@jbrowse/plugin-legacy-jbrowse 1.4.4 → 1.5.3
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.
- package/dist/JBrowse1Connection/jb1ToJb2.d.ts +1 -0
- package/dist/JBrowse1Connection/types.d.ts +2 -0
- package/dist/JBrowse1TextSeachAdapter/HttpMap.d.ts +1 -15
- package/dist/JBrowse1TextSeachAdapter/JBrowse1TextSearchAdapter.d.ts +12 -8
- package/dist/NCListAdapter/NCListAdapter.d.ts +3 -1
- package/dist/plugin-legacy-jbrowse.cjs.development.js +334 -398
- package/dist/plugin-legacy-jbrowse.cjs.development.js.map +1 -1
- package/dist/plugin-legacy-jbrowse.cjs.production.min.js +1 -1
- package/dist/plugin-legacy-jbrowse.cjs.production.min.js.map +1 -1
- package/dist/plugin-legacy-jbrowse.esm.js +336 -399
- package/dist/plugin-legacy-jbrowse.esm.js.map +1 -1
- package/package.json +5 -3
- package/src/JBrowse1Connection/configSchema.ts +4 -1
- package/src/JBrowse1Connection/jb1ConfigLoad.ts +24 -27
- package/src/JBrowse1Connection/jb1ConfigParse.ts +10 -12
- package/src/JBrowse1Connection/jb1ToJb2.ts +93 -43
- package/src/JBrowse1Connection/types.ts +2 -0
- package/src/JBrowse1TextSeachAdapter/HttpMap.test.ts +8 -20
- package/src/JBrowse1TextSeachAdapter/HttpMap.ts +17 -75
- package/src/JBrowse1TextSeachAdapter/JBrowse1TextSearchAdapter.test.ts +2 -4
- package/src/JBrowse1TextSeachAdapter/JBrowse1TextSearchAdapter.ts +42 -58
- package/src/JBrowse1TextSeachAdapter/configSchema.ts +2 -2
- package/src/NCListAdapter/NCListAdapter.test.ts +4 -1
- package/src/NCListAdapter/NCListAdapter.ts +15 -8
- package/src/NCListAdapter/configSchema.ts +4 -1
- package/src/__snapshots__/index.test.js.snap +3 -0
- package/src/index.test.js +1 -0
- package/src/index.ts +23 -0
- package/dist/JBrowse1TextSeachAdapter/Crc32.d.ts +0 -19
- package/src/JBrowse1TextSeachAdapter/Crc32.test.ts +0 -21
- package/src/JBrowse1TextSeachAdapter/Crc32.ts +0 -77
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@@ -10,17 +10,93 @@ var ConnectionType = _interopDefault(require('@jbrowse/core/pluggableElementType
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var Plugin = _interopDefault(require('@jbrowse/core/Plugin'));
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var configuration = require('@jbrowse/core/configuration');
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var BaseAdapter = require('@jbrowse/core/data_adapters/BaseAdapter');
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var BaseResult = require('@jbrowse/core/TextSearch/BaseResults');
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var
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var BaseResult = _interopDefault(require('@jbrowse/core/TextSearch/BaseResults'));
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var crc32 = _interopDefault(require('buffer-crc32'));
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var tracks = require('@jbrowse/core/util/tracks');
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var util = require('@jbrowse/core/util');
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var models = require('@jbrowse/core/pluggableElementTypes/models');
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var mobxStateTree = require('mobx-state-tree');
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var io = require('@jbrowse/core/util/io');
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var getValue = _interopDefault(require('get-value'));
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var setValue = _interopDefault(require('set-value'));
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var tracks = require('@jbrowse/core/util/tracks');
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var NCListStore = _interopDefault(require('@gmod/nclist'));
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var rxjs = require('@jbrowse/core/util/rxjs');
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var genericFilehandle = require('generic-filehandle');
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function _asyncIterator(iterable) {
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var method,
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async,
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sync,
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retry = 2;
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if (typeof Symbol !== "undefined") {
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async = Symbol.asyncIterator;
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sync = Symbol.iterator;
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}
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while (retry--) {
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if (async && (method = iterable[async]) != null) {
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return method.call(iterable);
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}
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if (sync && (method = iterable[sync]) != null) {
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return new AsyncFromSyncIterator(method.call(iterable));
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}
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async = "@@asyncIterator";
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sync = "@@iterator";
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}
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throw new TypeError("Object is not async iterable");
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}
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function AsyncFromSyncIterator(s) {
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AsyncFromSyncIterator = function (s) {
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this.s = s;
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this.n = s.next;
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};
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AsyncFromSyncIterator.prototype = {
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s: null,
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n: null,
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next: function () {
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return AsyncFromSyncIteratorContinuation(this.n.apply(this.s, arguments));
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},
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value: value,
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done: true
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});
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}
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return AsyncFromSyncIteratorContinuation(ret.apply(this.s, arguments));
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throw: function (value) {
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return AsyncFromSyncIteratorContinuation(thr.apply(this.s, arguments));
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}
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function AsyncFromSyncIteratorContinuation(r) {
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return Promise.reject(new TypeError(r + " is not an object."));
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}
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var done = r.done;
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return Promise.resolve(r.value).then(function (value) {
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return {
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value: value,
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done: done
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};
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});
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}
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return new AsyncFromSyncIterator(s);
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}
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function ownKeys(object, enumerableOnly) {
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var keys = Object.keys(object);
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}
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function _asyncIterator(iterable) {
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var method;
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if (typeof Symbol !== "undefined") {
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if (Symbol.asyncIterator) method = iterable[Symbol.asyncIterator];
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if (method == null && Symbol.iterator) method = iterable[Symbol.iterator];
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}
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if (method == null) method = iterable["@@asyncIterator"];
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if (method == null) method = iterable["@@iterator"];
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if (method == null) throw new TypeError("Object is not async iterable");
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}
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function asyncGeneratorStep(gen, resolve, reject, _next, _throw, key, arg) {
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try {
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var info = gen[key](arg);
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@@ -218,6 +280,8 @@ function _assertThisInitialized(self) {
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function _possibleConstructorReturn(self, call) {
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return _assertThisInitialized(self);
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rootUrlTemplate: {
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type: 'fileLocation',
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defaultValue: {
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uri: '/path/to/my/{refseq}/trackData.json'
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uri: '/path/to/my/{refseq}/trackData.json',
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locationType: 'UriLocation'
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refNames: {
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@@ -430,11 +495,9 @@ var runtime_1 = /*#__PURE__*/createCommonjsModule(function (module) {
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var IteratorPrototype = {};
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IteratorPrototype[iteratorSymbol] = function () {
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define(IteratorPrototype, iteratorSymbol, function () {
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var getProto = Object.getPrototypeOf;
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var NativeIteratorPrototype = getProto && getProto(getProto(values([])));
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var Gp = GeneratorFunctionPrototype.prototype = Generator.prototype = Object.create(IteratorPrototype);
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define(GeneratorFunctionPrototype, "constructor", GeneratorFunction);
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GeneratorFunction.displayName = define(GeneratorFunctionPrototype, toStringTagSymbol, "GeneratorFunction"); // Helper for defining the .next, .throw, and .return methods of the
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defineIteratorMethods(AsyncIterator.prototype);
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AsyncIterator.prototype[asyncIteratorSymbol] = function () {
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// the proper solution is to fix the accidental strict mode problem. If
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// CSP to forbid Function, and you're not willing to fix either of those
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var crc32Table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dapted from JBrowse1 crc32 implementation.
