Object.getOwnPropertySymbols) { var symbols = Object.getOwnPropertySymbols(object); enumerableOnly && (symbols = symbols.filter(function (sym) { return Object.getOwnPropertyDescriptor(object, sym).enumerable; })), keys.push.apply(keys, symbols); } return keys; }
+
+function _objectSpread(target) { for (var i = 1; i < arguments.length; i++) { var source = null != arguments[i] ? arguments[i] : {}; i % 2 ? ownKeys(Object(source), !0).forEach(function (key) { (0, _defineProperty2["default"])(target, key, source[key]); }) : Object.getOwnPropertyDescriptors ? Object.defineProperties(target, Object.getOwnPropertyDescriptors(source)) : ownKeys(Object(source)).forEach(function (key) { Object.defineProperty(target, key, Object.getOwnPropertyDescriptor(source, key)); }); } return target; }
+
+function _createSuper(Derived) { var hasNativeReflectConstruct = _isNativeReflectConstruct(); return function _createSuperInternal() { var Super = (0, _getPrototypeOf2["default"])(Derived), result; if (hasNativeReflectConstruct) { var NewTarget = (0, _getPrototypeOf2["default"])(this).constructor; result = Reflect.construct(Super, arguments, NewTarget); } else { result = Super.apply(this, arguments); } return (0, _possibleConstructorReturn2["default"])(this, result); }; }
+
+function _isNativeReflectConstruct() { if (typeof Reflect === "undefined" || !Reflect.construct) return false; if (Reflect.construct.sham) return false; if (typeof Proxy === "function") return true; try { Boolean.prototype.valueOf.call(Reflect.construct(Boolean, [], function () {})); return true; } catch (e) { return false; } }
+
+var FromConfigSequenceAdapter = /*#__PURE__*/function (_FromConfigAdapter) {
+  (0, _inherits2["default"])(FromConfigSequenceAdapter, _FromConfigAdapter);
+
+  var _super = _createSuper(FromConfigSequenceAdapter);
+
+  function FromConfigSequenceAdapter() {
+    (0, _classCallCheck2["default"])(this, FromConfigSequenceAdapter);
+    return _super.apply(this, arguments);
+  }
+
+  (0, _createClass2["default"])(FromConfigSequenceAdapter, [{
+    key: "getFeatures",
+    value:
+    /**
+     * Fetch features for a certain region
+     * @param region - Region
+     * @returns Observable of Feature objects in the region
+     */
+    function getFeatures(region) {
+      var _this = this;
+
+      // 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()
+      var superGetFeatures = (0, _get2["default"])((0, _getPrototypeOf2["default"])(FromConfigSequenceAdapter.prototype), "getFeatures", this);
+      return (0, _rxjs.ObservableCreate)( /*#__PURE__*/function () {
+        var _ref = (0, _asyncToGenerator2["default"])( /*#__PURE__*/_regenerator["default"].mark(function _callee(observer) {
+          var feats, feat;
+          return _regenerator["default"].wrap(function _callee$(_context) {
+            while (1) {
+              switch (_context.prev = _context.next) {
+                case 0:
+                  _context.next = 2;
+                  return superGetFeatures.call(_this, region).pipe((0, _operators.toArray)()).toPromise();
+
+                case 2:
+                  feats = _context.sent;
+                  feat = feats[0];
+                  observer.next(new _simpleFeature["default"](_objectSpread(_objectSpread({}, feat.toJSON()), {}, {
+                    uniqueId: "".concat(feat.id(), ":").concat(region.start, "-").concat(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();
+
+                case 6:
+                case "end":
+                  return _context.stop();
+              }
+            }
+          }, _callee);
+        }));
+
+        return function (_x) {
+          return _ref.apply(this, arguments);
+        };
+      }());
+    }
+    /**
+     * Get refName, start, and end for all features after collapsing any overlaps
+     */
+
+  }, {
+    key: "getRegions",
+    value: function () {
+      var _getRegions = (0, _asyncToGenerator2["default"])( /*#__PURE__*/_regenerator["default"].mark(function _callee2() {
+        var regions, _iterator, _step, _step$value, refName, features, currentRegion, _iterator2, _step2, feature;
+
+        return _regenerator["default"].wrap(function _callee2$(_context2) {
+          while (1) {
+            switch (_context2.prev = _context2.next) {
+              case 0:
+                regions = []; // recall: features are stored in this object sorted by start coordinate
+
+                _iterator = _createForOfIteratorHelper(this.features);
+
+                try {
+                  for (_iterator.s(); !(_step = _iterator.n()).done;) {
+                    _step$value = (0, _slicedToArray2["default"])(_step.value, 2), refName = _step$value[0], features = _step$value[1];
+                    currentRegion = void 0;
+                    _iterator2 = _createForOfIteratorHelper(features);
+
+                    try {
+                      for (_iterator2.s(); !(_step2 = _iterator2.n()).done;) {
+                        feature = _step2.value;
+
+                        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: refName,
+                            start: feature.get('start'),
+                            end: feature.get('end')
+                          };
+                        }
+                      }
+                    } catch (err) {
+                      _iterator2.e(err);
+                    } finally {
+                      _iterator2.f();
+                    }
+
+                    if (currentRegion) {
+                      regions.push(currentRegion);
+                    }
+                  }
+                } catch (err) {
+                  _iterator.e(err);
+                } finally {
+                  _iterator.f();
+                }
+
+                return _context2.abrupt("return", regions);
+
+              case 4:
+              case "end":
+                return _context2.stop();
+            }
+          }
+        }, _callee2, this);
+      }));
+
+      function getRegions() {
+        return _getRegions.apply(this, arguments);
+      }
+
+      return getRegions;
+    }()
+    /**
+     * 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
+     */
+
+  }, {
+    key: "freeResources",
+    value: function
+      /* { region } */
+    freeResources() {}
+  }]);
+  return FromConfigSequenceAdapter;
+}(_FromConfigAdapter2["default"]);
+
+exports["default"] = FromConfigSequenceAdapter;

