@jbrowse/plugin-legacy-jbrowse 2.1.0 → 2.1.2
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/configSchema.js +2 -2
- package/dist/JBrowse1Connection/configSchema.js.map +1 -1
- package/dist/JBrowse1Connection/jb1ConfigLoad.js +132 -285
- package/dist/JBrowse1Connection/jb1ConfigLoad.js.map +1 -1
- package/dist/JBrowse1Connection/jb1ConfigParse.js +58 -127
- package/dist/JBrowse1Connection/jb1ConfigParse.js.map +1 -1
- package/dist/JBrowse1Connection/jb1ToJb2.js +155 -159
- package/dist/JBrowse1Connection/jb1ToJb2.js.map +1 -1
- package/dist/JBrowse1Connection/model.js +20 -20
- package/dist/JBrowse1Connection/model.js.map +1 -1
- package/dist/JBrowse1Connection/util.js +18 -41
- package/dist/JBrowse1Connection/util.js.map +1 -1
- package/dist/JBrowse1TextSeachAdapter/HttpMap.js +58 -168
- package/dist/JBrowse1TextSeachAdapter/HttpMap.js.map +1 -1
- package/dist/JBrowse1TextSeachAdapter/JBrowse1TextSearchAdapter.js +48 -145
- package/dist/JBrowse1TextSeachAdapter/JBrowse1TextSearchAdapter.js.map +1 -1
- package/dist/JBrowse1TextSeachAdapter/configSchema.js +1 -1
- package/dist/JBrowse1TextSeachAdapter/configSchema.js.map +1 -1
- package/dist/NCListAdapter/NCListAdapter.js +38 -147
- package/dist/NCListAdapter/NCListAdapter.js.map +1 -1
- package/dist/NCListAdapter/NCListFeature.js +35 -39
- package/dist/NCListAdapter/NCListFeature.js.map +1 -1
- package/dist/NCListAdapter/configSchema.js +1 -1
- package/dist/NCListAdapter/configSchema.js.map +1 -1
- package/dist/index.js +39 -65
- package/dist/index.js.map +1 -1
- package/package.json +2 -3
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// eslint-disable-next-line @typescript-eslint/no-explicit-any
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function isTrack(arg) {
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* e.g., 'htp://foo/someurl?arg=valueforbaz'
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const empty = {};
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// the (!(name in empty) || empty[name] !== s) condition avoids copying
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// properties in "source" inherited from Object.prototype. For example,
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{"version":3,"file":"util.js","sourceRoot":"","sources":["../../src/JBrowse1Connection/util.ts"],"names":[],"mappings":"
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{"version":3,"file":"util.js","sourceRoot":"","sources":["../../src/JBrowse1Connection/util.ts"],"names":[],"mappings":";;;;;;AAAA,0DAAgC;AAGhC,8DAA8D;AAC9D,SAAgB,OAAO,CAAC,GAAQ;IAC9B,OAAO,GAAG,IAAI,GAAG,CAAC,KAAK,IAAI,OAAO,GAAG,CAAC,KAAK,KAAK,QAAQ,CAAA;AAC1D,CAAC;AAFD,0BAEC;AAED,8DAA8D;AAC9D,SAAgB,QAAQ,CAAC,GAAQ;IAC/B,OAAO,GAAG,IAAI,GAAG,CAAC,GAAG,IAAI,OAAO,GAAG,CAAC,GAAG,KAAK,QAAQ,CAAA;AACtD,CAAC;AAFD,4BAEC;AAOD,SAAgB,UAAU,CAAC,CAAM,EAAE,CAAM;IACvC,KAAK,MAAM,IAAI,IAAI,MAAM,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE;QACjC,IACE,IAAI,IAAI,CAAC;YACT,OAAO,CAAC,CAAC,IAAI,CAAC,KAAK,QAAQ;YAC3B,OAAO,CAAC,CAAC,IAAI,CAAC,KAAK,QAAQ,EAC3B;YACA,UAAU,CAAC,CAAC,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC,IAAI,CAAC,CAAC,CAAA;SAC7B;aAAM,IACL,OAAO,CAAC,CAAC,IAAI,CAAC,KAAK,WAAW;YAC9B,OAAO,CAAC,CAAC,IAAI,CAAC,KAAK,WAAW,EAC9B