@abi-software/mapintegratedvuer 1.12.4 → 1.12.6
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- package/dist/{ContentMixin-CSEGbP7G.js → ContentMixin-DE9Pk_KF.js} +200 -177
- package/dist/{Flatmap-DX7vdhah.js → Flatmap-BdSINIH3.js} +27 -39
- package/dist/{Iframe-CjY_VCK6.js → Iframe-DL3E0cnI.js} +2 -2
- package/dist/{MultiFlatmap-DLRSNwLa.js → MultiFlatmap-DKPBFc_Y.js} +21 -37
- package/dist/{Plot-nDa1teji.js → Plot-_ca3lFZI.js} +2 -2
- package/dist/{Scaffold-CAZt83-7.js → Scaffold-DxH7TMFn.js} +2 -2
- package/dist/{Simulation-DcJ--KHu.js → Simulation-ewRVK6sW.js} +2 -2
- package/dist/{index-QOPChEwx.js → index-BHZwLSRu.js} +7006 -6945
- package/dist/mapintegratedvuer.js +1 -1
- package/dist/mapintegratedvuer.umd.cjs +107 -107
- package/dist/style-IHXUSXDX.js +57 -0
- package/dist/style.css +1 -1
- package/package.json +6 -6
- package/src/App.vue +136 -3
- package/src/components/ContextCard.vue +9 -1
- package/src/components/MapContent.vue +20 -3
- package/src/components/SplitDialog.vue +2 -1
- package/src/components/SplitFlow.vue +48 -18
- package/src/components/viewers/Flatmap.vue +10 -26
- package/src/components/viewers/MultiFlatmap.vue +5 -25
- package/src/mixins/ContentMixin.js +43 -7
- package/src/mixins/DynamicMarkerMixin.js +2 -11
- package/src/stores/entries.js +12 -0
- package/src/stores/settings.js +1 -1
- package/dist/style-JL7U0dZL.js +0 -66
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import { markRaw as
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import {
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import { mapStores as
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import { markRaw as y } from "vue";
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import { c as C, u as E, d as O, e as N, E as f, T as b, f as R, h as x, i as w, l as P, J as B } from "./index-BHZwLSRu.js";
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import { mapStores as X } from "pinia";
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const M = function(e) {
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return e ? [...new Set(e.map((r) => JSON.stringify(r)))].map(
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(r) => JSON.parse(r)
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) : [];
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}, d = [], T = async function(e, r) {
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const t = r.filter(
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(s) => d.some((i) => i.taxon === s)
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), n = d.filter(
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(s) => t.includes(s.taxon)
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), a = r.filter(
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(s) => !t.includes(s)
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if (
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const s = await e.queryLabels(
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const s = await e.queryLabels(a);
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return s.forEach((i) => {
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let { entity: l, label: o } = i;
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o === "Mammalia" && (o = "Mammalia not otherwise specified");
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const c = { taxon: l, label: o };
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n.push(c),
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n.push(c), d.push(c);
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} else
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return n;
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},
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}, L = function(e, r) {
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let
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return
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let t = JSON.stringify(e), n = JSON.stringify(r);
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return t.indexOf(n) !== -1;
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const
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return
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const t = e.name ?? e, n = r.name ?? r, a = t.toUpperCase(), s = n.toUpperCase();
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return a < s ? -1 : a > s ? 1 : 0;
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};
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let S = function() {
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this.initialise = function(e) {
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this.flatmapAPI = e, this.destinations = [], this.origins = [], this.components = [], this.rawURLs = [], this.controller = void 0, this.uberons = [], this.lookUp = [], this.connectivitySource = "map", this.noMapConnectivity = !1;
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}, this.createTooltipData = async function(e, r) {
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let
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r.feature.hyperlinks && r.feature.hyperlinks.length > 0 ?
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let t = [];
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r.feature.hyperlinks && r.feature.hyperlinks.length > 0 ? t = r.feature.hyperlinks : t = this.rawURLs;
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let n;
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if (r.provenanceTaxonomy) {
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n = [];
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componentsWithDatasets: this.componentsWithDatasets,
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title: r.label,
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featureId: r.resource,
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hyperlinks:
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hyperlinks: t,
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provenanceTaxonomy: r.provenanceTaxonomy,
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provenanceTaxonomyLabel: n,
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connectivitySource: this.connectivitySource,
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noMapConnectivity: this.noMapConnectivity
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};
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}, this.createComponentsLabelList = function(e, r) {
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let
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}),
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t.push(this.createLabelFromNeuralNode(n[0]), r), n.length === 2 && t.push(this.createLabelFromNeuralNode(n[1]), r);
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}), t;
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}, this.createLabelLookup = function(e, r) {
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return new Promise(async (
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return new Promise(async (t) => {
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let n = {};
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this.uberons = [];
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const
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const a = await T(e, r);
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a.length && (a.forEach((s) => {
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const { taxon: i, label: l } = s;
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n[i] = l, this.uberons.push({
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id: i,
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name: l
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}),
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});
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}, this.buildConnectivitySqlStatement = function(e) {
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let r = "select knowledge from knowledge where entity in (";
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if (e.length === 1)
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r += `'${e[0]}')`;
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for (let
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r += `'${e[
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for (let t in e)
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r += `'${e[t]}'${t >= e.length - 1 ? ")" : ","} `;
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return r;
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}, this.buildLabelSqlStatement = function(e) {
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let r = "select entity, label from labels where entity in (";
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r += `'${e[0]}')`;
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for (let
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for (let t in e)
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r += `'${e[t]}'${t >= e.length - 1 ? ")" : ","} `;
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}, this.findAllIdsFromConnectivity = function(e) {
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let r = e.connectivity.flat(),
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return
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let r = e.connectivity.flat(), t = [...new Set(r)], n = [];
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return t.forEach((a) => {
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Array.isArray(a) ? n.push(a.flat()) : n.push(a);
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}), [...new Set(n.flat())];
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}, this.flattenConnectivity = function(e) {
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return
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let r = e.flat(), t = [...new Set(r)], n = [];
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return t.forEach((a) => {
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Array.isArray(a) ? n.push(a.flat()) : n.push(a);
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}, this.findComponents = function(e, r,
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let
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}, this.findComponents = function(e, r, t, n) {
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let a = e.connectivity.flat(), s = M(a), i = [], l = !1;
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return s.forEach((o) => {
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l = !1,
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l = !1, L(r, o) && (l = !0), n && L(n, o) && (l = !0), L(t, o) && (l = !0), l || i.push(o);
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}), i;
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}, this.retrieveFlatmapKnowledgeForEvent = async function(e, r) {
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this.controller && this.controller.abort(), this.controller = new AbortController(), this.controller.signal;
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const
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if (this.destinations = [], this.origins = [], this.components = [], this.rawURLs = [], !