package/dist/FromConfigAdapter/FromConfigSequenceAdapter.test.js

@@ -0,0 +1,110 @@
+"use strict";
+
+var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
+
+var _regenerator = _interopRequireDefault(require("@babel/runtime/regenerator"));
+
+var _asyncToGenerator2 = _interopRequireDefault(require("@babel/runtime/helpers/asyncToGenerator"));
+
+var _operators = require("rxjs/operators");
+
+var _FromConfigSequenceAdapter = _interopRequireDefault(require("./FromConfigSequenceAdapter"));
+
+var _configSchema = require("./configSchema");
+
+test('adapter can fetch sequences when there is just one feature representing whole refseq', /*#__PURE__*/(0, _asyncToGenerator2["default"])( /*#__PURE__*/_regenerator["default"].mark(function _callee() {
+  var features, adapter, result, featuresArray, result2, featuresArray2;
+  return _regenerator["default"].wrap(function _callee$(_context) {
+    while (1) {
+      switch (_context.prev = _context.next) {
+        case 0:
+          features = [{
+            uniqueId: 'one',
+            refName: 'ctgA',
+            start: 0,
+            end: 150,
+            seq: 'ccaaaccgtcaattaaccggtatcttctcggaaacggcggttctctcctagatagcgatctgtggtctcaccatgcaatttaaacaggtgagtaaagattgctacaaatacgagactagctgtcaccagatgctgttcatctgttggctc'
+          }];
+          adapter = new _FromConfigSequenceAdapter["default"](_configSchema.sequenceConfigSchema.create({
+            features: features
+          }));
+          result = adapter.getFeatures({
+            refName: 'ctgA',
+            start: 0,
+            end: 50
+          });
+          _context.next = 5;
+          return result.pipe((0, _operators.toArray)()).toPromise();
+
+        case 5:
+          featuresArray = _context.sent;
+          expect(featuresArray.length).toBe(1);
+          expect(featuresArray[0].get('seq')).toBe(features[0].seq.slice(0, 50));
+          result2 = adapter.getFeatures({
+            refName: 'ctgA',
+            start: 100,
+            end: 150
+          });
+          _context.next = 11;
+          return result2.pipe((0, _operators.toArray)()).toPromise();
+
+        case 11:
+          featuresArray2 = _context.sent;
+          expect(featuresArray2.length).toBe(1);
+          expect(featuresArray2[0].get('seq')).toBe(features[0].seq.slice(100, 150));
+
+        case 14:
+        case "end":
+          return _context.stop();
+      }
+    }
+  }, _callee);
+})));
+test("adapter can fetch sequences when the config's sequence doesn't start at 0", /*#__PURE__*/(0, _asyncToGenerator2["default"])( /*#__PURE__*/_regenerator["default"].mark(function _callee2() {
+  var features, adapter, result, featuresArray, result2, featuresArray2;
+  return _regenerator["default"].wrap(function _callee2$(_context2) {
+    while (1) {
+      switch (_context2.prev = _context2.next) {
+        case 0:
+          features = [{
+            uniqueId: 'one',
+            refName: 'ctgA',
+            start: 5000,
+            end: 5150,
+            seq: 'ccaaaccgtcaattaaccggtatcttctcggaaacggcggttctctcctagatagcgatctgtggtctcaccatgcaatttaaacaggtgagtaaagattgctacaaatacgagactagctgtcaccagatgctgttcatctgttggctc'
+          }];
+          adapter = new _FromConfigSequenceAdapter["default"](_configSchema.sequenceConfigSchema.create({
+            features: features
+          }));
+          result = adapter.getFeatures({
+            refName: 'ctgA',
+            start: 4950,
+            end: 5050
+          });
+          _context2.next = 5;
+          return result.pipe((0, _operators.toArray)()).toPromise();
+
+        case 5:
+          featuresArray = _context2.sent;
+          expect(featuresArray.length).toBe(1);
+          expect(featuresArray[0].get('seq')).toBe(features[0].seq.slice(0, 50));
+          result2 = adapter.getFeatures({
+            refName: 'ctgA',
+            start: 5050,
+            end: 5150
+          });
+          _context2.next = 11;
+          return result2.pipe((0, _operators.toArray)()).toPromise();
+
+        case 11:
+          featuresArray2 = _context2.sent;
+          expect(featuresArray2.length).toBe(1);
+          expect(featuresArray2[0].get('seq')).toBe(features[0].seq.slice(50, 150));
+
+        case 14:
+        case "end":
+          return _context2.stop();
+      }
+    }
+  }, _callee2);
+})));

