@jbrowse/plugin-rdf 2.6.1 → 2.6.2

package/dist/SPARQLAdapter/SPARQLAdapter.js

@@ -175,4 +175,3 @@ class SPARQLAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
     freeResources( /* { region } */) { }
 }
 exports.default = SPARQLAdapter;
-//# sourceMappingURL=SPARQLAdapter.js.map

package/dist/SPARQLAdapter/configSchema.js

@@ -31,4 +31,3 @@ exports.default = (0, configuration_1.ConfigurationSchema)('SPARQLAdapter', {
         description: 'Additional parameters to add to the query, e.g. "format=JSON"',
     },
 }, { explicitlyTyped: true });
-//# sourceMappingURL=configSchema.js.map

package/dist/SPARQLAdapter/index.js

@@ -8,4 +8,3 @@ var SPARQLAdapter_1 = require("./SPARQLAdapter");
 Object.defineProperty(exports, "AdapterClass", { enumerable: true, get: function () { return __importDefault(SPARQLAdapter_1).default; } });
 var configSchema_1 = require("./configSchema");
 Object.defineProperty(exports, "configSchema", { enumerable: true, get: function () { return __importDefault(configSchema_1).default; } });
-//# sourceMappingURL=index.js.map

package/dist/index.js

@@ -36,4 +36,3 @@ class RdfPlugin extends Plugin_1.default {
     }
 }
 exports.default = RdfPlugin;
-//# sourceMappingURL=index.js.map

package/esm/SPARQLAdapter/SPARQLAdapter.js

@@ -169,4 +169,3 @@ export default class SPARQLAdapter extends BaseFeatureDataAdapter {
     }
     freeResources( /* { region } */) { }
 }
-//# sourceMappingURL=SPARQLAdapter.js.map

package/esm/SPARQLAdapter/configSchema.js

@@ -29,4 +29,3 @@ export default ConfigurationSchema('SPARQLAdapter', {
         description: 'Additional parameters to add to the query, e.g. "format=JSON"',
     },
 }, { explicitlyTyped: true });
-//# sourceMappingURL=configSchema.js.map

package/esm/SPARQLAdapter/index.js

@@ -1,3 +1,2 @@
 export { default as AdapterClass } from './SPARQLAdapter';
 export { default as configSchema } from './configSchema';
-//# sourceMappingURL=index.js.map

package/esm/index.js

@@ -30,4 +30,3 @@ export default class RdfPlugin extends Plugin {
         });
     }
 }
-//# sourceMappingURL=index.js.map

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-rdf",
-  "version": "2.6.1",
+  "version": "2.6.2",
   "description": "JBrowse 2 RDF resources",
   "keywords": [
     "jbrowse",
@@ -20,7 +20,6 @@
   "main": "dist/index.js",
   "files": [
     "dist",
-    "src",
     "esm"
   ],
   "scripts": {
@@ -33,7 +32,7 @@
     "useSrc": "node ../../scripts/useSrc.js",
     "prebuild": "npm run clean",
     "build:esm": "tsc --build tsconfig.build.esm.json",
-    "build:es5": "tsc --build tsconfig.build.es5.json",
+    "build:commonjs": "tsc --build tsconfig.build.commonjs.json",
     "clean": "rimraf dist esm *.tsbuildinfo"
   },
   "dependencies": {
@@ -52,5 +51,5 @@
   "publishConfig": {
     "access": "public"
   },
-  "gitHead": "1cbe7ba097fb2d2763c776e5e429e4670cdd583c"
+  "gitHead": "bbea587a402d9974acdd804a33f4b77f31a2fd5f"
 }