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let n = this.queryForConnectivityNew(e,
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const t = r.resource;
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if (this.destinations = [], this.origins = [], this.components = [], this.rawURLs = [], !t || t.length === 0 || !t[0]) return;
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let n = this.queryForConnectivityNew(e, t[0]);
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return await Promise.all([n]);
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}, this.queryForConnectivityNew = function(e, r,
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return this.connectivitySource =
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(
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}, this.queryForConnectivityNew = function(e, r, t = "map", n = !0) {
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return this.connectivitySource = t, new Promise((a) => {
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(t === "map" ? this.queryMapConnectivity(e.mapMetadata.uuid, r) : e.queryKnowledge(r)).then((i) => {
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t === "map" && (this.noMapConnectivity = !1);
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n ? this.processConnectivity(e, l).then((o) => {
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}) :
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} else
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i.references && (this.rawURLs = [...i.references]), a(o);
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}) : a(l);
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} else t === "map" ? (this.connectivitySource = "sckan", this.noMapConnectivity = !0, e.queryKnowledge(r).then((l) => {
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}) :
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l.references && (this.rawURLs = [...l.references]), a(c);
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}) : a(o);
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} else
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}).catch(() =>
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a(!1);
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}).catch(() => a(!1))) : a(!1);
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}).catch((i) => {
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i.name === "AbortError" || console.warn(`Unable to get the knowledge for the entity ${r}.`), a(!1);
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});
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});
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}, this.queryMapConnectivity = async function(e, r) {
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const t = this.flatmapAPI + `flatmap/${e}/connectivity/${r}`;
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try {
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const n = await fetch(t);
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if (!n.ok)
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throw new Error(`Response status: ${n.status}`);
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}, this.queryForConnectivity = function(e, r, t, n = !0) {
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const a = { sql: this.buildConnectivitySqlStatement(r) }, s = {
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method: "POST",
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headers: {
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"Content-Type": "application/json"
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body: JSON.stringify(
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body: JSON.stringify(a),
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...t ? { signal: t } : {}
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};
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return new Promise((i) => {
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}, this.findIfNodeIsSingle = function(e) {
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return e.length === 1 ? (console.error("Server returns a single node", e), e[0]) : e.length === 2 && e[1].length === 0 ? e[0] : !1;
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return e.length === 2 && e[1].length > 0 && e[1].forEach((a) => {
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r[a] == null ? n += `, ${a}` : n += `, ${r[a]}`;
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}, this.flattenAndFindDatasets = function(e, r, t) {
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let n = this.flattenConnectivity(e), a = this.flattenConnectivity(r), s = this.flattenConnectivity(t);
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const o = ["ilxtr:hasSomaLocatedIn"], c = ["ilxtr:hasAxonPresynapticElementIn", "ilxtr:hasAxonSensorySubcellularElementIn"];
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o.forEach((u) => {
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u in r["node-phenotypes"] && n.push(...r["node-phenotypes"][u]);
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}), a = M(a);
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} else
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a = M(r.axons), r.somas && r.somas.length > 0 && n.push(...r.somas), r.dendrites && r.dendrites.length > 0 && n.push(...r.dendrites), n = M(n), s = r.somas;
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const i = this.findComponents(r, a, n, s), l = this.findAllIdsFromConnectivity(r);
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this.createLabelLookup(e, l).then((o) => {
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this.origins = n.map(
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(c) => this.createLabelFromNeuralNode(c, o)
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).sort(A), this.components = i.map(
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(c) => this.createLabelFromNeuralNode(c, o)
|
|
233
|
-
).sort(A), this.destinations =
|
|
233
|
+
).sort(A), this.destinations = a.map(
|
|
234
234
|
(c) => this.createLabelFromNeuralNode(c, o)
|
|
235
|
-
).sort(A), this.flattenAndFindDatasets(n, i,
|
|
235
|
+
).sort(A), this.flattenAndFindDatasets(n, i, a), t({
|
|
236
236
|
ids: {
|
|
237
237
|
dendrites: n,
|
|
238
238
|
components: i,
|
|
239
|
-
axons:
|
|
239
|
+
axons: a
|
|
240
240
|
},
|
|
241
241
|
labels: {
|
|
242
242
|
origins: this.origins,
|
|
@@ -251,22 +251,22 @@ let S = function() {
|
|
|
251
251
|
if (e.length === 1)
|
|
252
252
|
r += `'${e[0]}')`;
|
|
253
253
|
else if (e.length > 1)
|
|
254
|
-
for (let
|
|
255
|
-
r += `'${e[
|
|
254
|
+
for (let t in e)
|
|
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|
+
r += `'${e[t]}'${t >= e.length - 1 ? ")" : ","} `;
|
|
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256
|
return r;
|
|
257
257
|
}, this.buildPubmedSqlStatementForModels = function(e) {
|
|
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258
|
return `select distinct publication from publications where entity = '${e}'`;
|
|
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259
|
}, this.queryKnowledge = async (e, r) => {
|
|
260
|
-
const
|
|
260
|
+
const t = `${this.flatmapAPI}/knowledge/query/`, a = await fetch(t, {
|
|
261
261
|
method: "POST",
|
|
262
262
|
headers: {
|
|
263
263
|
Accept: "application/json"
|
|
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264
|
},
|
|
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265
|
body: JSON.stringify({ sql: e, params: r })
|
|
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266
|
});
|
|
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|
-
if (!
