@abi-software/flatmapvuer 0.4.1-beta.0 → 0.4.1-beta.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/flatmapvuer.common.js +450 -549
- package/dist/flatmapvuer.common.js.map +1 -1
- package/dist/flatmapvuer.css +1 -1
- package/dist/flatmapvuer.umd.js +450 -549
- package/dist/flatmapvuer.umd.js.map +1 -1
- package/dist/flatmapvuer.umd.min.js +2 -2
- package/dist/flatmapvuer.umd.min.js.map +1 -1
- package/package-lock.json +22 -4
- package/package.json +2 -2
- package/src/App.vue +1 -1
- package/src/components/FlatmapVuer.vue +27 -11
- package/src/components/SelectionsGroup.vue +2 -2
- package/src/services/flatmapQueries.js +32 -33
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/* harmony import */ var _node_modules_mini_css_extract_plugin_dist_loader_js_ref_9_oneOf_1_0_node_modules_css_loader_dist_cjs_js_ref_9_oneOf_1_1_node_modules_vue_loader_lib_loaders_stylePostLoader_js_node_modules_postcss_loader_src_index_js_ref_9_oneOf_1_2_node_modules_sass_loader_dist_cjs_js_ref_9_oneOf_1_3_node_modules_cache_loader_dist_cjs_js_ref_1_0_node_modules_vue_loader_lib_index_js_vue_loader_options_FlatmapVuer_vue_vue_type_style_index_0_id_3bcd7b15_prod_scoped_true_lang_scss___WEBPACK_IMPORTED_MODULE_0__ = __webpack_require__("ee41");
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/* harmony import */ var _node_modules_mini_css_extract_plugin_dist_loader_js_ref_9_oneOf_1_0_node_modules_css_loader_dist_cjs_js_ref_9_oneOf_1_1_node_modules_vue_loader_lib_loaders_stylePostLoader_js_node_modules_postcss_loader_src_index_js_ref_9_oneOf_1_2_node_modules_sass_loader_dist_cjs_js_ref_9_oneOf_1_3_node_modules_cache_loader_dist_cjs_js_ref_1_0_node_modules_vue_loader_lib_index_js_vue_loader_options_FlatmapVuer_vue_vue_type_style_index_0_id_3bcd7b15_prod_scoped_true_lang_scss___WEBPACK_IMPORTED_MODULE_0___default = /*#__PURE__*/__webpack_require__.n(_node_modules_mini_css_extract_plugin_dist_loader_js_ref_9_oneOf_1_0_node_modules_css_loader_dist_cjs_js_ref_9_oneOf_1_1_node_modules_vue_loader_lib_loaders_stylePostLoader_js_node_modules_postcss_loader_src_index_js_ref_9_oneOf_1_2_node_modules_sass_loader_dist_cjs_js_ref_9_oneOf_1_3_node_modules_cache_loader_dist_cjs_js_ref_1_0_node_modules_vue_loader_lib_index_js_vue_loader_options_FlatmapVuer_vue_vue_type_style_index_0_id_3bcd7b15_prod_scoped_true_lang_scss___WEBPACK_IMPORTED_MODULE_0__);
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/* harmony import */ var _node_modules_mini_css_extract_plugin_dist_loader_js_ref_9_oneOf_1_0_node_modules_css_loader_dist_cjs_js_ref_9_oneOf_1_1_node_modules_vue_loader_lib_loaders_stylePostLoader_js_node_modules_postcss_loader_src_index_js_ref_9_oneOf_1_2_node_modules_sass_loader_dist_cjs_js_ref_9_oneOf_1_3_node_modules_cache_loader_dist_cjs_js_ref_1_0_node_modules_vue_loader_lib_index_js_vue_loader_options_SelectionsGroup_vue_vue_type_style_index_0_id_1f69f0e7_prod_scoped_true_lang_scss___WEBPACK_IMPORTED_MODULE_0__ = __webpack_require__("06b8");
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/* harmony import */ var _node_modules_mini_css_extract_plugin_dist_loader_js_ref_9_oneOf_1_0_node_modules_css_loader_dist_cjs_js_ref_9_oneOf_1_1_node_modules_vue_loader_lib_loaders_stylePostLoader_js_node_modules_postcss_loader_src_index_js_ref_9_oneOf_1_2_node_modules_sass_loader_dist_cjs_js_ref_9_oneOf_1_3_node_modules_cache_loader_dist_cjs_js_ref_1_0_node_modules_vue_loader_lib_index_js_vue_loader_options_SelectionsGroup_vue_vue_type_style_index_0_id_1f69f0e7_prod_scoped_true_lang_scss___WEBPACK_IMPORTED_MODULE_0___default = /*#__PURE__*/__webpack_require__.n(_node_modules_mini_css_extract_plugin_dist_loader_js_ref_9_oneOf_1_0_node_modules_css_loader_dist_cjs_js_ref_9_oneOf_1_1_node_modules_vue_loader_lib_loaders_stylePostLoader_js_node_modules_postcss_loader_src_index_js_ref_9_oneOf_1_2_node_modules_sass_loader_dist_cjs_js_ref_9_oneOf_1_3_node_modules_cache_loader_dist_cjs_js_ref_1_0_node_modules_vue_loader_lib_index_js_vue_loader_options_SelectionsGroup_vue_vue_type_style_index_0_id_1f69f0e7_prod_scoped_true_lang_scss___WEBPACK_IMPORTED_MODULE_0__);
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/* harmony import */ var _node_modules_mini_css_extract_plugin_dist_loader_js_ref_9_oneOf_1_0_node_modules_css_loader_dist_cjs_js_ref_9_oneOf_1_1_node_modules_vue_loader_lib_loaders_stylePostLoader_js_node_modules_postcss_loader_src_index_js_ref_9_oneOf_1_2_node_modules_sass_loader_dist_cjs_js_ref_9_oneOf_1_3_node_modules_cache_loader_dist_cjs_js_ref_1_0_node_modules_vue_loader_lib_index_js_vue_loader_options_FlatmapVuer_vue_vue_type_style_index_0_id_01bcf386_prod_scoped_true_lang_scss___WEBPACK_IMPORTED_MODULE_0__ = __webpack_require__("abf8");
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/* harmony import */ var _node_modules_mini_css_extract_plugin_dist_loader_js_ref_9_oneOf_1_0_node_modules_css_loader_dist_cjs_js_ref_9_oneOf_1_1_node_modules_vue_loader_lib_loaders_stylePostLoader_js_node_modules_postcss_loader_src_index_js_ref_9_oneOf_1_2_node_modules_sass_loader_dist_cjs_js_ref_9_oneOf_1_3_node_modules_cache_loader_dist_cjs_js_ref_1_0_node_modules_vue_loader_lib_index_js_vue_loader_options_FlatmapVuer_vue_vue_type_style_index_0_id_01bcf386_prod_scoped_true_lang_scss___WEBPACK_IMPORTED_MODULE_0___default = /*#__PURE__*/__webpack_require__.n(_node_modules_mini_css_extract_plugin_dist_loader_js_ref_9_oneOf_1_0_node_modules_css_loader_dist_cjs_js_ref_9_oneOf_1_1_node_modules_vue_loader_lib_loaders_stylePostLoader_js_node_modules_postcss_loader_src_index_js_ref_9_oneOf_1_2_node_modules_sass_loader_dist_cjs_js_ref_9_oneOf_1_3_node_modules_cache_loader_dist_cjs_js_ref_1_0_node_modules_vue_loader_lib_index_js_vue_loader_options_FlatmapVuer_vue_vue_type_style_index_0_id_01bcf386_prod_scoped_true_lang_scss___WEBPACK_IMPORTED_MODULE_0__);
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/* harmony import */ var _node_modules_mini_css_extract_plugin_dist_loader_js_ref_9_oneOf_1_0_node_modules_css_loader_dist_cjs_js_ref_9_oneOf_1_1_node_modules_vue_loader_lib_loaders_stylePostLoader_js_node_modules_postcss_loader_src_index_js_ref_9_oneOf_1_2_node_modules_sass_loader_dist_cjs_js_ref_9_oneOf_1_3_node_modules_cache_loader_dist_cjs_js_ref_1_0_node_modules_vue_loader_lib_index_js_vue_loader_options_SelectionsGroup_vue_vue_type_style_index_0_id_404813f2_prod_scoped_true_lang_scss___WEBPACK_IMPORTED_MODULE_0__ = __webpack_require__("9b03");
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/* harmony import */ var _node_modules_mini_css_extract_plugin_dist_loader_js_ref_9_oneOf_1_0_node_modules_css_loader_dist_cjs_js_ref_9_oneOf_1_1_node_modules_vue_loader_lib_loaders_stylePostLoader_js_node_modules_postcss_loader_src_index_js_ref_9_oneOf_1_2_node_modules_sass_loader_dist_cjs_js_ref_9_oneOf_1_3_node_modules_cache_loader_dist_cjs_js_ref_1_0_node_modules_vue_loader_lib_index_js_vue_loader_options_SelectionsGroup_vue_vue_type_style_index_0_id_404813f2_prod_scoped_true_lang_scss___WEBPACK_IMPORTED_MODULE_0___default = /*#__PURE__*/__webpack_require__.n(_node_modules_mini_css_extract_plugin_dist_loader_js_ref_9_oneOf_1_0_node_modules_css_loader_dist_cjs_js_ref_9_oneOf_1_1_node_modules_vue_loader_lib_loaders_stylePostLoader_js_node_modules_postcss_loader_src_index_js_ref_9_oneOf_1_2_node_modules_sass_loader_dist_cjs_js_ref_9_oneOf_1_3_node_modules_cache_loader_dist_cjs_js_ref_1_0_node_modules_vue_loader_lib_index_js_vue_loader_options_SelectionsGroup_vue_vue_type_style_index_0_id_404813f2_prod_scoped_true_lang_scss___WEBPACK_IMPORTED_MODULE_0__);
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var EventBus = new external_vue_default.a();
|
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/* harmony default export */ var components_EventBus = (EventBus);
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// CONCATENATED MODULE: ./node_modules/cache-loader/dist/cjs.js?{"cacheDirectory":"node_modules/.cache/vue-loader","cacheIdentifier":"
|
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+
// CONCATENATED MODULE: ./node_modules/cache-loader/dist/cjs.js?{"cacheDirectory":"node_modules/.cache/vue-loader","cacheIdentifier":"1a046c7e-vue-loader-template"}!./node_modules/cache-loader/dist/cjs.js??ref--13-0!./node_modules/babel-loader/lib!./node_modules/vue-loader/lib/loaders/templateLoader.js??ref--6!./node_modules/cache-loader/dist/cjs.js??ref--1-0!./node_modules/vue-loader/lib??vue-loader-options!./src/components/ExternalResourceCard.vue?vue&type=template&id=14172b61&scoped=true&
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|
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var