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// done because chars have "wrong" endianness
|
|
1088
|
-
|
|
1089
|
-
|
|
1090
|
-
re = re.concat(st.reverse());
|
|
1091
|
-
}
|
|
1092
|
-
|
|
1093
|
-
return re;
|
|
1094
|
-
}
|
|
1095
|
-
/**
|
|
1096
|
-
* crc32 given a string
|
|
1097
|
-
* @param str - string
|
|
1098
|
-
* @param crc - number
|
|
1099
|
-
*/
|
|
1100
|
-
|
|
1101
|
-
function crc32(str) {
|
|
1102
|
-
var crc = arguments.length > 1 && arguments[1] !== undefined ? arguments[1] : 0;
|
|
1103
|
-
var bytes = stringToBytes(str);
|
|
1104
|
-
var n = 0; // a number between 0 and 255
|
|
1105
|
-
|
|
1106
|
-
var x; // a hex number
|
|
1107
|
-
|
|
1108
|
-
var table = crc32Table;
|
|
1109
|
-
crc ^= -1;
|
|
1110
|
-
|
|
1111
|
-
for (var i = 0, iTop = bytes.length; i < iTop; i++) {
|
|
1112
|
-
n = (crc ^ bytes[i]) & 0xff;
|
|
1113
|
-
x = "0x".concat(table.substr(n * 9, 8));
|
|
1114
|
-
crc = crc >>> 8 ^ parseInt(x, 16);
|
|
1115
|
-
}
|
|
1116
|
-
|
|
1117
|
-
crc ^= -1; // convert to unsigned 32-bit int if needed
|
|
1118
|
-
|
|
1119
|
-
if (crc < 0) {
|
|
1120
|
-
crc += 4294967296;
|
|
1121
|
-
}
|
|
1122
|
-
|
|
1123
|
-
return crc;
|
|
1124
|
-
}
|
|
1125
|
-
|
|
1126
1130
|
var HttpMap = /*#__PURE__*/function () {
|
|
1127
1131
|
function HttpMap(args) {
|
|
1128
1132
|
_classCallCheck(this, HttpMap);
|
|
1129
1133
|
|
|
1130
1134
|
// make sure url has a trailing slash
|
|
1131
1135
|
this.url = /\/$/.test(args.url) ? args.url : "".concat(args.url, "/");
|
|
1132
|
-
this.isElectron = args.isElectron;
|
|
1133
1136
|
}
|
|
1134
1137
|
/**
|
|
1135
1138
|
* loads meta.json file from names directory and reads number of hash_bits used
|
|
@@ -1145,47 +1148,25 @@ var HttpMap = /*#__PURE__*/function () {
|
|
|
1145
1148
|
while (1) {
|
|
1146
1149
|
switch (_context.prev = _context.next) {
|
|
1147
1150
|
case 0:
|
|
1148
|
-
_context.
|
|
1149
|
-
_context.next = 3;
|
|
1151
|
+
_context.next = 2;
|
|
1150
1152
|
return this.loadFile('meta.json');
|
|
1151
1153
|
|
|
1152
|
-
case
|
|
1154
|
+
case 2:
|
|
1153
1155
|
meta = _context.sent;
|
|
1154
|
-
|
|
1155
|
-
if (!(meta !== {})) {
|
|
1156
|
-
_context.next = 11;
|
|
1157
|
-
break;
|
|
1158
|
-
}
|
|
1159
|
-
|
|
1160
1156
|
compress = meta.compress, tracks = meta.track_names;
|
|
1161
|
-
this.compress = compress;
|
|
1162
1157
|
hashHexCharacters = Math.ceil(meta.hash_bits / 4);
|
|
1163
|
-
this.hash_hex_characters = hashHexCharacters;
|
|
1164
|
-
this.tracks = tracks;
|
|
1165
1158
|
return _context.abrupt("return", {
|
|
1166
1159
|
hashHexCharacters: hashHexCharacters,
|
|
1167
1160
|
compress: compress,
|
|
1168
1161
|
tracks: tracks
|
|
1169
1162
|
});
|
|
1170
1163
|
|
|
1171
|
-
case
|
|
1172
|
-
throw new Error('Error parsing meta.json');
|
|
1173
|
-
|
|
1174
|
-
case 14:
|
|
1175
|
-
_context.prev = 14;
|
|
1176
|
-
_context.t0 = _context["catch"](0);
|
|
1177
|
-
// throw Error(err)
|
|
1178
|
-
console.warn("Error: ".concat(_context.t0));
|
|
1179
|
-
|
|
1180
|
-
case 17:
|
|
1181
|
-
return _context.abrupt("return", {});
|
|
1182
|
-
|
|
1183
|
-
case 18:
|
|
1164
|
+
case 6:
|
|
1184
1165
|
case "end":
|
|
1185
1166
|
return _context.stop();
|
|
1186
1167
|
}
|
|
1187
1168
|
}
|
|
1188
|
-
}, _callee, this
|
|
1169
|
+
}, _callee, this);
|
|
1189
1170
|
}));
|
|
1190
1171
|
|
|
1191
1172
|
function readMeta() {
|
|
@@ -1203,22 +1184,14 @@ var HttpMap = /*#__PURE__*/function () {
|
|
|
1203
1184
|
while (1) {
|
|
1204
1185
|
switch (_context2.prev = _context2.next) {
|
|
1205
1186
|
case 0:
|
|
1206
|
-
|
|
1207
|
-
_context2.next = 2;
|
|
1208
|
-
break;
|
|
1209
|
-
}
|
|
1210
|
-
|
|
1211
|
-
return _context2.abrupt("return", this.hash_hex_characters);
|
|
1212
|
-
|
|
1213
|
-
case 2:
|
|
1214
|
-
_context2.next = 4;
|
|
1187
|
+
_context2.next = 2;
|
|
1215
1188
|
return this.readMeta();
|
|
1216
1189
|
|
|
1217
|
-
case
|
|
1190
|
+
case 2:
|
|
1218
1191
|
meta = _context2.sent;
|
|
1219
1192
|
return _context2.abrupt("return", meta.hashHexCharacters);
|
|
1220
1193
|
|
|
1221
|
-
case
|
|
1194
|
+
case 4:
|
|
1222
1195
|
case "end":
|
|
1223
1196
|
return _context2.stop();
|
|
1224
1197
|
}
|
|
@@ -1241,22 +1214,14 @@ var HttpMap = /*#__PURE__*/function () {
|
|
|
1241
1214
|
while (1) {
|
|
1242
1215
|
switch (_context3.prev = _context3.next) {
|
|
1243
1216
|
case 0:
|
|
1244
|
-
|
|
1245
|
-
_context3.next = 2;
|
|
1246
|
-
break;
|
|
1247
|
-
}
|
|
1248
|
-
|
|
1249
|
-
return _context3.abrupt("return", this.compress);
|
|
1250
|
-
|
|
1251
|
-
case 2:
|
|
1252
|
-
_context3.next = 4;
|
|
1217
|
+
_context3.next = 2;
|
|
1253
1218
|
return this.readMeta();
|
|
1254
1219
|
|
|
1255
|
-
case
|
|
1220
|
+
case 2:
|
|
1256
1221
|
meta = _context3.sent;
|
|
1257
1222
|
return _context3.abrupt("return", meta.compress);
|
|
1258
1223
|
|
|
1259
|
-
case
|
|
1224
|
+
case 4:
|
|
1260
1225
|
case "end":
|
|
1261
1226
|
return _context3.stop();
|
|
1262
1227
|
}
|
|
@@ -1279,22 +1244,14 @@ var HttpMap = /*#__PURE__*/function () {
|
|
|
1279
1244
|
while (1) {
|
|
1280
1245
|
switch (_context4.prev = _context4.next) {
|
|
1281
1246
|
case 0:
|
|
1282
|
-
|
|
1283
|
-
_context4.next = 2;
|
|
1284
|
-
break;
|
|
1285
|
-
}
|
|
1286
|
-
|
|
1287
|
-
return _context4.abrupt("return", this.tracks);
|
|
1288
|
-
|
|
1289
|
-
case 2:
|
|
1290
|
-
_context4.next = 4;
|
|
1247
|
+
_context4.next = 2;
|
|
1291
1248
|
return this.readMeta();
|
|
1292
1249
|
|
|
1293
|
-
case
|
|
1250
|
+
case 2:
|
|
1294
1251
|
meta = _context4.sent;
|
|
1295
1252
|
return _context4.abrupt("return", meta.tracks);
|
|
1296
1253
|
|
|
1297
|
-
case
|
|
1254
|
+
case 4:
|
|
1298
1255
|
case "end":
|
|
1299
1256
|
return _context4.stop();
|
|
1300
1257
|
}
|
|
@@ -1352,45 +1309,25 @@ var HttpMap = /*#__PURE__*/function () {
|
|
|
1352
1309
|
key: "getBucket",
|
|
1353
1310
|
value: function () {
|
|
1354
1311
|
var _getBucket = /*#__PURE__*/_asyncToGenerator( /*#__PURE__*/runtime_1.mark(function _callee6(key) {
|
|
1355
|
-
var bucketIdent, hexToDirPath
|
|
1312
|
+
var bucketIdent, hexToDirPath;
|
|
1356
1313
|
return runtime_1.wrap(function _callee6$(_context6) {
|
|
1357
1314
|
while (1) {
|
|
1358
1315
|
switch (_context6.prev = _context6.next) {
|
|
1359
1316
|
case 0:
|
|
1360
1317
|
bucketIdent = this.hash(key);
|
|
1361
|
-
_context6.