package/dist/SPARQLAdapter/SPARQLAdapter.js.map

@@ -1 +0,0 @@
-{"version":3,"file":"SPARQLAdapter.js","sourceRoot":"","sources":["../../src/SPARQLAdapter/SPARQLAdapter.ts"],"names":[],"mappings":";;;;;AAAA,yEAGgD;AAEhD,kDAA0D;AAC1D,qFAAyE;AACzE,sEAAoC;AAGpC,+DAA4D;AA0C5D,MAAqB,aAAc,SAAQ,oCAAsB;IAa/D,YACE,MAAuC,EACvC,aAAiC,EACjC,aAA6B;QAE7B,KAAK,CAAC,MAAM,EAAE,aAAa,EAAE,aAAa,CAAC,CAAA;QAC3C,IAAI,CAAC,QAAQ,GAAG,IAAA,8BAAc,EAAC,MAAM,EAAE,UAAU,CAAC,CAAC,GAAG,CAAA;QACtD,IAAI,CAAC,aAAa,GAAG,IAAA,8BAAc,EAAC,MAAM,EAAE,eAAe,CAAC,CAAA;QAC5D,IAAI,CAAC,qBAAqB,GAAG,IAAA,8BAAc,EAAC,MAAM,EAAE,uBAAuB,CAAC,CAAA;QAC5E,IAAI,CAAC,qBAAqB,GAAG,IAAA,8BAAc,EAAC,MAAM,EAAE,uBAAuB,CAAC,CAAA;QAC5E,IAAI,CAAC,cAAc,GAAG,IAAA,8BAAc,EAAC,MAAM,EAAE,UAAU,CAAC,CAAA;IAC1D,CAAC;IAEM,KAAK,CAAC,WAAW,CAAC,OAAoB,EAAE;QAC7C,IAAI,IAAI,CAAC,QAAQ,EAAE;YACjB,OAAO,IAAI,CAAC,QAAQ,CAAA;SACrB;QACD,IAAI,QAAQ,GAAG,EAAc,CAAA;QAC7B,IAAI,IAAI,CAAC,qBAAqB,EAAE;YAC9B,MAAM,aAAa,GAAG,kBAAkB,CAAC,IAAI,CAAC,qBAAqB,CAAC,CAAA;YACpE,MAAM,OAAO,GAAG,MAAM,IAAI,CAAC,WAAW,CAAC,aAAa,EAAE,IAAI,CAAC,CAAA;YAC3D,QAAQ,GAAG,IAAI,CAAC,iBAAiB,CAAC,OAAO,CAAC,CAAA;SAC3C;aAAM,IAAI,IAAI,CAAC,cAAc,EAAE;YAC9B,QAAQ,GAAG,IAAI,CAAC,cAAc,CAAA;SAC/B;QACD,IAAI,CAAC,QAAQ,GAAG,QAAQ,CAAA;QACxB,OAAO,QAAQ,CAAA;IACjB,CAAC;IAEM,WAAW,CAAC,KAAuB,EAAE,OAAoB,EAAE;QAChE,OAAO,IAAA,uBAAgB,EAAU,KAAK,EAAC,QAAQ,EAAC,EAAE;YAChD,MAAM,cAAc,GAAG,kBAAkB,CACvC,IAAA,yBAAM,EAAC,IAAI,CAAC,aAAa,EAAE,KAAK,CAAC,CAClC,CAAA;YACD,MAAM,EAAE,OAAO,EAAE,GAAG,KAAK,CAAA;YACzB,MAAM,OAAO,GAAG,MAAM,IAAI,CAAC,WAAW,CAAC,cAAc,EAAE,IAAI,CAAC,CAAA;YAC5D,IAAI,CAAC,iBAAiB,CAAC,OAAO,EAAE,OAAO,CAAC,CAAC,OAAO,CAAC,OAAO,CAAC,EAAE;gBACzD,QAAQ,CAAC,IAAI,CAAC,OAAO,CAAC,CAAA;YACxB,CAAC,CAAC,CAAA;YACF,QAAQ,CAAC,QAAQ,EAAE,CAAA;QACrB,CAAC,EAAE,IAAI,CAAC,MAAM,CAAC,CAAA;IACjB,CAAC;IAED,8DAA8D;IACtD,KAAK,CAAC,WAAW,CAAC,KAAa,EAAE,IAAkB;QACzD,IAAI,qBAAqB,GAAG,EAAE,CAAA;QAC9B,IAAI,IAAI,CAAC,qBAAqB,CAAC,MAAM,EAAE;YACrC,qBAAqB,GAAG,IAAI,IAAI,CAAC,qBAAqB,CAAC,IAAI,CAAC,GAAG,CAAC,EAAE,CAAA;SACnE;QACD,MAAM,MAAM,GAAG,IAAI,IAAI,IAAI,CAAC,MAAM,CAAA;QAClC,MAAM,QAAQ,GAAG,MAAM,KAAK,CAC1B,GAAG,IAAI,CAAC,QAAQ,UAAU,KAAK,GAAG,qBAAqB,EAAE,EACzD;YACE,OAAO,EAAE,EAAE,MAAM,EAAE,kDAAkD,EAAE;YACvE,MAAM;SACP,CACF,CAAA;QACD,OAAO,QAAQ,CAAC,IAAI,EAAE,CAAA;IACxB,CAAC;IAEO,iBAAiB,CAAC,QAAwB;QAChD,MAAM,IAAI,GAAG,CAAC,CAAC,QAAQ,IAAI,EAAE,CAAC,CAAC,OAAO,IAAI,EAAE,CAAC,CAAC,QAAQ,IAAI,EAAE,CAAA;QAC5D,IAAI,CAAC,IAAI,CAAC,MAAM,EAAE;YAChB,OAAO,EAAE,CAAA;SACV;QACD,MAAM,MAAM,GAAG,QAAQ,CAAC,IAAI,CAAC,IAAI,CAAA;QACjC,IAAI,CAAC,MAAM,CAAC,QAAQ,CAAC,SAAS,CAAC,EAAE;YAC/B,MAAM,IAAI,KAAK,CAAC,uDAAuD,CAAC,CAAA;SACzE;QACD,OAAO,IAAI,CAAC,GAAG,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,CAAC,OAAO,CAAC,KAAK,CAAC,CAAA;IAC3C,CAAC;IAEO,iBAAiB,CACvB,OAAuB,EACvB,OAAe;QAEf,MAAM,IAAI,GAAG,CAAC,CAAC,OAAO,IAAI,EAAE,CAAC,CAAC,OAAO,IAAI,EAAE,CAAC,CAAC,QAAQ,IAAI,EAAE,CAAA;QAC3D,IAAI,CAAC,IAAI,CAAC,MAAM,EAAE;YAChB,OAAO,EAAE,CAAA;SACV;QACD,MAAM,MAAM,GAAG,OAAO,CAAC,IAAI,CAAC,IAAI,CAAA;QAChC,MAAM,cAAc,GAAG,CAAC,OAAO,EAAE,KAAK,EAAE,UAAU,CAAC,CAAA;QACnD,cAAc,CAAC,OAAO,CAAC,aAAa,CAAC,EAAE;YACrC,IAAI,CAAC,MAAM,CAAC,QAAQ,CAAC,aAAa,CAAC,EAAE;gBACnC,OAAO,CAAC,KAAK,CACX,kBAAkB,aAAa,4BAA4B,CAC5D,CAAA;aACF;QACH,CAAC,CAAC,CAAA;QACF,MAAM,YAAY,GAAkC,EAAE,CAAA;QACtD,IAAI,CAAC,OAAO,CAAC,GAAG,CAAC,EAAE;YACjB,MAAM,OAAO,GAA6B,CAAC,EAAE,CAAC,CAAA;YAC9C,MAAM,CAAC,OAAO,CAAC,KAAK,CAAC,EAAE;gBACrB,IAAI,KAAK,IAAI,GAAG,EAAE;oBAChB,MAAM,EAAE,KAAK,EAAE,GAAG,GAAG,CAAC,KAAK,CAAC,CAAA;oBAC5B,IAAI,GAAG,GAAG,CAAC,CAAA;oBACX,OAAO,KAAK,CAAC,UAAU,CAAC,MAAM,CAAC,EAAE;wBAC/B,KAAK,GAAG,KAAK,CAAC,KAAK,CAAC,CAAC,CAAC,CAAA;wBACtB,GAAG,IAAI,CAAC,CAAA;qBACT;oBACD,OAAO,GAAG,GAAG,OAAO,CAAC,MAAM,GAAG,CAAC,EAAE;wBAC/B,OAAO,CAAC,IAAI,CAAC,EAAE,CAAC,CAAA;qBACjB;oBACD,OAAO,CAAC,GAAG,CAAC,CAAC,KAAK,CAAC,GAAG,KAAK,CAAA;iBAC5B;YACH,CAAC,CAAC,CAAA;YAEF,OAAO,CAAC,OAAO,CAAC,CAAC,EAAE,EAAE,GAAG,EAAE,EAAE;gBAC1B,MAAM,EAAE,QAAQ,EAAE,GAAG,EAAE,CAAA;gBACvB,IAAI,GAAG,GAAG,OAAO,CAAC,MAAM,GAAG,CAAC,EAAE;oBAC5B,OAAO,CAAC,GAAG,GAAG,CAAC,CAAC,CAAC,cAAc,GAAG,QAAQ,CAAA;iBAC3C;gBACD,YAAY,CAAC,QAAQ,CAAC,GAAG;oBACvB,IAAI,EAAE;wBACJ,GAAG,EAAE;wBACL,QAAQ;wBACR,OAAO;wBACP,KAAK,EAAE,QAAQ,CAAC,EAAE,CAAC,KAAK,EAAE,EAAE,CAAC;wBAC7B,GAAG,EAAE,QAAQ,CAAC,EAAE,CAAC,GAAG,EAAE,EAAE,CAAC;wBACzB,MAAM,EAAE,QAAQ,CAAC,EAAE,CAAC,MAAM,EAAE,EAAE,CAAC,IAAI,CAAC;qBACrC;iBACF,CAAA;YACH,CAAC,CAAC,CAAA;QACJ,CAAC,CAAC,CAAA;QAEF,uEAAuE;QACvE,KAAK,MAAM,CAAC,QAAQ,EAAE,CAAC,CAAC,IAAI,MAAM,CAAC,OAAO,CAAC,YAAY,CAAC,EAAE;YACxD,MAAM,GAAG,GAAG,CAAC,CAAC,IAAI,CAAC,cAAc,CAAA;YACjC,OAAO,CAAC,CAAC,IAAI,CAAC,cAAc,CAAA;YAC5B,IAAI,GAAG,EAAE;gBACP,MAAM,CAAC,GAAG,YAAY,CAAC,GAAG,CAAC,CAAA;gBAC3B,IAAI,CAAC,EAAE;oBACL,IAAI,CAAC,CAAC,CAAC,IAAI,CAAC,WAAW,EAAE;wBACvB,CAAC,CAAC,IAAI,CAAC,WAAW,GAAG,EAAE,CAAA;qBACxB;oBACD,CAAC,CAAC,IAAI,CAAC,WAAW,CAAC,IAAI,CAAC;wBACtB,GAAG,CAAC,CAAC,IAAI;wBACT,QAAQ;qBACT,CAAC,CAAA;oBACF,OAAO,YAAY,CAAC,QAAQ,CAAC,CAAA;iBAC9B;qBAAM;oBACL,MAAM,WAAW,GAAG,MAAM,CAAC,MAAM,CAAC,YAAY,CAAC;yBAC5C,GAAG,CAAC,EAAE,CAAC,EAAE,CAAC,EAAE,CAAC,IAAI,CAAC,WAAW,CAAC;yBAC9B,MAAM,CAAC,EAAE,CAAC,EAAE,CAAC,CAAC,CAAC,EAAE,CAAC;yBAClB,IAAI,EAAE,CAAA;oBACT,IAAI,KAAK,GAAG,KAAK,CAAA;oBACjB,KAAK,MAAM,UAAU,IAAI,WAAW,EAAE;wBACpC,IAAI,UAAU,IAAI,UAAU,CAAC,QAAQ,KAAK,GAAG,EAAE;4BAC7C,IAAI,CAAC,UAAU,CAAC,WAAW,EAAE;gCAC3B,UAAU,CAAC,WAAW,GAAG,EAAE,CAAA;6BAC5B;4BACD,UAAU,CAAC,WAAW,CAAC,IAAI,CAAC;gCAC1B,GAAG,CAAC,CAAC,IAAI;gCACT,QAAQ;6BACT,CAAC,CAAA;4BACF,OAAO,YAAY,CAAC,QAAQ,CAAC,CAAA;4BAC7B,KAAK,GAAG,IAAI,CAAA;4BACZ,MAAK;yBACN;6BAAM,IAAI,UAAU,IAAI,UAAU,CAAC,WAAW,EAAE;4BAC/C,WAAW,CAAC,IAAI,CAAC,GAAG,UAAU,CAAC,WAAW,CAAC,CAAA;yBAC5C;qBACF;oBACD,IAAI,CAAC,KAAK,EAAE;wBACV,OAAO,CAAC,KAAK,CAAC,2BAA2B,GAAG,EAAE,CAAC,CAAA;qBAChD;iBACF;aACF;SACF;QAED,OAAO,MAAM,CAAC,IAAI,CAAC,YAAY,CAAC,CAAC,GAAG,CAClC,WAAW,CAAC,EAAE,CACZ,IAAI,uBAAa,CAAC;YAChB,GAAG,YAAY,CAAC,WAAW,CAAC,CAAC,IAAI;YACjC,QAAQ,EAAE,WAAW;YACrB,WAAW,EAAE,YAAY,CAAC,WAAW,CAAC,CAAC,IAAI,CAAC,WAAW;SACxD,CAAC,CACL,CAAA;IACH,CAAC;IAEM,KAAK,CAAC,iBAAiB,CAC5B,OAAe,EACf,OAAoB,EAAE;QAEtB,MAAM,QAAQ,GAAG,MAAM,IAAI,CAAC,WAAW,CAAC,IAAI,CAAC,CAAA;QAC7C,IAAI,QAAQ,CAAC,MAAM,IAAI,CAAC,QAAQ,CAAC,QAAQ,CAAC,OAAO,CAAC,EAAE;YAClD,OAAO,KAAK,CAAA;SACb;QACD,OAAO,IAAI,CAAA;IACb,CAAC;IAEM,aAAa,EAAC,gBAAgB,IAAS,CAAC;CAChD;AA5MD,gCA4MC"}