|
|
268
|
-
throw new Error(`Cannot access ${
|
|
269
|
-
const s = await
|
|
267
|
+
if (!a.ok)
|
|
268
|
+
throw new Error(`Cannot access ${t}`);
|
|
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|
+
const s = await a.json();
|
|
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270
|
if ("error" in s)
|
|
271
271
|
throw new TypeError(s.error);
|
|
272
272
|
return s.values;
|
|
@@ -1085,50 +1085,50 @@ const I = [
|
|
|
1085
1085
|
"FMA subclasses (in human nerves)": ["FMA:6892", "FMA:6893"],
|
|
1086
1086
|
"subclass labels": ["Right T9 grey ramus communicans", "Left T9 grey ramus communicans"]
|
|
1087
1087
|
}
|
|
1088
|
-
],
|
|
1088
|
+
], U = () => {
|
|
1089
1089
|
const e = {};
|
|
1090
1090
|
return I.forEach((r) => {
|
|
1091
|
-
const
|
|
1092
|
-
if (
|
|
1093
|
-
if (!
|
|
1091
|
+
const t = r.nerve_id, n = r.label.toLowerCase(), a = r["subclass labels"];
|
|
1092
|
+
if (t && n !== "nerve") {
|
|
1093
|
+
if (!a.length)
|
|
1094
1094
|
return;
|
|
1095
|
-
|
|
1096
|
-
const s =
|
|
1097
|
-
e[
|
|
1095
|
+
t in e || (e[t] = {});
|
|
1096
|
+
const s = a.map((i) => i.toLowerCase()).sort();
|
|
1097
|
+
e[t] = {
|
|
1098
1098
|
nerve: n,
|
|
1099
1099
|
subNerves: s
|
|
1100
1100
|
};
|
|
1101
1101
|
}
|
|
1102
1102
|
}), e;
|
|
1103
|
-
},
|
|
1103
|
+
}, $ = () => {
|
|
1104
1104
|
let e = [], r = {
|
|
1105
1105
|
key: "scaffold.connectivity.nerve",
|
|
1106
1106
|
label: "Nerves",
|
|
1107
1107
|
children: []
|
|
1108
|
-
},
|
|
1108
|
+
}, t = [];
|
|
1109
1109
|
for (const n of I) {
|
|
1110
1110
|
if (n.label === "nerve")
|
|
1111
1111
|
continue;
|
|
1112
|
-
let
|
|
1112
|
+
let a = {
|
|
1113
1113
|
facetPropPath: "scaffold.connectivity.nerve",
|
|
1114
1114
|
label: "",
|
|
1115
1115
|
children: []
|
|
1116
1116
|
}, s = [];
|
|
1117
1117
|
for (const [i, l] of Object.entries(n))
|
|
1118
|
-
if (i === "label" && (
|
|
1118
|
+
if (i === "label" && (a.label = l), i === "subclass labels")
|
|
1119
1119
|
for (const o of l)
|
|
1120
1120
|
s.push({
|
|
1121
1121
|
facetPropPath: "scaffold.connectivity.subnerve",
|
|
1122
1122
|
label: o
|
|
1123
1123
|
});
|
|
1124
|
-
s.length && (
|
|
1124
|
+
s.length && (a.children = s.sort((i, l) => i.label.localeCompare(l.label)), t.push(a));
|
|
1125
1125
|
}
|
|
1126
|
-
return
|
|
1126
|
+
return t.length && (r.children = t.sort((n, a) => n.label.localeCompare(a.label)), e.push(r)), e;
|
|
1127
1127
|
};
|
|
1128
|
-
function
|
|
1128
|
+
function H(e) {
|
|
1129
1129
|
return e[0].toUpperCase() + e.substring(1);
|
|
1130
1130
|
}
|
|
1131
|
-
const
|
|
1131
|
+
const K = {
|
|
1132
1132
|
emits: ["flatmap-provenance-ready", "resource-selected", "species-changed"],
|
|
1133
1133
|
props: {
|
|
1134
1134
|
/**
|
|
@@ -1147,7 +1147,7 @@ const q = {
|
|
|
1147
1147
|
},
|
|
1148
1148
|
inject: ["showGlobalSettings", "showOpenMapButton"],
|
|
1149
1149
|
computed: {
|
|
1150
|
-
...