|
|
1362
|
-
_context6.next = 4;
|
|
1318
|
+
_context6.next = 3;
|
|
1363
1319
|
return this.hexToDirPath(bucketIdent);
|
|
1364
1320
|
|
|
1365
|
-
case
|
|
1321
|
+
case 3:
|
|
1366
1322
|
hexToDirPath = _context6.sent;
|
|
1367
|
-
_context6.
|
|
1368
|
-
return this.loadFile(hexToDirPath);
|
|
1323
|
+
return _context6.abrupt("return", this.loadFile(hexToDirPath));
|
|
1369
1324
|
|
|
1370
|
-
case
|
|
1371
|
-
value = _context6.sent;
|
|
1372
|
-
return _context6.abrupt("return", value);
|
|
1373
|
-
|
|
1374
|
-
case 11:
|
|
1375
|
-
_context6.prev = 11;
|
|
1376
|
-
_context6.t0 = _context6["catch"](1);
|
|
1377
|
-
|
|
1378
|
-
if (!(this.isElectron || _context6.t0.status === 404)) {
|
|
1379
|
-
_context6.next = 15;
|
|
1380
|
-
break;
|
|
1381
|
-
}
|
|
1382
|
-
|
|
1383
|
-
return _context6.abrupt("return", {});
|
|
1384
|
-
|
|
1385
|
-
case 15:
|
|
1386
|
-
return _context6.abrupt("return", {});
|
|
1387
|
-
|
|
1388
|
-
case 16:
|
|
1325
|
+
case 5:
|
|
1389
1326
|
case "end":
|
|
1390
1327
|
return _context6.stop();
|
|
1391
1328
|
}
|
|
1392
1329
|
}
|
|
1393
|
-
}, _callee6, this
|
|
1330
|
+
}, _callee6, this);
|
|
1394
1331
|
}));
|
|
1395
1332
|
|
|
1396
1333
|
function getBucket(_x2) {
|
|
@@ -1409,45 +1346,33 @@ var HttpMap = /*#__PURE__*/function () {
|
|
|
1409
1346
|
key: "loadFile",
|
|
1410
1347
|
value: function () {
|
|
1411
1348
|
var _loadFile = /*#__PURE__*/_asyncToGenerator( /*#__PURE__*/runtime_1.mark(function _callee7(id) {
|
|
1412
|
-
var response
|
|
1349
|
+
var response;
|
|
1413
1350
|
return runtime_1.wrap(function _callee7$(_context7) {
|
|
1414
1351
|
while (1) {
|
|
1415
1352
|
switch (_context7.prev = _context7.next) {
|
|
1416
1353
|
case 0:
|
|
1417
1354
|
_context7.next = 2;
|
|
1418
|
-
return fetch("".concat(this.url).concat(id)
|
|
1419
|
-
headers: {
|
|
1420
|
-
'Content-Type': 'application/json',
|
|
1421
|
-
'Access-Control-Allow-Origin': '*'
|
|
1422
|
-
}
|
|
1423
|
-
});
|
|
1355
|
+
return fetch("".concat(this.url).concat(id));
|
|
1424
1356
|
|
|
1425
1357
|
case 2:
|
|
1426
1358
|
response = _context7.sent;
|
|
1427
|
-
_context7.prev = 3;
|
|
1428
|
-
_context7.next = 6;
|
|
1429
|
-
return response.json();
|
|
1430
1359
|
|
|
1431
|
-
|
|
1432
|
-
|
|
1433
|
-
|
|
1360
|
+
if (response.ok) {
|
|
1361
|
+
_context7.next = 5;
|
|
1362
|
+
break;
|
|
1363
|
+
}
|
|
1434
1364
|
|
|
1435
|
-
|
|
1436
|
-
_context7.prev = 10;
|
|
1437
|
-
_context7.t0 = _context7["catch"](3);
|
|
1438
|
-
// handle error
|
|
1439
|
-
// throw Error(err)
|
|
1440
|
-
console.warn("Error: ".concat(_context7.t0));
|
|
1365
|
+
throw new Error("HTTP ".concat(response.status, " ").concat(response.statusText));
|
|
1441
1366
|
|
|
1442
|
-
case
|
|
1443
|
-
return _context7.abrupt("return",
|
|
1367
|
+
case 5:
|
|
1368
|
+
return _context7.abrupt("return", response.json());
|
|
1444
1369
|
|
|
1445
|
-
case
|
|
1370
|
+
case 6:
|
|
1446
1371
|
case "end":
|
|
1447
1372
|
return _context7.stop();
|
|
1448
1373
|
}
|
|
1449
1374
|
}
|
|
1450
|
-
}, _callee7, this
|
|
1375
|
+
}, _callee7, this);
|
|
1451
1376
|
}));
|
|
1452
1377
|
|
|
1453
1378
|
function loadFile(_x3) {
|
|
@@ -1517,33 +1442,29 @@ var HttpMap = /*#__PURE__*/function () {
|
|
|
1517
1442
|
|
|
1518
1443
|
return hexToDirPath;
|
|
1519
1444
|
}()
|
|
1520
|
-
/**
|
|
1521
|
-
* Returns crc32 hash given a string.
|
|
1522
|
-
* (Note: this is using JBrowse1 implementation of crc32.)
|
|
1523
|
-
* @param data - string
|
|
1524
|
-
*/
|
|
1525
|
-
|
|
1526
1445
|
}, {
|
|
1527
1446
|
key: "hash",
|
|
1528
1447
|
value: function hash(data) {
|
|
1529
|
-
return crc32(data).toString(
|
|
1448
|
+
return crc32(Buffer.from(data)).toString('hex').toLowerCase().replace('-', 'n');
|
|
1530
1449
|
}
|
|
1531
1450
|
}]);
|
|
1532
1451
|
|
|
1533
1452
|
return HttpMap;
|
|
1534
1453
|
}();
|
|
1535
1454
|
|
|
1455
|
+
// Uses index built by generate-names.pl
|
|
1456
|
+
|
|
1536
1457
|
var JBrowse1TextSearchAdapter = /*#__PURE__*/function (_BaseAdapter) {
|
|
1537
1458
|
_inherits(JBrowse1TextSearchAdapter, _BaseAdapter);
|
|
1538
1459
|
|
|
1539
1460
|
var _super = /*#__PURE__*/_createSuper(JBrowse1TextSearchAdapter);
|
|
1540
1461
|
|
|
1541
|
-
function JBrowse1TextSearchAdapter(config) {
|
|
1462
|
+
function JBrowse1TextSearchAdapter(config, getSubAdapter, pluginManager) {
|
|
1542
1463
|
var _this;
|
|
1543
1464
|
|
|
1544
1465
|
_classCallCheck(this, JBrowse1TextSearchAdapter);
|
|
1545
1466
|
|
|
1546
|
-
_this = _super.call(this, config);
|
|
1467
|
+
_this = _super.call(this, config, getSubAdapter, pluginManager);
|
|
1547
1468
|
var namesIndexLocation = configuration.readConfObject(config, 'namesIndexLocation');
|
|
1548
1469
|
|
|
1549
1470
|
if (!namesIndexLocation) {
|
|
@@ -1551,8 +1472,7 @@ var JBrowse1TextSearchAdapter = /*#__PURE__*/function (_BaseAdapter) {
|
|
|
1551
1472
|
}
|
|
1552
1473
|
|
|
1553
1474
|
_this.httpMap = new HttpMap({
|
|
1554
|
-
url: namesIndexLocation.baseUri ? new URL(namesIndexLocation.uri, namesIndexLocation.baseUri).href : namesIndexLocation.uri
|
|
1555
|
-
isElectron: util.isElectron
|
|
1475
|
+
url: namesIndexLocation.baseUri ? new URL(namesIndexLocation.uri, namesIndexLocation.baseUri).href : namesIndexLocation.uri
|
|
1556
1476
|
});
|
|
1557
1477
|
return _this;
|
|
1558
1478
|
}
|
|
@@ -1567,19 +1487,13 @@ var JBrowse1TextSearchAdapter = /*#__PURE__*/function (_BaseAdapter) {
|
|
|
1567
1487
|
key: "loadIndexFile",
|
|
1568
1488
|
value: function () {
|
|
1569
1489
|
var _loadIndexFile = /*#__PURE__*/_asyncToGenerator( /*#__PURE__*/runtime_1.mark(function _callee(query) {
|
|
1570
|
-
var bucketContents;
|
|
1571
1490
|
return runtime_1.wrap(function _callee$(_context) {
|
|
1572
1491
|
while (1) {
|
|
1573
1492
|
switch (_context.prev = _context.next) {
|
|
1574
1493
|
case 0:
|
|
1575
|
-
_context.