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// CONCATENATED MODULE: ./node_modules/cache-loader/dist/cjs.js?{"cacheDirectory":"node_modules/.cache/vue-loader","cacheIdentifier":"1a046c7e-vue-loader-template"}!./node_modules/cache-loader/dist/cjs.js??ref--13-0!./node_modules/babel-loader/lib!./node_modules/vue-loader/lib/loaders/templateLoader.js??ref--6!./node_modules/cache-loader/dist/cjs.js??ref--1-0!./node_modules/vue-loader/lib??vue-loader-options!./src/components/SelectionsGroup.vue?vue&type=template&id=404813f2&scoped=true&
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var SelectionsGroupvue_type_template_id_404813f2_scoped_true_render = function render() {
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|
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@@ -15075,7 +15055,7 @@ var SelectionsGroupvue_type_template_id_1f69f0e7_scoped_true_render = function r
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staticClass: "my-checkbox",
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|
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}, [_vm._v(" " + _vm._s(item[_vm.labelKey]) + " ")])])], 1)], 1)], 1)]);
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var SelectionsGroupvue_type_template_id_404813f2_scoped_true_staticRenderFns = [];
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// CONCATENATED MODULE: ./src/components/SelectionsGroup.vue?vue&type=template&id=
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// EXTERNAL MODULE: ./node_modules/element-ui/lib/theme-chalk/checkbox-group.css
|
|
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|
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@@ -15161,7 +15141,7 @@ external_vue_default.a.use(lib_row_default.a);
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this.checkAll = true;
|
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|
|
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|
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if (!('
|
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|
|
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|
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|
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// CONCATENATED MODULE: ./src/components/SelectionsGroup.vue?vue&type=script&lang=js&
|
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|
/* harmony default export */ var components_SelectionsGroupvue_type_script_lang_js_ = (SelectionsGroupvue_type_script_lang_js_);
|
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// EXTERNAL MODULE: ./src/components/SelectionsGroup.vue?vue&type=style&index=0&id=
|
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// EXTERNAL MODULE: ./src/components/SelectionsGroup.vue?vue&type=style&index=0&id=404813f2&prod&scoped=true&lang=scss&
|
|
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var SelectionsGroupvue_type_style_index_0_id_404813f2_prod_scoped_true_lang_scss_ = __webpack_require__("e777");
|
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// CONCATENATED MODULE: ./src/components/SelectionsGroup.vue
|
|
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15248
|
|
|
@@ -15275,11 +15255,11 @@ var SelectionsGroupvue_type_style_index_0_id_1f69f0e7_prod_scoped_true_lang_scss
|
|
|
15275
15255
|
|
|
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|
var SelectionsGroup_component = normalizeComponent(
|
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SelectionsGroupvue_type_template_id_404813f2_scoped_true_render,
|
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SelectionsGroupvue_type_template_id_404813f2_scoped_true_staticRenderFns,
|
|
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false,
|
|
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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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// CONCATENATED MODULE: ./node_modules/cache-loader/dist/cjs.js?{"cacheDirectory":"node_modules/.cache/vue-loader","cacheIdentifier":"
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|
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// CONCATENATED MODULE: ./node_modules/cache-loader/dist/cjs.js?{"cacheDirectory":"node_modules/.cache/vue-loader","cacheIdentifier":"1a046c7e-vue-loader-template"}!./node_modules/cache-loader/dist/cjs.js??ref--13-0!./node_modules/babel-loader/lib!./node_modules/vue-loader/lib/loaders/templateLoader.js??ref--6!./node_modules/cache-loader/dist/cjs.js??ref--1-0!./node_modules/vue-loader/lib??vue-loader-options!./src/components/legends/SvgLegends.vue?vue&type=template&id=3d3218c8&scoped=true&
|
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|
|
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|
|
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|
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|
|
@@ -15404,80 +15384,6 @@ var SvgLegends_component = normalizeComponent(
|
|
|
15404
15384
|
/* harmony default export */ var SvgLegends = (SvgLegends_component.exports);
|
|
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|
// CONCATENATED MODULE: ./src/icons/flatmap-marker.js
|
|
15406
15386
|
/* harmony default export */ var flatmap_marker = ('<div class="flatmap-marker"><svg display="block" height="41px" width="27px" viewBox="0 0 27 41"><g fill-rule="nonzero"><g transform="translate(3.0, 29.0)" fill="#000000"><ellipse opacity="0.04" cx="10.5" cy="5.80029008" rx="10.5" ry="5.25002273"></ellipse><ellipse opacity="0.04" cx="10.5" cy="5.80029008" rx="10.5" ry="5.25002273"></ellipse><ellipse opacity="0.04" cx="10.5" cy="5.80029008" rx="9.5" ry="4.77275007"></ellipse><ellipse opacity="0.04" cx="10.5" cy="5.80029008" rx="8.5" ry="4.29549936"></ellipse><ellipse opacity="0.04" cx="10.5" cy="5.80029008" rx="7.5" ry="3.81822308"></ellipse><ellipse opacity="0.04" cx="10.5" cy="5.80029008" rx="6.5" ry="3.34094679"></ellipse><ellipse opacity="0.04" cx="10.5" cy="5.80029008" rx="5.5" ry="2.86367051"></ellipse><ellipse opacity="0.04" cx="10.5" cy="5.80029008" rx="4.5" ry="2.38636864"></ellipse></g><g fill="#005974"><path d="M27,13.5 C27,19.074644 20.250001,27.000002 14.75,34.500002 C14.016665,35.500004 12.983335,35.500004 12.25,34.500002 C6.7499993,27.000002 0,19.222562 0,13.5 C0,6.0441559 6.0441559,0 13.5,0 C20.955844,0 27,6.0441559 27,13.5 Z"></path></g><g opacity="0.25" fill="#000000"><path d="M13.5,0 C6.0441559,0 0,6.0441559 0,13.5 C0,19.222562 6.7499993,27 12.25,34.5 C13,35.522727 14.016664,35.500004 14.75,34.5 C20.250001,27 27,19.074644 27,13.5 C27,6.0441559 20.955844,0 13.5,0 Z M13.5,1 C20.415404,1 26,6.584596 26,13.5 C26,15.898657 24.495584,19.181431 22.220703,22.738281 C19.945823,26.295132 16.705119,30.142167 13.943359,33.908203 C13.743445,34.180814 13.612715,34.322738 13.5,34.441406 C13.387285,34.322738 13.256555,34.180814 13.056641,33.908203 C10.284481,30.127985 7.4148684,26.314159 5.015625,22.773438 C2.6163816,19.232715 1,15.953538 1,13.5 C1,6.584596 6.584596,1 13.5,1 Z"></path></g><g transform="translate(6.0, 7.0)" fill="#FFFFFF"></g><g transform="translate(8.0, 8.0)"><circle fill="#000000" opacity="0.25" cx="5.5" cy="5.5" r="5.4999962"></circle><circle fill="#FFFFFF" cx="5.5" cy="5.5" r="5.4999962"></circle></g></g></svg></div>');
|
|
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|
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// CONCATENATED MODULE: ./node_modules/@babel/runtime/helpers/esm/classCallCheck.js
|
|
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|
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|
|
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|
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function _classCallCheck(instance, Constructor) {
|
|
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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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// EXTERNAL MODULE: external "core-js/modules/es.symbol.to-primitive.js"
|
|
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|
-
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|
|
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|
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|
|
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|
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// EXTERNAL MODULE: external "core-js/modules/es.date.to-primitive.js"
|
|
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|
-
var es_date_to_primitive_js_ = __webpack_require__("1f48");
|
|
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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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|
|
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|
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function _toPrimitive(input, hint) {
|
|
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|
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|
|
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|
-
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|