|
|
1150
|
+
...X(C, E, O, N),
|
|
1151
1151
|
idNamePair() {
|
|
1152
1152
|
return this.splitFlowStore.idNamePair;
|
|
1153
1153
|
},
|
|
@@ -1190,13 +1190,19 @@ const q = {
|
|
|
1190
1190
|
this.settingsStore.updateMapManager(e);
|
|
1191
1191
|
},
|
|
1192
1192
|
trackOpenMap: function(e) {
|
|
1193
|
-
|
|
1193
|
+
b.sendEvent({
|
|
1194
1194
|
event: "interaction_event",
|
|
1195
1195
|
event_name: "portal_maps_open_map",
|
|
1196
1196
|
category: e,
|
|
1197
1197
|
location: "open_new_map"
|
|
1198
1198
|
});
|
|
1199
1199
|
},
|
|
1200
|
+
updateEntryLabel: function(e) {
|
|
1201
|
+
e && this.entriesStore.updateLabelForEntry(this.entry, e);
|
|
1202
|
+
},
|
|
1203
|
+
updateEntryTitle: function(e) {
|
|
1204
|
+
e && this.entriesStore.updateTitleForEntry(this.entry, e);
|
|
1205
|
+
},
|
|
1200
1206
|
updateWithViewUrl: function() {
|
|
1201
1207
|
},
|
|
1202
1208
|
/**
|
|
@@ -1215,12 +1221,12 @@ const q = {
|
|
|
1215
1221
|
*/
|
|
1216
1222
|
resourceSelected: function(e, r) {
|
|
1217
1223
|
var i, l, o, c;
|
|
1218
|
-
const
|
|
1219
|
-
if (this.resourceHasAction(
|
|
1220
|
-
f.emit("PopoverActionClick",
|
|
1224
|
+
const t = r[0];
|
|
1225
|
+
if (this.resourceHasAction(t)) {
|
|
1226
|
+
f.emit("PopoverActionClick", t);
|
|
1221
1227
|
return;
|
|
1222
1228
|
}
|
|
1223
|
-
let n,
|
|
1229
|
+
let n, a = !1;
|
|
1224
1230
|
const s = {
|
|
1225
1231
|
paneIndex: this.entry.id,
|
|
1226
1232
|
type: e,
|
|
@@ -1229,13 +1235,13 @@ const q = {
|
|
|
1229
1235
|
eventType: void 0
|
|
1230
1236
|
};
|
|
1231
1237
|
if (e == "MultiFlatmap" || e == "Flatmap")
|
|
1232
|
-
if (s.internalName = (i =
|
|
1233
|
-
if (s.eventType = "selected",
|
|
1238
|
+
if (s.internalName = (i = t == null ? void 0 : t.feature) != null && i.label ? t.feature.label : this.idNamePair[t.feature.models], t.eventType == "click") {
|
|
1239
|
+
if (s.eventType = "selected", t.feature.type == "marker") {
|
|
1234
1240
|
let u = s.internalName;
|
|
1235
|
-
if (this.settingsStore.isFeaturedMarkerIdentifier(
|
|
1241
|
+
if (this.settingsStore.isFeaturedMarkerIdentifier(t.feature.id))
|
|
1236
1242
|
n = {
|
|
1237
1243
|
type: "Search",
|
|
1238
|
-
term: this.settingsStore.featuredMarkerDoi(
|
|
1244
|
+
term: this.settingsStore.featuredMarkerDoi(t.feature.id),
|
|
1239
1245
|
featuredDataset: !0
|
|
1240
1246
|
};
|
|
1241
1247
|
else {
|
|
@@ -1244,8 +1250,8 @@ const q = {
|
|
|
1244
1250
|
facets: [u]
|
|
1245
1251
|
};
|
|
1246
1252
|
let h = /* @__PURE__ */ new Set();
|
|
1247
|
-
if (
|
|
1248
|
-
h.add(m.label);
|
|
1253
|
+
if (t.feature["dataset-terms"].forEach((m) => {
|
|
1254
|
+
h.add(m.label ? m.label : m.term);
|
|
1249
1255
|
}), h.size === 0 && h.add(u), n.facets = [...h], this.settingsStore.hasAppliedFacets(h) && this.settingsStore.appliedFacets.length <= h.size)
|
|
1250
1256
|
return;
|
|
1251
1257
|
if (this.settingsStore.appliedFacets.length) {
|
|
@@ -1259,14 +1265,14 @@ const q = {
|
|
|
1259
1265
|
} else
|
|
1260
1266
|
h.size > 1 && (n.type = "Facets"), this.settingsStore.updateAppliedFacets(n.facets);
|
|
1261
1267
|
}
|
|
1262
|
-
|
|
1268
|
+
a = !0, e == "MultiFlatmap" && this.$refs.multiflatmap.getCurrentFlatmap().mapImp.clearSearchResults();
|
|
1263
1269
|
}
|
|
1264
|
-
} else
|
|
1265
|
-
else e == "Scaffold" && (
|
|
1270
|
+
} else t.eventType == "mouseenter" && (s.eventType = "highlighted", a = !0);
|
|
1271
|
+
else e == "Scaffold" && (t && ((((l = t.data) == null ? void 0 : l.id) === void 0 || ((o = t.data) == null ? void 0 : o.id) === "") && (t.data.id = (c = t.data) == null ? void 0 : c.group), s.internalName = t.data.id, t.data.lastActionOnMarker === !0 && (n = {
|
|
1266
1272
|
type: "Facet",
|
|
1267
|
-
facets: [
|
|
1268
|
-
})), s.eventType = "selected",
|
|
1269
|
-
n && f.emit("PopoverActionClick", n),
|
|
1273
|
+
facets: [H(t.data.id)]
|
|
1274
|
+
})), s.eventType = "selected", a = !0);
|
|
1275
|
+
n && f.emit("PopoverActionClick", n), a && this.$emit("resource-selected", s);
|
|
1270
1276
|
},
|
|
1271
1277
|
resourceHasAction: function(e) {
|
|
1272
1278
|
return e && (e.type === "URL" || e.type === "Search" || e.type === "Neuron Search" || e.type == "Facet" || e.type == "Facets");
|
|
@@ -1285,21 +1291,21 @@ const q = {
|
|
|
1285
1291
|
getNameAndIdFromSyncData: async function(e) {
|
|
1286
1292
|
let r = e.internalName;
|
|
1287
1293
|