;YACA,CAAC,CAAC,IAAI,CAAC,GAAG,CAAC,CAAC,IAAI,CAAC,CAAA;SAClB;KACF;IACD,OAAO,CAAC,CAAA;AACV,CAAC;AAhBD,gCAgBC;AAED;;;;;;;;GAQG;AACH,SAAgB,YAAY,CAAC,QAAgB,EAAE,QAAa;IAC1D,OAAO,QAAQ,CAAC,OAAO,CACrB,iBAAiB,EACjB,CAAC,KAAK,EAAE,OAAe,EAAU,EAAE;QACjC,OAAO,GAAG,OAAO,CAAC,OAAO,CAAC,MAAM,EAAE,EAAE,CAAC,CAAA,CAAC,wBAAwB;QAC9D,MAAM,IAAI,GAAG,IAAA,mBAAQ,EAAC,QAAQ,EAAE,OAAO,CAAC,CAAA;QACxC,IAAI,IAAI,KAAK,SAAS,EAAE;YACtB,IAAI,OAAO,IAAI,KAAK,UAAU,EAAE;gBAC9B,OAAO,IAAI,CAAC,OAAO,CAAC,CAAA;aACrB;YACD,OAAO,IAAI,CAAA;SACZ;QACD,IAAI,QAAQ,CAAC,QAAQ,EAAE;YACrB,aAAa;YACb,MAAM,CAAC,GAAG,QAAQ,CAAC,QAAQ,CAAC,IAAI,CAAC,IAAI,EAAE,OAAO,CAAC,CAAA;YAC/C,IAAI,CAAC,KAAK,SAAS,EAAE;gBACnB,OAAO,CAAC,CAAA;aACT;SACF;QACD,OAAO,KAAK,CAAA;IACd,CAAC,CACF,CAAA;AACH,CAAC;AAtBD,oCAsBC;AAED;;;;;GAKG;AACH,8DAA8D;AAC9D,SAAgB,KAAK,CAAC,GAAQ;IAC5B,IACE,CAAC,GAAG;QACJ,OAAO,GAAG,KAAK,QAAQ;QACvB,MAAM,CAAC,SAAS,CAAC,QAAQ,CAAC,IAAI,CAAC,GAAG,CAAC,KAAK,mBAAmB,EAC3D;QACA,+CAA+C;QAC/C,OAAO,GAAG,CAAA,CAAC,WAAW;KACvB;IACD,IAAI,GAAG,CAAC,QAAQ,IAAI,WAAW,IAAI,GAAG,EAAE;QACtC,WAAW;QACX,OAAO,GAAG,CAAC,SAAS,CAAC,IAAI,CAAC,CAAA,CAAC,OAAO;KACnC;IACD,IAAI,GAAG,YAAY,IAAI,EAAE;QACvB,OAAO;QACP,OAAO,IAAI,IAAI,CAAC,GAAG,CAAC,OAAO,EAAE,CAAC,CAAA,CAAC,OAAO;KACvC;IACD,IAAI,GAAG,YAAY,MAAM,EAAE;QACzB,SAAS;QACT,OAAO,IAAI,MAAM,CAAC,GAAG,CAAC,CAAA,CAAC,SAAS;KACjC;IACD,IAAI,CAAC,CAAA;IACL,IAAI,CAAC,CAAA;IACL,IAAI,CAAC,CAAA;IACL,IAAI,KAAK,CAAC,OAAO,CAAC,GAAG,CAAC,EAAE;QACtB,QAAQ;QACR,CAAC,GAAG,EAAE,CAAA;QACN,KAAK,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,GAAG,CAAC,MAAM,EAAE,CAAC,GAAG,CAAC,EAAE,EAAE,CAAC,EAAE;YACtC,IAAI,CAAC,IAAI,GAAG,EAAE;gBACZ,CAAC,CAAC,CAAC,CAAC,GAAG,KAAK,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,CAAA;aACrB;SACF;QACD,mDAAmD;QACnD,kCAAkC;QAClC,mBAAmB;QACnB,6DAA6D;KAC9D;SAAM;QACL,kBAAkB;QAClB,CAAC,GAAG,GAAG,CAAC,WAAW,CAAC,CAAC,CAAC,IAAI,GAAG,CAAC,WAAW,EAAE,CAAC,CAAC,CAAC,EAAE,CAAA;KACjD;IACD,OAAO,KAAK,CAAC,CAAC,EAAE,GAAG,EAAE,KAAK,CAAC,CAAA;AAC7B,CAAC;AAzCD,sBAyCC;AAED;;;;;;;;;;;;;;;;GAgBG;AACH,SAAS,KAAK,CAAC,IAAS,EAAE,MAAW,EAAE,QAAkB;IACvD,IAAI,IAAI,CAAA;IACR,IAAI,CAAC,CAAA;IACL,MAAM,KAAK,GAAG,EAAE,CAAA;IAChB,KAAK,IAAI,IAAI,MAAM,EAAE;QACnB,uEAAuE;QACvE,wEAAwE;QACxE,sEAAsE;QACtE,gEAAgE;QAChE,CAAC,GAAG,MAAM,CAAC,IAAI,CAAC,CAAA;QAChB,IACE,CAAC,CAAC,IAAI,IAAI,IAAI,CAAC;YACf,aAAa;YACb,CAAC,IAAI,CAAC,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,CAAC,CAAC,IAAI,IAAI,KAAK,CAAC,IAAI,KAAK,CAAC,IAAI,CAAC,KAAK,CAAC,CAAC,CAAC,EAC7D;YACA,IAAI,CAAC,IAAI,CAAC,GAAG,QAAQ,CAAC,CAAC,CAAC,QAAQ,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAA;SACxC;KACF;IAED,OAAO,IAAI,CAAA,CAAC,SAAS;AACvB,CAAC"}
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return __awaiter(this, void 0, void 0, function () {
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HttpMap.prototype.getTrackNames = function () {
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|
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|
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|
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|
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|
|
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|
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|
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|
