@jbrowse/plugin-legacy-jbrowse 1.7.3 → 1.7.6

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (21) hide show
  1. package/dist/JBrowse1Connection/configSchema.js +2 -2
  2. package/dist/JBrowse1Connection/index.js +2 -2
  3. package/dist/JBrowse1Connection/jb1ConfigLoad.js +16 -16
  4. package/dist/JBrowse1Connection/jb1ConfigParse.js +6 -6
  5. package/dist/JBrowse1Connection/jb1ToJb2.js +3 -3
  6. package/dist/JBrowse1Connection/model.js +3 -3
  7. package/dist/JBrowse1Connection/util.js +3 -3
  8. package/dist/JBrowse1TextSeachAdapter/HttpMap.js +22 -22
  9. package/dist/JBrowse1TextSeachAdapter/HttpMap.test.js +12 -12
  10. package/dist/JBrowse1TextSeachAdapter/JBrowse1TextSearchAdapter.js +18 -18
  11. package/dist/JBrowse1TextSeachAdapter/JBrowse1TextSearchAdapter.test.js +9 -9
  12. package/dist/JBrowse1TextSeachAdapter/configSchema.js +2 -2
  13. package/dist/JBrowse1TextSeachAdapter/index.js +2 -2
  14. package/dist/NCListAdapter/NCListAdapter.js +17 -17
  15. package/dist/NCListAdapter/NCListAdapter.test.js +5 -5
  16. package/dist/NCListAdapter/NCListFeature.js +6 -6
  17. package/dist/NCListAdapter/configSchema.js +2 -2
  18. package/dist/NCListAdapter/index.js +1 -1
  19. package/dist/index.js +13 -13
  20. package/dist/index.test.js +3 -3
  21. package/package.json +3 -2
package/dist/JBrowse1Connection/configSchema.js CHANGED
@@ -3,7 +3,7 @@
3
3
  Object.defineProperty(exports, "__esModule", {
4
4
  value: true
5
5
  });
6
- exports["default"] = void 0;
6
+ exports.default = void 0;
7
7
 
8
8
  var _models = require("@jbrowse/core/pluggableElementTypes/models");
9
9
 
@@ -27,4 +27,4 @@ var _default = (0, _configuration.ConfigurationSchema)('JBrowse1Connection', {
27
27
  baseConfiguration: _models.baseConnectionConfig
28
28
  });
29
29
 
30
- exports["default"] = _default;
30
+ exports.default = _default;
package/dist/JBrowse1Connection/index.js CHANGED
@@ -8,13 +8,13 @@ Object.defineProperty(exports, "__esModule", {
8
8
  Object.defineProperty(exports, "configSchema", {
9
9
  enumerable: true,
10
10
  get: function get() {
11
- return _configSchema["default"];
11
+ return _configSchema.default;
12
12
  }
13
13
  });
14
14
  Object.defineProperty(exports, "modelFactory", {
15
15
  enumerable: true,
16
16
  get: function get() {
17
- return _model["default"];
17
+ return _model.default;
18
18
  }
19
19
  });
20
20
 
package/dist/JBrowse1Connection/jb1ConfigLoad.js CHANGED
@@ -37,7 +37,7 @@ function fetchJb1() {
37
37
  }
38
38
 
39
39
  function _fetchJb() {
40
- _fetchJb = (0, _asyncToGenerator2["default"])( /*#__PURE__*/_regenerator["default"].mark(function _callee() {
40
+ _fetchJb = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee() {
41
41
  var dataRoot,
42
42
  baseConfig,
43
43
  baseConfigRoot,
@@ -54,7 +54,7 @@ function _fetchJb() {
54
54
  newConfig,
55
55
  _args = arguments;
56
56
 
57
- return _regenerator["default"].wrap(function _callee$(_context) {
57
+ return _regenerator.default.wrap(function _callee$(_context) {
58
58
  while (1) {
59
59
  switch (_context.prev = _context.next) {
60
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  case 0:
@@ -118,7 +118,7 @@ function _fetchJb() {
118
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  fetchedConfig = null;
119
119
  _context.prev = 20;
120
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  _context.next = 23;
121
- return fetchConfigFile((0, _defineProperty2["default"])({}, baseProtocol, "".concat(baseConfigLocation, "/").concat(conf)));
121
+ return fetchConfigFile((0, _defineProperty2.default)({}, baseProtocol, "".concat(baseConfigLocation, "/").concat(conf)));
122
122
 
123
123
  case 23:
124
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  fetchedConfig = _context.sent;
@@ -169,12 +169,12 @@ function createFinalConfig(_x) {
169
169
  }
170
170
 
171
171
  function _createFinalConfig() {
172
- _createFinalConfig = (0, _asyncToGenerator2["default"])( /*#__PURE__*/_regenerator["default"].mark(function _callee2(baseConfig) {
172
+ _createFinalConfig = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee2(baseConfig) {
173
173
  var defaults,
174
174
  configWithDefaults,
175
175
  finalConfig,
176
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  _args2 = arguments;
177
- return _regenerator["default"].wrap(function _callee2$(_context2) {
177
+ return _regenerator.default.wrap(function _callee2$(_context2) {
178
178
  while (1) {
179
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  switch (_context2.prev = _context2.next) {
180
180
  case 0:
@@ -205,9 +205,9 @@ function fetchConfigFile(_x2) {
205
205
  }
206
206
 
207
207
  function _fetchConfigFile() {
208
- _fetchConfigFile = (0, _asyncToGenerator2["default"])( /*#__PURE__*/_regenerator["default"].mark(function _callee3(location) {
208
+ _fetchConfigFile = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee3(location) {
209
209
  var result;
210
- return _regenerator["default"].wrap(function _callee3$(_context3) {
210
+ return _regenerator.default.wrap(function _callee3$(_context3) {
211
211
  while (1) {
212
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  switch (_context3.prev = _context3.next) {
213
213
  case 0:
@@ -281,8 +281,8 @@ function mergeConfigs(a, b) {
281
281
  throw new Error("Track config has not been properly regularized: ".concat(aTracks, " ").concat(bTracks));
282
282
  }
283
283
  } else if (!noRecursiveMerge(prop) && prop in a && // @ts-ignore
284
- (0, _typeof2["default"])(b[prop]) === 'object' && // @ts-ignore
285
- (0, _typeof2["default"])(a[prop]) === 'object') {
284
+ (0, _typeof2.default)(b[prop]) === 'object' && // @ts-ignore
285
+ (0, _typeof2.default)(a[prop]) === 'object') {
286
286
  // @ts-ignore
287
287
  a[prop] = (0, _util.deepUpdate)(a[prop], b[prop]);
288
288
  } else if (prop === 'dataRoot') {
@@ -337,17 +337,17 @@ function loadIncludes(_x3) {
337
337
  }
338
338
 
339
339
  function _loadIncludes() {
340
- _loadIncludes = (0, _asyncToGenerator2["default"])( /*#__PURE__*/_regenerator["default"].mark(function _callee6(inputConfig) {
340
+ _loadIncludes = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee6(inputConfig) {
341
341
  var loadRecur, _loadRecur;
342
342
 