r === void 0 && e.resource && (r = e.resource.label);
|
|
1288
|
-
let
|
|
1289
|
-
if (e.resource && e.resource.resource && (
|
|
1294
|
+
let t;
|
|
1295
|
+
if (e.resource && e.resource.resource && (t = e.resource.resource[0]), this.entry.type === "Scaffold") {
|
|
1290
1296
|
if (this.$refs.scaffold.findObjectsWithGroupName(r).length === 0) {
|
|
1291
1297
|
if (e.resource && e.resource.feature) {
|
|
1292
1298
|
const s = R(e.resource.feature.models);
|
|
1293
1299
|
if (s.length > 0) return s;
|
|
1294
1300
|
}
|
|
1295
|
-
let
|
|
1296
|
-
if (
|
|
1297
|
-
return
|
|
1298
|
-
if (
|
|
1299
|
-
return fetch(`${this.apiLocation}get-related-terms/${
|
|
1301
|
+
let a = x(r);
|
|
1302
|
+
if (a)
|
|
1303
|
+
return a;
|
|
1304
|
+
if (t && e.eventType === "selected")
|
|
1305
|
+
return fetch(`${this.apiLocation}get-related-terms/${t}`).then((s) => s.json()).then((s) => {
|
|
1300
1306
|
var i;
|
|
1301
1307
|
if (((i = s.uberon) == null ? void 0 : i.array.length) > 0)
|
|
1302
|
-
return r = s.uberon.array[0].name.charAt(0).toUpperCase() + s.uberon.array[0].name.slice(1),
|
|
1308
|
+
return r = s.uberon.array[0].name.charAt(0).toUpperCase() + s.uberon.array[0].name.slice(1), t = s.uberon.array[0].id.toUpperCase(), { id: t, name: r };
|
|
1303
1309
|
});
|
|
1304
1310
|
}
|
|
1305
1311
|
} else if (this.entry.type === "MultiFlatmap")
|
|
@@ -1309,29 +1315,29 @@ const q = {
|
|
|
1309
1315
|
const n = R(r);
|
|
1310
1316
|
n.length > 0 && (r = n[0]);
|
|
1311
1317
|
}
|
|
1312
|
-
return { id:
|
|
1318
|
+
return { id: t, name: r };
|
|
1313
1319
|
},
|
|
1314
1320
|
// Get the species and andaotmy info for the featured datasets
|
|
1315
1321
|
getDatasetAnatomyInfo: function(e) {
|
|
1316
1322
|
fetch(`${this.apiLocation}dataset_info/anatomy?identifier=${e}`).then((r) => r.json()).then((r) => {
|
|
1317
|
-
const
|
|
1323
|
+
const t = r.result[0];
|
|
1318
1324
|
let n;
|
|
1319
1325
|
try {
|
|
1320
|
-
n =
|
|
1326
|
+
n = t.anatomy.organ[0].curie;
|
|
1321
1327
|
} catch {
|
|
1322
1328
|
n = void 0;
|
|
1323
1329
|
}
|
|
1324
|
-
let
|
|
1330
|
+
let a;
|
|
1325
1331
|
try {
|
|
1326
|
-
|
|
1332
|
+
a = t.item.curie;
|
|
1327
1333
|
} catch {
|
|
1328
|
-
|
|
1334
|
+
a = void 0;
|
|
1329
1335
|
}
|
|
1330
1336
|
let s;
|
|
1331
1337
|
try {
|
|
1332
1338
|
let i = 0, l = !1;
|
|
1333
|
-
for (; !l && i <
|
|
1334
|
-
const o =
|
|
1339
|
+
for (; !l && i < t.organisms.subject.length; ) {
|
|
1340
|
+
const o = t.organisms.subject[i];
|
|
1335
1341
|
o.species && (s = o.species.name, l = !0), i += 1;
|
|
1336
1342
|
}
|
|
1337
1343
|
} catch {
|
|
@@ -1340,7 +1346,7 @@ const q = {
|
|
|
1340
1346
|
this.settingsStore.updateFeaturedMarker({
|
|
1341
1347
|
identifier: e,
|
|
1342
1348
|
marker: n,
|
|
1343
|
-
doi:
|
|
1349
|
+
doi: a,
|
|
1344
1350
|
species: s
|
|
1345
1351
|
});
|
|
1346
1352
|
});
|
|
@@ -1353,7 +1359,24 @@ const q = {
|
|
|
1353
1359
|
// Check if the new featured dataset api has any info
|
|
1354
1360
|
newFeaturedDatasetApiHasInfo: async function() {
|
|
1355
1361
|
let r = await (await fetch(`${this.apiLocation}get_featured_dataset`)).json();
|
|
1356
|
-
return !r.datasets || r.datasets.length == 0 ? !1 : r.datasets.map((
|
|
1362
|
+
return !r.datasets || r.datasets.length == 0 ? !1 : r.datasets.map((t) => t.id);
|
|
1363
|
+
},
|
|
1364
|
+
flatmapResourceSelected: function(e, r) {
|
|
1365
|
+
var i;
|
|
1366
|
+
this.resourceSelected(e, r);
|
|
1367
|
+
const t = r[0], { eventType: n, feature: a } = t, { viewingMode: s } = this.settingsStore.globalSettings;
|
|
1368
|
+
if (n === "click" && a.type === "feature" && ((i = a.models) != null && i.startsWith("ilxtr:"))) {
|
|
1369
|
+
const l = [];
|
|
1370
|
+
r.forEach((o) => {
|
|
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|
+
const { models: c } = o.feature;
|
|
1372
|
+
l.push(c);
|
|
1373
|
+
}), b.sendEvent({
|
|
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|
+
event: "interaction_event",
|
|
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|
+
event_name: "portal_maps_connectivity",
|
|
1376
|
+
category: l.join(", "),
|
|
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|
+
location: e + " " + s
|
|
1378
|
+
});
|
|
1379
|
+
}
|
|
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|
},
|
|
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1381
|
/**
|
|
1359
1382
|
* Get a list of featured datasets to display.