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|
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|
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|
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|
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async getTrackNames() {
|
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|
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|
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|
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|
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|
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|
|
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|
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|
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|
-
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|
|
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|
+
async getBucket(key) {
|
|
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|
+
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|
|
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|
+
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|
|
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|
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return this.loadFile(hexToDirPath);
|
|
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|
+
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|
|
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54
|
/**
|
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55
|
* Loads a file using the url and provided id.
|
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56
|
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|
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|
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|
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|
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|
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|
-
throw new Error("HTTP ".concat(response.status, " ").concat(response.statusText));
|
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|
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|
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|
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|
|
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|
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|
|
59
|
+
async loadFile(id) {
|
|
60
|
+
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|
|
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|
+
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|
|
62
|
+
throw new Error(`HTTP ${response.status} ${response.statusText}`);
|
|
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|
+
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|
|
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|
+
return response.json();
|
|
65
|
+
}
|
|
166
66
|
/**
|
|
167
67
|
* Returns the corresponding path of the file given a hex string
|
|
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68
|
* @param hex - hex string
|
|
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69
|
*/
|
|
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|
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|
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|
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|
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|
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|
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|
|
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|
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|
|
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|
-
dirpath.push(hex.substring(i, i + 3));
|
|
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|
-
}
|
|
190
|
-
return [2 /*return*/, "".concat(dirpath.join('/'), ".json").concat(compress ? 'z' : '')];
|
|
191
|
-
case 3: return [2 /*return*/, ''];
|
|
192
|
-
}
|
|
193
|
-
});
|
|
194
|
-
});
|
|
195
|
-
};
|
|
196
|
-
HttpMap.prototype.hash = function (data) {
|
|
70
|
+
async hexToDirPath(hex) {
|
|
71
|
+
// zero-pad the hex string to be 8 chars if necessary
|
|
72
|
+
const hashHexCharacters = await this.getHashHexCharacters();
|
|
73
|
+
if (hashHexCharacters) {
|
|
74
|
+
const compress = await this.getCompress();
|
|
75
|
+
while (hex.length < 8) {
|
|
76
|
+
hex = `0${hex}`;
|
|
77
|
+
}
|
|
78
|
+
hex = hex.substr(8 - hashHexCharacters);
|
|
79
|
+
const dirpath = [];
|
|
80
|
+
for (let i = 0; i < hex.length; i += 3) {
|
|
81
|
+
dirpath.push(hex.substring(i, i + 3));
|
|
82
|
+
}
|
|
83
|
+
return `${dirpath.join('/')}.json${compress ? 'z' : ''}`;
|
|
84
|
+
}
|
|
85
|
+
return '';
|
|
86
|
+
}
|
|
87
|
+
hash(data) {
|
|
197
88
|
return (0, buffer_crc32_1.default)(Buffer.from(data))
|
|
198
89
|
.toString('hex')
|
|
199
90
|
.toLowerCase()
|
|
200
91
|
.replace('-', 'n');
|
|
201
|
-
}
|
|
202
|
-
|
|
203
|
-
}());
|
|
92
|
+
}
|
|
93
|
+
}
|
|
204
94
|
exports.default = HttpMap;
|
|
205
95
|
//# sourceMappingURL=HttpMap.js.map
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"HttpMap.js","sourceRoot":"","sources":["../../src/JBrowse1TextSeachAdapter/HttpMap.ts"],"names":[],"mappings":"
|
|
1
|
+
{"version":3,"file":"HttpMap.js","sourceRoot":"","sources":["../../src/JBrowse1TextSeachAdapter/HttpMap.ts"],"names":[],"mappings":";;;;;AAAA;;;GAGG;AACH,gEAAgC;AAEhC,MAAqB,OAAO;IAG1B,YAAY,IAAqB;QAC/B,qCAAqC;QACrC,IAAI,CAAC,GAAG,GAAG,KAAK,CAAC,IAAI,CAAC,IAAI,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,GAAG,CAAC,CAAC,CAAC,GAAG,IAAI,CAAC,GAAG,GAAG,CAAA;IAC7D,CAAC;IAED;;OAEG;IACH,KAAK,CAAC,QAAQ;QACZ,MAAM,IAAI,GAAG,MAAM,IAAI,CAAC,QAAQ,CAAC,WAAW,CAAC,CAAA;QAC7C,MAAM,EAAE,QAAQ,EAAE,WAAW,EAAE,MAAM,EAAE,GAAG,IAAI,CAAA;QAC9C,MAAM,iBAAiB,GAAG,IAAI,CAAC,IAAI,CAAC,IAAI,CAAC,SAAS,GAAG,CAAC,CAAC,CAAA;QACvD,OAAO,EAAE,iBAAiB,EAAE,QAAQ,EAAE,MAAM,EAAE,CAAA;IAChD,CAAC;IAED,KAAK,CAAC,oBAAoB;QACxB,MAAM,IAAI,GAAG,MAAM,IAAI,CAAC,QAAQ,EAAE,CAAA;QAClC,OAAO,IAAI,CAAC,iBAAiB,CAAA;IAC/B,CAAC;IAED,KAAK,CAAC,WAAW;QACf,MAAM,IAAI,GAAG,MAAM,IAAI,CAAC,QAAQ,EAAE,CAAA;QAClC,OAAO,IAAI,CAAC,QAAQ,CAAA;IACtB,CAAC;IAED,KAAK,CAAC,aAAa;QACjB,MAAM,IAAI,GAAG,MAAM,IAAI,CAAC,QAAQ,EAAE,CAAA;QAClC,OAAO,IAAI,CAAC,MAAM,CAAA;IACpB,CAAC;IAED;;;OAGG;IACH,KAAK,CAAC,GAAG,CAAC,GAAW;QACnB,MAAM,MAAM,GAAG,MAAM,IAAI,CAAC,SAAS,CAAC,GAAG,CAAC,CAAA;QACxC,OAAO,MAAM,CAAC,GAAG,CAAC,CAAA;IACpB,CAAC;IAED;;;OAGG;IACH,KAAK,CAAC,SAAS,CAAC,GAAW;QACzB,MAAM,WAAW,GAAG,IAAI,CAAC,IAAI,CAAC,GAAG,CAAC,CAAA;QAClC,MAAM,YAAY,GAAG,MAAM,IAAI,CAAC,YAAY,CAAC,WAAW,CAAC,CAAA;QACzD,OAAO,IAAI,CAAC,QAAQ,CAAC,YAAY,CAAC,CAAA;IACpC,CAAC;IAED;;;;OAIG;IACH,KAAK,CAAC,QAAQ,CAAC,EAAU;QACvB,MAAM,QAAQ,GAAG,MAAM,KAAK,CAAC,GAAG,IAAI,CAAC,GAAG,GAAG,EAAE,EAAE,CAAC,CAAA;QAChD,IAAI,CAAC,QAAQ,CAAC,EAAE,EAAE;YAChB,MAAM,IAAI,KAAK,CAAC,QAAQ,QAAQ,CAAC,MAAM,IAAI,QAAQ,CAAC,UAAU,EAAE,CAAC,CAAA;SAClE;QACD,OAAO,QAAQ,CAAC,IAAI,EAAE,CAAA;IACxB,CAAC;IAED;;;OAGG;IACH,KAAK,CAAC,YAAY,CAAC,GAAW;QAC5B,qDAAqD;QACrD,MAAM,iBAAiB,GAAG,MAAM,IAAI,CAAC,oBAAoB,EAAE,CAAA;QAC3D,IAAI,iBAAiB,EAAE;YACrB,MAAM,QAAQ,GAAG,MAAM,IAAI,CAAC,WAAW,EAAE,CAAA;YACzC,OAAO,GAAG,CAAC,MAAM,GAAG,CAAC,EAAE;gBACrB,GAAG,GAAG,IAAI,GAAG,EAAE,CAAA;aAChB;YACD,GAAG,GAAG,GAAG,CAAC,MAAM,CAAC,CAAC,GAAG,iBAAiB,CAAC,CAAA;YACvC,MAAM,OAAO,GAAG,EAAE,CAAA;YAClB,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,GAAG,CAAC,MAAM,EAAE,CAAC,IAAI,CAAC,EAAE;gBACtC,OAAO,CAAC,IAAI,CAAC,GAAG,CAAC,SAAS,CAAC,CAAC,EAAE,CAAC,GAAG,CAAC,CAAC,CAAC,CAAA;aACtC;YACD,OAAO,GAAG,OAAO,CAAC,IAAI,CAAC,GAAG,CAAC,QAAQ,QAAQ,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,EAAE,CAAA;SACzD;QACD,OAAO,EAAE,CAAA;IACX,CAAC;IAED,IAAI,CAAC,IAAY;QACf,OAAO,IAAA,sBAAK,EAAC,MAAM,CAAC,IAAI,CAAC,IAAI,CAAC,CAAC;aAC5B,QAAQ,CAAC,KAAK,CAAC;aACf,WAAW,EAAE;aACb,OAAO,CAAC,GAAG,EAAE,GAAG,CAAC,CAAA;IACtB,CAAC;CACF;AA7FD,0BA6FC"}
|
|
@@ -1,170 +1,73 @@
|
|
|
1
1
|
"use strict";
|
|
2
|
-
var __extends = (this && this.__extends) || (function () {
|
|
3
|
-
var extendStatics = function (d, b) {
|
|
4
|
-
extendStatics = Object.setPrototypeOf ||
|
|
5
|
-
({ __proto__: [] } instanceof Array && function (d, b) { d.__proto__ = b; }) ||
|
|
6
|
-
function (d, b) { for (var p in b) if (Object.prototype.hasOwnProperty.call(b, p)) d[p] = b[p]; };
|
|
7
|
-
return extendStatics(d, b);
|
|
8
|
-
};
|
|
9
|
-
return function (d, b) {
|
|
10
|
-
if (typeof b !== "function" && b !== null)
|
|
11
|
-
throw new TypeError("Class extends value " + String(b) + " is not a constructor or null");
|
|
12
|
-
extendStatics(d, b);
|
|
13
|
-
function __() { this.constructor = d; }
|
|
14
|
-
d.prototype = b === null ? Object.create(b) : (__.prototype = b.prototype, new __());
|
|
15
|
-
};
|
|
16
|
-
})();
|
|
17
|
-
var __awaiter = (this && this.__awaiter) || function (thisArg, _arguments, P, generator) {
|
|
18
|
-
function adopt(value) { return value instanceof P ? value : new P(function (resolve) { resolve(value); }); }
|
|
19
|
-
return new (P || (P = Promise))(function (resolve, reject) {
|
|
20
|
-
function fulfilled(value) { try { step(generator.next(value)); } catch (e) { reject(e); } }
|
|
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|
-
function rejected(value) { try { step(generator["throw"](value)); } catch (e) { reject(e); } }
|
|
22
|
-
function step(result) { result.done ? resolve(result.value) : adopt(result.value).then(fulfilled, rejected); }
|
|
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|
-
step((generator = generator.apply(thisArg, _arguments || [])).next());
|
|
24
|
-
});
|
|
25
|
-
};
|
|
26
|
-
var __generator = (this && this.__generator) || function (thisArg, body) {
|
|
27
|
-
var _ = { label: 0, sent: function() { if (t[0] & 1) throw t[1]; return t[1]; }, trys: [], ops: [] }, f, y, t, g;
|
|
28
|
-