|
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|
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if (prim !== undefined) {
|
|
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|
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|
|
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|
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if (_typeof(res) !== "object") return res;
|
|
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|
-
throw new TypeError("@@toPrimitive must return a primitive value.");
|
|
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|
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}
|
|
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|
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return (hint === "string" ? String : Number)(input);
|
|
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|
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}
|
|
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|
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// CONCATENATED MODULE: ./node_modules/@babel/runtime/helpers/esm/toPropertyKey.js
|
|
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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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|
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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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|
|
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|
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Object.defineProperty(target, _toPropertyKey(descriptor.key), descriptor);
|
|
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|
-
}
|
|
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|
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}
|
|
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|
-
function _createClass(Constructor, protoProps, staticProps) {
|
|
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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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|
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|
|
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|
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// CONCATENATED MODULE: ./node_modules/@babel/runtime/helpers/esm/defineProperty.js
|
|
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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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|
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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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|
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|
|
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|
|
|
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|
function _arrayWithoutHoles(arr) {
|
|
@@ -15517,15 +15423,15 @@ var es_array_flat_js_ = __webpack_require__("da6e");
|
|
|
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15423
|
// EXTERNAL MODULE: external "core-js/modules/es.array.unscopables.flat.js"
|
|
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|
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|
|
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|
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|
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|
|
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|
+
var es_array_filter_js_ = __webpack_require__("1a89");
|
|
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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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|
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// EXTERNAL MODULE: external "core-js/modules/es.array.filter.js"
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|
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|
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|
|
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|
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|
|
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|
// CONCATENATED MODULE: ./src/services/flatmapQueries.js
|
|
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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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15466
|
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|
|
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15467
|
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|
|
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|
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|
|
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|
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var flatmapQueries_FlatmapQueries =
|
|
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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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|
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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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|
|
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|
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_defineProperty(this, "getOrganCuries", 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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|
-
}).then(function (data) {
|
|
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|
-
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|
|
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|
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|
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|
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|
-
_defineProperty(this, "createComponentsLabelList", function (components, lookUp) {
|
|
15600
|
-
var _this2 = this;
|
|
15601
|
-
var labelList = [];
|
|
15602
|
-
components.forEach(function (n) {
|
|
15603
|
-
labelList.push(_this2.createLabelFromNeuralNode(n[0]), lookUp);
|
|
15604
|
-
if (n.length === 2) {
|
|
15605
|
-
labelList.push(_this2.createLabelFromNeuralNode(n[1]), lookUp);
|
|
15606
|
-
}
|
|
15469
|
+
var flatmapQueries_FlatmapQueries = function FlatmapQueries() {
|
|
15470
|
+
this.initialise = function (sparcApi, flatmapApi) {
|
|
15471
|
+
var _this = this;
|
|
15472
|
+
this.sparcApi = sparcApi;
|
|
15473
|
+
this.flatmapApi = flatmapApi;
|
|
15474
|
+
this.destinations = [];
|
|
15475
|
+
this.origins = [];
|
|
15476
|
+
this.components = [];
|
|
15477
|
+
this.uberons = [];
|
|
15478
|
+
this.urls = [];
|
|
15479
|
+
this.controller = undefined;
|
|
15480
|
+
this.getOrganCuries().then(function (uberons) {
|
|
15481
|
+
_this.uberons = uberons;
|
|
15482
|
+
_this.createLabelLookup(uberons).then(function (lookUp) {
|
|
15483
|
+
_this.lookUp = lookUp;
|
|
15607
15484
|
});
|
|
15608
|
-
return labelList;
|
|
15609
15485
|
});
|
|
15610
|
-
|
|
15611
|
-
|
|
15612
|
-
|
|
15613
|
-
|
|
15614
|
-
|
|
15615
|
-
|
|
15486
|
+
};
|
|
15487
|
+
this.createTooltipData = function (eventData) {
|
|
15488
|
+
var tooltipData = {
|
|
15489
|
+
destinations: this.destinations,
|
|
15490
|
+
origins: this.origins,
|
|
15491
|
+
components: this.components,
|
|
15492
|
+
destinationsWithDatasets: this.destinationsWithDatasets,
|
|
15493
|
+
originsWithDatasets: this.originsWithDatasets,
|
|
15494
|
+
componentsWithDatasets: this.componentsWithDatasets,
|
|
15495
|
+
title: eventData.label,
|
|
15496
|
+
featureId: eventData.resource,
|
|
15497
|
+
hyperlinks: eventData.feature.hyperlinks ? eventData.feature.hyperlinks : this.urls.map(function (url) {
|
|
15498
|
+
return {
|
|
15499
|
+
url: url,
|
|
15500
|
+
id: "pubmed"
|
|
15616
15501
|
};
|
|
15617
|
-
|
|
15618
|
-
|
|
15619
|
-
|
|
15620
|
-
|
|
15621
|
-
|
|
15622
|
-
|
|
15623
|
-
|
|
15624
|
-
|
|
15625
|
-
|
|
15626
|
-
|
|
15627
|
-
|
|
15628
|
-
if (entity > -1 && label > -1) {
|
|
15629
|
-
payload.values.forEach(function (pair) {
|
|
15630
|
-
uberonMap[pair[entity]] = pair[label];
|
|
15631
|
-
});
|
|
15632
|
-
}
|
|
15633
|
-
resolve(uberonMap);
|
|
15634
|
-
});
|
|
15635
|
-
});
|
|
15636
|
-
});
|
|
15637
|
-
_defineProperty(this, "buildConnectivitySqlStatement", function (keastIds) {
|
|
15638
|
-
var sql = 'select knowledge from knowledge where entity in (';
|
|
15639
|
-
if (keastIds.length === 1) {
|
|
15640
|
-
sql += "'".concat(keastIds[0], "')");
|
|
15641
|
-
} else if (keastIds.length > 1) {
|
|
15642
|
-
for (var i in keastIds) {
|
|
15643
|
-
sql += "'".concat(keastIds[i], "'").concat(i >= keastIds.length - 1 ? ')' : ',', " ");
|
|
15644
|
-
}
|
|
15645
|
-
}
|
|
15646
|
-
return sql;
|
|
15647
|
-
});
|
|
15648
|
-
_defineProperty(this, "buildLabelSqlStatement", function (uberons) {
|
|
15649
|
-
var sql = 'select entity, label from labels where entity in (';