343
- return _regenerator["default"].wrap(function _callee6$(_context6) {
343
+ return _regenerator.default.wrap(function _callee6$(_context6) {
344
344
  while (1) {
345
345
  switch (_context6.prev = _context6.next) {
346
346
  case 0:
347
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  _loadRecur = function _loadRecur3() {
348
- _loadRecur = (0, _asyncToGenerator2["default"])( /*#__PURE__*/_regenerator["default"].mark(function _callee5(config, upstreamConf) {
348
+ _loadRecur = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee5(config, upstreamConf) {
349
349
  var sourceUrl, newUpstreamConf, includes, loads, includedDataObjects;
350
- return _regenerator["default"].wrap(function _callee5$(_context5) {
350
+ return _regenerator.default.wrap(function _callee5$(_context5) {
351
351
  while (1) {
352
352
  switch (_context5.prev = _context5.next) {
353
353
  case 0:
@@ -374,9 +374,9 @@ function _loadIncludes() {
374
374
  includes = fillTemplates(regularizeIncludes(config.include || []), newUpstreamConf);
375
375
  delete config.include;
376
376
  loads = includes.map( /*#__PURE__*/function () {
377
- var _ref = (0, _asyncToGenerator2["default"])( /*#__PURE__*/_regenerator["default"].mark(function _callee4(include) {
377
+ var _ref = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee4(include) {
378
378
  var includedData;
379
- return _regenerator["default"].wrap(function _callee4$(_context4) {
379
+ return _regenerator.default.wrap(function _callee4$(_context4) {
380
380
  while (1) {
381
381
  switch (_context4.prev = _context4.next) {
382
382
  case 0:
@@ -481,7 +481,7 @@ function fillTemplates(subconfig, config) {
481
481
  for (var i = 0; i < subconfig.length; i += 1) {
482
482
  subconfig[i] = fillTemplates(subconfig[i], config);
483
483
  }
484
- } else if ((0, _typeof2["default"])(subconfig) === 'object') {
484
+ } else if ((0, _typeof2.default)(subconfig) === 'object') {
485
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  // eslint-disable-next-line @typescript-eslint/no-explicit-any
486
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  var sub = subconfig;
487
487
 
package/dist/JBrowse1Connection/jb1ConfigParse.js CHANGED
@@ -25,7 +25,7 @@ var _util2 = require("./util");
25
25
 
26
26
  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; }
27
27
 
28
- 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; }
28
+ 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; }
29
29
 
30
30
  function parseJB1Json(config, url) {
31
31
  if (typeof config === 'string') {
@@ -97,7 +97,7 @@ function parse(text, url) {
97
97
  var path = section.concat(keyPath).join('.');
98
98
 
99
99
  if (operation === '+=') {
100
- var existing = (0, _getValue["default"])(data, path);
100
+ var existing = (0, _getValue.default)(data, path);
101
101
 
102
102
  if (existing) {
103
103
  if (!Array.isArray(existing)) {
@@ -119,7 +119,7 @@ function parse(text, url) {
119
119
  parsedValue = false;
120
120
  }
121
121
 
122
- (0, _setValue["default"])(data, path, parsedValue);
122
+ (0, _setValue.default)(data, path, parsedValue);
123
123
  } catch (e) {
124
124
  throw new Error("syntax error".concat(url ? " in ".concat(url) : '').concat(lineNumber ? " at line ".concat(lineNumber - 1) : ''));
125
125
  }
@@ -148,7 +148,7 @@ function parse(text, url) {
148
148
  keyPath = match[1].trim().split(/\s*\.\s*/);
149
149
  var _match = match;
150
150
 
151
- var _match2 = (0, _slicedToArray2["default"])(_match, 3);
151
+ var _match2 = (0, _slicedToArray2.default)(_match, 3);
152
152
 
153
153
  operation = _match2[2];
154
154
 
@@ -278,11 +278,11 @@ function regularizeConf(conf, url) {
278
278
  var addBase = [];
279
279
 
280
280
  if (conf.tracks) {
281
- addBase.push.apply(addBase, (0, _toConsumableArray2["default"])(conf.tracks));
281
+ addBase.push.apply(addBase, (0, _toConsumableArray2.default)(conf.tracks));
282
282
  }
283
283
 
284
284
  if (conf.stores) {
285
- addBase.push.apply(addBase, (0, _toConsumableArray2["default"])(Object.values(conf.stores)));
285
+ addBase.push.apply(addBase, (0, _toConsumableArray2.default)(Object.values(conf.stores)));
286
286
  }
287
287
 
288
288
  if (conf.names) {
package/dist/JBrowse1Connection/jb1ToJb2.js CHANGED
@@ -22,7 +22,7 @@ var _tracks = require("@jbrowse/core/util/tracks");
22
22
 
23
23
  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; }
24
24
 
25
- 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; }
25
+ 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; }
26
26
 
27
27
  function convertTrackConfig(jb1TrackConfig, dataRoot, sequenceAdapter) {
28
28
  var jb2TrackConfig = {
@@ -441,9 +441,9 @@ function createRefSeqsAdapter(_x) {
441
441
  }
442
442
 
443
443
  function _createRefSeqsAdapter() {
444
- _createRefSeqsAdapter = (0, _asyncToGenerator2["default"])( /*#__PURE__*/_regenerator["default"].mark(function _callee(refSeqs) {
444
+ _createRefSeqsAdapter = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee(refSeqs) {
445
445
  var refSeqsJson, refSeqsData;
446
- return _regenerator["default"].wrap(function _callee$(_context) {
446
+ return _regenerator.default.wrap(function _callee$(_context) {
447
447
  while (1) {
448
448
  switch (_context.prev = _context.next) {
449
449
  case 0:
package/dist/JBrowse1Connection/model.js CHANGED
@@ -5,7 +5,7 @@ var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefau
5
5
  Object.defineProperty(exports, "__esModule", {
6
6
  value: true
7
7
  });
8
- exports["default"] = _default;
8
+ exports.default = _default;
9
9
 
10
10
  var _configuration = require("@jbrowse/core/configuration");
11
11
 
@@ -23,7 +23,7 @@ var _jb1ToJb = require("./jb1ToJb2");
23
23
 
24
24
  function _default(pluginManager) {
25
25
  return _mobxStateTree.types.compose('JBrowse1Connection', (0, _models.BaseConnectionModelFactory)(pluginManager), _mobxStateTree.types.model({
26
- configuration: (0, _configuration.ConfigurationReference)(_configSchema["default"]),
26
+ configuration: (0, _configuration.ConfigurationReference)(_configSchema.default),
27
27
  type: _mobxStateTree.types.literal('JBrowse1Connection')
28
28
  }).actions(function (self) {
29
29
  return {
@@ -47,7 +47,7 @@ function _default(pluginManager) {
47
47
  return jb2Track;
48
48
  });
49
49
  self.setTrackConfs(jb2Tracks);
50
- })["catch"](function (error) {
50
+ }).catch(function (error) {
51
51
  console.error(error);
52
52
  session.notify("There was a problem connecting to the JBrowse 1 data directory \"".concat(self.name, "\". Please make sure you have entered a valid location. The error that was thrown is: \"").concat(error, "\""), 'error');
53
53
  session.breakConnection(self.configuration);
package/dist/JBrowse1Connection/util.js CHANGED
@@ -34,7 +34,7 @@ function deepUpdate(a, b) {
34
34
  for (var _i = 0, _Object$keys = Object.keys(b); _i < _Object$keys.length; _i++) {
35
35
  var prop = _Object$keys[_i];
36
36
 
37
- if (prop in a && (0, _typeof2["default"])(b[prop]) === 'object' && (0, _typeof2["default"])(a[prop]) === 'object') {
37
+ if (prop in a && (0, _typeof2.default)(b[prop]) === 'object' && (0, _typeof2.default)(a[prop]) === 'object') {
38
38
  deepUpdate(a[prop], b[prop]);
39
39
  } else if (typeof a[prop] === 'undefined' || typeof b[prop] !== 'undefined') {
40
40
  a[prop] = b[prop];
@@ -60,7 +60,7 @@ function fillTemplate(template, fillWith) {
60
60
  return template.replace(/\{([\w\s.]+)\}/g, function (match, varName) {
61
61
  varName = varName.replace(/\s+/g, ''); // remove all whitespace
62
62
 