|
|
1576
|
-
return this.httpMap.getBucket(query);
|
|
1577
|
-
|
|
1578
|
-
case 2:
|
|
1579
|
-
bucketContents = _context.sent;
|
|
1580
|
-
return _context.abrupt("return", bucketContents);
|
|
1494
|
+
return _context.abrupt("return", this.httpMap.getBucket(query));
|
|
1581
1495
|
|
|
1582
|
-
case
|
|
1496
|
+
case 1:
|
|
1583
1497
|
case "end":
|
|
1584
1498
|
return _context.stop();
|
|
1585
1499
|
}
|
|
@@ -1593,12 +1507,6 @@ var JBrowse1TextSearchAdapter = /*#__PURE__*/function (_BaseAdapter) {
|
|
|
1593
1507
|
|
|
1594
1508
|
return loadIndexFile;
|
|
1595
1509
|
}()
|
|
1596
|
-
/**
|
|
1597
|
-
* Returns list of results
|
|
1598
|
-
* @param args - search options/arguments include: search query
|
|
1599
|
-
* limit of results to return, SearchType...prefix | full | exact", etc.
|
|
1600
|
-
*/
|
|
1601
|
-
|
|
1602
1510
|
}, {
|
|
1603
1511
|
key: "searchIndex",
|
|
1604
1512
|
value: function () {
|
|
@@ -1609,42 +1517,38 @@ var JBrowse1TextSearchAdapter = /*#__PURE__*/function (_BaseAdapter) {
|
|
|
1609
1517
|
switch (_context2.prev = _context2.next) {
|
|
1610
1518
|
case 0:
|
|
1611
1519
|
searchType = args.searchType, queryString = args.queryString;
|
|
1520
|
+
_context2.t0 = this.tracksNames;
|
|
1612
1521
|
|
|
1613
|
-
if (
|
|
1614
|
-
_context2.next =
|
|
1522
|
+
if (_context2.t0) {
|
|
1523
|
+
_context2.next = 6;
|
|
1615
1524
|
break;
|
|
1616
1525
|
}
|
|
1617
1526
|
|
|
1618
|
-
_context2.
|
|
1619
|
-
_context2.next = 8;
|
|
1620
|
-
break;
|
|
1621
|
-
|
|
1622
|
-
case 5:
|
|
1623
|
-
_context2.next = 7;
|
|
1527
|
+
_context2.next = 5;
|
|
1624
1528
|
return this.httpMap.getTrackNames();
|
|
1625
1529
|
|
|
1626
|
-
case
|
|
1530
|
+
case 5:
|
|
1627
1531
|
_context2.t0 = _context2.sent;
|
|
1628
1532
|
|
|
1629
|
-
case
|
|
1533
|
+
case 6:
|
|
1630
1534
|
tracks = _context2.t0;
|
|
1631
|
-
_context2.next =
|
|
1632
|
-
return this.loadIndexFile(queryString);
|
|
1535
|
+
_context2.next = 9;
|
|
1536
|
+
return this.loadIndexFile(queryString.toLowerCase());
|
|
1633
1537
|
|
|
1634
|
-
case
|
|
1538
|
+
case 9:
|
|
1635
1539
|
entries = _context2.sent;
|
|
1636
1540
|
|
|
1637
|
-
if (!
|
|
1638
|
-
_context2.next =
|
|
1541
|
+
if (!entries[queryString]) {
|
|
1542
|
+
_context2.next = 12;
|
|
1639
1543
|
break;
|
|
1640
1544
|
}
|
|
1641
1545
|
|
|
1642
|
-
return _context2.abrupt("return", this.formatResults(entries[queryString]
|
|
1546
|
+
return _context2.abrupt("return", this.formatResults(entries[queryString], tracks, searchType));
|
|
1643
1547
|
|
|
1644
|
-
case
|
|
1548
|
+
case 12:
|
|
1645
1549
|
return _context2.abrupt("return", []);
|
|
1646
1550
|
|
|
1647
|
-
case
|
|
1551
|
+
case 13:
|
|
1648
1552
|
case "end":
|
|
1649
1553
|
return _context2.stop();
|
|
1650
1554
|
}
|
|
@@ -1660,41 +1564,30 @@ var JBrowse1TextSearchAdapter = /*#__PURE__*/function (_BaseAdapter) {
|
|
|
1660
1564
|
}()
|
|
1661
1565
|
}, {
|
|
1662
1566
|
key: "formatResults",
|
|
1663
|
-
value: function formatResults(results,
|
|
1664
|
-
|
|
1665
|
-
return
|
|
1666
|
-
|
|
1667
|
-
|
|
1668
|
-
var formattedResults = results.map(function (result) {
|
|
1669
|
-
if (result && Array.isArray(result)) {
|
|
1670
|
-
var name = result[0];
|
|
1671
|
-
var trackIndex = result[1];
|
|
1672
|
-
var refName = result[3];
|
|
1673
|
-
var start = result[4];
|
|
1674
|
-
var end = result[5];
|
|
1675
|
-
var locstring = "".concat(refName || name, ":").concat(start, "-").concat(end);
|
|
1676
|
-
var formattedResult = new BaseResult.LocStringResult({
|
|
1677
|
-
locString: locstring,
|
|
1678
|
-
label: name,
|
|
1679
|
-
matchedAttribute: 'name',
|
|
1680
|
-
matchedObject: result,
|
|
1681
|
-
trackId: tracksNames[trackIndex]
|
|
1682
|
-
});
|
|
1683
|
-
return formattedResult;
|
|
1684
|
-
} // {"name":"too many matches","hitLimit":1}
|
|
1685
|
-
|
|
1686
|
-
|
|
1687
|
-
var defaultLabel = _typeof(result) === 'object' ? result.name : result;
|
|
1688
|
-
var defaultResult = new BaseResult__default({
|
|
1689
|
-
label: defaultLabel,
|
|
1567
|
+
value: function formatResults(results, tracks, searchType) {
|
|
1568
|
+
return [].concat(_toConsumableArray(searchType === 'exact' ? [] : results.prefix.map(function (result) {
|
|
1569
|
+
return new BaseResult({
|
|
1570
|
+
label: _typeof(result) === 'object' ? result.name : result,
|
|
1690
1571
|
matchedAttribute: 'name',
|
|
1691
1572
|
matchedObject: {
|
|
1692
1573
|
result: result
|
|
1693
1574
|
}
|
|
1694
1575
|
});
|
|
1695
|
-
|
|
1696
|
-
|
|
1697
|
-
|
|
1576
|
+
})), _toConsumableArray(results.exact.map(function (result) {
|
|
1577
|
+
var name = result[0];
|
|
1578
|
+
var trackIndex = result[1];
|
|
1579
|
+
var refName = result[3];
|
|
1580
|
+
var start = result[4];
|
|
1581
|
+
var end = result[5];
|
|
1582
|
+
var locstring = "".concat(refName || name, ":").concat(start, "-").concat(end);
|
|
1583
|
+
return new BaseResult({
|
|
1584
|
+
locString: locstring,
|
|
1585
|
+
label: name,
|
|
1586
|
+
matchedAttribute: 'name',
|
|
1587
|
+
matchedObject: result,
|
|
1588
|
+
trackId: tracks[trackIndex]
|
|
1589
|
+
});
|
|
1590
|
+
}))).filter(function (result) {
|
|
1698
1591
|
return result.getLabel() !== 'too many matches';
|
|
1699
1592
|
});
|
|
1700
1593
|
}
|
|
@@ -1711,7 +1604,8 @@ var jbrowse1AdapterConfigSchema = /*#__PURE__*/configuration.ConfigurationSchema
|
|
|
1711
1604
|
namesIndexLocation: {
|
|
1712
1605
|
type: 'fileLocation',
|
|
1713
1606
|
defaultValue: {
|
|
1714
|
-
uri: '/volvox/names'
|
|
1607
|
+
uri: '/volvox/names',
|
|
1608
|
+
locationType: 'UriLocation'
|
|
1715