package/dist/SPARQLAdapter/configSchema.js.map

@@ -1 +0,0 @@
-{"version":3,"file":"configSchema.js","sourceRoot":"","sources":["../../src/SPARQLAdapter/configSchema.ts"],"names":[],"mappings":";;AAAA,+DAAiE;AAEjE,kBAAe,IAAA,mCAAmB,EAChC,eAAe,EACf;IACE,QAAQ,EAAE;QACR,IAAI,EAAE,cAAc;QACpB,YAAY,EAAE;YACZ,GAAG,EAAE,6BAA6B;YAClC,YAAY,EAAE,aAAa;SAC5B;QACD,WAAW,EAAE,4BAA4B;KAC1C;IACD,aAAa,EAAE;QACb,IAAI,EAAE,MAAM;QACZ,YAAY,EAAE,EAAE;QAChB,WAAW,EACT,gFAAgF;KACnF;IACD,qBAAqB,EAAE;QACrB,IAAI,EAAE,MAAM;QACZ,YAAY,EAAE,EAAE;QAChB,WAAW,EACT,sEAAsE;KACzE;IACD,QAAQ,EAAE;QACR,IAAI,EAAE,aAAa;QACnB,YAAY,EAAE,EAAE;QAChB,WAAW,EACT,gGAAgG;KACnG;IACD,qBAAqB,EAAE;QACrB,IAAI,EAAE,aAAa;QACnB,YAAY,EAAE,EAAE;QAChB,WAAW,EACT,+DAA+D;KAClE;CACF,EACD,EAAE,eAAe,EAAE,IAAI,EAAE,CAC1B,CAAA"}

package/dist/SPARQLAdapter/index.js.map

@@ -1 +0,0 @@
-{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/SPARQLAdapter/index.ts"],"names":[],"mappings":";;;;;;AAAA,iDAAyD;AAAhD,8HAAA,OAAO,OAAgB;AAChC,+CAAwD;AAA/C,6HAAA,OAAO,OAAgB"}

package/dist/index.js.map

@@ -1 +0,0 @@
-{"version":3,"file":"index.js","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":";;;;;AAAA,kGAAyE;AACzE,kEAAyC;AAGzC,mDAGwB;AACxB,sDAAuE;AAEvE,MAAqB,SAAU,SAAQ,gBAAM;IAA7C;;QACE,SAAI,GAAG,WAAW,CAAA;IAkCpB,CAAC;IAhCC,OAAO,CAAC,aAA4B;QAClC,aAAa,CAAC,cAAc,CAC1B,GAAG,EAAE,CACH,IAAI,qBAAW,CAAC;YACd,IAAI,EAAE,eAAe;YACrB,WAAW,EAAE,gBAAgB;YAC7B,YAAY,EAAE,4BAAyB;YACvC,YAAY,EAAE,4BAAkB;SACjC,CAAC,CACL,CAAA;QACD,aAAa,CAAC,mBAAmB,CAC/B,8BAA8B,EAC9B,CAAC,cAA8B,EAAE,EAAE;YACjC,OAAO,CACL,IAAkB,EAClB,KAAoB,EACpB,WAAoB,EACpB,EAAE;gBACF,MAAM,UAAU,GAAG,YAAY,CAAA;gBAC/B,MAAM,WAAW,GAAG,eAAe,CAAA;gBACnC,MAAM,QAAQ,GAAG,IAAA,oBAAW,EAAC,IAAI,CAAC,CAAA;gBAClC,IAAI,UAAU,CAAC,IAAI,CAAC,QAAQ,CAAC,IAAI,WAAW,KAAK,WAAW,EAAE;oBAC5D,OAAO;wBACL,IAAI,EAAE,WAAW;wBACjB,QAAQ,EAAE,IAAI;qBACf,CAAA;iBACF;gBACD,OAAO,cAAc,CAAC,IAAI,EAAE,KAAK,EAAE,WAAW,CAAC,CAAA;YACjD,CAAC,CAAA;QACH,CAAC,CACF,CAAA;IACH,CAAC;CACF;AAnCD,4BAmCC"}

