@abi-software/mapintegratedvuer 1.5.0 → 1.5.1-beta-1

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@abi-software/mapintegratedvuer",
-  "version": "1.5.0",
+  "version": "1.5.1-beta-1",
   "license": "Apache-2.0",
   "scripts": {
     "serve": "vite --host --force",
@@ -55,7 +55,7 @@
     "@abi-software/map-utilities": "^1.1.0",
     "@abi-software/plotvuer": "1.0.0",
     "@abi-software/scaffoldvuer": "^1.4.1",
-    "@abi-software/simulationvuer": "1.0.0",
+    "@abi-software/simulationvuer": "2.0.6",
     "@abi-software/svg-sprite": "1.0.0",
     "@element-plus/icons-vue": "^2.3.1",
     "@pinia/testing": "^0.1.3",
@@ -66,7 +66,7 @@
     "mitt": "^3.0.1",
     "pinia": "^2.1.7",
     "splitpanes": "^3.1.5",
-    "vue": "^3.4.15",
+    "vue": "^3.5.11",
     "vue-router": "^4.2.5",
     "vuex": "^4.1.0",
     "xss": "^1.0.14"

package/src/components/SimulatedData.js

@@ -203,441 +203,6 @@ const nerveMaps = [
   }
 ];
 
-
-
-/* eslint-disable no-alert, no-console */
-function getGenericMarkerInfo(term ,label, dataset, scaffold, simulations) {
-  let data = {};
-  data.dataset = dataset;
-  data.scaffold = scaffold;
-  data.simulations = simulations;
-  if (label)
-    data.title = label;
-  else
-    data.title = term;
-  data.description = "";
-  data.actions = [];
-  if (term) {
-    switch (term) {
-    case "ICN":
-        data.title = "RNA";
-        data.description = "The distribution of neurons in the intrinsic cardiac nervous system (ICN) were mapped and visualized in a 3D reconstruction of a male rat heart.";
-        data.actions = {
-          search: {
-            title: "Explore data",
-            resource: "icn",
-            type: "Search",
-            label: "ICN",
-            filter: {
-              facet: 'genotype',
-              term: 'heart'
-            },
-          },
-          plot: {
-            title: "View plot",
-            label: "ICN",
-            resource: "https://mapcore-bucket1.s3-us-west-2.amazonaws.com/ISAN/csv-data/use-case-4/RNA_Seq.csv",
-            type: "Plot",
-            plotType: "heatmap",
-            datasetTitle: "Molecular Phenotype Distribution of Single Rat Intracardiac Neurons",
-            datasetDescription: "Images collected from serial cryostat sectioning of a cryopreserved heart was used to reconstruct the 3D context. Transcriptional profiles taken from isolated single neurons and mapped back into the previously generated 3D context.",
-            datasetUrl: "https://discover.pennsieve.io/datasets/29",
-            datasetImage: "https://assets.discover.pennsieve.io/dataset-assets/29/6/revisions/1/banner.jpg"
-          },
-        };
-        break;
-      default:
-        break;
-    }
-  } else {
-    data.actions = [];
-  }
-  return data;
-}
-
-
-function getHumanData(term, label, dataset, scaffold, simulations) {
-  if (term || label) {
-    let data = {};
-    switch (term) {
-      case "UBERON:0001157":
-        data.title = "Colon";
-        data.description = "";
-        data.actions = {
-          search: {
-            title: "Explore data",
-            label: "Colon",
-            resource: "https://sparc.science/data?type=dataset&q=colon",
-            type: "Search",
-            filter: {
-              facet: 'genotype',
-              term: 'colon'
-            },
-          },
-          scaffold: {
-            title: "View 3D scaffold",
-            label: "Colon",
-            resource: "https://mapcore-bucket1.s3-us-west-2.amazonaws.com/Generic+Scaffold/Colon/human/humanColon_metadata.json",
-            type: "Scaffold"
-          },
-        };
-        break;
-        case "UBERON:0000948":
-        case "UBERON:0002080": {
-          data.title = "Heart";
-          data.description = "";
-          data.actions = {
-            search: {
-              title: "Explore data",
-              label: "Heart",
-              resource: "https://sparc.science/data?type=dataset&q=colon",
-              type: "Search",
-              filter: {
-                facet: 'genotype',
-                term: 'heart'
-              },
-            },
-            scaffold: {
-              title: "View 3D scaffold",
-              label: "Heart",
-              resource: "https://mapcore-bucket1.s3-us-west-2.amazonaws.com/Generic+Scaffold/Heart/human/humanHeart_metadata.json",
-              type: "Scaffold"
-            },
-          };
-        }
-        break;
-        case "UBERON:0002048":
-            data.title = "Lung";
-            data.description = "";
-            data.actions = {
-              search: {
-                title: "Explore data",
-                label: "Lung",
-                resource: "https://sparc.science/data?type=dataset&q=lung",
-                type: "Search"
-              },
-              scaffold: {
-                title: "View 3D scaffold",
-                label: "Lung",
-                resource: "https://mapcore-bucket1.s3-us-west-2.amazonaws.com/Generic+Scaffold/Lungs/human/humanLeftLung_metadata.json",
-                type: "Scaffold"
-              },
-            };
-            break;
-      default:
-        data = getGenericMarkerInfo(term, label, dataset, scaffold, simulations);
-        break;
-    }
-    return data;
-  }
-  return undefined;
-}
-
-function getRatData(term, label, dataset, scaffold, simulations) {
