@abi-software/flatmapvuer 1.1.4-beta.0 → 1.1.4-beta.2

package/dist/flatmapvuer.js

@@ -12391,6 +12391,19 @@ let xit = function() {
     }), n.flat();
   }, this.stripPMIDPrefix = function(e) {
     return e.split(":")[1];
+  }, this.extractTermFromURLString = function(e) {
+    if (!e)
+      return;
+    const t = decodeURIComponent(e);
+    let r = "";
+    return [
+      "doi.org/",
+      "nih.gov/pubmed/",
+      "pubmed.ncbi.nlm.nih.gov/"
+    ].forEach((i) => {
+      const o = t.lastIndexOf(i);
+      o !== -1 && (r = t.slice(o + i.length));
+    }), r.endsWith("/") && (r = r.slice(0, -1)), r;
   }, this.buildPubmedSqlStatement = function(e) {
     let t = "select distinct publication from publications where entity in (";
     if (e.length === 1)
@@ -12419,11 +12432,7 @@ let xit = function() {
         return;
       const i = this.buildPubmedSqlStatement(r);
       this.flatmapQuery(i).then((o) => {
-        o.values.length > 0 ? (this.urls = [
-          this.pubmedSearchUrl(
-            o.values.map((a) => this.stripPMIDPrefix(a[0]))
-          )
-        ], t(!0)) : this.pubmedQueryOnModels(n).then((a) => {
+        o.values.length > 0 ? (this.urls = this.getURLsForPubMed(o), t(!0)) : this.pubmedQueryOnModels(n).then((a) => {
           t(a);
         });
       });
@@ -12431,11 +12440,14 @@ let xit = function() {
   }, this.pubmedQueryOnModels = function(e) {
     return this.flatmapQuery(
       this.buildPubmedSqlStatementForModels(e)
-    ).then((t) => Array.isArray(t.values) && t.values.length > 0 ? (this.urls = [
-      this.pubmedSearchUrl(
-        t.values.map((r) => this.stripPMIDPrefix(r[0]))
-      )
-    ], !0) : (this.urls = [], !1));
+    ).then((t) => Array.isArray(t.values) && t.values.length > 0 ? (this.urls = this.getURLsForPubMed(t), !0) : (this.urls = [], !1));
+  }, this.getURLsForPubMed = function(e) {
+    const t = e.values.map((n) => this.extractTermFromURLString(n[0])), r = this.transformPubMedSearchTerms(t);
+    return [
+      this.pubmedSearchUrl(r)
+    ];
+  }, this.transformPubMedSearchTerms = function(e) {
+    return e.join(" OR ");
   }, this.pubmedSearchUrl = function(e) {
     let t = "https://pubmed.ncbi.nlm.nih.gov/?", r = new URLSearchParams();
     return r.append("term", e), t + r.toString();
@@ -99532,7 +99544,7 @@ const rOt = tOt("main", {
     popUpCssHacks: function() {
       const e = document.querySelector(".flatmap-tooltip-popup"), t = document.querySelector(".maplibregl-popup-close-button");
       e && (e.style.display = "none"), t.style.display = "block", this.$refs.tooltip.$el.style.display = "flex", t.onclick = () => {
-        this.$emit("provenance-popup-close"), e && (e.style.display = "block");
+        this.$emit("connectivity-info-close"), e && (e.style.display = "block");
       };
     },
     /**
@@ -99651,11 +99663,11 @@ const rOt = tOt("main", {
     displayTooltip: function(e, t = void 0) {
       this.tooltipDisplay = !0;
       let r, n = { className: "flatmapvuer-popover" };
-      if (t ? (r = e, n.annotationFeatureGeometry = t) : (r = this.mapImp.modelFeatureIds(e)[0], this.activeDrawTool || (n.positionAtLastClick = !0)), this.provenanceSidebar) {