63
- var fill = (0, _getValue["default"])(fillWith, varName);
63
+ var fill = (0, _getValue.default)(fillWith, varName);
64
64
 
65
65
  if (fill !== undefined) {
66
66
  if (typeof fill === 'function') {
@@ -92,7 +92,7 @@ function fillTemplate(template, fillWith) {
92
92
 
93
93
 
94
94
  function clone(src) {
95
- if (!src || (0, _typeof2["default"])(src) !== 'object' || Object.prototype.toString.call(src) === '[object Function]') {
95
+ if (!src || (0, _typeof2.default)(src) !== 'object' || Object.prototype.toString.call(src) === '[object Function]') {
96
96
  // null, undefined, any non-object, or function
97
97
  return src; // anything
98
98
  }
package/dist/JBrowse1TextSeachAdapter/HttpMap.js CHANGED
@@ -5,7 +5,7 @@ var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefau
5
5
  Object.defineProperty(exports, "__esModule", {
6
6
  value: true
7
7
  });
8
- exports["default"] = void 0;
8
+ exports.default = void 0;
9
9
 
10
10
  var _regenerator = _interopRequireDefault(require("@babel/runtime/regenerator"));
11
11
 
@@ -25,8 +25,8 @@ var _bufferCrc = _interopRequireDefault(require("buffer-crc32"));
25
25
  */
26
26
  var HttpMap = /*#__PURE__*/function () {
27
27
  function HttpMap(args) {
28
- (0, _classCallCheck2["default"])(this, HttpMap);
29
- (0, _defineProperty2["default"])(this, "url", void 0);
28
+ (0, _classCallCheck2.default)(this, HttpMap);
29
+ (0, _defineProperty2.default)(this, "url", void 0);
30
30
  // make sure url has a trailing slash
31
31
  this.url = /\/$/.test(args.url) ? args.url : "".concat(args.url, "/");
32
32
  }
@@ -35,12 +35,12 @@ var HttpMap = /*#__PURE__*/function () {
35
35
  */
36
36
 
37
37
 
38
- (0, _createClass2["default"])(HttpMap, [{
38
+ (0, _createClass2.default)(HttpMap, [{
39
39
  key: "readMeta",
40
40
  value: function () {
41
- var _readMeta = (0, _asyncToGenerator2["default"])( /*#__PURE__*/_regenerator["default"].mark(function _callee() {
41
+ var _readMeta = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee() {
42
42
  var meta, compress, tracks, hashHexCharacters;
43
- return _regenerator["default"].wrap(function _callee$(_context) {
43
+ return _regenerator.default.wrap(function _callee$(_context) {
44
44
  while (1) {
45
45
  switch (_context.prev = _context.next) {
46
46
  case 0:
@@ -74,9 +74,9 @@ var HttpMap = /*#__PURE__*/function () {
74
74
  }, {
75
75
  key: "getHashHexCharacters",
76
76
  value: function () {
77
- var _getHashHexCharacters = (0, _asyncToGenerator2["default"])( /*#__PURE__*/_regenerator["default"].mark(function _callee2() {
77
+ var _getHashHexCharacters = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee2() {
78
78
  var meta;
79
- return _regenerator["default"].wrap(function _callee2$(_context2) {
79
+ return _regenerator.default.wrap(function _callee2$(_context2) {
80
80
  while (1) {
81
81
  switch (_context2.prev = _context2.next) {
82
82
  case 0:
@@ -104,9 +104,9 @@ var HttpMap = /*#__PURE__*/function () {
104
104
  }, {
105
105
  key: "getCompress",
106
106
  value: function () {
107
- var _getCompress = (0, _asyncToGenerator2["default"])( /*#__PURE__*/_regenerator["default"].mark(function _callee3() {
107
+ var _getCompress = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee3() {
108
108
  var meta;
109
- return _regenerator["default"].wrap(function _callee3$(_context3) {
109
+ return _regenerator.default.wrap(function _callee3$(_context3) {
110
110
  while (1) {
111
111
  switch (_context3.prev = _context3.next) {
112
112
  case 0:
@@ -134,9 +134,9 @@ var HttpMap = /*#__PURE__*/function () {
134
134
  }, {
135
135
  key: "getTrackNames",
136
136
  value: function () {
137
- var _getTrackNames = (0, _asyncToGenerator2["default"])( /*#__PURE__*/_regenerator["default"].mark(function _callee4() {
137
+ var _getTrackNames = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee4() {
138
138
  var meta;
139
- return _regenerator["default"].wrap(function _callee4$(_context4) {
139
+ return _regenerator.default.wrap(function _callee4$(_context4) {
140
140
  while (1) {
141
141
  switch (_context4.prev = _context4.next) {
142
142
  case 0:
@@ -169,9 +169,9 @@ var HttpMap = /*#__PURE__*/function () {
169
169
  }, {
170
170
  key: "get",
171
171
  value: function () {
172
- var _get = (0, _asyncToGenerator2["default"])( /*#__PURE__*/_regenerator["default"].mark(function _callee5(key) {
172
+ var _get = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee5(key) {
173
173
  var bucket;
174
- return _regenerator["default"].wrap(function _callee5$(_context5) {
174
+ return _regenerator.default.wrap(function _callee5$(_context5) {
175
175
  while (1) {
176
176
  switch (_context5.prev = _context5.next) {
177
177
  case 0:
@@ -204,9 +204,9 @@ var HttpMap = /*#__PURE__*/function () {
204
204
  }, {
205
205
  key: "getBucket",
206
206
  value: function () {
207
- var _getBucket = (0, _asyncToGenerator2["default"])( /*#__PURE__*/_regenerator["default"].mark(function _callee6(key) {
207
+ var _getBucket = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee6(key) {
208
208
  var bucketIdent, hexToDirPath;
209
- return _regenerator["default"].wrap(function _callee6$(_context6) {
209
+ return _regenerator.default.wrap(function _callee6$(_context6) {
210
210
  while (1) {
211
211
  switch (_context6.prev = _context6.next) {
212
212
  case 0:
@@ -241,9 +241,9 @@ var HttpMap = /*#__PURE__*/function () {
241
241
  }, {
242
242
  key: "loadFile",
243
243
  value: function () {
244
- var _loadFile = (0, _asyncToGenerator2["default"])( /*#__PURE__*/_regenerator["default"].mark(function _callee7(id) {
244
+ var _loadFile = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee7(id) {
245
245
  var response;
246
- return _regenerator["default"].wrap(function _callee7$(_context7) {
246
+ return _regenerator.default.wrap(function _callee7$(_context7) {
247
247
  while (1) {
248
248
  switch (_context7.prev = _context7.next) {
249
249
  case 0:
@@ -285,9 +285,9 @@ var HttpMap = /*#__PURE__*/function () {
285
285
  }, {
286
286
  key: "hexToDirPath",
287
287
  value: function () {
288
- var _hexToDirPath = (0, _asyncToGenerator2["default"])( /*#__PURE__*/_regenerator["default"].mark(function _callee8(hex) {
288
+ var _hexToDirPath = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee8(hex) {
289
289
  var hashHexCharacters, compress, dirpath, i;
290
- return _regenerator["default"].wrap(function _callee8$(_context8) {
290
+ return _regenerator.default.wrap(function _callee8$(_context8) {
291
291
  while (1) {
292
292
  switch (_context8.prev = _context8.next) {
293
293
  case 0:
@@ -341,10 +341,10 @@ var HttpMap = /*#__PURE__*/function () {
341
341
  }, {
342
342
  key: "hash",
343
343
  value: function hash(data) {
344
- return (0, _bufferCrc["default"])(Buffer.from(data)).toString('hex').toLowerCase().replace('-', 'n');
344
+ return (0, _bufferCrc.default)(Buffer.from(data)).toString('hex').toLowerCase().replace('-', 'n');
345
345
  }
346
346
  }]);
347
347
  return HttpMap;
348
348
  }();
349
349
 