1609
|
},
|
|
1716
1610
|
description: 'the location of the JBrowse1 names index data directory'
|
|
1717
1611
|
},
|
|
@@ -1720,7 +1614,7 @@ var jbrowse1AdapterConfigSchema = /*#__PURE__*/configuration.ConfigurationSchema
|
|
|
1720
1614
|
defaultValue: [],
|
|
1721
1615
|
description: 'List of tracks covered by text search adapter'
|
|
1722
1616
|
},
|
|
1723
|
-
|
|
1617
|
+
assemblyNames: {
|
|
1724
1618
|
type: 'stringArray',
|
|
1725
1619
|
defaultValue: [],
|
|
1726
1620
|
description: 'List of assemblies covered by text search adapter'
|
|
@@ -1734,7 +1628,8 @@ var jbrowse1ConfigSchema = /*#__PURE__*/configuration.ConfigurationSchema('JBrow
|
|
|
1734
1628
|
dataDirLocation: {
|
|
1735
1629
|
type: 'fileLocation',
|
|
1736
1630
|
defaultValue: {
|
|
1737
|
-
uri: 'http://mysite.com/jbrowse/data/'
|
|
1631
|
+
uri: 'http://mysite.com/jbrowse/data/',
|
|
1632
|
+
locationType: 'UriLocation'
|
|
1738
1633
|
},
|
|
1739
1634
|
description: 'the location of the JBrowse 1 data directory, often something like http://mysite.com/jbrowse/data/'
|
|
1740
1635
|
},
|
|
@@ -1954,10 +1849,10 @@ function parse(text, url) {
|
|
|
1954
1849
|
parsedValue = JSON.parse(match[1]);
|
|
1955
1850
|
} // parse numbers if it looks numeric
|
|
1956
1851
|
else if (/^[+-]?[\d.,]+([eE][-+]?\d+)?$/.test(value)) {
|
|
1957
|
-
|
|
1958
|
-
|
|
1959
|
-
|
|
1960
|
-
|
|
1852
|
+
parsedValue = parseFloat(value.replace(/,/g, ''));
|
|
1853
|
+
} else {
|
|
1854
|
+
parsedValue = value;
|
|
1855
|
+
}
|
|
1961
1856
|
|
|
1962
1857
|
if (!keyPath) {
|
|
1963
1858
|
throw new Error("Error parsing in section ".concat(section.join(' - ')));
|
|
@@ -2013,33 +1908,33 @@ function parse(text, url) {
|
|
|
2013
1908
|
}
|
|
2014
1909
|
} // new value
|
|
2015
1910
|
else if (match = line.match(value === undefined ? /^([^+=]+)(\+?=)(.*)/ : /^(\S[^+=]+)(\+?=)(.*)/)) {
|
|
2016
|
-
|
|
2017
|
-
|
|
2018
|
-
|
|
1911
|
+
recordVal();
|
|
1912
|
+
keyPath = match[1].trim().split(/\s*\.\s*/);
|
|
1913
|
+
var _match = match;
|
|
2019
1914
|
|
|
2020
|
-
|
|
1915
|
+
var _match2 = _slicedToArray(_match, 3);
|
|
2021
1916
|
|
|
2022
|
-
|
|
1917
|
+
operation = _match2[2];
|
|
2023
1918
|
|
|
2024
|
-
|
|
2025
|
-
|
|
2026
|
-
|
|
1919
|
+
if (isAlwaysArray(section.concat(keyPath).join('.'))) {
|
|
1920
|
+
operation = '+=';
|
|
1921
|
+
}
|
|
2027
1922
|
|
|
2028
|
-
|
|
2029
|
-
|
|
2030
|
-
|
|
2031
|
-
|
|
2032
|
-
|
|
2033
|
-
|
|
2034
|
-
|
|
2035
|
-
|
|
2036
|
-
|
|
2037
|
-
|
|
2038
|
-
|
|
2039
|
-
|
|
2040
|
-
|
|
2041
|
-
|
|
2042
|
-
|
|
1923
|
+
value = match[3].trim();
|
|
1924
|
+
} // add to existing array value
|
|
1925
|
+
else if (keyPath !== undefined && (match = line.match(/^\s{0,4}\+\s*(.+)/))) {
|
|
1926
|
+
recordVal();
|
|
1927
|
+
operation = '+=';
|
|
1928
|
+
value = match[1].trim();
|
|
1929
|
+
} // add to existing value
|
|
1930
|
+
else if (value !== undefined && (match = line.match(/^\s+(\S.*)/))) {
|
|
1931
|
+
value += value.length ? " ".concat(match[1].trim()) : match[1].trim();
|
|
1932
|
+
} // done with last value
|
|
1933
|
+
else {
|
|
1934
|
+
recordVal();
|
|
1935
|
+
keyPath = undefined;
|
|
1936
|
+
value = undefined;
|
|
1937
|
+
}
|
|
2043
1938
|
});
|
|
2044
1939
|
recordVal();
|
|
2045
1940
|
return data;
|
|
@@ -2061,23 +1956,23 @@ function regularizeConf(conf, url) {
|
|
|
2061
1956
|
conf.tracks = [conf.tracks];
|
|
2062
1957
|
} // otherwise, coerce it to an array
|
|
2063
1958
|
else {
|
|
2064
|
-
|
|
1959
|
+
var tracks = [];
|
|
2065
1960
|
|
|
2066
|
-
|
|
2067
|
-
|
|
2068
|
-
|
|
1961
|
+
for (var _i = 0, _Object$keys = Object.keys(conf.tracks); _i < _Object$keys.length; _i++) {
|
|
1962
|
+
var label = _Object$keys[_i];
|
|
1963
|
+
var track = conf.tracks[label];
|
|
2069
1964
|
|
|
2070
|
-
|
|
2071
|
-
|
|
2072
|
-
|
|
2073
|
-
|
|
2074
|
-
|
|
2075
|
-
|
|
2076
|
-
}
|
|
1965
|
+
if (isTrack(track)) {
|
|
1966
|
+
tracks.push(track);
|
|
1967
|
+
} else {
|
|
1968
|
+
tracks.push(_objectSpread2({
|
|
1969
|
+
label: label
|
|
1970
|
+
}, track));
|
|
2077
1971
|
}
|
|
2078
|
-
|
|
2079
|
-
conf.tracks = tracks;
|
|
2080
1972
|
}
|
|
1973
|
+
|
|
1974
|
+
conf.tracks = tracks;
|
|
1975
|
+
}
|
|
2081
1976
|
} // regularize trackMetadata.sources
|
|
2082
1977
|
|
|
2083
1978
|
|
|
@@ -2378,13 +2273,15 @@ function _fetchJb() {
|
|
|
2378
2273
|
switch (_context.prev = _context.next) {
|
|
2379
2274
|
case 0:
|
|
2380
2275
|
dataRoot = _args.length > 0 && _args[0] !== undefined ? _args[0] : {
|
|
2381
|
-
uri: ''
|
|
2276
|
+
uri: '',
|
|
2277
|
+
locationType: 'UriLocation'
|
|
2382
2278
|
};
|
|
2383
2279
|
baseConfig = _args.length > 1 && _args[1] !== undefined ? _args[1] : {
|
|
2384
2280
|
include: ['{dataRoot}/trackList.json', '{dataRoot}/tracks.conf']
|
|
2385
2281
|
};
|
|
2386
2282
|
baseConfigRoot = _args.length > 2 && _args[2] !== undefined ? _args[2] : {
|
|
2387
|
-
uri: ''
|
|
2283
|
+
uri: '',
|
|
2284
|
+
locationType: 'UriLocation'
|
|
2388
2285
|
};
|
|
2389
2286
|
protocol = 'uri' in dataRoot ? 'uri' : 'localPath';
|
|
2390
2287
|
dataRootReg = JSON.parse(JSON.stringify(dataRoot));
|
|
@@ -2707,7 +2604,8 @@ function _loadIncludes() {
|
|
|
2707
2604
|
include.cacheBuster = inputConfig.cacheBuster;
|
|
2708
2605
|
_context4.next = 3;
|
|
2709
2606
|
return fetchConfigFile({
|
|
2710
|
-
uri: new URL(include.url, sourceUrl).href
|
|
2607
|
+
uri: new URL(include.url, sourceUrl).href,
|
|
2608
|
+
locationType: 'UriLocation'
|
|
2711
2609
|
});
|
|
2712
2610
|
|
|
2713
2611
|
case 3:
|
|
@@ -2913,27 +2811,31 @@ function convertTrackConfig(jb1TrackConfig, dataRoot, sequenceAdapter) {