|
|
@@ -1362,11 +1385,11 @@ const q = {
|
|
|
1362
1385
|
let e = [], r = await this.oldFeaturedDatasetApiHasInfo();
|
|
1363
1386
|
if (r) e = r;
|
|
1364
1387
|
else {
|
|
1365
|
-
let
|
|
1366
|
-
|
|
1388
|
+
let t = await this.newFeaturedDatasetApiHasInfo();
|
|
1389
|
+
t && (e = t);
|
|
1367
1390
|
}
|
|
1368
|
-
this.settingsStore.updateFeatured(e), e.forEach((
|
|
1369
|
-
this.getDatasetAnatomyInfo(
|
|
1391
|
+
this.settingsStore.updateFeatured(e), e.forEach((t) => {
|
|
1392
|
+
this.getDatasetAnatomyInfo(t);
|
|
1370
1393
|
});
|
|
1371
1394
|
},
|
|
1372
1395
|
flatmapMarkerUpdate() {
|
|
@@ -1404,26 +1427,26 @@ const q = {
|
|
|
1404
1427
|
checkEndHelpMouseDown: function(e) {
|
|
1405
1428
|
e.target.closest(".help-mode-dialog") || this.endHelp();
|
|
1406
1429
|
},
|
|
1407
|
-
flatmapHighlight: async function(e, r,
|
|
1408
|
-
let
|
|
1430
|
+
flatmapHighlight: async function(e, r, t, n) {
|
|
1431
|
+
let a = [...r, ...n];
|
|
1409
1432
|
const s = this.settingsStore.globalSettings;
|
|
1410
1433
|
if (s.highlightConnectedPaths) {
|
|
1411
1434
|
const i = r.length ? r : n.length ? n : [], l = await e.retrieveConnectedPaths(i);
|
|
1412
|
-
l &&
|
|
1435
|
+
l && a.push(...l);
|
|
1413
1436
|
}
|
|
1414
1437
|
if (s.highlightDOIPaths) {
|
|
1415
|
-
const i = await e.searchConnectivitiesByReference(
|
|
1416
|
-
i &&
|
|
1438
|
+
const i = await e.searchConnectivitiesByReference(t);
|
|
1439
|
+
i && a.push(...i);
|
|
1417
1440
|
}
|
|
1418
|
-
return
|
|
1441
|
+
return a = [...new Set(a)], a;
|
|
1419
1442
|
},
|
|
1420
1443
|
sidebarHoverHighlight: function(e) {
|
|
1421
|
-
var r,
|
|
1444
|
+
var r, t;
|
|
1422
1445
|
if (this.visible && ((this.flatmapRef || this.multiflatmapRef) && this.flatmapReady || this.scaffoldRef && this.scaffoldLoaded)) {
|
|
1423
|
-
const n = this.settingsStore.hoverAnatomies,
|
|
1446
|
+
const n = this.settingsStore.hoverAnatomies, a = this.settingsStore.hoverOrgans, s = this.settingsStore.hoverDOI, i = this.settingsStore.hoverConnectivity;
|
|
1424
1447
|
let l = null, o = null;
|
|
1425
|
-
this.flatmapRef && (l = this.flatmapRef), this.multiflatmapRef && (l = this.multiflatmapRef.getCurrentFlatmap()), this.scaffoldRef && (o = this.scaffoldRef), clearTimeout(this.highlightDelay), !n.length && !