+      if (t ? (r = e, n.annotationFeatureGeometry = t) : (r = this.mapImp.modelFeatureIds(e)[0], this.activeDrawTool || (n.positionAtLastClick = !0)), this.connectivityInfoSidebar) {
         const i = [e];
-        this.moveMap(i), this.$emit("provenance-popup-open", this.tooltipEntry);
+        this.moveMap(i), this.$emit("connectivity-info-open", this.tooltipEntry);
       }
-      !this.disableUI && !this.provenanceSidebar && this.$nextTick(() => {
+      !this.disableUI && !this.connectivityInfoSidebar && this.$nextTick(() => {
         this.mapImp.showPopup(r, this.$refs.tooltip.$el, n), this.popUpCssHacks();
       });
     },
@@ -99827,7 +99839,7 @@ const rOt = tOt("main", {
     handleMapClick: function() {
       const e = this.mapImp._map;
       e && e.on("click", (t) => {
-        this.tooltipEntry.featureId && this.$emit("provenance-popup-close");
+        this.tooltipEntry.featureId && this.$emit("connectivity-info-close");
       });
     },
     /**
@@ -100071,9 +100083,9 @@ const rOt = tOt("main", {
       default: !1
     },
     /**
-     * The option to show provenance information in sidebar
+     * The option to show connectivity information in sidebar
      */
-    provenanceSidebar: {
+    connectivityInfoSidebar: {
       type: Boolean,
       default: !1
     }
@@ -100260,7 +100272,7 @@ const rOt = tOt("main", {
   mounted: function() {
     this.openMapRef = oa(this.$refs.openMapRef), this.backgroundIconRef = oa(this.$refs.backgroundIconRef), this.tooltipWait = [], this.tooltipWait.length = this.hoverVisibilities.length, this.mapManager = new tM(this.flatmapAPI), this.flatmapQueries = new xit(), this.flatmapQueries.initialise(this.flatmapAPI), this.state ? this.setStateRequired && this.setState(this.state) : this.renderAtMounted && this.createFlatmap();
   }
-}, Xa = (e) => (Q6("data-v-80d59da9"), e = e(), m6(), e), aOt = {
+}, Xa = (e) => (Q6("data-v-78a7555b"), e = e(), m6(), e), aOt = {
   class: "flatmap-container",
   ref: "flatmapContainer",
   "element-loading-text": "Loading...",
@@ -101009,14 +101021,14 @@ function SOt(e, t, r, n, i, o) {
         annotationDisplay: o.viewingMode === "Annotation",
         onAnnotation: o.commitAnnotationEvent
       }, null, 8, ["annotationEntry", "entry", "annotationDisplay", "onAnnotation"]), [
-        [Dn, e.tooltipDisplay && !r.provenanceSidebar]
+        [Dn, e.tooltipDisplay && !r.connectivityInfoSidebar]
       ])
     ])
   ])), [
     [ot, e.loading]
   ]);
 }
-const Gz = /* @__PURE__ */ fa(oOt, [["render", SOt], ["__scopeId", "data-v-80d59da9"]]), Vk = {
+const Gz = /* @__PURE__ */ fa(oOt, [["render", SOt], ["__scopeId", "data-v-78a7555b"]]), Vk = {
   "NCBITaxon:10114": "01fedbf9-d783-509c-a10c-827941ab13da",
   "NCBITaxon:9823": "a336ac04-24db-561f-a25f-1c994fe17410",
   "NCBITaxon:9606": "42ed6323-f645-5fbe-bada-9581819cf689",
@@ -101115,11 +101127,11 @@ const Gz = /* @__PURE__ */ fa(oOt, [["render", SOt], ["__scopeId", "data-v-80d59
     panZoomCallback: function(e) {
       this.$emit("pan-zoom-callback", e);
     },
-    onProvenancePopupClose: function() {
-      this.$emit("provenance-popup-close");
+    onConnectivityInfoClose: function() {
+      this.$emit("connectivity-info-close");
     },