|
|
|
2913
2811
|
var adapter = {
|
|
2914
2812
|
type: 'BamAdapter',
|
|
2915
2813
|
bamLocation: {
|
|
2916
|
-
uri: urlTemplate
|
|
2814
|
+
uri: urlTemplate,
|
|
2815
|
+
locationType: 'UriLocation'
|
|
2917
2816
|
}
|
|
2918
2817
|
};
|
|
2919
2818
|
|
|
2920
2819
|
if (jb1TrackConfig.baiUrlTemplate) {
|
|
2921
2820
|
adapter.index = {
|
|
2922
2821
|
location: {
|
|
2923
|
-
uri: resolveUrlTemplate(jb1TrackConfig.baiUrlTemplate)
|
|
2822
|
+
uri: resolveUrlTemplate(jb1TrackConfig.baiUrlTemplate),
|
|
2823
|
+
locationType: 'UriLocation'
|
|
2924
2824
|
}
|
|
2925
2825
|
};
|
|
2926
2826
|
} else if (jb1TrackConfig.csiUrlTemplate) {
|
|
2927
2827
|
adapter.index = {
|
|
2928
2828
|
location: {
|
|
2929
|
-
uri: resolveUrlTemplate(jb1TrackConfig.csiUrlTemplate)
|
|
2829
|
+
uri: resolveUrlTemplate(jb1TrackConfig.csiUrlTemplate),
|
|
2830
|
+
locationType: 'UriLocation'
|
|
2930
2831
|
},
|
|
2931
2832
|
indexType: 'CSI'
|
|
2932
2833
|
};
|
|
2933
2834
|
} else {
|
|
2934
2835
|
adapter.index = {
|
|
2935
2836
|
location: {
|
|
2936
|
-
uri: "".concat(urlTemplate, ".bai")
|
|
2837
|
+
uri: "".concat(urlTemplate, ".bai"),
|
|
2838
|
+
locationType: 'UriLocation'
|
|
2937
2839
|
}
|
|
2938
2840
|
};
|
|
2939
2841
|
}
|
|
@@ -2948,18 +2850,21 @@ function convertTrackConfig(jb1TrackConfig, dataRoot, sequenceAdapter) {
|
|
|
2948
2850
|
var _adapter = {
|
|
2949
2851
|
type: 'CramAdapter',
|
|
2950
2852
|
cramLocation: {
|
|
2951
|
-
uri: urlTemplate
|
|
2853
|
+
uri: urlTemplate,
|
|
2854
|
+
locationType: 'UriLocation'
|
|
2952
2855
|
},
|
|
2953
2856
|
sequenceAdapter: sequenceAdapter
|
|
2954
2857
|
};
|
|
2955
2858
|
|
|
2956
2859
|
if (jb1TrackConfig.craiUrlTemplate) {
|
|
2957
2860
|
_adapter.craiLocation = {
|
|
2958
|
-
uri: resolveUrlTemplate(jb1TrackConfig.craiUrlTemplate)
|
|
2861
|
+
uri: resolveUrlTemplate(jb1TrackConfig.craiUrlTemplate),
|
|
2862
|
+
locationType: 'UriLocation'
|
|
2959
2863
|
};
|
|
2960
2864
|
} else {
|
|
2961
2865
|
_adapter.craiLocation = {
|
|
2962
|
-
uri: "".concat(urlTemplate, ".crai")
|
|
2866
|
+
uri: "".concat(urlTemplate, ".crai"),
|
|
2867
|
+
locationType: 'UriLocation'
|
|
2963
2868
|
};
|
|
2964
2869
|
}
|
|
2965
2870
|
|
|
@@ -2975,7 +2880,8 @@ function convertTrackConfig(jb1TrackConfig, dataRoot, sequenceAdapter) {
|
|
|
2975
2880
|
adapter: {
|
|
2976
2881
|
type: 'NCListAdapter',
|
|
2977
2882
|
rootUrlTemplate: {
|
|
2978
|
-
uri: urlTemplate
|
|
2883
|
+
uri: urlTemplate,
|
|
2884
|
+
locationType: 'UriLocation'
|
|
2979
2885
|
}
|
|
2980
2886
|
}
|
|
2981
2887
|
});
|
|
@@ -2993,7 +2899,8 @@ function convertTrackConfig(jb1TrackConfig, dataRoot, sequenceAdapter) {
|
|
|
2993
2899
|
adapter: {
|
|
2994
2900
|
type: 'BigWigAdapter',
|
|
2995
2901
|
bigWigLocation: {
|
|
2996
|
-
uri: urlTemplate
|
|
2902
|
+
uri: urlTemplate,
|
|
2903
|
+
locationType: 'UriLocation'
|
|
2997
2904
|
}
|
|
2998
2905
|
}
|
|
2999
2906
|
});
|
|
@@ -3003,27 +2910,31 @@ function convertTrackConfig(jb1TrackConfig, dataRoot, sequenceAdapter) {
|
|
|
3003
2910
|
var _adapter2 = {
|
|
3004
2911
|
type: 'VcfTabixAdapter',
|
|
3005
2912
|
vcfGzLocation: {
|
|
3006
|
-
uri: urlTemplate
|
|
2913
|
+
uri: urlTemplate,
|
|
2914
|
+
locationType: 'UriLocation'
|
|
3007
2915
|
}
|
|
3008
2916
|
};
|
|
3009
2917
|
|
|
3010
2918
|
if (jb1TrackConfig.tbiUrlTemplate) {
|
|
3011
2919
|
_adapter2.index = {
|
|
3012
2920
|
location: {
|
|
3013
|
-
uri: resolveUrlTemplate(jb1TrackConfig.tbiUrlTemplate)
|
|
2921
|
+
uri: resolveUrlTemplate(jb1TrackConfig.tbiUrlTemplate),
|
|
2922
|
+
locationType: 'UriLocation'
|
|
3014
2923
|
}
|
|
3015
2924
|
};
|
|
3016
2925
|
} else if (jb1TrackConfig.csiUrlTemplate) {
|
|
3017
2926
|
_adapter2.index = {
|
|
3018
2927
|
location: {
|
|
3019
|
-
uri: resolveUrlTemplate(jb1TrackConfig.csiUrlTemplate)
|
|
2928
|
+
uri: resolveUrlTemplate(jb1TrackConfig.csiUrlTemplate),
|
|
2929
|
+
locationType: 'UriLocation'
|
|
3020
2930
|
},
|
|
3021
2931
|
indexType: 'CSI'
|
|
3022
2932
|
};
|
|
3023
2933
|
} else {
|
|
3024
2934
|
_adapter2.index = {
|
|
3025
2935
|
location: {
|
|
3026
|
-
uri: "".concat(urlTemplate, ".tbi")
|
|
2936
|
+
uri: "".concat(urlTemplate, ".tbi"),
|
|
2937
|
+
locationType: 'UriLocation'
|
|
3027
2938
|
}
|
|
3028
2939
|
};
|
|
3029
2940
|
}
|
|
@@ -3048,7 +2959,8 @@ function convertTrackConfig(jb1TrackConfig, dataRoot, sequenceAdapter) {
|
|
|
3048
2959
|
adapter: {
|
|
3049
2960
|
type: 'BigBedAdapter',
|
|
3050
2961
|
bigBedLocation: {
|
|
3051
|
-
uri: urlTemplate
|
|
2962
|
+
uri: urlTemplate,
|
|
2963
|
+
locationType: 'UriLocation'
|
|
3052
2964
|
}
|
|
3053
2965
|
}
|
|
3054
2966
|
});
|
|
@@ -3058,27 +2970,31 @@ function convertTrackConfig(jb1TrackConfig, dataRoot, sequenceAdapter) {
|
|
|
3058
2970
|
var _adapter3 = {
|
|
3059
2971
|
type: 'Gff3TabixAdapter',
|
|
3060
2972
|
gffGzLocation: {
|
|
3061
|
-
uri: urlTemplate
|
|
2973
|
+
uri: urlTemplate,
|
|
2974
|
+
locationType: 'UriLocation'
|
|
3062
2975
|
}
|
|
3063
2976
|
};
|
|
3064
2977
|
|
|
3065
2978
|
if (jb1TrackConfig.tbiUrlTemplate) {
|
|
3066
2979
|
_adapter3.index = {
|
|
3067
2980
|
location: {
|
|
3068
|
-
uri: resolveUrlTemplate(jb1TrackConfig.tbiUrlTemplate)
|
|
2981
|
+
uri: resolveUrlTemplate(jb1TrackConfig.tbiUrlTemplate),
|
|
2982
|
+
locationType: 'UriLocation'
|
|
3069
2983
|
}
|
|
3070
2984
|
};
|
|
3071
2985
|
} else if (jb1TrackConfig.csiUrlTemplate) {
|
|
3072
2986
|
_adapter3.index = {
|
|
3073
2987
|
location: {
|
|
3074
|
-
uri: resolveUrlTemplate(jb1TrackConfig.csiUrlTemplate)
|
|
2988