350
- exports["default"] = HttpMap;
350
+ exports.default = HttpMap;
package/dist/JBrowse1TextSeachAdapter/HttpMap.test.js CHANGED
@@ -17,9 +17,9 @@ var _f = _interopRequireDefault(require("../../test_data/names/f.json"));
17
17
  var _HttpMap = _interopRequireDefault(require("./HttpMap"));
18
18
 
19
19
  describe('test JBrowse1 hash implementation', function () {
20
- test('read from meta', /*#__PURE__*/(0, _asyncToGenerator2["default"])( /*#__PURE__*/_regenerator["default"].mark(function _callee() {
20
+ test('read from meta', /*#__PURE__*/(0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee() {
21
21
  var mockFetch, rootTemplate, spy, hashMap;
22
- return _regenerator["default"].wrap(function _callee$(_context) {
22
+ return _regenerator.default.wrap(function _callee$(_context) {
23
23
  while (1) {
24
24
  switch (_context.prev = _context.next) {
25
25
  case 0:
@@ -27,17 +27,17 @@ describe('test JBrowse1 hash implementation', function () {
27
27
  var response = {};
28
28
 
29
29
  if (url.includes('names/meta.json')) {
30
- response = _meta["default"];
30
+ response = _meta.default;
31
31
  }
32
32
 
33
33
  return Promise.resolve(new Response(JSON.stringify(response)));
34
34
  };
35
35
 
36
- rootTemplate = _path["default"].join(__dirname, '..', '..', '..', '..', 'test_data', 'names').replace(/\\/g, '\\\\');
36
+ rootTemplate = _path.default.join(__dirname, '..', '..', '..', '..', 'test_data', 'names').replace(/\\/g, '\\\\');
37
37
  spy = jest.spyOn(global, 'fetch'); // eslint-disable-next-line @typescript-eslint/no-explicit-any
38
38
 
39
39
  spy.mockImplementation(mockFetch);
40
- hashMap = new _HttpMap["default"]({
40
+ hashMap = new _HttpMap.default({
41
41
  url: rootTemplate
42
42
  });
43
43
  _context.next = 7;
@@ -66,9 +66,9 @@ describe('test JBrowse1 hash implementation', function () {
66
66
  }
67
67
  }, _callee);
68
68
  })));
69
- test('get bucket contents', /*#__PURE__*/(0, _asyncToGenerator2["default"])( /*#__PURE__*/_regenerator["default"].mark(function _callee2() {
69
+ test('get bucket contents', /*#__PURE__*/(0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee2() {
70
70
  var mockFetch, rootTemplate, spy, hashMap;
71
- return _regenerator["default"].wrap(function _callee2$(_context2) {
71
+ return _regenerator.default.wrap(function _callee2$(_context2) {
72
72
  while (1) {
73
73
  switch (_context2.prev = _context2.next) {
74
74
  case 0:
@@ -76,25 +76,25 @@ describe('test JBrowse1 hash implementation', function () {
76
76
  var response = {};
77
77
 
78
78
  if (url.includes('names/meta.json')) {
79
- response = _meta["default"];
79
+ response = _meta.default;
80
80
  }
81
81
 
82
82
  if (url.includes('names/0.json')) {
83
- response = _["default"];
83
+ response = _.default;
84
84
  }
85
85
 
86
86
  if (url.includes('names/f.json')) {
87
- response = _f["default"];
87
+ response = _f.default;
88
88
  }
89
89
 
90
90
  return Promise.resolve(new Response(JSON.stringify(response)));
91
91
  };
92
92
 
93
- rootTemplate = _path["default"].join(__dirname, '..', '..', '..', '..', 'test_data', 'names').replace(/\\/g, '\\\\');
93
+ rootTemplate = _path.default.join(__dirname, '..', '..', '..', '..', 'test_data', 'names').replace(/\\/g, '\\\\');
94
94
  spy = jest.spyOn(global, 'fetch'); // eslint-disable-next-line @typescript-eslint/no-explicit-any
95
95
 
96
96
  spy.mockImplementation(mockFetch);
97
- hashMap = new _HttpMap["default"]({
97
+ hashMap = new _HttpMap.default({
98
98
  url: rootTemplate
99
99
  });
100
100
  _context2.next = 7;
package/dist/JBrowse1TextSeachAdapter/JBrowse1TextSearchAdapter.js CHANGED
@@ -5,7 +5,7 @@ var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefau
5
5
  Object.defineProperty(exports, "__esModule", {
6
6
  value: true
7
7
  });
8
- exports["default"] = void 0;
8
+ exports.default = void 0;
9
9
 
10
10
  var _regenerator = _interopRequireDefault(require("@babel/runtime/regenerator"));
11
11
 
@@ -37,31 +37,31 @@ var _configuration = require("@jbrowse/core/configuration");
37
37
 
38
38
  var _HttpMap = _interopRequireDefault(require("./HttpMap"));
39
39
 
40
- 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); }; }
40
+ 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); }; }
41
41
 
42
42
  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; } }
43
43
 
44
44
  // Jbrowse1 text search adapter
45
45
  // Uses index built by generate-names.pl
46
46
  var JBrowse1TextSearchAdapter = /*#__PURE__*/function (_BaseAdapter) {
47
- (0, _inherits2["default"])(JBrowse1TextSearchAdapter, _BaseAdapter);
47
+ (0, _inherits2.default)(JBrowse1TextSearchAdapter, _BaseAdapter);
48
48
 
49
49
  var _super = _createSuper(JBrowse1TextSearchAdapter);
50
50
 
51
51
  function JBrowse1TextSearchAdapter(config, getSubAdapter, pluginManager) {
52
52
  var _this;
53
53
 
54
- (0, _classCallCheck2["default"])(this, JBrowse1TextSearchAdapter);
54
+ (0, _classCallCheck2.default)(this, JBrowse1TextSearchAdapter);
55
55
  _this = _super.call(this, config, getSubAdapter, pluginManager);
56
- (0, _defineProperty2["default"])((0, _assertThisInitialized2["default"])(_this), "httpMap", void 0);
57
- (0, _defineProperty2["default"])((0, _assertThisInitialized2["default"])(_this), "tracksNames", void 0);
56
+ (0, _defineProperty2.default)((0, _assertThisInitialized2.default)(_this), "httpMap", void 0);
57
+ (0, _defineProperty2.default)((0, _assertThisInitialized2.default)(_this), "tracksNames", void 0);
58
58
  var namesIndexLocation = (0, _configuration.readConfObject)(config, 'namesIndexLocation');
59
59
 
60
60
  if (!namesIndexLocation) {
61
61
  throw new Error('must provide namesIndexLocation');
62
62
  }
63
63
 
64
- _this.httpMap = new _HttpMap["default"]({
64
+ _this.httpMap = new _HttpMap.default({
65
65
  url: namesIndexLocation.baseUri ? new URL(namesIndexLocation.uri, namesIndexLocation.baseUri).href : namesIndexLocation.uri
66
66
  });
67
67
  return _this;
@@ -73,11 +73,11 @@ var JBrowse1TextSearchAdapter = /*#__PURE__*/function (_BaseAdapter) {
73
73
  */
74
74
 