-    onProvenancePopupOpen: function(e) {
-      this.$emit("provenance-popup-open", e);
+    onConnectivityInfoOpen: function(e) {
+      this.$emit("connectivity-info-open", e);
     },
     onSelectionsDataChanged: function(e) {
       this.$emit("pathway-selection-changed", e);
@@ -101497,9 +101509,9 @@ const Gz = /* @__PURE__ */ fa(oOt, [["render", SOt], ["__scopeId", "data-v-80d59
       default: !1
     },
     /**
-     * The option to show provenance information in sidebar
+     * The option to show connectivity information in sidebar
      */
-    provenanceSidebar: {
+    connectivityInfoSidebar: {
       type: Boolean,
       default: !1
     }
@@ -101520,7 +101532,7 @@ const Gz = /* @__PURE__ */ fa(oOt, [["render", SOt], ["__scopeId", "data-v-80d59
       deep: !0
     }
   }
-}, COt = (e) => (Q6("data-v-f78570a0"), e = e(), m6(), e), OOt = {
+}, COt = (e) => (Q6("data-v-c373f9aa"), e = e(), m6(), e), OOt = {
   class: "multi-container",
   ref: "multiContainer"
 }, POt = {
@@ -101593,9 +101605,9 @@ function VOt(e, t, r, n, i, o) {
       onResourceSelected: o.resourceSelected,
       onReady: o.FlatmapReady,
       onPanZoomCallback: o.panZoomCallback,
-      provenanceSidebar: r.provenanceSidebar,
-      onProvenancePopupOpen: o.onProvenancePopupOpen,
-      onProvenancePopupClose: o.onProvenancePopupClose,
+      connectivityInfoSidebar: r.connectivityInfoSidebar,
+      onConnectivityInfoOpen: o.onConnectivityInfoOpen,
+      onConnectivityInfoClose: o.onConnectivityInfoClose,
       onOpenMap: t[1] || (t[1] = (Q) => (
         /**
          * This event is emitted when the user chooses a different map option
@@ -101619,12 +101631,12 @@ function VOt(e, t, r, n, i, o) {
       style: { height: "100%" },
       flatmapAPI: r.flatmapAPI,
       sparcAPI: r.sparcAPI
-    }, null, 8, ["entry", "uuid", "biologicalSex", "displayWarning", "displayLatestChanges", "isLegacy", "enableOpenMapUI", "openMapOptions", "disableUI", "onViewLatestMap", "onResourceSelected", "onReady", "onPanZoomCallback", "provenanceSidebar", "onProvenancePopupOpen", "onProvenancePopupClose", "onPathwaySelectionChanged", "minZoom", "helpMode", "helpModeActiveItem", "helpModeDialog", "onHelpModeLastItem", "onShownTooltip", "onShownMapTooltip", "renderAtMounted", "displayMinimap", "showStarInLegend", "flatmapAPI", "sparcAPI"])), [
+    }, null, 8, ["entry", "uuid", "biologicalSex", "displayWarning", "displayLatestChanges", "isLegacy", "enableOpenMapUI", "openMapOptions", "disableUI", "onViewLatestMap", "onResourceSelected", "onReady", "onPanZoomCallback", "connectivityInfoSidebar", "onConnectivityInfoOpen", "onConnectivityInfoClose", "onPathwaySelectionChanged", "minZoom", "helpMode", "helpModeActiveItem", "helpModeDialog", "onHelpModeLastItem", "onShownTooltip", "onShownMapTooltip", "renderAtMounted", "displayMinimap", "showStarInLegend", "flatmapAPI", "sparcAPI"])), [
       [Dn, e.activeSpecies == f]
     ])), 128))
   ], 512);
 }
-const GOt = /* @__PURE__ */ fa(AOt, [["render", VOt], ["__scopeId", "data-v-f78570a0"]]), ROt = {
+const GOt = /* @__PURE__ */ fa(AOt, [["render", VOt], ["__scopeId", "data-v-c373f9aa"]]), ROt = {
   name: "HelpModeDialog",
   components: {
     Button: h2