-  if (term || label) {
-    let data = {};
-    switch (term) {
-      case "UBERON:0000948":
-      case "UBERON:0002080":
-        if (!simulations) {
-          data.title = "Heart";
-          data.description = "";
-          data.actions = {
-            search: {
-              title: "Explore data",
-              label: "Heart",
-              resource: "https://sparc.science/data?type=dataset&q=heart",
-              type: "Search",
-              filter: {
-                facet: 'genotype',
-                term: 'heart'
-              },
-            },
-            scaffold: {
-              title: "View 3D scaffold",
-              label: "Heart",
-              resource: "https://mapcore-bucket1.s3-us-west-2.amazonaws.com/Generic+Scaffold/Heart/rat/ratHeart_metadata.json",
-              type: "Scaffold"
-            },
-            simulation: {
-              title: "Explore simulations",
-              label: "Heart",
-              resource: "https://sparc.science/data?type=simulation&q=heart",
-              type: "URL"
-            },
-          };
-        } else {
-          data = getGenericMarkerInfo(term, label, dataset, scaffold, simulations);
-        }
-        break;
-      case "UBERON:0001156":
-        data.title = "Colon";
-        data.description = "";
-        data.actions = {
-          search: {
-            title: "Explore data",
-            label: "Colon",
-            resource: "https://sparc.science/data?type=dataset&q=colon",
-            type: "Search"
-          },
-        };
-        break;
-        case "UBERON:0002108":
-          data.title = "Small intestines";
-          data.description = "";
-          data.actions = {
-            search: {
-              title: "Explore data",
-              label: "Colon",
-              resource: "https://sparc.science/data?type=dataset&q=small+intestines",
-              type: "Search"
-            },
-          };
-          break;
-        case "UBERON:0001255":
-          data.title = "Urinary bladder";
-          data.description = "";
-          data.actions = {
-            search: {
-              title: "Explore data",
-              label: "Urinary Bladder",
-              resource: "https://sparc.science/data?type=dataset&q=bladder",
-              type: "Search"
-            },
-            scaffold: {
-              title: "View 3D scaffold",
-              label: "Bladder",
-              resource: "https://mapcore-bucket1.s3-us-west-2.amazonaws.com/Generic+Scaffold/Bladder/rat/ratBladder_metadata.json",
-              type: "Scaffold"
-            },
-          };
-        break;
-        case "UBERON:0002048":
-          data.title = "Lung";
-          data.description = "";
-          data.actions = {
-            search: {
-              title: "Explore data",
-              label: "Lung",
-              resource: "https://sparc.science/data?type=dataset&q=lung",
-              type: "Search"
-            },
-          };
-          break;
-      case "ICN":
-        data.title = "RNA";
-        data.description = "The distribution of neurons in the intrinsic cardiac nervous system (ICN) were mapped and visualized in a 3D reconstruction of a male rat heart.";
-        data.actions = {
-          search: {
-            title: "Explore data",
-            resource: "icn",
-            type: "Search"
-          },
-          plot: {
-            title: "View plot",
-            label: "ICN",
-            resource: "https://mapcore-bucket1.s3-us-west-2.amazonaws.com/ISAN/csv-data/use-case-4/RNA_Seq.csv",
-            type: "Plot",
-            plotType: "heatmap",
-            datasetTitle: "Molecular Phenotype Distribution of Single Rat Intracardiac Neurons",
-            datasetDescription: "Images collected from serial cryostat sectioning of a cryopreserved heart was used to reconstruct the 3D context. Transcriptional profiles taken from isolated single neurons and mapped back into the previously generated 3D context.",
-            datasetUrl: "https://discover.pennsieve.io/datasets/29",
-            datasetImage: "https://assets.discover.pennsieve.io/dataset-assets/29/6/revisions/1/banner.jpg"
-          },
-        };
-        break;
-      case "UBERON:0000945":
-      case "UBERON:0001160":
-      case "UBERON:0001161":
-        data.title = "Stomach";
-        data.description = "";
-        data.actions = {
-          search: {
-            title: "Explore data",
-            label: "Stomach",
-            resource: "https://sparc.science/data?type=dataset&q=stomach",
-            type: "Search"
-          },
-          scaffold: {
-            title: "View 3D scaffold",
-            label: "Stomach",
-            resource: "https://mapcore-bucket1.s3-us-west-2.amazonaws.com/Generic+Scaffold/Stomach/rat/ratStomach_metadata.json",
-            type: "Scaffold"
-          },
-        };
-        break;
-      case "UBERON:0001759":
-        if (label)
-          data.title = label;
-        else
-          data.title = "Vagus nerve";
-        data.actions = {
-          search: {
-            title: "Explore data",
-            label: "Vagus nerve",
-            resource: "https://sparc.science/data?type=dataset&q=vagus+nerve",
-            type: "Search"
-          },
-          simulation: {