package/dist/FromConfigAdapter/configSchema.js

@@ -0,0 +1,51 @@
+"use strict";
+
+Object.defineProperty(exports, "__esModule", {
+  value: true
+});
+exports.sequenceConfigSchema = exports.regionsConfigSchema = exports.configSchema = void 0;
+
+var _configuration = require("@jbrowse/core/configuration");
+
+var configSchema = (0, _configuration.ConfigurationSchema)('FromConfigAdapter', {
+  features: {
+    type: 'frozen',
+    defaultValue: []
+  },
+  featureClass: {
+    type: 'string',
+    defaultValue: 'SimpleFeature'
+  }
+}, {
+  explicitlyTyped: true,
+  implicitIdentifier: 'adapterId'
+});
+exports.configSchema = configSchema;
+var regionsConfigSchema = (0, _configuration.ConfigurationSchema)('FromConfigRegionsAdapter', {
+  features: {
+    type: 'frozen',
+    defaultValue: []
+  },
+  featureClass: {
+    type: 'string',
+    defaultValue: 'SimpleFeature'
+  }
+}, {
+  explicitlyTyped: true,
+  implicitIdentifier: 'adapterId'
+});
+exports.regionsConfigSchema = regionsConfigSchema;
+var sequenceConfigSchema = (0, _configuration.ConfigurationSchema)('FromConfigSequenceAdapter', {
+  features: {
+    type: 'frozen',
+    defaultValue: []
+  },
+  featureClass: {
+    type: 'string',
+    defaultValue: 'SimpleFeature'
+  }
+}, {
+  explicitlyTyped: true,
+  implicitIdentifier: 'adapterId'
+});
+exports.sequenceConfigSchema = sequenceConfigSchema;

package/dist/FromConfigAdapter/index.js

@@ -0,0 +1,51 @@
+"use strict";
+
+var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
+
+Object.defineProperty(exports, "__esModule", {
+  value: true
+});
+Object.defineProperty(exports, "AdapterClass", {
+  enumerable: true,
+  get: function get() {
+    return _FromConfigAdapter["default"];
+  }
+});
+Object.defineProperty(exports, "RegionsAdapterClass", {
+  enumerable: true,
+  get: function get() {
+    return _FromConfigRegionsAdapter["default"];
+  }
+});
+Object.defineProperty(exports, "SequenceAdapterClass", {
+  enumerable: true,
+  get: function get() {
+    return _FromConfigSequenceAdapter["default"];
+  }
+});
+Object.defineProperty(exports, "configSchema", {
+  enumerable: true,
+  get: function get() {
+    return _configSchema.configSchema;
+  }
+});
+Object.defineProperty(exports, "regionsConfigSchema", {
+  enumerable: true,
+  get: function get() {
+    return _configSchema.regionsConfigSchema;
+  }
+});
+Object.defineProperty(exports, "sequenceConfigSchema", {
+  enumerable: true,
+  get: function get() {
+    return _configSchema.sequenceConfigSchema;
+  }
+});
+
+var _FromConfigAdapter = _interopRequireDefault(require("./FromConfigAdapter"));
+
+var _FromConfigRegionsAdapter = _interopRequireDefault(require("./FromConfigRegionsAdapter"));
+
+var _FromConfigSequenceAdapter = _interopRequireDefault(require("./FromConfigSequenceAdapter"));
+
+var _configSchema = require("./configSchema");