|
|
15650
|
-
if (uberons.length === 1) {
|
|
15651
|
-
sql += "'".concat(uberons[0], "')");
|
|
15652
|
-
} else if (uberons.length > 1) {
|
|
15653
|
-
for (var i in uberons) {
|
|
15654
|
-
sql += "'".concat(uberons[i], "'").concat(i >= uberons.length - 1 ? ')' : ',', " ");
|
|
15655
|
-
}
|
|
15656
|
-
}
|
|
15657
|
-
return sql;
|
|
15658
|
-
});
|
|
15659
|
-
_defineProperty(this, "findAllIdsFromConnectivity", function (connectivity) {
|
|
15660
|
-
var dnodes = connectivity.connectivity.flat(); // get nodes from edgelist
|
|
15661
|
-
var nodes = _toConsumableArray(new Set(dnodes)); // remove duplicates
|
|
15662
|
-
var found = [];
|
|
15663
|
-
nodes.forEach(function (n) {
|
|
15664
|
-
if (Array.isArray(n)) {
|
|
15665
|
-
found.push(n.flat());
|
|
15666
|
-
} else {
|
|
15667
|
-
found.push(n);
|
|
15668
|
-
}
|
|
15669
|
-
});
|
|
15670
|
-
return _toConsumableArray(new Set(found.flat()));
|
|
15671
|
-
});
|
|
15672
|
-
_defineProperty(this, "flattenConntectivity", function (connectivity) {
|
|
15673
|
-
var dnodes = connectivity.flat(); // get nodes from edgelist
|
|
15674
|
-
var nodes = _toConsumableArray(new Set(dnodes)); // remove duplicates
|
|
15675
|
-
var found = [];
|
|
15676
|
-
nodes.forEach(function (n) {
|
|
15677
|
-
if (Array.isArray(n)) {
|
|
15678
|
-
found.push(n.flat());
|
|
15679
|
-
} else {
|
|
15680
|
-
found.push(n);
|
|
15681
|
-
}
|
|
15682
|
-
});
|
|
15683
|
-
return found.flat();
|
|
15684
|
-
});
|
|
15685
|
-
_defineProperty(this, "findComponents", function (connectivity) {
|
|
15686
|
-
var dnodes = connectivity.connectivity.flat(); // get nodes from edgelist
|
|
15687
|
-
var nodes = flatmapQueries_removeDuplicates(dnodes);
|
|
15688
|
-
var found = [];
|
|
15689
|
-
var terminal = false;
|
|
15690
|
-
nodes.forEach(function (node) {
|
|
15691
|
-
terminal = false;
|
|
15692
|
-
// Check if the node is an destination or origin (note that they are labelled dendrite and axon as opposed to origin and destination)
|
|
15693
|
-
if (inArray(connectivity.axons, node)) {
|
|
15694
|
-
terminal = true;
|
|
15695
|
-
}
|
|
15696
|
-
if (inArray(connectivity.dendrites, node)) {
|
|
15697
|
-
terminal = true;
|
|
15698
|
-
}
|
|
15699
|
-
if (!terminal) {
|
|
15700
|
-
found.push(node);
|
|
15701
|
-
}
|
|
15702
|
-
});
|
|
15703
|
-
return found;
|
|
15704
|
-
});
|
|
15705
|
-
_defineProperty(this, "retrieveFlatmapKnowledgeForEvent", /*#__PURE__*/function () {
|
|
15706
|
-
var _ref = _asyncToGenerator( /*#__PURE__*/_regeneratorRuntime().mark(function _callee(eventData) {
|
|
15707
|
-
var _this4 = this;
|
|
15708
|
-
var signal, keastIds, data, prom1, prom2;
|
|
15709
|
-
return _regeneratorRuntime().wrap(function _callee$(_context) {
|
|
15710
|
-
while (1) {
|
|
15711
|
-
switch (_context.prev = _context.next) {
|
|
15712
|
-
case 0:
|
|
15713
|
-
// check if there is an existing query
|
|
15714
|
-
if (this.controller) this.controller.abort();
|
|
15715
|
-
|
|
15716
|
-
// set up the abort controller
|
|
15717
|
-
this.controller = new AbortController();
|
|
15718
|
-
signal = this.controller.signal;
|
|
15719
|
-
keastIds = eventData.resource;
|
|
15720
|
-
this.destinations = [];
|
|
15721
|
-
this.origins = [];
|
|
15722
|
-
this.components = [];
|
|
15723
|
-
if (!(!keastIds || keastIds.length == 0)) {
|
|
15724
|
-
_context.next = 9;
|
|
15725
|
-
break;
|
|
15726
|
-
}
|
|
15727
|
-
return _context.abrupt("return");
|
|
15728
|
-
case 9:
|
|
15729
|
-
data = {
|
|
15730
|
-
sql: this.buildConnectivitySqlStatement(keastIds)
|
|
15731
|
-
};
|
|
15732
|
-
prom1 = new Promise(function (resolve) {
|
|
15733
|
-
fetch("".concat(_this4.flatmapApi, "knowledge/query/"), {
|
|
15734
|
-
method: 'POST',
|
|
15735
|
-
headers: {
|
|
15736
|
-
'Content-Type': 'application/json'
|
|
15737
|
-
},
|
|
15738
|
-
body: JSON.stringify(data),
|
|
15739
|
-
signal: signal
|
|
15740
|
-
}).then(function (response) {
|
|
15741
|
-
return response.json();
|
|
15742
|
-
}).then(function (data) {
|
|
15743
|
-
if (_this4.connectivityExists(data)) {
|
|
15744
|
-
var connectivity = JSON.parse(data.values[0][0]);
|
|
15745
|
-
_this4.processConnectivity(connectivity).then(function () {
|
|
15746
|
-
resolve(true);
|
|
15747
|
-
});
|
|
15748
|
-
} else {
|
|
15749
|
-
console.log('No connectivity data found');
|
|
15750
|
-
resolve(true);
|
|
15751
|
-
}
|
|
15752
|
-
}).catch(function (error) {
|
|
15753
|
-
console.error('Error:', error);
|
|
15754
|
-
resolve(false);
|
|
15755
|
-
});
|
|
15756
|
-
});
|
|
15757
|
-
prom2 = this.pubmedQueryOnIds(eventData);
|
|
15758
|
-
_context.next = 14;
|
|
15759
|
-
return Promise.all([prom1, prom2]);
|
|
15760
|
-
case 14:
|
|
15761
|
-
return _context.abrupt("return", _context.sent);
|
|
15762
|
-
case 15:
|
|
15763
|
-
case "end":
|
|
15764
|
-
return _context.stop();
|
|
15765
|
-
}
|
|
15766
|
-
}
|
|
15767
|
-
}, _callee, this);
|
|
15768
|
-
}));
|
|
15769
|
-
return function (_x) {
|
|
15770
|
-
return _ref.apply(this, arguments);
|
|
15771
|
-
};
|
|
15772
|
-
}());
|
|
15773
|
-
_defineProperty(this, "connectivityExists", function (data) {
|
|
15774
|
-
if (data.values && data.values.length > 0 && JSON.parse(data.values[0][0]).connectivity && JSON.parse(data.values[0][0]).connectivity.length > 0) {
|
|
15775
|
-
return true;
|
|
15776
|
-
} else {
|
|
15777
|
-
return false;
|
|
15778
|
-
}
|
|
15779
|
-
});
|
|
15780
|
-
_defineProperty(this, "createLabelFromNeuralNode", function (node, lookUp) {
|
|
15781
|
-
var label = lookUp[node[0]];
|
|
15782
|
-
if (node.length === 2 && node[1].length > 0) {
|
|
15783
|
-
node[1].forEach(function (n) {
|
|
15784
|
-
if (lookUp[n] == undefined) {
|
|
15785
|
-
label += ", ".concat(n);
|
|
15786
|
-
} else {
|
|
15787
|
-
label += ", ".concat(lookUp[n]);
|
|
15788
|
-
}
|
|
15789
|
-
});
|
|
15790
|
-
}
|
|
15791
|
-
return label;
|
|
15792
|
-
});
|
|
15793
|
-
_defineProperty(this, "findComponents", function (connectivity) {
|
|
15794
|
-
var dnodes = connectivity.connectivity.flat(); // get nodes from edgelist
|
|
15795
|
-
var nodes = flatmapQueries_removeDuplicates(dnodes);
|
|
15796
|
-
var found = [];
|
|
15797
|
-
var terminal = false;
|
|
15798
|
-
nodes.forEach(function (node) {
|
|
15799
|
-
terminal = false;
|
|
15800
|
-
// Check if the node is an destination or origin (note that they are labelled dendrite and axon as opposed to origin and destination)
|
|
15801
|
-
if (inArray(connectivity.axons, node)) {
|
|
15802
|
-
terminal = true;
|
|
15803
|
-
}
|
|
15804
|
-
if (inArray(connectivity.dendrites, node)) {
|
|
15805
|
-
terminal = true;
|
|
15806
|
-
}
|
|
15807
|
-
if (!terminal) {
|
|
15808
|
-
found.push(node);
|
|
15809
|
-
}
|
|
15502
|
+
})
|
|
15503
|
+
};
|
|
15504
|
+
return tooltipData;
|
|
15505
|
+
};
|
|
15506
|
+
this.getOrganCuries = function () {
|
|
15507
|
+
var _this2 = this;
|
|
15508
|
+
return new Promise(function (resolve) {
|
|
15509
|
+
fetch("".concat(_this2.sparcAPI, "get-organ-curies/")).then(function (response) {
|
|
15510
|
+
return response.json();
|
|
15511
|
+
}).then(function (data) {
|
|
15512
|
+
resolve(data.uberon.array);
|
|
15810
15513
|
});
|
|
15811
|
-
return found;
|
|
15812
|
-
});
|
|
15813
|
-
_defineProperty(this, "stripPMIDPrefix", function (pubmedId) {
|
|
15814
|
-
return pubmedId.split(':')[1];
|
|
15815
15514
|
});
|
|
15816
|
-
|
|
15817
|
-
|
|
15818
|
-
|
|
15819
|
-
|
|
15820
|
-
|
|
15821
|
-
|
|
15822
|
-
|
|
15823
|
-
|
|
15515
|
+
};
|
|
15516
|
+
this.createComponentsLabelList = function (components, lookUp) {
|
|
15517
|
+
var _this3 = this;
|
|
15518
|
+
var labelList = [];
|
|
15519
|
+
components.forEach(function (n) {
|
|
15520
|
+
labelList.push(_this3.createLabelFromNeuralNode(n[0]), lookUp);
|
|
15521
|
+
if (n.length === 2) {
|
|
15522
|
+
labelList.push(_this3.createLabelFromNeuralNode(n[1]), lookUp);
|
|
15824
15523
|
}
|
|
15825
|
-
return sql;
|
|
15826
15524
|
});
|
|
15827
|
-
|
|
15828
|
-
|
|
15829
|
-
|
|
15830
|
-
|
|
15525
|
+
return labelList;
|
|
15526
|
+
};
|
|
15527
|
+
this.createLabelLookup = function (uberons) {
|
|
15528
|
+
var _this4 = this;
|
|
15529
|
+
return new Promise(function (resolve) {
|
|
15530
|
+
var uberonMap = {};
|
|
15831
15531
|
var data = {
|
|
15832
|
-
sql:
|
|
15532
|
+
sql: _this4.buildLabelSqlStatement(uberons)
|
|
15833
15533
|
};
|
|
15834
|
-
|
|
15534
|
+
fetch("".concat(_this4.flatmapApi, "knowledge/query/"), {
|
|
15835
15535
|
method: 'POST',
|
|
15836
15536
|
headers: {
|
|
15837
15537
|
'Content-Type': 'application/json'
|
|
@@ -15839,135 +15539,331 @@ var flatmapQueries_FlatmapQueries = /*#__PURE__*/function () {
|
|
|
15839
15539
|
body: JSON.stringify(data)
|
|
15840
15540
|
}).then(function (response) {
|
|
15841
15541
|
return response.json();
|
|
15842
|
-
}).