|
+
uri: resolveUrlTemplate(jb1TrackConfig.csiUrlTemplate),
|
|
2989
|
+
locationType: 'UriLocation'
|
|
3075
2990
|
},
|
|
3076
2991
|
indexType: 'CSI'
|
|
3077
2992
|
};
|
|
3078
2993
|
} else {
|
|
3079
2994
|
_adapter3.index = {
|
|
3080
2995
|
location: {
|
|
3081
|
-
uri: "".concat(urlTemplate, ".tbi")
|
|
2996
|
+
uri: "".concat(urlTemplate, ".tbi"),
|
|
2997
|
+
locationType: 'UriLocation'
|
|
3082
2998
|
}
|
|
3083
2999
|
};
|
|
3084
3000
|
}
|
|
@@ -3097,27 +3013,31 @@ function convertTrackConfig(jb1TrackConfig, dataRoot, sequenceAdapter) {
|
|
|
3097
3013
|
var _adapter4 = {
|
|
3098
3014
|
type: 'BedTabixAdapter',
|
|
3099
3015
|
bedGzLocation: {
|
|
3100
|
-
uri: urlTemplate
|
|
3016
|
+
uri: urlTemplate,
|
|
3017
|
+
locationType: 'UriLocation'
|
|
3101
3018
|
}
|
|
3102
3019
|
};
|
|
3103
3020
|
|
|
3104
3021
|
if (jb1TrackConfig.tbiUrlTemplate) {
|
|
3105
3022
|
_adapter4.index = {
|
|
3106
3023
|
location: {
|
|
3107
|
-
uri: resolveUrlTemplate(jb1TrackConfig.tbiUrlTemplate)
|
|
3024
|
+
uri: resolveUrlTemplate(jb1TrackConfig.tbiUrlTemplate),
|
|
3025
|
+
locationType: 'UriLocation'
|
|
3108
3026
|
}
|
|
3109
3027
|
};
|
|
3110
3028
|
} else if (jb1TrackConfig.csiUrlTemplate) {
|
|
3111
3029
|
_adapter4.index = {
|
|
3112
3030
|
location: {
|
|
3113
|
-
uri: resolveUrlTemplate(jb1TrackConfig.csiUrlTemplate)
|
|
3031
|
+
uri: resolveUrlTemplate(jb1TrackConfig.csiUrlTemplate),
|
|
3032
|
+
locationType: 'UriLocation'
|
|
3114
3033
|
},
|
|
3115
3034
|
indexType: 'CSI'
|
|
3116
3035
|
};
|
|
3117
3036
|
} else {
|
|
3118
3037
|
_adapter4.index = {
|
|
3119
3038
|
location: {
|
|
3120
|
-
uri: "".concat(urlTemplate, ".tbi")
|
|
3039
|
+
uri: "".concat(urlTemplate, ".tbi"),
|
|
3040
|
+
locationType: 'UriLocation'
|
|
3121
3041
|
}
|
|
3122
3042
|
};
|
|
3123
3043
|
}
|
|
@@ -3144,17 +3064,20 @@ function convertTrackConfig(jb1TrackConfig, dataRoot, sequenceAdapter) {
|
|
|
3144
3064
|
var _adapter5 = {
|
|
3145
3065
|
type: 'IndexedFastaAdapter',
|
|
3146
3066
|
fastaLocation: {
|
|
3147
|
-
uri: urlTemplate
|
|
3067
|
+
uri: urlTemplate,
|
|
3068
|
+
locationType: 'UriLocation'
|
|
3148
3069
|
}
|
|
3149
3070
|
};
|
|
3150
3071
|
|
|
3151
3072
|
if (jb1TrackConfig.faiUrlTemplate) {
|
|
3152
3073
|
_adapter5.faiLocation = {
|
|
3153
|
-
uri: resolveUrlTemplate(jb1TrackConfig.faiUrlTemplate)
|
|
3074
|
+
uri: resolveUrlTemplate(jb1TrackConfig.faiUrlTemplate),
|
|
3075
|
+
locationType: 'UriLocation'
|
|
3154
3076
|
};
|
|
3155
3077
|
} else {
|
|
3156
3078
|
_adapter5.faiLocation = {
|
|
3157
|
-
uri: "".concat(urlTemplate, ".fai")
|
|
3079
|
+
uri: "".concat(urlTemplate, ".fai"),
|
|
3080
|
+
locationType: 'UriLocation'
|
|
3158
3081
|
};
|
|
3159
3082
|
}
|
|
3160
3083
|
|
|
@@ -3168,27 +3091,32 @@ function convertTrackConfig(jb1TrackConfig, dataRoot, sequenceAdapter) {
|
|
|
3168
3091
|
var _adapter6 = {
|
|
3169
3092
|
type: 'BgzipFastaAdapter',
|
|
3170
3093
|
fastaLocation: {
|
|
3171
|
-
uri: urlTemplate
|
|
3094
|
+
uri: urlTemplate,
|
|
3095
|
+
locationType: 'UriLocation'
|
|
3172
3096
|
}
|
|
3173
3097
|
};
|
|
3174
3098
|
|
|
3175
3099
|
if (jb1TrackConfig.faiUrlTemplate) {
|
|
3176
3100
|
_adapter6.faiLocation = {
|
|
3177
|
-
uri: resolveUrlTemplate(jb1TrackConfig.faiUrlTemplate)
|
|
3101
|
+
uri: resolveUrlTemplate(jb1TrackConfig.faiUrlTemplate),
|
|
3102
|
+
locationType: 'UriLocation'
|
|
3178
3103
|
};
|
|
3179
3104
|
} else {
|
|
3180
3105
|
_adapter6.faiLocation = {
|
|
3181
|
-
uri: "".concat(urlTemplate, ".fai")
|
|
3106
|
+
uri: "".concat(urlTemplate, ".fai"),
|
|
3107
|
+
locationType: 'UriLocation'
|
|
3182
3108
|
};
|
|
3183
3109
|
}
|
|
3184
3110
|
|
|
3185
3111
|
if (jb1TrackConfig.gziUrlTemplate) {
|
|
3186
3112
|
_adapter6.gziLocation = {
|
|
3187
|
-
uri: resolveUrlTemplate(jb1TrackConfig.gziUrlTemplate)
|
|
3113
|
+
uri: resolveUrlTemplate(jb1TrackConfig.gziUrlTemplate),
|
|
3114
|
+
locationType: 'UriLocation'
|
|
3188
3115
|
};
|
|
3189
3116
|
} else {
|
|
3190
3117
|
_adapter6.gziLocation = {
|
|
3191
|
-
uri: "".concat(urlTemplate, ".gzi")
|
|
3118
|
+
uri: "".concat(urlTemplate, ".gzi"),
|
|
3119
|
+
locationType: 'UriLocation'
|
|
3192
3120
|
};
|
|
3193
3121
|
}
|
|
3194
3122
|
|
|
@@ -3204,7 +3132,8 @@ function convertTrackConfig(jb1TrackConfig, dataRoot, sequenceAdapter) {
|
|
|
3204
3132
|
adapter: {
|
|
3205
3133
|
type: 'TwoBitAdapter',
|
|
3206
3134
|
twoBitLocation: {
|
|
3207
|
-
uri: urlTemplate
|
|
3135
|
+
uri: urlTemplate,
|
|
3136
|
+
locationType: 'UriLocation'
|
|
3208
3137
|
}
|
|
3209
3138
|
}
|
|
3210
3139
|
});
|
|
@@ -3213,10 +3142,9 @@ function convertTrackConfig(jb1TrackConfig, dataRoot, sequenceAdapter) {
|
|
|
3213
3142
|
|
|
3214
3143
|
|
|
3215
3144
|
jb2TrackConfig.adapter = tracks.guessAdapter({
|
|
3216
|
-
uri: urlTemplate
|
|
3217
|
-
|
|
3218
|
-
|
|
3219
|
-
});
|
|
3145
|
+
uri: urlTemplate,
|
|
3146
|
+
locationType: 'UriLocation'
|
|
3147
|
+
}, undefined, urlTemplate);
|
|
3220
3148
|
|
|
3221
3149
|
if (!jb2TrackConfig.adapter) {
|
|
3222
3150
|
throw new Error('Could not determine adapter');
|
|
@@ -3324,6 +3252,22 @@ var LegacyJBrowsePlugin = /*#__PURE__*/function (_Plugin) {
|
|
|
3324
3252
|
}
|
|
3325
3253
|
});
|
|
3326
3254
|
});
|
|
3255
|
+
pluginManager.addToExtensionPoint('Core-guessAdapterForLocation', function (adapterGuesser) {
|
|
3256
|
+
return function (file, index, adapterHint) {
|
|
3257
|
+
var regexGuess = /trackData.jsonz?$/i;
|
|
3258
|
+
var adapterName = 'NCListAdapter';
|
|
3259
|
+
var fileName = tracks.getFileName(file);
|
|
3260
|
+
|
|
3261
|
+