package/esm/SPARQLAdapter/SPARQLAdapter.js.map

@@ -1 +0,0 @@
-{"version":3,"file":"SPARQLAdapter.js","sourceRoot":"","sources":["../../src/SPARQLAdapter/SPARQLAdapter.ts"],"names":[],"mappings":"AAAA,OAAO,EACL,sBAAsB,GAEvB,MAAM,yCAAyC,CAAA;AAEhD,OAAO,EAAE,gBAAgB,EAAE,MAAM,yBAAyB,CAAA;AAC1D,OAAO,aAA0B,MAAM,kCAAkC,CAAA;AACzE,OAAO,MAAM,MAAM,iBAAiB,CAAA;AAGpC,OAAO,EAAE,cAAc,EAAE,MAAM,6BAA6B,CAAA;AA0C5D,MAAM,CAAC,OAAO,OAAO,aAAc,SAAQ,sBAAsB;IAa/D,YACE,MAAuC,EACvC,aAAiC,EACjC,aAA6B;QAE7B,KAAK,CAAC,MAAM,EAAE,aAAa,EAAE,aAAa,CAAC,CAAA;QAC3C,IAAI,CAAC,QAAQ,GAAG,cAAc,CAAC,MAAM,EAAE,UAAU,CAAC,CAAC,GAAG,CAAA;QACtD,IAAI,CAAC,aAAa,GAAG,cAAc,CAAC,MAAM,EAAE,eAAe,CAAC,CAAA;QAC5D,IAAI,CAAC,qBAAqB,GAAG,cAAc,CAAC,MAAM,EAAE,uBAAuB,CAAC,CAAA;QAC5E,IAAI,CAAC,qBAAqB,GAAG,cAAc,CAAC,MAAM,EAAE,uBAAuB,CAAC,CAAA;QAC5E,IAAI,CAAC,cAAc,GAAG,cAAc,CAAC,MAAM,EAAE,UAAU,CAAC,CAAA;IAC1D,CAAC;IAEM,KAAK,CAAC,WAAW,CAAC,OAAoB,EAAE;QAC7C,IAAI,IAAI,CAAC,QAAQ,EAAE;YACjB,OAAO,IAAI,CAAC,QAAQ,CAAA;SACrB;QACD,IAAI,QAAQ,GAAG,EAAc,CAAA;QAC7B,IAAI,IAAI,CAAC,qBAAqB,EAAE;YAC9B,MAAM,aAAa,GAAG,kBAAkB,CAAC,IAAI,CAAC,qBAAqB,CAAC,CAAA;YACpE,MAAM,OAAO,GAAG,MAAM,IAAI,CAAC,WAAW,CAAC,aAAa,EAAE,IAAI,CAAC,CAAA;YAC3D,QAAQ,GAAG,IAAI,CAAC,iBAAiB,CAAC,OAAO,CAAC,CAAA;SAC3C;aAAM,IAAI,IAAI,CAAC,cAAc,EAAE;YAC9B,QAAQ,GAAG,IAAI,CAAC,cAAc,CAAA;SAC/B;QACD,IAAI,CAAC,QAAQ,GAAG,QAAQ,CAAA;QACxB,OAAO,QAAQ,CAAA;IACjB,CAAC;IAEM,WAAW,CAAC,KAAuB,EAAE,OAAoB,EAAE;QAChE,OAAO,gBAAgB,CAAU,KAAK,EAAC,QAAQ,EAAC,EAAE;YAChD,MAAM,cAAc,GAAG,kBAAkB,CACvC,MAAM,CAAC,IAAI,CAAC,aAAa,EAAE,KAAK,CAAC,CAClC,CAAA;YACD,MAAM,EAAE,OAAO,EAAE,GAAG,KAAK,CAAA;YACzB,MAAM,OAAO,GAAG,MAAM,IAAI,CAAC,WAAW,CAAC,cAAc,EAAE,IAAI,CAAC,CAAA;YAC5D,IAAI,CAAC,iBAAiB,CAAC,OAAO,EAAE,OAAO,CAAC,CAAC,OAAO,CAAC,OAAO,CAAC,EAAE;gBACzD,QAAQ,CAAC,IAAI,CAAC,OAAO,CAAC,CAAA;YACxB,CAAC,CAAC,CAAA;YACF,QAAQ,CAAC,QAAQ,EAAE,CAAA;QACrB,CAAC,EAAE,IAAI,CAAC,MAAM,CAAC,CAAA;IACjB,CAAC;IAED,8DAA8D;IACtD,KAAK,CAAC,WAAW,CAAC,KAAa,EAAE,IAAkB;QACzD,IAAI,qBAAqB,GAAG,EAAE,CAAA;QAC9B,IAAI,IAAI,CAAC,qBAAqB,CAAC,MAAM,EAAE;YACrC,qBAAqB,GAAG,IAAI,IAAI,CAAC,qBAAqB,CAAC,IAAI,CAAC,GAAG,CAAC,EAAE,CAAA;SACnE;QACD,MAAM,MAAM,GAAG,IAAI,IAAI,IAAI,CAAC,MAAM,CAAA;QAClC,MAAM,QAAQ,GAAG,MAAM,KAAK,CAC1B,GAAG,IAAI,CAAC,QAAQ,UAAU,KAAK,GAAG,qBAAqB,EAAE,EACzD;YACE,OAAO,EAAE,EAAE,MAAM,EAAE,kDAAkD,EAAE;YACvE,MAAM;SACP,CACF,CAAA;QACD,OAAO,QAAQ,CAAC,IAAI,EAAE,CAAA;IACxB,CAAC;IAEO,iBAAiB,CAAC,QAAwB;QAChD,MAAM,IAAI,GAAG,CAAC,CAAC,QAAQ,IAAI,EAAE,CAAC,CAAC,OAAO,IAAI,EAAE,CAAC,CAAC,QAAQ,IAAI,EAAE,CAAA;QAC5D,IAAI,CAAC,IAAI,CAAC,MAAM,EAAE;YAChB,OAAO,EAAE,CAAA;SACV;QACD,MAAM,MAAM,GAAG,QAAQ,CAAC,IAAI,CAAC,IAAI,CAAA;QACjC,IAAI,CAAC,MAAM,CAAC,QAAQ,CAAC,SAAS,CAAC,EAAE;YAC/B,MAAM,IAAI,KAAK,CAAC,uDAAuD,CAAC,CAAA;SACzE;QACD,OAAO,IAAI,CAAC,GAAG,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,CAAC,OAAO,CAAC,KAAK,CAAC,CAAA;IAC3C,CAAC;IAEO,iBAAiB,CACvB,OAAuB,EACvB,OAAe;QAEf,MAAM,IAAI,GAAG,CAAC,CAAC,OAAO,IAAI,EAAE,CAAC,CAAC,OAAO,IAAI,EAAE,CAAC,CAAC,QAAQ,IAAI,EAAE,CAAA;QAC3D,IAAI,CAAC,IAAI,CAAC,MAAM,EAAE;YAChB,OAAO,EAAE,CAAA;SACV;QACD,MAAM,MAAM,GAAG,OAAO,CAAC,IAAI,CAAC,IAAI,CAAA;QAChC,MAAM,cAAc,GAAG,CAAC,OAAO,EAAE,KAAK,EAAE,UAAU,CAAC,CAAA;QACnD,cAAc,CAAC,OAAO,CAAC,aAAa,CAAC,EAAE;YACrC,IAAI,CAAC,MAAM,CAAC,QAAQ,CAAC,aAAa,CAAC,EAAE;gBACnC,OAAO,CAAC,KAAK,CACX,kBAAkB,aAAa,4BAA4B,CAC5D,CAAA;aACF;QACH,CAAC,CAAC,CAAA;QACF,MAAM,YAAY,GAAkC,EAAE,CAAA;QACtD,IAAI,CAAC,OAAO,CAAC,GAAG,CAAC,EAAE;YACjB,MAAM,OAAO,GAA6B,CAAC,EAAE,CAAC,CAAA;YAC9C,MAAM,CAAC,OAAO,CAAC,KAAK,CAAC,EAAE;gBACrB,IAAI,KAAK,IAAI,GAAG,EAAE;oBAChB,MAAM,EAAE,KAAK,EAAE,GAAG,GAAG,CAAC,KAAK,CAAC,CAAA;oBAC5B,IAAI,GAAG,GAAG,CAAC,CAAA;oBACX,OAAO,KAAK,CAAC,UAAU,CAAC,MAAM,CAAC,EAAE;wBAC/B,KAAK,GAAG,KAAK,CAAC,KAAK,CAAC,CAAC,CAAC,CAAA;wBACtB,GAAG,IAAI,CAAC,CAAA;qBACT;oBACD,OAAO,GAAG,GAAG,OAAO,CAAC,MAAM,GAAG,CAAC,EAAE;wBAC/B,OAAO,CAAC,IAAI,CAAC,EAAE,CAAC,CAAA;qBACjB;oBACD,OAAO,CAAC,GAAG,CAAC,CAAC,KAAK,CAAC,GAAG,KAAK,CAAA;iBAC5B;YACH,CAAC,CAAC,CAAA;YAEF,OAAO,CAAC,OAAO,CAAC,CAAC,EAAE,EAAE,GAAG,EAAE,EAAE;gBAC1B,MAAM,EAAE,QAAQ,EAAE,GAAG,EAAE,CAAA;gBACvB,IAAI,GAAG,GAAG,OAAO,CAAC,MAAM,GAAG,CAAC,EAAE;oBAC5B,OAAO,CAAC,GAAG,GAAG,CAAC,CAAC,CAAC,cAAc,GAAG,QAAQ,CAAA;iBAC3C;gBACD,YAAY,CAAC,QAAQ,CAAC,GAAG;oBACvB,IAAI,EAAE;wBACJ,GAAG,EAAE;wBACL,QAAQ;wBACR,OAAO;wBACP,KAAK,EAAE,QAAQ,CAAC,EAAE,CAAC,KAAK,EAAE,EAAE,CAAC;wBAC7B,GAAG,EAAE,QAAQ,CAAC,EAAE,CAAC,GAAG,EAAE,EAAE,CAAC;wBACzB,MAAM,EAAE,QAAQ,CAAC,EAAE,CAAC,MAAM,EAAE,EAAE,CAAC,IAAI,CAAC;qBACrC;iBACF,CAAA;YACH,CAAC,CAAC,CAAA;QACJ,CAAC,CAAC,CAAA;QAEF,uEAAuE;QACvE,KAAK,MAAM,CAAC,QAAQ,EAAE,CAAC,CAAC,IAAI,MAAM,CAAC,OAAO,CAAC,YAAY,CAAC,EAAE;YACxD,MAAM,GAAG,GAAG,CAAC,CAAC,IAAI,CAAC,cAAc,CAAA;YACjC,OAAO,CAAC,CAAC,IAAI,CAAC,cAAc,CAAA;YAC5B,IAAI,GAAG,EAAE;gBACP,MAAM,CAAC,GAAG,YAAY,CAAC,GAAG,CAAC,CAAA;gBAC3B,IAAI,CAAC,EAAE;oBACL,IAAI,CAAC,CAAC,CAAC,IAAI,CAAC,WAAW,EAAE;wBACvB,CAAC,CAAC,IAAI,CAAC,WAAW,GAAG,EAAE,CAAA;qBACxB;oBACD,CAAC,CAAC,IAAI,CAAC,WAAW,CAAC,IAAI,CAAC;wBACtB,GAAG,CAAC,CAAC,IAAI;wBACT,QAAQ;qBACT,CAAC,CAAA;oBACF,OAAO,YAAY,CAAC,QAAQ,CAAC,CAAA;iBAC9B;qBAAM;oBACL,MAAM,WAAW,GAAG,MAAM,CAAC,MAAM,CAAC,YAAY,CAAC;yBAC5C,GAAG,CAAC,EAAE,CAAC,EAAE,CAAC,EAAE,CAAC,IAAI,CAAC,WAAW,CAAC;yBAC9B,MAAM,CAAC,EAAE,CAAC,EAAE,CAAC,CAAC,CAAC,EAAE,CAAC;yBAClB,IAAI,EAAE,CAAA;oBACT,IAAI,KAAK,GAAG,KAAK,CAAA;oBACjB,KAAK,MAAM,UAAU,IAAI,WAAW,EAAE;wBACpC,IAAI,UAAU,IAAI,UAAU,CAAC,QAAQ,KAAK,GAAG,EAAE;4BAC7C,IAAI,CAAC,UAAU,CAAC,WAAW,EAAE;gCAC3B,UAAU,CAAC,WAAW,GAAG,EAAE,CAAA;6BAC5B;4BACD,UAAU,CAAC,WAAW,CAAC,IAAI,CAAC;gCAC1B,GAAG,CAAC,CAAC,IAAI;gCACT,QAAQ;6BACT,CAAC,CAAA;4BACF,OAAO,YAAY,CAAC,QAAQ,CAAC,CAAA;4BAC7B,KAAK,GAAG,IAAI,CAAA;4BACZ,MAAK;yBACN;6BAAM,IAAI,UAAU,IAAI,UAAU,CAAC,WAAW,EAAE;4BAC/C,WAAW,CAAC,IAAI,CAAC,GAAG,UAAU,CAAC,WAAW,CAAC,CAAA;yBAC5C;qBACF;oBACD,IAAI,CAAC,KAAK,EAAE;wBACV,OAAO,CAAC,KAAK,CAAC,2BAA2B,GAAG,EAAE,CAAC,CAAA;qBAChD;iBACF;aACF;SACF;QAED,OAAO,MAAM,CAAC,IAAI,CAAC,YAAY,CAAC,CAAC,GAAG,CAClC,WAAW,CAAC,EAAE,CACZ,IAAI,aAAa,CAAC;YAChB,GAAG,YAAY,CAAC,WAAW,CAAC,CAAC,IAAI;YACjC,QAAQ,EAAE,WAAW;YACrB,WAAW,EAAE,YAAY,CAAC,WAAW,CAAC,CAAC,IAAI,CAAC,WAAW;SACxD,CAAC,CACL,CAAA;IACH,CAAC;IAEM,KAAK,CAAC,iBAAiB,CAC5B,OAAe,EACf,OAAoB,EAAE;QAEtB,MAAM,QAAQ,GAAG,MAAM,IAAI,CAAC,WAAW,CAAC,IAAI,CAAC,CAAA;QAC7C,IAAI,QAAQ,CAAC,MAAM,IAAI,CAAC,QAAQ,CAAC,QAAQ,CAAC,OAAO,CAAC,EAAE;YAClD,OAAO,KAAK,CAAA;SACb;QACD,OAAO,IAAI,CAAA;IACb,CAAC;IAEM,aAAa,EAAC,gBAAgB,IAAS,CAAC;CAChD"}