|
|
15843
|
-
|
|
15844
|
-
|
|
15845
|
-
|
|
15846
|
-
|
|
15847
|
-
|
|
15848
|
-
var keastIds = eventData.resource;
|
|
15849
|
-
var source = eventData.feature.source;
|
|
15850
|
-
if (!keastIds || keastIds.length === 0) return;
|
|
15851
|
-
var sql = this.buildPubmedSqlStatement(keastIds);
|
|
15852
|
-
return this.flatmapQuery(sql).then(function (data) {
|
|
15853
|
-
// Create pubmed url on paths if we have them
|
|
15854
|
-
if (data.values.length > 0) {
|
|
15855
|
-
_this5.urls = [_this5.pubmedSearchUrl(data.values.map(function (id) {
|
|
15856
|
-
return _this5.stripPMIDPrefix(id[0]);
|
|
15857
|
-
}))];
|
|
15858
|
-
return true;
|
|
15859
|
-
} else {
|
|
15860
|
-
// Create pubmed url on models
|
|
15861
|
-
_this5.pubmedQueryOnModels(source).then(function () {
|
|
15862
|
-
return true;
|
|
15542
|
+
}).then(function (payload) {
|
|
15543
|
+
var entity = payload.keys.indexOf("entity");
|
|
15544
|
+
var label = payload.keys.indexOf("label");
|
|
15545
|
+
if (entity > -1 && label > -1) {
|
|
15546
|
+
payload.values.forEach(function (pair) {
|
|
15547
|
+
uberonMap[pair[entity]] = pair[label];
|
|
15863
15548
|
});
|
|
15864
15549
|
}
|
|
15550
|
+
resolve(uberonMap);
|
|
15865
15551
|
});
|
|
15866
15552
|
});
|
|
15867
|
-
|
|
15868
|
-
|
|
15869
|
-
|
|
15870
|
-
|
|
15871
|
-
|
|
15872
|
-
|
|
15873
|
-
|
|
15553
|
+
};
|
|
15554
|
+
this.buildConnectivitySqlStatement = function (keastIds) {
|
|
15555
|
+
var sql = 'select knowledge from knowledge where entity in (';
|
|
15556
|
+
if (keastIds.length === 1) {
|
|
15557
|
+
sql += "'".concat(keastIds[0], "')");
|
|
15558
|
+
} else if (keastIds.length > 1) {
|
|
15559
|
+
for (var i in keastIds) {
|
|
15560
|
+
sql += "'".concat(keastIds[i], "'").concat(i >= keastIds.length - 1 ? ')' : ',', " ");
|
|
15561
|
+
}
|
|
15562
|
+
}
|
|
15563
|
+
return sql;
|
|
15564
|
+
};
|
|
15565
|
+
this.buildLabelSqlStatement = function (uberons) {
|
|
15566
|
+
var sql = 'select entity, label from labels where entity in (';
|
|
15567
|
+
if (uberons.length === 1) {
|
|
15568
|
+
sql += "'".concat(uberons[0], "')");
|
|
15569
|
+
} else if (uberons.length > 1) {
|
|
15570
|
+
for (var i in uberons) {
|
|
15571
|
+
sql += "'".concat(uberons[i], "'").concat(i >= uberons.length - 1 ? ')' : ',', " ");
|
|
15572
|
+
}
|
|
15573
|
+
}
|
|
15574
|
+
return sql;
|
|
15575
|
+
};
|
|
15576
|
+
this.findAllIdsFromConnectivity = function (connectivity) {
|
|
15577
|
+
var dnodes = connectivity.connectivity.flat(); // get nodes from edgelist
|
|
15578
|
+
var nodes = _toConsumableArray(new Set(dnodes)); // remove duplicates
|
|
15579
|
+
var found = [];
|
|
15580
|
+
nodes.forEach(function (n) {
|
|
15581
|
+
if (Array.isArray(n)) {
|
|
15582
|
+
found.push(n.flat());
|
|
15583
|
+
} else {
|
|
15584
|
+
found.push(n);
|
|
15585
|
+
}
|
|
15586
|
+
});
|
|
15587
|
+
return _toConsumableArray(new Set(found.flat()));
|
|
15588
|
+
};
|
|
15589
|
+
this.flattenConntectivity = function (connectivity) {
|
|
15590
|
+
var dnodes = connectivity.flat(); // get nodes from edgelist
|
|
15591
|
+
var nodes = _toConsumableArray(new Set(dnodes)); // remove duplicates
|
|
15592
|
+
var found = [];
|
|
15593
|
+
nodes.forEach(function (n) {
|
|
15594
|
+
if (Array.isArray(n)) {
|
|
15595
|
+
found.push(n.flat());
|
|
15596
|
+
} else {
|
|
15597
|
+
found.push(n);
|
|
15598
|
+
}
|
|
15599
|
+
});
|
|
15600
|
+
return found.flat();
|
|
15601
|
+
};
|
|
15602
|
+
this.findComponents = function (connectivity) {
|
|
15603
|
+
var dnodes = connectivity.connectivity.flat(); // get nodes from edgelist
|
|
15604
|
+
var nodes = flatmapQueries_removeDuplicates(dnodes);
|
|
15605
|
+
var found = [];
|
|
15606
|
+
var terminal = false;
|
|
15607
|
+
nodes.forEach(function (node) {
|
|
15608
|
+
terminal = false;
|
|
15609
|
+
// Check if the node is an destination or origin (note that they are labelled dendrite and axon as opposed to origin and destination)
|
|
15610
|
+
if (inArray(connectivity.axons, node)) {
|
|
15611
|
+
terminal = true;
|
|
15612
|
+
}
|
|
15613
|
+
if (inArray(connectivity.dendrites, node)) {
|
|
15614
|
+
terminal = true;
|
|
15615
|
+
}
|
|
15616
|
+
if (!terminal) {
|
|
15617
|
+
found.push(node);
|
|
15618
|
+
}
|
|
15619
|
+
});
|
|
15620
|
+
return found;
|
|
15621
|
+
};
|
|
15622
|
+
this.retrieveFlatmapKnowledgeForEvent = /*#__PURE__*/function () {
|
|
15623
|
+
var _ref = _asyncToGenerator( /*#__PURE__*/_regeneratorRuntime().mark(function _callee(eventData) {
|
|
15624
|
+
var _this5 = this;
|
|
15625
|
+
var signal, keastIds, data, prom1, prom2, results;
|
|
15626
|
+
return _regeneratorRuntime().wrap(function _callee$(_context) {
|
|
15627
|
+
while (1) {
|
|
15628
|
+
switch (_context.prev = _context.next) {
|
|
15629
|
+
case 0:
|
|
15630
|
+
// check if there is an existing query
|
|
15631
|
+
if (this.controller) this.controller.abort();
|
|
15632
|
+
|
|
15633
|
+
// set up the abort controller
|
|
15634
|
+
this.controller = new AbortController();
|
|
15635
|
+
signal = this.controller.signal;
|
|
15636
|
+
keastIds = eventData.resource;
|
|
15637
|
+
this.destinations = [];
|
|
15638
|
+
this.origins = [];
|
|
15639
|
+
this.components = [];
|
|
15640
|
+
if (!(!keastIds || keastIds.length == 0)) {
|
|
15641
|
+
_context.next = 9;
|
|
15642
|
+
break;
|
|
15643
|
+
}
|
|
15644
|
+
return _context.abrupt("return");
|
|
15645
|
+
case 9:
|
|
15646
|
+
data = {
|
|
15647
|
+
sql: this.buildConnectivitySqlStatement(keastIds)
|
|
15648
|
+
};
|
|
15649
|
+
prom1 = new Promise(function (resolve) {
|
|
15650
|
+
fetch("".concat(_this5.flatmapApi, "knowledge/query/"), {
|
|
15651
|
+
method: 'POST',
|
|
15652
|
+
headers: {
|
|
15653
|
+
'Content-Type': 'application/json'
|
|
15654
|
+
},
|
|
15655
|
+
body: JSON.stringify(data),
|
|
15656
|
+
signal: signal
|
|
15657
|
+
}).then(function (response) {
|
|
15658
|
+
return response.json();
|
|
15659
|
+
}).then(function (data) {
|
|
15660
|
+
if (_this5.connectivityExists(data)) {
|
|
15661
|
+
var connectivity = JSON.parse(data.values[0][0]);
|
|
15662
|
+
_this5.processConnectivity(connectivity).then(function () {
|
|
15663
|
+
resolve(true);
|
|
15664
|
+
});
|
|
15665
|
+
} else {
|
|
15666
|
+
console.log('No connectivity data found');
|
|
15667
|