return g = { next: verb(0), "throw": verb(1), "return": verb(2) }, typeof Symbol === "function" && (g[Symbol.iterator] = function() { return this; }), g;
|
|
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|
-
function verb(n) { return function (v) { return step([n, v]); }; }
|
|
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|
-
function step(op) {
|
|
31
|
-
if (f) throw new TypeError("Generator is already executing.");
|
|
32
|
-
while (_) try {
|
|
33
|
-
if (f = 1, y && (t = op[0] & 2 ? y["return"] : op[0] ? y["throw"] || ((t = y["return"]) && t.call(y), 0) : y.next) && !(t = t.call(y, op[1])).done) return t;
|
|
34
|
-
if (y = 0, t) op = [op[0] & 2, t.value];
|
|
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|
-
switch (op[0]) {
|
|
36
|
-
case 0: case 1: t = op; break;
|
|
37
|
-
case 4: _.label++; return { value: op[1], done: false };
|
|
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|
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case 5: _.label++; y = op[1]; op = [0]; continue;
|
|
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|
-
case 7: op = _.ops.pop(); _.trys.pop(); continue;
|
|
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|
-
default:
|
|
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|
-
if (!(t = _.trys, t = t.length > 0 && t[t.length - 1]) && (op[0] === 6 || op[0] === 2)) { _ = 0; continue; }
|
|
42
|
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if (op[0] === 3 && (!t || (op[1] > t[0] && op[1] < t[3]))) { _.label = op[1]; break; }
|
|
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|
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if (op[0] === 6 && _.label < t[1]) { _.label = t[1]; t = op; break; }
|
|
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|
-
if (t && _.label < t[2]) { _.label = t[2]; _.ops.push(op); break; }
|
|
45
|
-
if (t[2]) _.ops.pop();
|
|
46
|
-
_.trys.pop(); continue;
|
|
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|
-
}
|
|
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|
-
op = body.call(thisArg, _);
|
|
49
|
-
} catch (e) { op = [6, e]; y = 0; } finally { f = t = 0; }
|
|
50
|
-
if (op[0] & 5) throw op[1]; return { value: op[0] ? op[1] : void 0, done: true };
|
|
51
|
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}
|
|
52
|
-
};
|
|
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|
-
var __read = (this && this.__read) || function (o, n) {
|
|
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|
-
var m = typeof Symbol === "function" && o[Symbol.iterator];
|
|
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|
-
if (!m) return o;
|
|
56
|
-
var i = m.call(o), r, ar = [], e;
|
|
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|
-
try {
|
|
58
|
-
while ((n === void 0 || n-- > 0) && !(r = i.next()).done) ar.push(r.value);
|
|
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|
-
}
|
|
60
|
-
catch (error) { e = { error: error }; }
|
|
61
|
-
finally {
|
|
62
|
-
try {
|
|
63
|
-
if (r && !r.done && (m = i["return"])) m.call(i);
|
|
64
|
-
}
|
|
65
|
-
finally { if (e) throw e.error; }
|
|
66
|
-
}
|
|
67
|
-
return ar;
|
|
68
|
-
};
|
|
69
|
-
var __spreadArray = (this && this.__spreadArray) || function (to, from, pack) {
|
|
70
|
-