if (regexGuess.test(fileName) || adapterHint === adapterName) {
|
|
3262
|
+
return {
|
|
3263
|
+
type: adapterName,
|
|
3264
|
+
rootUrlTemplate: file
|
|
3265
|
+
};
|
|
3266
|
+
}
|
|
3267
|
+
|
|
3268
|
+
return adapterGuesser(file, index, adapterHint);
|
|
3269
|
+
};
|
|
3270
|
+
});
|
|
3327
3271
|
pluginManager.addTextSearchAdapterType(function () {
|
|
3328
3272
|
return new TextSearchAdapterType({
|
|
3329
3273
|
name: 'JBrowse1TextSearchAdapter',
|
|
@@ -3479,12 +3423,12 @@ var NCListAdapter = /*#__PURE__*/function (_BaseFeatureDataAdapt) {
|
|
|
3479
3423
|
|
|
3480
3424
|
var _super = /*#__PURE__*/_createSuper(NCListAdapter);
|
|
3481
3425
|
|
|
3482
|
-
function NCListAdapter(config) {
|
|
3426
|
+
function NCListAdapter(config, getSubAdapter, pluginManager) {
|
|
3483
3427
|
var _this;
|
|
3484
3428
|
|
|
3485
3429
|
_classCallCheck(this, NCListAdapter);
|
|
3486
3430
|
|
|
3487
|
-
_this = _super.call(this, config);
|
|
3431
|
+
_this = _super.call(this, config, getSubAdapter, pluginManager);
|
|
3488
3432
|
var refNames = configuration.readConfObject(config, 'refNames');
|
|
3489
3433
|
var rootUrlTemplate = configuration.readConfObject(config, 'rootUrlTemplate');
|
|
3490
3434
|
_this.configRefNames = refNames;
|
|
@@ -3492,7 +3436,7 @@ var NCListAdapter = /*#__PURE__*/function (_BaseFeatureDataAdapt) {
|
|
|
3492
3436
|
baseUrl: '',
|
|
3493
3437
|
urlTemplate: rootUrlTemplate.uri,
|
|
3494
3438
|
readFile: function readFile(url) {
|
|
3495
|
-
return
|
|
3439
|
+
return new genericFilehandle.RemoteFile(String(rootUrlTemplate.baseUri ? new URL(url, rootUrlTemplate.baseUri).toString() : url)).readFile();
|
|
3496
3440
|
}
|
|
3497
3441
|
});
|
|
3498
3442
|
return _this;
|
|
@@ -3515,14 +3459,14 @@ var NCListAdapter = /*#__PURE__*/function (_BaseFeatureDataAdapt) {
|
|
|
3515
3459
|
var opts = arguments.length > 1 && arguments[1] !== undefined ? arguments[1] : {};
|
|
3516
3460
|
return rxjs.ObservableCreate( /*#__PURE__*/function () {
|
|
3517
3461
|
var _ref = _asyncToGenerator( /*#__PURE__*/runtime_1.mark(function _callee(observer) {
|
|
3518
|
-
var signal,
|
|
3462
|
+
var signal, _iteratorAbruptCompletion, _didIteratorError, _iteratorError, _iterator, _step, feature;
|
|
3519
3463
|
|
|
3520
3464
|
return runtime_1.wrap(function _callee$(_context) {
|
|
3521
3465
|
while (1) {
|
|
3522
3466
|
switch (_context.prev = _context.next) {
|
|
3523
3467
|
case 0:
|
|
3524
3468
|
signal = opts.signal;
|
|
3525
|
-
|
|
3469
|
+
_iteratorAbruptCompletion = false;
|
|
3526
3470
|
_didIteratorError = false;
|
|
3527
3471
|
_context.prev = 3;
|
|
3528
3472
|
_iterator = _asyncIterator(_this2.nclist.getFeatures(region, opts));
|
|
@@ -3532,75 +3476,67 @@ var NCListAdapter = /*#__PURE__*/function (_BaseFeatureDataAdapt) {
|
|
|
3532
3476
|
return _iterator.next();
|
|
3533
3477
|
|
|
3534
3478
|
case 7:
|
|
3535
|
-
_step = _context.sent
|
|
3536
|
-
|
|
3537
|
-
_context.next = 11;
|
|
3538
|
-
return _step.value;
|
|
3539
|
-
|
|
3540
|
-
case 11:
|
|
3541
|
-
_value = _context.sent;
|
|
3542
|
-
|
|
3543
|
-
if (_iteratorNormalCompletion) {
|
|
3544
|
-
_context.next = 19;
|
|
3479
|
+
if (!(_iteratorAbruptCompletion = !(_step = _context.sent).done)) {
|
|
3480
|
+
_context.next = 14;
|
|
3545
3481
|
break;
|
|
3546
3482
|
}
|
|
3547
3483
|
|
|
3548
|
-
feature =
|
|
3484
|
+
feature = _step.value;
|
|
3549
3485
|
util.checkAbortSignal(signal);
|
|
3550
3486
|
observer.next(_this2.wrapFeature(feature));
|
|
3551
3487
|
|
|
3552
|
-
case
|
|
3553
|
-
|
|
3488
|
+
case 11:
|
|
3489
|
+
_iteratorAbruptCompletion = false;
|
|
3554
3490
|
_context.next = 5;
|
|
3555
3491
|
break;
|
|
3556
3492
|
|
|
3557
|
-
case
|
|
3558
|
-
_context.next =
|
|
3493
|
+
case 14:
|
|
3494
|
+
_context.next = 20;
|
|
3559
3495
|
break;
|
|
3560
3496
|
|
|
3561
|
-
case
|
|
3562
|
-
_context.prev =
|
|
3497
|
+
case 16:
|
|
3498
|
+
_context.prev = 16;
|
|
3563
3499
|
_context.t0 = _context["catch"](3);
|
|
3564
3500
|
_didIteratorError = true;
|
|
3565
3501
|
_iteratorError = _context.t0;
|
|
3566
3502
|
|
|
3567
|
-
case
|
|
3568
|
-
_context.prev =
|
|
3569
|
-
_context.prev =
|
|
3503
|
+
case 20:
|
|
3504
|
+
_context.prev = 20;
|
|
3505
|
+
_context.prev = 21;
|
|
3570
3506
|
|
|
3571
|
-
if (!(
|
|
3572
|
-
_context.next =
|
|
3507
|
+
if (!(_iteratorAbruptCompletion && _iterator["return"] != null)) {
|
|
3508
|
+
_context.next = 25;
|
|
3573
3509
|
break;
|
|
3574
3510
|
}
|
|
3575
3511
|
|
|
3576
|
-
_context.next =
|
|
3512
|
+
_context.next = 25;
|
|
3577
3513
|
return _iterator["return"]();
|
|
3578
3514
|
|
|
3579
|
-
case
|
|
3580
|
-
_context.prev =
|
|
3515
|
+
case 25:
|
|
3516
|
+
_context.prev = 25;
|
|
3581
3517
|
|
|
3582
3518
|
if (!_didIteratorError) {
|
|
3583
|
-
_context.next =
|
|
3519
|
+
_context.next = 28;
|
|
3584
3520
|
break;
|
|
3585
3521
|
}
|
|
3586
3522
|
|
|
3587
3523
|
throw _iteratorError;
|
|
3588
3524
|
|
|
3589
|
-
case
|
|
3590
|
-
return _context.finish(30);
|
|
3591
|
-
|
|
3592
|
-
case 34:
|
|
3525
|
+
case 28:
|
|
3593
3526
|
return _context.finish(25);
|
|
3594
3527
|
|
|
3595
|
-
case
|
|
3528
|
+
case 29:
|
|
3529
|
+
return _context.finish(20);
|
|
3530
|
+
|
|
3531
|
+
case 30:
|
|
3596
3532
|
observer.complete();
|
|
3597
3533
|
|
|
3598
|
-
case
|
|
3534
|
+
case 31:
|
|
3599
3535
|
case "end":
|
|
3600
3536
|
return _context.stop();
|
|
3601
3537
|
}
|
|
3602
3538
|
}
|
|
3603
|
-
}, _callee, null, [[3,
|
|
3539
|
+
}, _callee, null, [[3, 16, 20, 30], [21,, 25, 29]]);
|
|
3604
3540
|
}));
|
|
3605
3541
|
|
|
3606
3542
|
return function (_x) {
|