+
resolve(false);
|
|
15668
|
+
}
|
|
15669
|
+
}).catch(function (error) {
|
|
15670
|
+
console.error('Error:', error);
|
|
15671
|
+
resolve(false);
|
|
15672
|
+
});
|
|
15673
|
+
});
|
|
15674
|
+
prom2 = this.pubmedQueryOnIds(eventData);
|
|
15675
|
+
_context.next = 14;
|
|
15676
|
+
return Promise.all([prom1, prom2]);
|
|
15677
|
+
case 14:
|
|
15678
|
+
results = _context.sent;
|
|
15679
|
+
return _context.abrupt("return", results.every(Boolean));
|
|
15680
|
+
case 16:
|
|
15681
|
+
case "end":
|
|
15682
|
+
return _context.stop();
|
|
15683
|
+
}
|
|
15684
|
+
}
|
|
15685
|
+
}, _callee, this);
|
|
15686
|
+
}));
|
|
15687
|
+
return function (_x) {
|
|
15688
|
+
return _ref.apply(this, arguments);
|
|
15689
|
+
};
|
|
15690
|
+
}();
|
|
15691
|
+
this.connectivityExists = function (data) {
|
|
15692
|
+
if (data.values && data.values.length > 0 && JSON.parse(data.values[0][0]).connectivity && JSON.parse(data.values[0][0]).connectivity.length > 0) {
|
|
15693
|
+
return true;
|
|
15694
|
+
} else {
|
|
15695
|
+
return false;
|
|
15696
|
+
}
|
|
15697
|
+
};
|
|
15698
|
+
this.createLabelFromNeuralNode = function (node, lookUp) {
|
|
15699
|
+
var label = lookUp[node[0]];
|
|
15700
|
+
if (node.length === 2 && node[1].length > 0) {
|
|
15701
|
+
node[1].forEach(function (n) {
|
|
15702
|
+
if (lookUp[n] == undefined) {
|
|
15703
|
+
label += ", ".concat(n);
|
|
15874
15704
|
} else {
|
|
15875
|
-
|
|
15705
|
+
label += ", ".concat(lookUp[n]);
|
|
15876
15706
|
}
|
|
15877
|
-
|
|
15878
|
-
return;
|
|
15879
15707
|
});
|
|
15708
|
+
}
|
|
15709
|
+
return label;
|
|
15710
|
+
};
|
|
15711
|
+
this.flattenAndFindDatasets = function (components, axons, dendrites) {
|
|
15712
|
+
// process the nodes for finding datasets (Note this is not critical to the tooltip, only for the 'search on components' button)
|
|
15713
|
+
var componentsFlat = this.flattenConntectivity(components);
|
|
15714
|
+
var axonsFlat = this.flattenConntectivity(axons);
|
|
15715
|
+
var dendritesFlat = this.flattenConntectivity(dendrites);
|
|
15716
|
+
|
|
15717
|
+
// Filter for the anatomy which is annotated on datasets
|
|
15718
|
+
this.destinationsWithDatasets = this.uberons.filter(function (ub) {
|
|
15719
|
+
return axonsFlat.indexOf(ub.id) !== -1;
|
|
15880
15720
|
});
|
|
15881
|
-
|
|
15882
|
-
|
|
15883
|
-
var params = new URLSearchParams();
|
|
15884
|
-
params.append('term', ids);
|
|
15885
|
-
return url + params.toString();
|
|
15721
|
+
this.originsWithDatasets = this.uberons.filter(function (ub) {
|
|
15722
|
+
return dendritesFlat.indexOf(ub.id) !== -1;
|
|
15886
15723
|
});
|
|
15887
|
-
this.
|
|
15888
|
-
|
|
15889
|
-
this.destinations = [];
|
|
15890
|
-
this.origins = [];
|
|
15891
|
-
this.components = [];
|
|
15892
|
-
this.uberons = [];
|
|
15893
|
-
this.urls = [];
|
|
15894
|
-
this.controller = undefined;
|
|
15895
|
-
this.getOrganCuries().then(function (uberons) {
|
|
15896
|
-
_this7.uberons = uberons;
|
|
15897
|
-
_this7.createLabelLookup(uberons).then(function (lookUp) {
|
|
15898
|
-
_this7.lookUp = lookUp;
|
|
15899
|
-
});
|
|
15724
|
+
this.componentsWithDatasets = this.uberons.filter(function (ub) {
|
|
15725
|
+
return componentsFlat.indexOf(ub.id) !== -1;
|
|
15900
15726
|
});
|
|
15901
|
-
}
|
|
15902
|
-
|
|
15903
|
-
|
|
15904
|
-
|
|
15905
|
-
//
|
|
15906
|
-
var
|
|
15907
|
-
|
|
15908
|
-
|
|
15909
|
-
|
|
15910
|
-
|
|
15911
|
-
|
|
15912
|
-
|
|
15913
|
-
|
|
15914
|
-
|
|
15915
|
-
|
|
15916
|
-
|
|
15917
|
-
|
|
15918
|
-
|
|
15727
|
+
};
|
|
15728
|
+
this.processConnectivity = function (connectivity) {
|
|
15729
|
+
var _this6 = this;
|
|
15730
|
+
return new Promise(function (resolve) {
|
|
15731
|
+
// Filter the origin and destinations from components
|
|
15732
|
+
var components = _this6.findComponents(connectivity);
|
|
15733
|
+
|
|
15734
|
+
// Remove duplicates
|
|
15735
|
+
var axons = flatmapQueries_removeDuplicates(connectivity.axons);
|
|
15736
|
+
var dendrites = flatmapQueries_removeDuplicates(connectivity.dendrites);
|
|
15737
|
+
|
|
15738
|
+
// Create list of ids to get labels for
|
|
15739
|
+
var conIds = _this6.findAllIdsFromConnectivity(connectivity);
|
|
15740
|
+
|
|
15741
|
+
// Create readable labels from the nodes. Setting this to 'this.origins' updates the display
|
|
15742
|
+
_this6.createLabelLookup(conIds).then(function (lookUp) {
|
|
15743
|
+
_this6.destinations = axons.map(function (a) {
|
|
15744
|
+
return _this6.createLabelFromNeuralNode(a, lookUp);
|
|
15745
|
+
});
|
|
15746
|
+
_this6.origins = dendrites.map(function (d) {
|
|
15747
|
+
return _this6.createLabelFromNeuralNode(d, lookUp);
|
|
15748
|
+
});
|
|
15749
|
+
_this6.components = components.map(function (c) {
|
|
15750
|
+
return _this6.createLabelFromNeuralNode(c, lookUp);
|
|
15751
|
+
});
|
|
15752
|
+
_this6.flattenAndFindDatasets(components, axons, dendrites);
|
|
15753
|
+
resolve(true);
|
|
15919
15754
|
});
|
|
15755
|
+
});
|
|
15756
|
+
};
|
|
15757
|
+
this.flattenConntectivity = function (connectivity) {
|
|
15758
|
+
var dnodes = connectivity.flat(); // get nodes from edgelist
|
|
15759
|
+
var nodes = _toConsumableArray(new Set(dnodes)); // remove duplicates
|
|
15760
|
+
var found = [];
|
|
15761
|
+
nodes.forEach(function (n) {
|
|
15762
|
+
if (Array.isArray(n)) {
|
|
15763
|
+
found.push(n.flat());
|
|
15764
|
+
} else {
|
|
15765
|
+
found.push(n);
|
|
15766
|
+
}
|
|
15767
|
+
});
|
|
15768
|
+
return found.flat();
|
|
15769
|
+
};
|
|
15770
|
+
this.findComponents = function (connectivity) {
|
|
15771
|
+
var dnodes = connectivity.connectivity.flat(); // get nodes from edgelist
|
|
15772
|
+
var nodes = flatmapQueries_removeDuplicates(dnodes);
|
|
15773
|
+
var found = [];
|
|
15774
|
+
var terminal = false;
|
|
15775
|
+
nodes.forEach(function (node) {
|
|
15776
|
+
terminal = false;
|
|
15777
|
+
// Check if the node is an destination or origin (note that they are labelled dendrite and axon as opposed to origin and destination)
|
|
15778
|
+
if (inArray(connectivity.axons, node)) {
|
|
15779
|
+
terminal = true;
|
|
15780
|
+
}
|
|
15781
|
+
if (inArray(connectivity.dendrites, node)) {
|
|
15782
|
+
terminal = true;
|
|
15783
|
+
}
|
|
15784
|
+
if (!terminal) {
|
|
15785
|
+
found.push(node);