|
|
1426
|
-
(n.length ||
|
|
1448
|
+
this.flatmapRef && (l = this.flatmapRef), this.multiflatmapRef && (l = this.multiflatmapRef.getCurrentFlatmap()), this.scaffoldRef && (o = this.scaffoldRef), clearTimeout(this.highlightDelay), !n.length && !a.length && !s && !i.length && ((this.multiflatmapRef || this.flatmapRef) && l ? ((r = l.mapImp) == null || r.clearSearchResults(), e.connectivityProcessed && ((t = l.mapImp) == null || t.setPaint({ dimmed: !0 }))) : this.scaffoldRef && o && o.changeHighlightedByName(a, "", !1)), this.highlightDelay = setTimeout(() => {
|
|
1449
|
+
(n.length || a.length || s || i.length) && ((this.multiflatmapRef || this.flatmapRef) && l ? this.flatmapHighlight(l, n, s, i).then((c) => {
|
|
1427
1450
|
try {
|
|
1428
1451
|
l.showConnectivityTooltips({
|
|
1429
1452
|
connectivityInfo: { featureId: c },
|
|
@@ -1439,7 +1462,7 @@ const q = {
|
|
|
1439
1462
|
) || l.mapImp.clearSearchResults();
|
|
1440
1463
|
}
|
|
1441
1464
|
}
|
|
1442
|
-
}) : this.scaffoldRef && o && o.changeHighlightedByName(
|
|
1465
|
+
}) : this.scaffoldRef && o && o.changeHighlightedByName(a, "", !1));
|
|
1443
1466
|
}, 100);
|
|
1444
1467
|
}
|
|
1445
1468
|
},
|
|
@@ -1476,24 +1499,24 @@ const q = {
|
|
|
1476
1499
|
this.flatmapService = await this.mockUpFlatmapService(), this.loadConnectivityExplorerConfig(this.flatmapService);
|
|
1477
1500
|
},
|
|
1478
1501
|
mockUpFlatmapService: async function() {
|
|
1479
|
-
const
|
|
1480
|
-
this.flatmapQueries =
|
|
1502
|
+
const t = (await (await fetch(this.flatmapAPI)).json()).filter((u) => u.id === "human-flatmap_male").sort((u, h) => h.created.localeCompare(u.created))[0], n = t.uuid, a = t.sckan["knowledge-source"], i = await (await fetch(`${this.flatmapAPI}/flatmap/${n}/pathways`)).json();
|
|
1503
|
+
this.flatmapQueries = y(new S()), this.flatmapQueries.initialise(this.flatmapAPI);
|
|
1481
1504
|
const l = {
|
|
1482
|
-
|
|
1505
|
+
mapMetadata: {
|
|
1483
1506
|
uuid: n,
|
|
1484
1507
|
connectivity: {
|
|
1485
|
-
...
|
|
1508
|
+
...t.sckan
|
|
1486
1509
|
}
|
|
1487
1510
|
},
|
|
1488
1511
|
pathways: i,
|
|
1489
1512
|
resource: this.entry.resource,
|
|
1490
|
-
knowledgeSource:
|
|
1513
|
+
knowledgeSource: a,
|
|
1491
1514
|
queryKnowledge: async (u) => {
|
|
1492
|
-
const h = "select knowledge from knowledge where (source=? or source is null) and entity=? order by source desc", m = [
|
|
1515
|
+
const h = "select knowledge from knowledge where (source=? or source is null) and entity=? order by source desc", m = [a, u], v = await this.flatmapQueries.queryKnowledge(h, m);
|
|
1493
1516
|
return JSON.parse(v);
|
|
1494
1517
|
},
|
|
1495
1518
|
queryLabels: async (u) => {
|
|
1496
|
-
const h = `select source, entity, knowledge from knowledge where (source=? or source is null) and entity in (?${", ?".repeat(u.length - 1)}) order by entity, source desc`, m = [
|
|
1519
|
+
const h = `select source, entity, knowledge from knowledge where (source=? or source is null) and entity in (?${", ?".repeat(u.length - 1)}) order by entity, source desc`, m = [a, ...u], v = await this.flatmapQueries.queryKnowledge(h, m), p = [];
|
|
1497
1520
|
let g;
|
|
1498
1521
|
for (const F of v)
|
|
1499
1522
|
if (F[1] !== g) {
|
|
@@ -1505,32 +1528,32 @@ const q = {
|
|
|
1505
1528
|
}
|
|
1506
1529
|
return p;
|
|
1507
1530
|
}
|
|
1508
|
-
}, o =
|
|
1531
|
+
}, o = $();
|
|
1509
1532
|
return {
|
|
1510
1533
|
mockup: !0,
|
|
1511
1534
|
getFilterOptions: async (u, h) => {
|
|
1512
|
-
const v = await
|
|
1535
|
+
const v = await B(this.flatmapAPI, u, h, void 0);
|
|
1513
1536
|
return [...o, ...v];
|
|
1514
1537
|
},
|
|
1515
|
-
getTermNerveMaps:
|
|
1538
|
+
getTermNerveMaps: U,
|
|
1516
1539
|
mapImp: l
|
|
1517
1540
|
};
|
|
1518
1541
|
},
|
|
1519
1542
|
loadConnectivityExplorerConfig: async function(e) {
|
|
1520
1543
|
var s;
|
|
1521
|
-
const r = e.mapImp,
|
|
1522
|
-
let
|
|
1523
|
-
if (!this.connectivityKnowledge[
|
|
1524
|
-
this.flatmapQueries =
|
|
1525
|
-
const i = await
|
|
1526
|
-
this.connectivityKnowledge[
|
|
1544
|
+
const r = e.mapImp, t = w(r), n = e.mockup ? r.resource : r.uuid;
|
|
1545
|
+
let a = [];
|
|
1546
|
+
if (!this.connectivityKnowledge[t]) {