package/esm/SPARQLAdapter/configSchema.js.map

@@ -1 +0,0 @@
-{"version":3,"file":"configSchema.js","sourceRoot":"","sources":["../../src/SPARQLAdapter/configSchema.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,mBAAmB,EAAE,MAAM,6BAA6B,CAAA;AAEjE,eAAe,mBAAmB,CAChC,eAAe,EACf;IACE,QAAQ,EAAE;QACR,IAAI,EAAE,cAAc;QACpB,YAAY,EAAE;YACZ,GAAG,EAAE,6BAA6B;YAClC,YAAY,EAAE,aAAa;SAC5B;QACD,WAAW,EAAE,4BAA4B;KAC1C;IACD,aAAa,EAAE;QACb,IAAI,EAAE,MAAM;QACZ,YAAY,EAAE,EAAE;QAChB,WAAW,EACT,gFAAgF;KACnF;IACD,qBAAqB,EAAE;QACrB,IAAI,EAAE,MAAM;QACZ,YAAY,EAAE,EAAE;QAChB,WAAW,EACT,sEAAsE;KACzE;IACD,QAAQ,EAAE;QACR,IAAI,EAAE,aAAa;QACnB,YAAY,EAAE,EAAE;QAChB,WAAW,EACT,gGAAgG;KACnG;IACD,qBAAqB,EAAE;QACrB,IAAI,EAAE,aAAa;QACnB,YAAY,EAAE,EAAE;QAChB,WAAW,EACT,+DAA+D;KAClE;CACF,EACD,EAAE,eAAe,EAAE,IAAI,EAAE,CAC1B,CAAA"}

package/esm/SPARQLAdapter/index.js.map

@@ -1 +0,0 @@
-{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/SPARQLAdapter/index.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,OAAO,IAAI,YAAY,EAAE,MAAM,iBAAiB,CAAA;AACzD,OAAO,EAAE,OAAO,IAAI,YAAY,EAAE,MAAM,gBAAgB,CAAA"}

package/esm/index.js.map

@@ -1 +0,0 @@
-{"version":3,"file":"index.js","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":"AAAA,OAAO,WAAW,MAAM,iDAAiD,CAAA;AACzE,OAAO,MAAM,MAAM,sBAAsB,CAAA;AAGzC,OAAO,EACL,YAAY,IAAI,kBAAkB,EAClC,YAAY,IAAI,yBAAyB,GAC1C,MAAM,iBAAiB,CAAA;AACxB,OAAO,EAAkB,WAAW,EAAE,MAAM,2BAA2B,CAAA;AAEvE,MAAM,CAAC,OAAO,OAAO,SAAU,SAAQ,MAAM;IAA7C;;QACE,SAAI,GAAG,WAAW,CAAA;IAkCpB,CAAC;IAhCC,OAAO,CAAC,aAA4B;QAClC,aAAa,CAAC,cAAc,CAC1B,GAAG,EAAE,CACH,IAAI,WAAW,CAAC;YACd,IAAI,EAAE,eAAe;YACrB,WAAW,EAAE,gBAAgB;YAC7B,YAAY,EAAE,yBAAyB;YACvC,YAAY,EAAE,kBAAkB;SACjC,CAAC,CACL,CAAA;QACD,aAAa,CAAC,mBAAmB,CAC/B,8BAA8B,EAC9B,CAAC,cAA8B,EAAE,EAAE;YACjC,OAAO,CACL,IAAkB,EAClB,KAAoB,EACpB,WAAoB,EACpB,EAAE;gBACF,MAAM,UAAU,GAAG,YAAY,CAAA;gBAC/B,MAAM,WAAW,GAAG,eAAe,CAAA;gBACnC,MAAM,QAAQ,GAAG,WAAW,CAAC,IAAI,CAAC,CAAA;gBAClC,IAAI,UAAU,CAAC,IAAI,CAAC,QAAQ,CAAC,IAAI,WAAW,KAAK,WAAW,EAAE;oBAC5D,OAAO;wBACL,IAAI,EAAE,WAAW;wBACjB,QAAQ,EAAE,IAAI;qBACf,CAAA;iBACF;gBACD,OAAO,cAAc,CAAC,IAAI,EAAE,KAAK,EAAE,WAAW,CAAC,CAAA;YACjD,CAAC,CAAA;QACH,CAAC,CACF,CAAA;IACH,CAAC;CACF"}