75
75
 
76
- (0, _createClass2["default"])(JBrowse1TextSearchAdapter, [{
76
+ (0, _createClass2.default)(JBrowse1TextSearchAdapter, [{
77
77
  key: "loadIndexFile",
78
78
  value: function () {
79
- var _loadIndexFile = (0, _asyncToGenerator2["default"])( /*#__PURE__*/_regenerator["default"].mark(function _callee(query) {
80
- return _regenerator["default"].wrap(function _callee$(_context) {
79
+ var _loadIndexFile = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee(query) {
80
+ return _regenerator.default.wrap(function _callee$(_context) {
81
81
  while (1) {
82
82
  switch (_context.prev = _context.next) {
83
83
  case 0:
@@ -100,9 +100,9 @@ var JBrowse1TextSearchAdapter = /*#__PURE__*/function (_BaseAdapter) {
100
100
  }, {
101
101
  key: "searchIndex",
102
102
  value: function () {
103
- var _searchIndex = (0, _asyncToGenerator2["default"])( /*#__PURE__*/_regenerator["default"].mark(function _callee2(args) {
103
+ var _searchIndex = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee2(args) {
104
104
  var searchType, queryString, tracks, entries;
105
- return _regenerator["default"].wrap(function _callee2$(_context2) {
105
+ return _regenerator.default.wrap(function _callee2$(_context2) {
106
106
  while (1) {
107
107
  switch (_context2.prev = _context2.next) {
108
108
  case 0:
@@ -155,22 +155,22 @@ var JBrowse1TextSearchAdapter = /*#__PURE__*/function (_BaseAdapter) {
155
155
  }, {
156
156
  key: "formatResults",
157
157
  value: function formatResults(results, tracks, searchType) {
158
- return [].concat((0, _toConsumableArray2["default"])(searchType === 'exact' ? [] : results.prefix.map(function (result) {
159
- return new _BaseResults["default"]({
160
- label: (0, _typeof2["default"])(result) === 'object' ? result.name : result,
158
+ return [].concat((0, _toConsumableArray2.default)(searchType === 'exact' ? [] : results.prefix.map(function (result) {
159
+ return new _BaseResults.default({
160
+ label: (0, _typeof2.default)(result) === 'object' ? result.name : result,
161
161
  matchedAttribute: 'name',
162
162
  matchedObject: {
163
163
  result: result
164
164
  }
165
165
  });
166
- })), (0, _toConsumableArray2["default"])(results.exact.map(function (result) {
166
+ })), (0, _toConsumableArray2.default)(results.exact.map(function (result) {
167
167
  var name = result[0];
168
168
  var trackIndex = result[1];
169
169
  var refName = result[3];
170
170
  var start = result[4];
171
171
  var end = result[5];
172
172
  var locstring = "".concat(refName || name, ":").concat(start, "-").concat(end);
173
- return new _BaseResults["default"]({
173
+ return new _BaseResults.default({
174
174
  locString: locstring,
175
175
  label: name,
176
176
  matchedAttribute: 'name',
@@ -188,4 +188,4 @@ var JBrowse1TextSearchAdapter = /*#__PURE__*/function (_BaseAdapter) {
188
188
  return JBrowse1TextSearchAdapter;
189
189
  }(_BaseAdapter2.BaseAdapter);
190
190
 
191
- exports["default"] = JBrowse1TextSearchAdapter;
191
+ exports.default = JBrowse1TextSearchAdapter;
package/dist/JBrowse1TextSeachAdapter/JBrowse1TextSearchAdapter.test.js CHANGED
@@ -20,9 +20,9 @@ var _JBrowse1TextSearchAdapter = _interopRequireDefault(require("./JBrowse1TextS
20
20
 
21
21
  var _configSchema = _interopRequireDefault(require("./configSchema"));
22
22
 
23
- test('adapter can fetch files from names index', /*#__PURE__*/(0, _asyncToGenerator2["default"])( /*#__PURE__*/_regenerator["default"].mark(function _callee() {
23
+ test('adapter can fetch files from names index', /*#__PURE__*/(0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee() {
24
24
  var mockFetch, rootTemplate, spy, urlPath, args, adapter, results, results2, test2;
25
- return _regenerator["default"].wrap(function _callee$(_context) {
25
+ return _regenerator.default.wrap(function _callee$(_context) {
26
26
  while (1) {
27
27
  switch (_context.prev = _context.next) {
28
28
  case 0:
@@ -30,21 +30,21 @@ test('adapter can fetch files from names index', /*#__PURE__*/(0, _asyncToGenera
30
30
  var response = {};
31
31
 
32
32
  if (url.includes('names/meta.json')) {
33
- response = _meta["default"];
33
+ response = _meta.default;
34
34
  }
35
35
 
36
36
  if (url.includes('names/0.json')) {
37
- response = _["default"];
37
+ response = _.default;
38
38
  }
39
39
 
40
40
  if (url.includes('names/f.json')) {
41
- response = _f["default"];
41
+ response = _f.default;
42
42
  }
43
43
 
44
44
  return Promise.resolve(new Response(JSON.stringify(response)));
45
45
  };
46
46
 
47
- rootTemplate = _path["default"].join(__dirname, '..', '..', '..', '..', 'test_data', 'names').replace(/\\/g, '\\\\');
47
+ rootTemplate = _path.default.join(__dirname, '..', '..', '..', '..', 'test_data', 'names').replace(/\\/g, '\\\\');
48
48
  spy = jest.spyOn(global, 'fetch'); // eslint-disable-next-line @typescript-eslint/no-explicit-any
49
49
 
50
50
  spy.mockImplementation(mockFetch);
@@ -58,7 +58,7 @@ test('adapter can fetch files from names index', /*#__PURE__*/(0, _asyncToGenera
58
58
  }
59
59
  }; // create adapter
60
60
 
61
- adapter = new _JBrowse1TextSearchAdapter["default"](_configSchema["default"].create(args)); // prefix search
61
+ adapter = new _JBrowse1TextSearchAdapter.default(_configSchema.default.create(args)); // prefix search
62
62
 
63
63
  _context.next = 9;
64
64
  return adapter.searchIndex({
@@ -69,7 +69,7 @@ test('adapter can fetch files from names index', /*#__PURE__*/(0, _asyncToGenera
69
69
  case 9:
70
70
  results = _context.sent;
71
71
  // check results are of type BaseResult for prefix search
72
- expect(results[0] instanceof _BaseResults["default"]).toBeTruthy();
72
+ expect(results[0] instanceof _BaseResults.default).toBeTruthy();
73
73
  expect(results[0].getLabel()).toEqual('Apple1');
74
74
  expect(results[1].getLabel()).toEqual('Apple2');
75
75
  expect(results[2].getLabel()).toEqual('Apple3'); // exact search
@@ -85,7 +85,7 @@ test('adapter can fetch files from names index', /*#__PURE__*/(0, _asyncToGenera
85
85
  // check results are of type location for exact search
86
86
  expect(results2.length).toEqual(5);
87
87
  test2 = results2[0];
88
- expect(test2 instanceof _BaseResults["default"]).toBeTruthy();
88
+ expect(test2 instanceof _BaseResults.default).toBeTruthy();
89
89
  expect(test2.getLabel()).toEqual('Apple3');
90
90
  expect(test2.getLocation()).toEqual('ctgA:17399-23000');
91
91
 
package/dist/JBrowse1TextSeachAdapter/configSchema.js CHANGED
@@ -3,7 +3,7 @@
3
3
  Object.defineProperty(exports, "__esModule", {
4
4
  value: true
5
5
  });
6
- exports["default"] = void 0;
6
+ exports.default = void 0;
7
7
 
8
8
  var _configuration = require("@jbrowse/core/configuration");
9
9
 
@@ -32,4 +32,4 @@ var _default = (0, _configuration.ConfigurationSchema)('JBrowse1TextSearchAdapte
32
32
  explicitIdentifier: 'textSearchAdapterId'
33
33
  });
34
34
 