if (pack || arguments.length === 2) for (var i = 0, l = from.length, ar; i < l; i++) {
|
|
71
|
-
if (ar || !(i in from)) {
|
|
72
|
-
if (!ar) ar = Array.prototype.slice.call(from, 0, i);
|
|
73
|
-
ar[i] = from[i];
|
|
74
|
-
}
|
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}
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76
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-
return to.concat(ar || Array.prototype.slice.call(from));
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};
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78
2
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var __importDefault = (this && this.__importDefault) || function (mod) {
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79
3
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return (mod && mod.__esModule) ? mod : { "default": mod };
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80
4
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};
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81
5
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Object.defineProperty(exports, "__esModule", { value: true });
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82
|
-
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83
|
-
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84
|
-
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85
|
-
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6
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+
const BaseAdapter_1 = require("@jbrowse/core/data_adapters/BaseAdapter");
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7
|
+
const BaseResults_1 = __importDefault(require("@jbrowse/core/TextSearch/BaseResults"));
|
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8
|
+
const configuration_1 = require("@jbrowse/core/configuration");
|
|
9
|
+
const HttpMap_1 = __importDefault(require("./HttpMap"));
|
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86
10
|
// Jbrowse1 text search adapter
|
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87
11
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// Uses index built by generate-names.pl
|
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88
|
-
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|
89
|
-
|
|
90
|
-
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91
|
-
|
|
92
|
-
var namesIndexLocation = (0, configuration_1.readConfObject)(config, 'namesIndexLocation');
|
|
12
|
+
class JBrowse1TextSearchAdapter extends BaseAdapter_1.BaseAdapter {
|
|
13
|
+
constructor(config, getSubAdapter, pluginManager) {
|
|
14
|
+
super(config, getSubAdapter, pluginManager);
|
|
15
|
+
const namesIndexLocation = (0, configuration_1.readConfObject)(config, 'namesIndexLocation');
|
|
93
16
|
if (!namesIndexLocation) {
|
|
94
17
|
throw new Error('must provide namesIndexLocation');
|
|
95
18
|
}
|
|
96
|
-
|
|
19
|
+
this.httpMap = new HttpMap_1.default({
|
|
97
20
|
url: namesIndexLocation.baseUri
|
|
98
21
|
? new URL(namesIndexLocation.uri, namesIndexLocation.baseUri).href
|
|
99
22
|
: namesIndexLocation.uri,
|
|
100
23
|
});
|
|
101
|
-
return _this;
|
|
102
24
|
}
|
|
103
25
|
/**
|
|
104
26
|
* Returns the contents of the file containing the query if it exists