|
|
1547
|
+
this.flatmapQueries = y(new S()), this.flatmapQueries.initialise(this.flatmapAPI);
|
|
1548
|
+
const i = await P(r, this.flatmapQueries);
|
|
1549
|
+
this.connectivityKnowledge[t] = i.filter((l) => {
|
|
1527
1550
|
var o;
|
|
1528
|
-
return
|
|
1551
|
+
return (o = l.connectivity) == null ? void 0 : o.length;
|
|
1529
1552
|
}).sort((l, o) => l.label.localeCompare(o.label));
|
|
1530
1553
|
}
|
|
1531
1554
|
if (!this.connectivityKnowledge[n]) {
|
|
1532
1555
|
const i = ((s = r.pathways) == null ? void 0 : s.paths) || {};
|
|
1533
|
-
this.connectivityKnowledge[n] = this.connectivityKnowledge[
|
|
1556
|
+
this.connectivityKnowledge[n] = this.connectivityKnowledge[t].filter((l) => l.id in i);
|
|
1534
1557
|
}
|
|
1535
1558
|
if (!this.connectivityFilterOptions[n] && !e.mockup && (this.connectivityFilterOptions[n] = await e.getFilterOptions(r, this.connectivityKnowledge[n])), e.mockup) {
|
|
1536
1559
|
const i = e.getTermNerveMaps() || {}, l = JSON.parse(JSON.stringify(this.connectivityKnowledge[n]));
|
|
@@ -1539,14 +1562,14 @@ const q = {
|
|
|
1539
1562
|
let u = c;
|
|
1540
1563
|
if ((h = c.nerves) != null && h.length) {
|
|
1541
1564
|
const v = c.nerves.flat(1 / 0).reduce((p, g) => (g in i && p.push(i[g]), p), []);
|
|
1542
|
-
v != null && v.length && (
|
|
1565
|
+
v != null && v.length && (a.push(...v), u["nerve-label"] = v.sort((p, g) => p.nerve.localeCompare(g.nerve)));
|
|
1543
1566
|
}
|
|
1544
1567
|
return u;
|
|
1545
|
-
}).filter((c) => c["nerve-label"]), this.connectivityFilterOptions[n] || (this.connectivityFilterOptions[n] = await e.getFilterOptions(r, this.connectivityKnowledge[n])),
|
|
1568
|
+
}).filter((c) => c["nerve-label"]), this.connectivityFilterOptions[n] || (this.connectivityFilterOptions[n] = await e.getFilterOptions(r, this.connectivityKnowledge[n])), a = a.map((c) => c.nerve.toLowerCase());
|
|
1546
1569
|
const o = JSON.parse(JSON.stringify(this.connectivityFilterOptions[n]));
|
|
1547
1570
|
this.connectivityFilterOptions[n] = o.map((c) => {
|
|
1548
1571
|
if (c.key === "scaffold.connectivity.nerve") {
|
|
1549
|
-
const u = c.children.filter((h) =>
|
|
1572
|
+
const u = c.children.filter((h) => a.includes(h.label.toLowerCase()));
|
|
1550
1573
|
return { ...c, children: u };
|
|
1551
1574
|
} else
|
|
1552
1575
|
return c;
|
|
@@ -1563,7 +1586,7 @@ const q = {
|
|
|
1563
1586
|
provenanceTaxonomy: e.taxons,
|
|
1564
1587
|
feature: []
|
|
1565
1588
|
});
|
|
1566
|
-
return r.knowledgeSource = w(this.flatmapService.mapImp), r.mapId = this.flatmapService.mapImp.
|
|
1589
|
+
return r.knowledgeSource = w(this.flatmapService.mapImp), r.mapId = this.flatmapService.mapImp.mapMetadata.id, r.mapuuid = this.flatmapService.mapImp.mapMetadata.uuid, r["nerve-label"] = e["nerve-label"], r.ready = !0, r;
|
|
1567
1590
|
},
|
|
1568
1591
|
getKnowledgeTooltip: async function(e) {
|
|
1569
1592
|
this.tooltipEntry = [], e.data.forEach((n) => this.tooltipEntry.push({ title: n.label, featureId: [n.id], ready: !1 })), f.emit("connectivity-info-open", this.tooltipEntry);
|
|
@@ -1573,11 +1596,11 @@ const q = {
|
|
|
1573
1596
|
this.tooltipEntry = await Promise.all(r), this.tooltipEntry.map((n) => n.featureId[0]).length > 0 && f.emit("connectivity-info-open", this.tooltipEntry);
|
|
1574
1597
|
},
|
|
1575
1598
|
changeConnectivitySource: async function(e) {
|
|
1576
|
-
const { entry: r, connectivitySource:
|
|
1577
|
-
await this.flatmapQueries.queryForConnectivityNew(this.flatmapService.mapImp, r.featureId[0],
|
|
1599
|
+
const { entry: r, connectivitySource: t } = e;
|
|
1600
|
+
await this.flatmapQueries.queryForConnectivityNew(this.flatmapService.mapImp, r.featureId[0], t), this.tooltipEntry = this.tooltipEntry.map((n) => n.featureId[0] === r.featureId[0] ? this.flatmapQueries.updateTooltipData(n) : n), f.emit("connectivity-info-open", this.tooltipEntry);
|
|
1578
1601
|
},
|
|
1579
1602
|
trackEvent: function(e) {
|
|
1580
|
-
|
|
1603
|
+
b.sendEvent(e);
|
|
1581
1604
|
}
|
|
1582
1605
|
},
|
|
1583
1606
|
data: function() {
|
|
@@ -1619,5 +1642,5 @@ const q = {
|
|
|
1619
1642
|
}
|
|
1620
1643
|
};
|
|
1621
1644
|
export {
|
|
1622
|
-
|
|
1645
|
+
K as C
|
|
1623
1646
|
};
|