35
- exports["default"] = _default;
35
+ exports.default = _default;
package/dist/JBrowse1TextSeachAdapter/index.js CHANGED
@@ -8,13 +8,13 @@ Object.defineProperty(exports, "__esModule", {
8
8
  Object.defineProperty(exports, "AdapterClass", {
9
9
  enumerable: true,
10
10
  get: function get() {
11
- return _JBrowse1TextSearchAdapter["default"];
11
+ return _JBrowse1TextSearchAdapter.default;
12
12
  }
13
13
  });
14
14
  Object.defineProperty(exports, "configSchema", {
15
15
  enumerable: true,
16
16
  get: function get() {
17
- return _configSchema["default"];
17
+ return _configSchema.default;
18
18
  }
19
19
  });
20
20
 
package/dist/NCListAdapter/NCListAdapter.js CHANGED
@@ -5,7 +5,7 @@ var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefau
5
5
  Object.defineProperty(exports, "__esModule", {
6
6
  value: true
7
7
  });
8
- exports["default"] = void 0;
8
+ exports.default = void 0;
9
9
 
10
10
  var _regenerator = _interopRequireDefault(require("@babel/runtime/regenerator"));
11
11
 
@@ -39,16 +39,16 @@ var _configuration = require("@jbrowse/core/configuration");
39
39
 
40
40
  var _NCListFeature = _interopRequireDefault(require("./NCListFeature"));
41
41
 
42
- 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); }; }
42
+ 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); }; }
43
43
 
44
44
  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; } }
45
45
 
46
46
  function _asyncIterator(iterable) { var method, async, sync, retry = 2; for ("undefined" != typeof Symbol && (async = Symbol.asyncIterator, sync = Symbol.iterator); retry--;) { if (async && null != (method = iterable[async])) return method.call(iterable); if (sync && null != (method = iterable[sync])) return new AsyncFromSyncIterator(method.call(iterable)); async = "@@asyncIterator", sync = "@@iterator"; } throw new TypeError("Object is not async iterable"); }
47
47
 
48
- function AsyncFromSyncIterator(s) { function AsyncFromSyncIteratorContinuation(r) { if (Object(r) !== r) return Promise.reject(new TypeError(r + " is not an object.")); var done = r.done; return Promise.resolve(r.value).then(function (value) { return { value: value, done: done }; }); } return AsyncFromSyncIterator = function AsyncFromSyncIterator(s) { this.s = s, this.n = s.next; }, AsyncFromSyncIterator.prototype = { s: null, n: null, next: function next() { return AsyncFromSyncIteratorContinuation(this.n.apply(this.s, arguments)); }, "return": function _return(value) { var ret = this.s["return"]; return void 0 === ret ? Promise.resolve({ value: value, done: !0 }) : AsyncFromSyncIteratorContinuation(ret.apply(this.s, arguments)); }, "throw": function _throw(value) { var thr = this.s["return"]; return void 0 === thr ? Promise.reject(value) : AsyncFromSyncIteratorContinuation(thr.apply(this.s, arguments)); } }, new AsyncFromSyncIterator(s); }
48
+ function AsyncFromSyncIterator(s) { function AsyncFromSyncIteratorContinuation(r) { if (Object(r) !== r) return Promise.reject(new TypeError(r + " is not an object.")); var done = r.done; return Promise.resolve(r.value).then(function (value) { return { value: value, done: done }; }); } return AsyncFromSyncIterator = function AsyncFromSyncIterator(s) { this.s = s, this.n = s.next; }, AsyncFromSyncIterator.prototype = { s: null, n: null, next: function next() { return AsyncFromSyncIteratorContinuation(this.n.apply(this.s, arguments)); }, return: function _return(value) { var ret = this.s.return; return void 0 === ret ? Promise.resolve({ value: value, done: !0 }) : AsyncFromSyncIteratorContinuation(ret.apply(this.s, arguments)); }, throw: function _throw(value) { var thr = this.s.return; return void 0 === thr ? Promise.reject(value) : AsyncFromSyncIteratorContinuation(thr.apply(this.s, arguments)); } }, new AsyncFromSyncIterator(s); }
49
49
 
50
50
  var NCListAdapter = /*#__PURE__*/function (_BaseFeatureDataAdapt) {
51
- (0, _inherits2["default"])(NCListAdapter, _BaseFeatureDataAdapt);
51
+ (0, _inherits2.default)(NCListAdapter, _BaseFeatureDataAdapt);
52
52
 
53
53
  var _super = _createSuper(NCListAdapter);
54
54
 
@@ -56,14 +56,14 @@ var NCListAdapter = /*#__PURE__*/function (_BaseFeatureDataAdapt) {
56
56
  function NCListAdapter(config, getSubAdapter, pluginManager) {
57
57
  var _this;
58
58
 
59
- (0, _classCallCheck2["default"])(this, NCListAdapter);
59
+ (0, _classCallCheck2.default)(this, NCListAdapter);
60
60
  _this = _super.call(this, config, getSubAdapter, pluginManager);
61
- (0, _defineProperty2["default"])((0, _assertThisInitialized2["default"])(_this), "nclist", void 0);
62
- (0, _defineProperty2["default"])((0, _assertThisInitialized2["default"])(_this), "configRefNames", void 0);
61
+ (0, _defineProperty2.default)((0, _assertThisInitialized2.default)(_this), "nclist", void 0);
62
+ (0, _defineProperty2.default)((0, _assertThisInitialized2.default)(_this), "configRefNames", void 0);
63
63
  var refNames = (0, _configuration.readConfObject)(config, 'refNames');
64
64
  var rootUrlTemplate = (0, _configuration.readConfObject)(config, 'rootUrlTemplate');
65
65
  _this.configRefNames = refNames;
66
- _this.nclist = new _nclist["default"]({
66
+ _this.nclist = new _nclist.default({
67
67
  baseUrl: '',
68
68
  urlTemplate: rootUrlTemplate.uri,
69
69
  readFile: function readFile(url) {
@@ -82,17 +82,17 @@ var NCListAdapter = /*#__PURE__*/function (_BaseFeatureDataAdapt) {
82
82
  */
83
83
 
84
84
 
85
- (0, _createClass2["default"])(NCListAdapter, [{
85
+ (0, _createClass2.default)(NCListAdapter, [{
86
86
  key: "getFeatures",
87
87
  value: function getFeatures(region) {
88
88
  var _this2 = this;
89
89
 
90
90
  var opts = arguments.length > 1 && arguments[1] !== undefined ? arguments[1] : {};
91
91
  return (0, _rxjs.ObservableCreate)( /*#__PURE__*/function () {
92
- var _ref = (0, _asyncToGenerator2["default"])( /*#__PURE__*/_regenerator["default"].mark(function _callee(observer) {
92
+ var _ref = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee(observer) {
93
93
  var signal, _iteratorAbruptCompletion, _didIteratorError, _iteratorError, _iterator, _step, feature;
94
94
 
95
- return _regenerator["default"].wrap(function _callee$(_context) {
95
+ return _regenerator.default.wrap(function _callee$(_context) {
96
96
  while (1) {
97
97
  switch (_context.prev = _context.next) {
98
98
  case 0:
@@ -135,13 +135,13 @@ var NCListAdapter = /*#__PURE__*/function (_BaseFeatureDataAdapt) {
135
135
  _context.prev = 20;
136
136
  _context.prev = 21;
137
137
 
138
- if (!(_iteratorAbruptCompletion && _iterator["return"] != null)) {
138
+ if (!(_iteratorAbruptCompletion && _iterator.return != null)) {
139
139
  _context.next = 25;
140
140
  break;
141
141
  }
142
142
 
143
143
  _context.next = 25;
144
- return _iterator["return"]();
144
+ return _iterator.return();
145
145
 