|
|
15786
|
+
}
|
|
15787
|
+
});
|
|
15788
|
+
return found;
|
|
15789
|
+
};
|
|
15790
|
+
this.stripPMIDPrefix = function (pubmedId) {
|
|
15791
|
+
return pubmedId.split(':')[1];
|
|
15792
|
+
};
|
|
15793
|
+
this.buildPubmedSqlStatement = function (keastIds) {
|
|
15794
|
+
var sql = 'select distinct publication from publications where entity in (';
|
|
15795
|
+
if (keastIds.length === 1) {
|
|
15796
|
+
sql += "'".concat(keastIds[0], "')");
|
|
15797
|
+
} else if (keastIds.length > 1) {
|
|
15798
|
+
for (var i in keastIds) {
|
|
15799
|
+
sql += "'".concat(keastIds[i], "'").concat(i >= keastIds.length - 1 ? ')' : ',', " ");
|
|
15800
|
+
}
|
|
15920
15801
|
}
|
|
15921
|
-
|
|
15922
|
-
|
|
15923
|
-
|
|
15924
|
-
|
|
15925
|
-
|
|
15926
|
-
|
|
15927
|
-
|
|
15928
|
-
|
|
15929
|
-
|
|
15930
|
-
|
|
15931
|
-
|
|
15802
|
+
return sql;
|
|
15803
|
+
};
|
|
15804
|
+
this.buildPubmedSqlStatementForModels = function (model) {
|
|
15805
|
+
return "select distinct publication from publications where entity = '".concat(model, "'");
|
|
15806
|
+
};
|
|
15807
|
+
this.flatmapQuery = function (sql) {
|
|
15808
|
+
var data = {
|
|
15809
|
+
sql: sql
|
|
15810
|
+
};
|
|
15811
|
+
return fetch("".concat(this.flatmapApi, "knowledge/query/"), {
|
|
15812
|
+
method: 'POST',
|
|
15813
|
+
headers: {
|
|
15814
|
+
'Content-Type': 'application/json'
|
|
15815
|
+
},
|
|
15816
|
+
body: JSON.stringify(data)
|
|
15817
|
+
}).then(function (response) {
|
|
15818
|
+
return response.json();
|
|
15819
|
+
}).catch(function (error) {
|
|
15820
|
+
console.error('Error:', error);
|
|
15821
|
+
});
|
|
15822
|
+
};
|
|
15823
|
+
this.pubmedQueryOnIds = function (eventData) {
|
|
15824
|
+
var _this7 = this;
|
|
15825
|
+
var keastIds = eventData.resource;
|
|
15826
|
+
var source = eventData.feature.source;
|
|
15827
|
+
if (!keastIds || keastIds.length === 0) return;
|
|
15828
|
+
var sql = this.buildPubmedSqlStatement(keastIds);
|
|
15829
|
+
return this.flatmapQuery(sql).then(function (data) {
|
|
15830
|
+
// Create pubmed url on paths if we have them
|
|
15831
|
+
if (data.values.length > 0) {
|
|
15832
|
+
_this7.urls = [_this7.pubmedSearchUrl(data.values.map(function (id) {
|
|
15833
|
+
return _this7.stripPMIDPrefix(id[0]);
|
|
15834
|
+
}))];
|
|
15835
|
+
return true;
|
|
15836
|
+
} else {
|
|
15837
|
+
// Create pubmed url on models
|
|
15838
|
+
_this7.pubmedQueryOnModels(source).then(function () {
|
|
15839
|
+
return true;
|
|
15840
|
+
});
|
|
15841
|
+
}
|
|
15842
|
+
return false;
|
|
15843
|
+
});
|
|
15844
|
+
};
|
|
15845
|
+
this.pubmedQueryOnModels = function (source) {
|
|
15846
|
+
var _this8 = this;
|
|
15847
|
+
return this.flatmapQuery(this.buildPubmedSqlStatementForModels(source)).then(function (data) {
|
|
15848
|
+
if (Array.isArray(data.values) && data.values.length > 0) {
|
|
15849
|
+
_this8.urls = [_this8.pubmedSearchUrl(data.values.map(function (id) {
|
|
15850
|
+
return _this8.stripPMIDPrefix(id[0]);
|
|
15851
|
+
}))];
|
|
15852
|
+
} else {
|
|
15853
|
+
_this8.urls = []; // Clears the pubmed search button
|
|
15854
|
+
}
|
|
15932
15855
|
|
|
15933
|
-
|
|
15934
|
-
|
|
15856
|
+
return;
|
|
15857
|
+
});
|
|
15858
|
+
};
|
|
15859
|
+
this.pubmedSearchUrl = function (ids) {
|
|
15860
|
+
var url = 'https://pubmed.ncbi.nlm.nih.gov/?';
|
|
15861
|
+
var params = new URLSearchParams();
|
|
15862
|
+
params.append('term', ids);
|
|
15863
|
+
return url + params.toString();
|
|
15864
|
+
};
|
|
15865
|
+
};
|
|
15935
15866
|
|
|
15936
|
-
// Create readable labels from the nodes. Setting this to 'this.origins' updates the display
|
|
15937
|
-
_this8.createLabelLookup(conIds).then(function (lookUp) {
|
|
15938
|
-
_this8.destinations = axons.map(function (a) {
|
|
15939
|
-
return _this8.createLabelFromNeuralNode(a, lookUp);
|
|
15940
|
-
});
|
|
15941
|
-
_this8.origins = dendrites.map(function (d) {
|
|
15942
|
-
return _this8.createLabelFromNeuralNode(d, lookUp);
|
|
15943
|
-
});
|
|
15944
|
-
_this8.components = components.map(function (c) {
|
|
15945
|
-
return _this8.createLabelFromNeuralNode(c, lookUp);
|
|
15946
|
-
});
|
|
15947
|
-
_this8.flattenAndFindDatasets(components, axons, dendrites);
|
|
15948
|
-
resolve(true);
|
|
15949
|
-
});
|
|
15950
|
-
});
|
|
15951
|
-
}
|
|
15952
|
-
}, {
|
|
15953
|
-
key: "flattenConntectivity",
|
|
15954
|
-
value: function flattenConntectivity(connectivity) {
|
|
15955
|
-
var dnodes = connectivity.flat(); // get nodes from edgelist
|
|
15956
|
-
var nodes = _toConsumableArray(new Set(dnodes)); // remove duplicates
|
|
15957
|
-
var found = [];
|
|
15958
|
-
nodes.forEach(function (n) {
|
|
15959
|
-
if (Array.isArray(n)) {
|
|
15960
|
-
found.push(n.flat());
|
|
15961
|
-
} else {
|
|
15962
|
-
found.push(n);
|
|
15963
|
-
}
|
|
15964
|
-
});
|
|
15965
|
-
return found.flat();
|
|
15966
|
-
}
|
|
15967
|
-
}]);
|
|
15968
|
-
return FlatmapQueries;
|
|
15969
|
-
}();
|
|
15970
|
-
/* harmony default export */ var flatmapQueries = (flatmapQueries_FlatmapQueries);
|
|
15971
15867
|
// CONCATENATED MODULE: ./node_modules/cache-loader/dist/cjs.js??ref--13-0!./node_modules/thread-loader/dist/cjs.js!./node_modules/babel-loader/lib!./node_modules/cache-loader/dist/cjs.js??ref--1-0!./node_modules/vue-loader/lib??vue-loader-options!./src/components/FlatmapVuer.vue?vue&type=script&lang=js&
|
|
15972
15868
|
|
|
15973
15869
|
|
|
@@ -16221,7 +16117,7 @@ var createUnfilledTooltipData = function createUnfilledTooltipData() {
|
|
|
16221
16117
|
// checkNeuronClicked shows a neuron path pop up if a path was recently clicked
|
|
16222
16118
|
checkAndCreatePopups: function () {
|
|
16223
16119
|
var _checkAndCreatePopups = _asyncToGenerator( /*#__PURE__*/_regeneratorRuntime().mark(function _callee(data) {
|
|
16224
|
-
var
|
|
16120
|
+
var results;
|
|
16225
16121
|
return _regeneratorRuntime().wrap(function _callee$(_context) {
|
|
16226
16122
|
while (1) {
|
|
16227
16123
|
switch (_context.prev = _context.next) {
|
|
@@ -16229,9 +16125,9 @@ var createUnfilledTooltipData = function createUnfilledTooltipData() {
|
|
|
16229
16125
|
_context.next = 2;
|
|
16230
16126
|
return this.flatmapQueries.retrieveFlatmapKnowledgeForEvent(data);
|
|
16231
16127
|
case 2:
|
|
16232
|
-
|
|
16233
|
-
if (!