-            title: "Explore simulations",
-            label: "Vagus nerve",
-            resource: "https://sparc.science/data?type=simulation&q=vagus%20nerve",
-            type: "simulation"
-          },
-        };
-        break;
-      default:
-        data = getGenericMarkerInfo(term, label, dataset, scaffold, simulations);
-        break;
-    }
-    return data;
-  }
-  return undefined;
-}
-
-function getMouseData(term, label, dataset, scaffold, simulations) {
-  if (term || label) {
-    let data = {};
-    switch (term) {
-      case "UBERON:0001156":
-        data.title = "Colon";
-        data.description = "";
-        data.actions = {
-          search: {
-            title: "Explore data",
-            label: "Colon",
-            resource: "https://sparc.science/data?type=dataset&q=colon",
-            type: "Search"
-          },
-          scaffold: {
-            title: "View 3D scaffold",
-            label: "Colon",
-            resource: "https://mapcore-bucket1.s3-us-west-2.amazonaws.com/Generic+Scaffold/Colon/mouse/mouseColon_metadata.json",
-            type: "Scaffold"
-          },
-        };
-        break;
-      case "UBERON:0002048":
-        data.title = "Lung";
-        data.description = "";
-        data.actions = {
-          search: {
-            title: "Explore data",
-            label: "Lung",
-            resource: "https://sparc.science/data?type=dataset&q=lung",
-            type: "Search"
-          },
-          scaffold: {
-            title: "View 3D scaffold",
-            label: "Lung",
-            resource: "https://mapcore-bucket1.s3-us-west-2.amazonaws.com/Generic+Scaffold/Lungs/mouse/mouseLeftLung_metadata.json",
-            type: "Scaffold"
-          },
-        };
-        break;
-        case "UBERON:0002108":
-          data.title = "Small intestines";
-          data.description = "";
-          data.actions = {
-            search: {
-              title: "Explore data",
-              label: "Colon",
-              resource: "https://sparc.science/data?type=dataset&q=small+intestines",
-              type: "Search"
-            },
-          };
-          break;
-      default:
-        data = getGenericMarkerInfo(term, label, dataset, scaffold, simulations);
-        break;
-    }
-    return data;
-  }
-  return undefined;
-}
-
-function getPigData(term, label, dataset, scaffold, simulations) {
-  if (term || label) {
-    let data = {};
-    switch (term) {
-      case "UBERON:0008972":
-        data.title = "Colon";
-        data.description = "";
-        data.actions = {
-          search: {
-            title: "Explore data",
-            label: "Colon",
-            resource: "https://sparc.science/data?type=dataset&q=colon",
-            type: "Search"
-          },
-          scaffold: {
-            title: "View 3D scaffold",
-            label: "Colon",
-            resource: "https://mapcore-bucket1.s3-us-west-2.amazonaws.com/Generic+Scaffold/Colon/pig/pigColon_metadata.json",
-            type: "Scaffold"
-          },
-        };
-        break;
-        case "UBERON:0002108":
-          data.title = "Small intestines";
-          data.description = "";
-          data.actions = {
-            search: {
-              title: "Explore data",
-              label: "Colon",
-              resource: "https://sparc.science/data?type=dataset&q=small+intestines",
-              type: "Search"
-            },
-          };
-          break;
-          case "UBERON:0000948":
-            case "UBERON:0002080": {
-              data.title = "Heart";
-              data.description = "";
-              data.actions = {
-                search: {
-                  title: "Explore data",
-                  label: "Heart",
-                  resource: "https://sparc.science/data?type=dataset&q=colon",
-                  type: "Search",
-                  filter: {
-                    facet: 'genotype',
-                    term: 'heart'
-                  },
-                },
-                scaffold: {
-                  title: "View 3D scaffold",
-                  label: "Heart",
-                  resource: "https://mapcore-bucket1.s3-us-west-2.amazonaws.com/Generic+Scaffold/Heart/pig/pigHeart_metadata.json",
-                  type: "Scaffold"
-                },
-              };
-            }
-            break;
-      default:
-        data = getGenericMarkerInfo(term, label, dataset, scaffold, simulations);
-        break;
-    }
-    return data;
-  }
-  return undefined;
-}
-
-function simulatedData(term, taxonomy, label, dataset, scaffold, simulations) {
-  switch (taxonomy) {
-    case "NCBITaxon:9606":
-        return getHumanData(term, label, dataset, scaffold, simulations);
-    case "NCBITaxon:9823":
-        return getPigData(term, label, dataset, scaffold, simulations);
-    case "NCBITaxon:10090":
-      return getMouseData(term, label, dataset, scaffold, simulations);
-    case "NCBITaxon:10114":
-      return getRatData(term, label, dataset, scaffold, simulations);
-    default:
-      return getGenericMarkerInfo(term, taxonomy, label, dataset, scaffold, simulations);
-  }
-}
-
 function getRatTerms() {
   return [
     {id: "UBERON:0000948", name: "Heart", type:"simulation"},
@@ -687,35 +252,3 @@ export function getParentsRegion(name) {
   return undefined;
 }
 