146
146
  case 25:
147
147
  _context.prev = 25;
@@ -179,14 +179,14 @@ var NCListAdapter = /*#__PURE__*/function (_BaseFeatureDataAdapt) {
179
179
  }, {
180
180
  key: "wrapFeature",
181
181
  value: function wrapFeature(ncFeature) {
182
- return new _NCListFeature["default"](ncFeature, undefined, "".concat(this.id, "-").concat(ncFeature.id()));
182
+ return new _NCListFeature.default(ncFeature, undefined, "".concat(this.id, "-").concat(ncFeature.id()));
183
183
  }
184
184
  }, {
185
185
  key: "hasDataForRefName",
186
186
  value: function () {
187
- var _hasDataForRefName = (0, _asyncToGenerator2["default"])( /*#__PURE__*/_regenerator["default"].mark(function _callee2(refName) {
187
+ var _hasDataForRefName = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee2(refName) {
188
188
  var root;
189
- return _regenerator["default"].wrap(function _callee2$(_context2) {
189
+ return _regenerator.default.wrap(function _callee2$(_context2) {
190
190
  while (1) {
191
191
  switch (_context2.prev = _context2.next) {
192
192
  case 0:
@@ -234,4 +234,4 @@ var NCListAdapter = /*#__PURE__*/function (_BaseFeatureDataAdapt) {
234
234
  return NCListAdapter;
235
235
  }(_BaseAdapter.BaseFeatureDataAdapter);
236
236
 
237
- exports["default"] = NCListAdapter;
237
+ exports.default = NCListAdapter;
package/dist/NCListAdapter/NCListAdapter.test.js CHANGED
@@ -18,20 +18,20 @@ var _NCListAdapter = _interopRequireDefault(require("./NCListAdapter"));
18
18
 
19
19
  var _configSchema = _interopRequireDefault(require("./configSchema"));
20
20
 
21
- 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; } } }; }
21
+ 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; } } }; }
22
22
 
23
23
  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); }
24
24
 
25
25
  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; }
26
26
 
27
- test('adapter can fetch features from ensembl_genes test set', /*#__PURE__*/(0, _asyncToGenerator2["default"])( /*#__PURE__*/_regenerator["default"].mark(function _callee() {
27
+ test('adapter can fetch features from ensembl_genes test set', /*#__PURE__*/(0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee() {
28
28
  var rootTemplate, args, adapter, features, featuresArray, featuresJsonArray, _iterator, _step, feature;
29
29
 
30
- return _regenerator["default"].wrap(function _callee$(_context) {
30
+ return _regenerator.default.wrap(function _callee$(_context) {
31
31
  while (1) {
32
32
  switch (_context.prev = _context.next) {
33
33
  case 0:
34
- rootTemplate = _path["default"].join(__dirname, '..', '..', 'test_data', 'ensembl_genes', '{refseq}', 'trackData.json').replace(/\\/g, '\\\\');
34
+ rootTemplate = _path.default.join(__dirname, '..', '..', 'test_data', 'ensembl_genes', '{refseq}', 'trackData.json').replace(/\\/g, '\\\\');
35
35
  _context.next = 3;
36
36
  return _fs.promises.stat(rootTemplate.replace('{refseq}', '21'));
37
37
 
@@ -44,7 +44,7 @@ test('adapter can fetch features from ensembl_genes test set', /*#__PURE__*/(0,
44
44
  locationType: 'UriLocation'
45
45
  }
46
46
  };
47
- adapter = new _NCListAdapter["default"](_configSchema["default"].create(args));
47
+ adapter = new _NCListAdapter.default(_configSchema.default.create(args));
48
48
  features = adapter.getFeatures({
49
49
  assemblyName: 'volvox',
50
50
  refName: '21',
package/dist/NCListAdapter/NCListFeature.js CHANGED
@@ -5,7 +5,7 @@ var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefau
5
5
  Object.defineProperty(exports, "__esModule", {
6
6
  value: true
7
7
  });
8
- exports["default"] = void 0;
8
+ exports.default = void 0;
9
9
 
10
10
  var _classCallCheck2 = _interopRequireDefault(require("@babel/runtime/helpers/classCallCheck"));
11
11
 
@@ -26,15 +26,15 @@ var jb1ToJb2 = {
26
26
  var NCListFeature = /*#__PURE__*/function () {
27
27
  // eslint-disable-next-line @typescript-eslint/no-explicit-any
28
28
  function NCListFeature(ncFeature, parent, id) {
29
- (0, _classCallCheck2["default"])(this, NCListFeature);
29
+ (0, _classCallCheck2.default)(this, NCListFeature);
30
30
  this.ncFeature = ncFeature;
31
- (0, _defineProperty2["default"])(this, "parentHandle", void 0);
32
- (0, _defineProperty2["default"])(this, "uniqueId", void 0);
31
+ (0, _defineProperty2.default)(this, "parentHandle", void 0);
32
+ (0, _defineProperty2.default)(this, "uniqueId", void 0);
33
33
  this.uniqueId = id || ncFeature.id();
34
34
  this.parentHandle = parent;
35
35
  }
36
36
 
37
- (0, _createClass2["default"])(NCListFeature, [{
37
+ (0, _createClass2.default)(NCListFeature, [{
38
38
  key: "set",
39
39
  value: function set() {
40
40
  throw new Error('not implemented');
@@ -139,4 +139,4 @@ var NCListFeature = /*#__PURE__*/function () {
139
139
  return NCListFeature;
140
140
  }();
141
141
 
142
- exports["default"] = NCListFeature;
142
+ exports.default = NCListFeature;
package/dist/NCListAdapter/configSchema.js CHANGED
@@ -3,7 +3,7 @@
3
3
  Object.defineProperty(exports, "__esModule", {
4
4
  value: true
5
5
  });
6
- exports["default"] = void 0;
6
+ exports.default = void 0;
7
7
 
8
8
  var _configuration = require("@jbrowse/core/configuration");
9
9
 
@@ -24,4 +24,4 @@ var _default = (0, _configuration.ConfigurationSchema)('NCListAdapter', {
24
24
  explicitlyTyped: true
25
25
  });
26
26
 
27
- exports["default"] = _default;
27
+ exports.default = _default;
package/dist/NCListAdapter/index.js CHANGED
@@ -8,7 +8,7 @@ Object.defineProperty(exports, "__esModule", {
8
8
  Object.defineProperty(exports, "configSchema", {
9
9
  enumerable: true,
10
10
  get: function get() {
11
- return _configSchema["default"];
11
+ return _configSchema.default;
12
12
  }
13
13
  });
14
14
 
package/dist/index.js CHANGED
@@ -7,7 +7,7 @@ var _typeof = require("@babel/runtime/helpers/typeof");
7
7
  Object.defineProperty(exports, "__esModule", {
8
8
  value: true
9
9
  });
10
- exports["default"] = void 0;
10
+ exports.default = void 0;
11
11
 
12
12
  var _classCallCheck2 = _interopRequireDefault(require("@babel/runtime/helpers/classCallCheck"));
13
13
 
@@ -41,43 +41,43 @@ var _JBrowse1Connection = require("./JBrowse1Connection");
41
41
 
42
42
  function _getRequireWildcardCache(nodeInterop) { if (typeof WeakMap !== "function") return null; var cacheBabelInterop = new WeakMap(); var cacheNodeInterop = new WeakMap(); return (_getRequireWildcardCache = function _getRequireWildcardCache(nodeInterop) { return nodeInterop ? cacheNodeInterop : cacheBabelInterop; })(nodeInterop); }
43
43
 