|
|
105
27
|
* else it returns empty
|
|
106
28
|
* @param query - string query
|
|
107
29
|
*/
|
|
108
|
-
|
|
109
|
-
return
|
|
110
|
-
|
|
111
|
-
|
|
112
|
-
|
|
113
|
-
|
|
114
|
-
|
|
115
|
-
|
|
116
|
-
|
|
117
|
-
|
|
118
|
-
|
|
119
|
-
|
|
120
|
-
|
|
121
|
-
|
|
122
|
-
|
|
123
|
-
|
|
124
|
-
|
|
125
|
-
|
|
126
|
-
|
|
127
|
-
|
|
128
|
-
|
|
129
|
-
|
|
130
|
-
|
|
131
|
-
|
|
132
|
-
|
|
133
|
-
|
|
134
|
-
|
|
135
|
-
|
|
136
|
-
|
|
137
|
-
}
|
|
138
|
-
});
|
|
139
|
-
});
|
|
140
|
-
};
|
|
141
|
-
JBrowse1TextSearchAdapter.prototype.formatResults = function (results, tracks, searchType) {
|
|
142
|
-
return __spreadArray(__spreadArray([], __read((searchType === 'exact'
|
|
143
|
-
? []
|
|
144
|
-
: results.prefix.map(function (result) {
|
|
30
|
+
async loadIndexFile(query) {
|
|
31
|
+
return this.httpMap.getBucket(query);
|
|
32
|
+
}
|
|
33
|
+
async searchIndex(args) {
|
|
34
|
+
const { searchType, queryString } = args;
|
|
35
|
+
const tracks = this.tracksNames || (await this.httpMap.getTrackNames());
|
|
36
|
+
const entries = await this.loadIndexFile(queryString.toLowerCase());
|
|
37
|
+
if (entries[queryString]) {
|
|
38
|
+
return this.formatResults(entries[queryString], tracks, searchType);
|
|
39
|
+
}
|
|
40
|
+
return [];
|
|
41
|
+
}
|
|
42
|
+
formatResults(results, tracks, searchType) {
|
|
43
|
+
return [
|
|
44
|
+
...(searchType === 'exact'
|
|
45
|
+
? []
|
|
46
|
+
: results.prefix.map(result => {
|
|
47
|
+
return new BaseResults_1.default({
|
|
48
|
+
label: typeof result === 'object' ? result.name : result,
|
|
49
|
+
matchedAttribute: 'name',
|
|
50
|
+
matchedObject: { result: result },
|
|
51
|
+
});
|
|
52
|
+
})),
|
|
53
|
+
...results.exact.map(result => {
|
|
54
|
+
const name = result[0];
|
|
55
|
+
const trackIndex = result[1];
|
|
56
|
+
const refName = result[3];
|
|
57
|
+
const start = result[4];
|
|
58
|
+
const end = result[5];
|
|
59
|
+
const locstring = `${refName || name}:${start}-${end}`;
|
|
145
60
|
return new BaseResults_1.default({
|
|
146
|
-
|
|
61
|
+
locString: locstring,
|
|
62
|
+
label: name,
|
|
147
63
|
matchedAttribute: 'name',
|
|
148
|
-
matchedObject:
|
|
64
|
+
matchedObject: result,
|
|
65
|
+
trackId: tracks[trackIndex],
|
|
149
66
|
});
|
|
150
|
-
})
|
|
151
|
-
|
|
152
|
-
|
|
153
|
-
|
|
154
|
-
|
|
155
|
-
var end = result[5];
|
|
156
|
-
var locstring = "".concat(refName || name, ":").concat(start, "-").concat(end);
|
|
157
|
-
return new BaseResults_1.default({
|
|
158
|
-
locString: locstring,
|
|
159
|
-
label: name,
|
|
160
|
-
matchedAttribute: 'name',
|
|
161
|
-
matchedObject: result,
|
|
162
|
-
trackId: tracks[trackIndex],
|
|
163
|
-
});
|
|
164
|
-
})), false).filter(function (result) { return result.getLabel() !== 'too many matches'; });
|
|
165
|
-
};
|
|
166
|
-
JBrowse1TextSearchAdapter.prototype.freeResources = function () { };
|
|
167
|
-
return JBrowse1TextSearchAdapter;
|
|
168
|
-
}(BaseAdapter_1.BaseAdapter));
|
|
67
|
+
}),
|
|
68
|
+
].filter(result => result.getLabel() !== 'too many matches');
|
|
69
|
+
}
|
|
70
|
+
freeResources() { }
|
|
71
|
+
}
|
|
169
72
|
exports.default = JBrowse1TextSearchAdapter;
|
|
170
73
|
//# sourceMappingURL=JBrowse1TextSearchAdapter.js.map
|