package/src/SPARQLAdapter/README.md

@@ -1,115 +0,0 @@
-# SPARQL Adapter
-
-JBrowse can display genomic information stored in RDF data stores by accessing
-them via a SPARQL endpoint. This is done by configuring a SPARQL adapter.
-
-## Query template
-
-The most basic configuration starts with a SPARQL query that returns features in
-a genomic range, i.e. on a particular chromosome/contig and between a start and
-end position. In such a query, replace the chromosome/contig name with
-`{refName}` and the start and end with `{start}` and `{end}`. For example
-
-```sparql
-PREFIX  rdfs: <http://www.w3.org/2000/01/rdf-schema#>
-PREFIX  rdf:  <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
-PREFIX  faldo: <http://biohackathon.org/resource/faldo#>
-PREFIX  dc:   <http://purl.org/dc/elements/1.1/>
-
-SELECT DISTINCT  ?gene (?id AS ?uniqueId) (?label AS ?name) (?desc AS ?note) ?strand ?start ?end
-WHERE
-  { VALUES ?location_type { faldo:ForwardStrandPosition faldo:ReverseStrandPosition faldo:BothStrandsPosition }
-    ?location  faldo:begin     _:b0 .
-    _:b0      rdf:type         ?location_type ;
-              faldo:position   ?faldo_begin .
-    ?location  faldo:end       _:b1 .
-    _:b1      rdf:type         ?location_type ;
-              faldo:position   ?faldo_end .
-    ?location  faldo:reference  <http://rdf.ebi.ac.uk/resource/ensembl/97/homo_sapiens/GRCh38/{refName}> .
-    ?gene     rdf:type         ?type ;
-              rdfs:label       ?label ;
-              dc:description   ?desc ;
-              dc:identifier    ?id ;
-              faldo:location   ?location
-    BIND(if(( ?location_type = faldo:ForwardStrandPosition ), 1, if(( ?location_type = faldo:ReverseStrandPosition ), -1, 0)) AS ?strand)
-    BIND(if(( ?strand = -1 ), ?faldo_end, ?faldo_begin) AS ?start)
-    BIND(if(( ?strand = -1 ), ?faldo_begin, ?faldo_end) AS ?end)
-    FILTER ( ( ?start >= {start} ) && ( ?end <= {end} ) )
-  }
-```
-
-The SELECT in the the query must provide at least the variables `?start`,
-`?end`, and `?uniqueId`. Any other variables will be added to the feature data.
-
-## Adding a track
-
-From a JBrowse track selector, click the "+" icon and choose "Add track". When
-asked for the location of the data source, enter the SPARQL endpoint. If the
-endpoint ends with `/sparql`, JBrowse will automatically choose the SPARQL
-adapter. If not, choose "SPARQL adapter" in the resulting dialog. (You can use
-https://www.ebi.ac.uk/rdf/services/sparql as the endpoint to demonstrate the
-above example.)
-
-You will then be able to choose a track name and type as well as the assembly to
-which the track should be added. BasicTrack is suggested for most
-configurations, and using other track types is covered below. Click the "Add"
-button to add the track.
-
-Next, in the track selector click the settings icon next to the track which was
-just added. Paste the query template (see above) in the "queryTemplate" section.
-You can also configure other aspects of the track such as a description,
-category, etc.
-
-## Advanced configuration
-
-### Subfeatures
-
-There are two ways to provide subfeature information. The first is to include a
-`?parentUniqueId` variable with a feature. It will be created as a subfeature of
-the feature with a matching `?uniqueId`.
-
-The second way is useful if a single query response line contains information
-for more than one feature, e.g. gene, transcript, and exon information on a
-single line. For this type of data prefix all variables for the subfeature with
-`sub_`, which will allow you to define multiple features from the same line. It
-also works for deeper nested features, too, by using `sub_sub_`, etc. Parent
-features that are duplicated across lines will be resolved into a single
-feature. For example, take the following SPARQL query result lines:
-
-| uniqueId   | type | start    | end      | sub_uniqueId     | sub_type   | sub_start | sub_end  | sub_sub_uniqueId | sub_sub_type | sub_sub_start | sub_sub_end |
-| ---------- | ---- | -------- | -------- | ---------------- | ---------- | --------- | -------- | ---------------- | ------------ | ------------- | ----------- |
-| geneId0001 | gene | 10430102 | 10452003 | transcriptId0001 | transcript | 10430518  | 10442405 | exonId0001       | exon         | 10430518      | 10430568    |
-| geneId0001 | gene | 10430102 | 10452003 | transcriptId0001 | transcript | 10430518  | 10442405 | exonId0002       | exon         | 10432568      | 10433965    |
-
-These two lines will resolve into a singe feature "geneId0001" with one child
-feature "transcriptId0001", which will then itself have two child features
-"exonId0001" and "exonId0002".
-
-### Additional query parameters
-
-JBrowse will automatically send a header stating that it expects responses to be
-in the `application/json` or `application/sparql-results+json` format. Some
-SPARQL endpoints, however, require additional query parameters to be passed in
-order for the results be returned in JSON format, for example `format=json`.
-These can be added to the "additionalQueryParams" section and will be appended
-to each SPARQL request.
-
-### Reference sequence renaming
-
-In order for the track to take advantage of JBrowse's reference name aliasing,
-it must know what reference name the SPARQL store uses. These can be entered in
-one of two ways. The first is by entering a SPARQL query in the
-"refNamesQueryTemplate" config section. This query should return a line for each
-reference name in a `refName` column.
-
-The second option is to enumerate the reference names explicitly in the
-"refNames" config section. These will be ignored if a "refNamesQueryTemplate" is
-defined.
-
-### Other track types
-
-BasicTracks are flexible because they don't require any additional information,
-any any additional info provided in the query is just added to the feature. You
-can use other tracks as well, though, as long as you make sure the SPARQL query
-provides any info the track requires. For example, if you want to use a
-VariantTrack, the SPARQL query must provide REF, ALT, QUAL, etc.

package/src/SPARQLAdapter/SPARQLAdapter.test.ts

@@ -1,84 +0,0 @@
-import { toArray } from 'rxjs/operators'
-import 'whatwg-fetch'
-import Adapter from './SPARQLAdapter'
-import emptyQueryResponse from './test_data/emptyQueryResponse.json'
-import queryResponse from './test_data/queryResponse.json'
-import refNamesResponse from './test_data/refNamesResponse.json'
-
-import configSchema from './configSchema'
-
-// window.fetch = jest.fn(url => new Promise(resolve => resolve()))
-
-test('adapter can fetch variants from volvox.vcf.gz', async () => {
-  function mockFetch(url: RequestInfo | URL) {
-    let response = {}
-    if (`${url}`.includes('chr1')) {
-      response = queryResponse
-    }
-    if (`${url}`.includes('chr80')) {
-      response = emptyQueryResponse
-    } else if (`${url}`.includes('fakeRefNamesQuery')) {
-      response = refNamesResponse
-    }
-
-    return Promise.resolve(new Response(JSON.stringify(response)))
-  }
-
-  const spy = jest.spyOn(global, 'fetch')
-  spy.mockImplementation(mockFetch)
-  const adapter = new Adapter(
-    configSchema.create({
-      endpoint: {
-        uri: 'http://somesite.com/sparql',
-        locationType: 'UriLocation',
-      },
-      queryTemplate: 'fakeSPARQLQuery-start{start}-end{end}-{refName}',
-      refNamesQueryTemplate: 'fakeRefNamesQuery',
-      additionalQueryParams: ['format=json'],
-      refNames: [],
-    }),
-  )
-
-  const refNames = await adapter.getRefNames()
-  expect(spy).toHaveBeenLastCalledWith(
-    'http://somesite.com/sparql?query=fakeRefNamesQuery&format=json',
-    {
-      headers: { accept: 'application/json,application/sparql-results+json' },
-      signal: undefined,
-    },
-  )
-  expect(refNames.length).toBe(17)
-  expect(refNames[0]).toBe('NC_004353.4')
-
-  const features = adapter.getFeatures({
-    refName: 'chr1',
-    start: 0,
-    end: 20000,
-  })
-  const featuresArray = await features.pipe(toArray()).toPromise()
-  expect(featuresArray).toMatchSnapshot()
-  expect(spy).toHaveBeenLastCalledWith(
-    'http://somesite.com/sparql?query=fakeSPARQLQuery-start0-end20000-chr1&format=json',
-    {
-      headers: { accept: 'application/json,application/sparql-results+json' },
-      signal: undefined,
-    },
-  )
-
-  const featuresNonExist = adapter.getFeatures({
-    refName: 'chr80',
-    start: 0,
-    end: 20000,
-  })
-  const featuresArrayNonExist = await featuresNonExist
-    .pipe(toArray())
-    .toPromise()
-  expect(featuresArrayNonExist).toEqual([])
-  expect(spy).toHaveBeenLastCalledWith(
-    'http://somesite.com/sparql?query=fakeSPARQLQuery-start0-end20000-chr80&format=json',
-    {
-      headers: { accept: 'application/json,application/sparql-results+json' },
-      signal: undefined,
-    },
-  )
-})