44
- function _interopRequireWildcard(obj, nodeInterop) { if (!nodeInterop && obj && obj.__esModule) { return obj; } if (obj === null || _typeof(obj) !== "object" && typeof obj !== "function") { return { "default": obj }; } var cache = _getRequireWildcardCache(nodeInterop); if (cache && cache.has(obj)) { return cache.get(obj); } var newObj = {}; var hasPropertyDescriptor = Object.defineProperty && Object.getOwnPropertyDescriptor; for (var key in obj) { if (key !== "default" && Object.prototype.hasOwnProperty.call(obj, key)) { var desc = hasPropertyDescriptor ? Object.getOwnPropertyDescriptor(obj, key) : null; if (desc && (desc.get || desc.set)) { Object.defineProperty(newObj, key, desc); } else { newObj[key] = obj[key]; } } } newObj["default"] = obj; if (cache) { cache.set(obj, newObj); } return newObj; }
44
+ function _interopRequireWildcard(obj, nodeInterop) { if (!nodeInterop && obj && obj.__esModule) { return obj; } if (obj === null || _typeof(obj) !== "object" && typeof obj !== "function") { return { default: obj }; } var cache = _getRequireWildcardCache(nodeInterop); if (cache && cache.has(obj)) { return cache.get(obj); } var newObj = {}; var hasPropertyDescriptor = Object.defineProperty && Object.getOwnPropertyDescriptor; for (var key in obj) { if (key !== "default" && Object.prototype.hasOwnProperty.call(obj, key)) { var desc = hasPropertyDescriptor ? Object.getOwnPropertyDescriptor(obj, key) : null; if (desc && (desc.get || desc.set)) { Object.defineProperty(newObj, key, desc); } else { newObj[key] = obj[key]; } } } newObj.default = obj; if (cache) { cache.set(obj, newObj); } return newObj; }
45
45
 
46
- 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); }; }
46
+ 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); }; }
47
47
 
48
48
  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; } }
49
49
 
50
50
  var LegacyJBrowsePlugin = /*#__PURE__*/function (_Plugin) {
51
- (0, _inherits2["default"])(LegacyJBrowsePlugin, _Plugin);
51
+ (0, _inherits2.default)(LegacyJBrowsePlugin, _Plugin);
52
52
 
53
53
  var _super = _createSuper(LegacyJBrowsePlugin);
54
54
 
55
55
  function LegacyJBrowsePlugin() {
56
56
  var _this;
57
57
 
58
- (0, _classCallCheck2["default"])(this, LegacyJBrowsePlugin);
58
+ (0, _classCallCheck2.default)(this, LegacyJBrowsePlugin);
59
59
 
60
60
  for (var _len = arguments.length, args = new Array(_len), _key = 0; _key < _len; _key++) {
61
61
  args[_key] = arguments[_key];
62
62
  }
63
63
 
64
64
  _this = _super.call.apply(_super, [this].concat(args));
65
- (0, _defineProperty2["default"])((0, _assertThisInitialized2["default"])(_this), "name", 'LegacyJBrowsePlugin');
65
+ (0, _defineProperty2.default)((0, _assertThisInitialized2.default)(_this), "name", 'LegacyJBrowsePlugin');
66
66
  return _this;
67
67
  }
68
68
 
69
- (0, _createClass2["default"])(LegacyJBrowsePlugin, [{
69
+ (0, _createClass2.default)(LegacyJBrowsePlugin, [{
70
70
  key: "install",
71
71
  value: function install(pluginManager) {
72
72
  pluginManager.addAdapterType(function () {
73
- return new _AdapterType["default"]({
73
+ return new _AdapterType.default({
74
74
  name: 'NCListAdapter',
75
75
  configSchema: _NCListAdapter.configSchema,
76
76
  getAdapterClass: function getAdapterClass() {
77
77
  return Promise.resolve().then(function () {
78
78
  return _interopRequireWildcard(require('./NCListAdapter/NCListAdapter'));
79
79
  }).then(function (r) {
80
- return r["default"];
80
+ return r.default;
81
81
  });
82
82
  }
83
83
  });
@@ -99,7 +99,7 @@ var LegacyJBrowsePlugin = /*#__PURE__*/function (_Plugin) {
99
99
  };
100
100
  });
101
101
  pluginManager.addTextSearchAdapterType(function () {
102
- return new _TextSearchAdapterType["default"]({
102
+ return new _TextSearchAdapterType.default({
103
103
  name: 'JBrowse1TextSearchAdapter',
104
104
  configSchema: _JBrowse1TextSeachAdapter.configSchema,
105
105
  AdapterClass: _JBrowse1TextSeachAdapter.AdapterClass,
@@ -107,7 +107,7 @@ var LegacyJBrowsePlugin = /*#__PURE__*/function (_Plugin) {
107
107
  });
108
108
  });
109
109
  pluginManager.addConnectionType(function () {
110
- return new _ConnectionType["default"]({
110
+ return new _ConnectionType.default({
111
111
  name: 'JBrowse1Connection',
112
112
  configSchema: _JBrowse1Connection.configSchema,
113
113
  stateModel: (0, _JBrowse1Connection.modelFactory)(pluginManager),
@@ -119,6 +119,6 @@ var LegacyJBrowsePlugin = /*#__PURE__*/function (_Plugin) {
119
119
  }
120
120
  }]);
121
121
  return LegacyJBrowsePlugin;
122
- }(_Plugin2["default"]);
122
+ }(_Plugin2.default);
123
123
 
124
- exports["default"] = LegacyJBrowsePlugin;
124
+ exports.default = LegacyJBrowsePlugin;
package/dist/index.test.js CHANGED
@@ -11,12 +11,12 @@ var _ = _interopRequireDefault(require("."));
11
11
  test('plugin in a stock JBrowse', function () {
12
12
  var originalConsoleWarn = console.warn;
13
13
  console.warn = jest.fn();
14
- var pluginManager = new _PluginManager["default"]([new _["default"]()]);
14
+ var pluginManager = new _PluginManager.default([new _.default()]);
15
15
  pluginManager.createPluggableElements();
16
16
  pluginManager.configure();
17
17
  console.warn = originalConsoleWarn;
18
18
  expect(function () {
19
- return pluginManager.addPlugin(new _["default"]());
19
+ return pluginManager.addPlugin(new _.default());
20
20
  }).toThrow(/JBrowse already configured, cannot add plugins/);
21
21
  var NCListAdapter = pluginManager.getAdapterType('NCListAdapter');
22
22
  var config = NCListAdapter.configSchema.create({
@@ -26,7 +26,7 @@ test('plugin in a stock JBrowse', function () {
26
26
  });
27
27
  test('test creating a text search adapter', function () {
28
28
  console.warn = jest.fn();
29
- var pluginManager = new _PluginManager["default"]([new _["default"]()]);
29
+ var pluginManager = new _PluginManager.default([new _.default()]);
30
30
  pluginManager.createPluggableElements();
31
31
  pluginManager.configure();
32
32
  var JB1TextSearchAdapter = pluginManager.getTextSearchAdapterType('JBrowse1TextSearchAdapter');
package/package.json CHANGED
@@ -1,6 +1,6 @@
1
1
  {
2
2
  "name": "@jbrowse/plugin-legacy-jbrowse",
3
- "version": "1.7.3",
3
+ "version": "1.7.6",
4
4
  "description": "JBrowse 2 plugin for connecting to and reading JBrowse 1 data",
5
5
  "keywords": [
6
6
  "jbrowse",
@@ -33,6 +33,7 @@
33
33
  "postbuild": "tsc --build tsconfig.build.json"
34
34
  },
35
35
  "dependencies": {
36
+ "@babel/runtime": "^7.17.9",
36
37
  "@gmod/nclist": "^0.2.1",
37
38
  "buffer-crc32": "^0.2.13",
38
39
  "generic-filehandle": "^2.2.2",
@@ -47,5 +48,5 @@
47
48
  "publishConfig": {
48
49
  "access": "public"
49
50
  },
50
- "gitHead": "09b13c85acf4ac68dd71ab23af87656c7552fdaf"
51
+ "gitHead": "dbd73f99714e395cf20877d5e05d26855857a0e3"
51
52
  }