|
|
16234
|
-
if (data.feature.hyperlinks) {
|
|
16128
|
+
results = _context.sent;
|
|
16129
|
+
if (!results) {
|
|
16130
|
+
if (data.feature.hyperlinks && data.feature.hyperlinks.length > 0) {
|
|
16235
16131
|
this.resourceForTooltip = data.resource[0];
|
|
16236
16132
|
this.createTooltipFromNeuronCuration(data);
|
|
16237
16133
|
}
|
|
@@ -16497,10 +16393,18 @@ var createUnfilledTooltipData = function createUnfilledTooltipData() {
|
|
|
16497
16393
|
}
|
|
16498
16394
|
},
|
|
16499
16395
|
mapResize: function mapResize() {
|
|
16500
|
-
|
|
16501
|
-
this.mapImp
|
|
16396
|
+
try {
|
|
16397
|
+
if (this.mapImp) {
|
|
16398
|
+
this.mapImp.resize();
|
|
16399
|
+
this.showMinimap(this.displayMinimap);
|
|
16400
|
+
if (this.mapImp._minimap) {
|
|
16401
|
+
this.mapImp._minimap.resize();
|
|
16402
|
+
}
|
|
16403
|
+
}
|
|
16404
|
+
this.computePathControlsMaximumHeight();
|
|
16405
|
+
} catch (_unused) {
|
|
16406
|
+
console.error("Map resize error");
|
|
16502
16407
|
}
|
|
16503
|
-
this.computePathControlsMaximumHeight();
|
|
16504
16408
|
},
|
|
16505
16409
|
onFlatmapReady: function onFlatmapReady() {
|
|
16506
16410
|
// onFlatmapReady is used for functions that need to run immediately after the flatmap is loaded
|
|
@@ -16512,12 +16416,14 @@ var createUnfilledTooltipData = function createUnfilledTooltipData() {
|
|
|
16512
16416
|
this.backgroundChangeCallback(this.currentBackground);
|
|
16513
16417
|
this.pathways = this.mapImp.pathTypes();
|
|
16514
16418
|
this.mapImp.enableCentrelines(false);
|
|
16515
|
-
|
|
16419
|
+
//Disable layers for now
|
|
16420
|
+
//this.layers = this.mapImp.getLayers();
|
|
16516
16421
|
this.systems = this.mapImp.getSystems();
|
|
16517
16422
|
this.addResizeButtonToMinimap();
|
|
16518
16423
|
this.loading = false;
|
|
16519
16424
|
this.computePathControlsMaximumHeight();
|
|
16520
16425
|
this.drawerOpen = true;
|
|
16426
|
+
this.mapResize();
|
|
16521
16427
|
this.$emit("ready", this);
|
|
16522
16428
|
},
|
|
16523
16429
|
showMinimap: function showMinimap(flag) {
|
|
@@ -16656,7 +16562,8 @@ var createUnfilledTooltipData = function createUnfilledTooltipData() {
|
|
|
16656
16562
|
}],
|
|
16657
16563
|
centreLines: [{
|
|
16658
16564
|
label: "Display Nerves",
|
|
16659
|
-
key: "centrelines"
|
|
16565
|
+
key: "centrelines",
|
|
16566
|
+
enabled: false
|
|
16660
16567
|
}],
|
|
16661
16568
|
systems: [],
|
|
16662
16569
|
pathwaysMaxHeight: 1000,
|
|
@@ -16712,13 +16619,14 @@ var createUnfilledTooltipData = function createUnfilledTooltipData() {
|
|
|
16712
16619
|
var flatmap = __webpack_require__("4979");
|
|
16713
16620
|
this.mapManager = new flatmap.MapManager(this.flatmapAPI);
|
|
16714
16621
|
if (this.renderAtMounted) this.createFlatmap();
|
|
16715
|
-
this.flatmapQueries = new flatmapQueries_FlatmapQueries(
|
|
16622
|
+
this.flatmapQueries = new flatmapQueries_FlatmapQueries();
|
|
16623
|
+
this.flatmapQueries.initialise(this.sparcAPI, this.flatmapAPI);
|
|
16716
16624
|
}
|
|
16717
16625
|
});
|
|
16718
16626
|
// CONCATENATED MODULE: ./src/components/FlatmapVuer.vue?vue&type=script&lang=js&
|
|
16719
16627
|
/* harmony default export */ var components_FlatmapVuervue_type_script_lang_js_ = (FlatmapVuervue_type_script_lang_js_);
|
|
16720
|
-
// EXTERNAL MODULE: ./src/components/FlatmapVuer.vue?vue&type=style&index=0&id=
|
|
16721
|
-
var
|
|
16628
|
+
// EXTERNAL MODULE: ./src/components/FlatmapVuer.vue?vue&type=style&index=0&id=01bcf386&prod&scoped=true&lang=scss&
|
|
16629
|
+
var FlatmapVuervue_type_style_index_0_id_01bcf386_prod_scoped_true_lang_scss_ = __webpack_require__("9382");
|
|
16722
16630
|
|
|
16723
16631
|
// CONCATENATED MODULE: ./src/components/FlatmapVuer.vue
|
|
16724
16632
|
|
|
@@ -16735,13 +16643,13 @@ var FlatmapVuer_component = normalizeComponent(
|
|
|
16735
16643
|
staticRenderFns,
|
|
16736
16644
|
false,
|
|
16737
16645
|
null,
|
|
16738
|
-
"
|
|
16646
|
+
"01bcf386",
|
|
16739
16647
|
null
|
|
16740
16648
|
|
|
16741
16649
|
)
|
|
16742
16650
|
|
|
16743
16651
|
/* harmony default export */ var FlatmapVuer = (FlatmapVuer_component.exports);
|
|
16744
|
-
// CONCATENATED MODULE: ./node_modules/cache-loader/dist/cjs.js?{"cacheDirectory":"node_modules/.cache/vue-loader","cacheIdentifier":"
|
|
16652
|
+
// CONCATENATED MODULE: ./node_modules/cache-loader/dist/cjs.js?{"cacheDirectory":"node_modules/.cache/vue-loader","cacheIdentifier":"1a046c7e-vue-loader-template"}!./node_modules/cache-loader/dist/cjs.js??ref--13-0!./node_modules/babel-loader/lib!./node_modules/vue-loader/lib/loaders/templateLoader.js??ref--6!./node_modules/cache-loader/dist/cjs.js??ref--1-0!./node_modules/vue-loader/lib??vue-loader-options!./src/components/MultiFlatmapVuer.vue?vue&type=template&id=bf82e340&scoped=true&
|
|
16745
16653
|
var MultiFlatmapVuervue_type_template_id_bf82e340_scoped_true_render = function render() {
|
|
16746
16654
|
var _vm = this,
|
|
16747
16655
|
_c = _vm._self._c;
|
|
@@ -17334,13 +17242,6 @@ var MultiFlatmapVuer_component = normalizeComponent(
|
|
|
17334
17242
|
|
|
17335
17243
|
|
|
17336
17244
|
|
|
17337
|
-
/***/ }),
|
|
17338
|
-
|
|
17339
|
-
/***/ "fb89":
|
|
17340
|
-
/***/ (function(module, exports) {
|
|
17341
|
-
|
|
17342
|
-
module.exports = require("core-js/modules/es.symbol.to-primitive.js");
|
|
17343
|
-
|
|
17344
17245
|
/***/ }),
|
|
17345
17246
|
|
|
17346
17247
|
/***/ "fd22":
|