package/src/SPARQLAdapter/SPARQLAdapter.ts

@@ -1,257 +0,0 @@
-import {
-  BaseFeatureDataAdapter,
-  BaseOptions,
-} from '@jbrowse/core/data_adapters/BaseAdapter'
-import { NoAssemblyRegion } from '@jbrowse/core/util/types'
-import { ObservableCreate } from '@jbrowse/core/util/rxjs'
-import SimpleFeature, { Feature } from '@jbrowse/core/util/simpleFeature'
-import format from 'string-template'
-
-import { Instance } from 'mobx-state-tree'
-import { readConfObject } from '@jbrowse/core/configuration'
-import MyConfigSchema from './configSchema'
-import PluginManager from '@jbrowse/core/PluginManager'
-import { getSubAdapterType } from '@jbrowse/core/data_adapters/dataAdapterCache'
-
-interface SPARQLEntry {
-  type: string
-  value: string
-  dataTypes?: string
-}
-
-interface SPARQLBinding {
-  [key: string]: SPARQLEntry
-}
-
-interface SPARQLResponseHead {
-  vars: string[]
-}
-
-interface SPARQLResponseResults {
-  bindings: SPARQLBinding[]
-}
-
-interface SPARQLResponse {
-  head: SPARQLResponseHead
-  results: SPARQLResponseResults
-}
-
-interface SPARQLFeatureData {
-  start: number
-  end: number
-  strand: number
-  subfeatures?: SPARQLFeatureData[]
-  uniqueId: string
-  // eslint-disable-next-line @typescript-eslint/no-explicit-any
-  [propName: string]: any
-}
-
-interface SPARQLFeature {
-  data: SPARQLFeatureData
-}
-
-export default class SPARQLAdapter extends BaseFeatureDataAdapter {
-  private endpoint: string
-
-  private queryTemplate: string
-
-  private refNamesQueryTemplate: string
-
-  private additionalQueryParams: string[]
-
-  private configRefNames: string[]
-
-  private refNames: string[] | undefined
-
-  public constructor(
-    config: Instance<typeof MyConfigSchema>,
-    getSubAdapter?: getSubAdapterType,
-    pluginManager?: PluginManager,
-  ) {
-    super(config, getSubAdapter, pluginManager)
-    this.endpoint = readConfObject(config, 'endpoint').uri
-    this.queryTemplate = readConfObject(config, 'queryTemplate')
-    this.additionalQueryParams = readConfObject(config, 'additionalQueryParams')
-    this.refNamesQueryTemplate = readConfObject(config, 'refNamesQueryTemplate')
-    this.configRefNames = readConfObject(config, 'refNames')
-  }
-
-  public async getRefNames(opts: BaseOptions = {}): Promise<string[]> {
-    if (this.refNames) {
-      return this.refNames
-    }
-    let refNames = [] as string[]
-    if (this.refNamesQueryTemplate) {
-      const queryTemplate = encodeURIComponent(this.refNamesQueryTemplate)
-      const results = await this.querySparql(queryTemplate, opts)
-      refNames = this.resultsToRefNames(results)
-    } else if (this.configRefNames) {
-      refNames = this.configRefNames
-    }
-    this.refNames = refNames
-    return refNames
-  }
-
-  public getFeatures(query: NoAssemblyRegion, opts: BaseOptions = {}) {
-    return ObservableCreate<Feature>(async observer => {
-      const filledTemplate = encodeURIComponent(
-        format(this.queryTemplate, query),
-      )
-      const { refName } = query
-      const results = await this.querySparql(filledTemplate, opts)
-      this.resultsToFeatures(results, refName).forEach(feature => {
-        observer.next(feature)
-      })
-      observer.complete()
-    }, opts.signal)
-  }
-
-  // eslint-disable-next-line @typescript-eslint/no-explicit-any
-  private async querySparql(query: string, opts?: BaseOptions): Promise<any> {
-    let additionalQueryParams = ''
-    if (this.additionalQueryParams.length) {
-      additionalQueryParams = `&${this.additionalQueryParams.join('&')}`
-    }
-    const signal = opts && opts.signal
-    const response = await fetch(
-      `${this.endpoint}?query=${query}${additionalQueryParams}`,
-      {
-        headers: { accept: 'application/json,application/sparql-results+json' },
-        signal,
-      },
-    )
-    return response.json()
-  }
-
-  private resultsToRefNames(response: SPARQLResponse): string[] {
-    const rows = ((response || {}).results || {}).bindings || []
-    if (!rows.length) {
-      return []
-    }
-    const fields = response.head.vars
-    if (!fields.includes('refName')) {
-      throw new Error('"refName" not found in refNamesQueryTemplate response')
-    }
-    return rows.map(row => row.refName.value)
-  }
-
-  private resultsToFeatures(
-    results: SPARQLResponse,
-    refName: string,
-  ): SimpleFeature[] {
-    const rows = ((results || {}).results || {}).bindings || []
-    if (!rows.length) {
-      return []
-    }
-    const fields = results.head.vars
-    const requiredFields = ['start', 'end', 'uniqueId']
-    requiredFields.forEach(requiredField => {
-      if (!fields.includes(requiredField)) {
-        console.error(
-          `Required field ${requiredField} missing from feature data`,
-        )
-      }
-    })
-    const seenFeatures: Record<string, SPARQLFeature> = {}
-    rows.forEach(row => {
-      const rawData: Record<string, string>[] = [{}]
-      fields.forEach(field => {
-        if (field in row) {
-          const { value } = row[field]
-          let idx = 0
-          while (field.startsWith('sub_')) {
-            field = field.slice(4)
-            idx += 1
-          }
-          while (idx > rawData.length - 1) {
-            rawData.push({})
-          }
-          rawData[idx][field] = value
-        }
-      })
-
-      rawData.forEach((rd, idx) => {
-        const { uniqueId } = rd
-        if (idx < rawData.length - 1) {
-          rawData[idx + 1].parentUniqueId = uniqueId
-        }
-        seenFeatures[uniqueId] = {
-          data: {
-            ...rd,
-            uniqueId,
-            refName,
-            start: parseInt(rd.start, 10),
-            end: parseInt(rd.end, 10),
-            strand: parseInt(rd.strand, 10) || 0,
-          },
-        }
-      })
-    })
-
-    // resolve subfeatures, keeping only top-level features in seenFeatures
-    for (const [uniqueId, f] of Object.entries(seenFeatures)) {
-      const pid = f.data.parentUniqueId
-      delete f.data.parentUniqueId
-      if (pid) {
-        const p = seenFeatures[pid]
-        if (p) {
-          if (!p.data.subfeatures) {
-            p.data.subfeatures = []
-          }
-          p.data.subfeatures.push({
-            ...f.data,
-            uniqueId,
-          })
-          delete seenFeatures[uniqueId]
-        } else {
-          const subfeatures = Object.values(seenFeatures)
-            .map(sf => sf.data.subfeatures)
-            .filter(sf => !!sf)
-            .flat()
-          let found = false
-          for (const subfeature of subfeatures) {
-            if (subfeature && subfeature.uniqueId === pid) {
-              if (!subfeature.subfeatures) {
-                subfeature.subfeatures = []
-              }
-              subfeature.subfeatures.push({
-                ...f.data,
-                uniqueId,
-              })
-              delete seenFeatures[uniqueId]
-              found = true
-              break
-            } else if (subfeature && subfeature.subfeatures) {
-              subfeatures.push(...subfeature.subfeatures)
-            }
-          }
-          if (!found) {
-            console.error(`Could not find parentID ${pid}`)
-          }
-        }
-      }
-    }
-
-    return Object.keys(seenFeatures).map(
-      seenFeature =>
-        new SimpleFeature({
-          ...seenFeatures[seenFeature].data,
-          uniqueId: seenFeature,
-          subfeatures: seenFeatures[seenFeature].data.subfeatures,
-        }),
-    )
-  }
-
-  public async hasDataForRefName(
-    refName: string,
-    opts: BaseOptions = {},
-  ): Promise<boolean> {
-    const refNames = await this.getRefNames(opts)
-    if (refNames.length && !refNames.includes(refName)) {
-      return false
-    }
-    return true
-  }
-
-  public freeResources(/* { region } */): void {}
-}