-export function getInteractiveAction(result, action) {
-  if (result && result.resource) {
-    let resource = result.resource;
-    if (Array.isArray(resource) && resource[0])
-      resource = resource[0];
-    let term = undefined;
-    let label = undefined;
-    let dataset = undefined;
-    let scaffold = undefined;
-    let simulations = undefined;
-    let taxonomy = resource.taxonomy;
-    if (resource.data && resource.data.id) {
-      term = resource.data.id;
-      label = resource.data.id;
-    } else if (resource.feature) {
-      term = resource.feature.models;
-      label = resource.feature.label;
-      dataset = resource.feature.dataset;
-      scaffold = resource.feature.scaffold;
-      simulations = resource.feature.simulations;
-    }
-    if (term || label) {
-      let data = simulatedData(term, taxonomy, label, dataset, scaffold, simulations);
-      if (data && data.actions) {
-        return data.actions[action];
-      }
-    }
-  }
-  return undefined;
-}
-
-export { simulatedData };

package/src/components/viewers/Flatmap.vue

@@ -75,8 +75,7 @@ export default {
       return this.$refs.flatmap?.mapImp;
     },
     flatmaprResourceSelected: function (type, resource) {
-      this.resourceSelected(
-        type, resource, (this.$refs.flatmap.viewingMode === "Exploration"));
+      this.resourceSelected(type, resource);
 
       if (resource.eventType === 'click' && resource.feature.type === 'feature') {
         const eventData = {

package/src/components/viewers/MultiFlatmap.vue

@@ -188,7 +188,7 @@ export default {
     },
     flatmaprResourceSelected: function (type, resource) {
       const map = this.$refs.multiflatmap.getCurrentFlatmap();
-      this.resourceSelected(type, resource, (map.viewingMode === "Exploration"));
+      this.resourceSelected(type, resource);
 
       if (resource.eventType === 'click' && resource.feature.type === 'feature') {
         const eventData = {

package/src/mixins/ContentMixin.js

@@ -1,5 +1,4 @@
 import {
-  getInteractiveAction,
   getNerveNames,
   getParentsRegion,
 } from "../components/SimulatedData.js";
@@ -102,7 +101,7 @@ export default {
     /**
      * Callback when the vuers emit a selected event.
      */
-    resourceSelected: function (type, resource, augmented) {
+    resourceSelected: function (type, resource) {
       // Skip processing if resources already has actions
       if (this.resourceHasAction(resource)) {
         EventBus.emit("PopoverActionClick", resource);
@@ -200,9 +199,6 @@ export default {
         fireResourceSelected = true;
         action = "search";
       }
-      if ((returnedAction === undefined) && augmented) {
-        returnedAction = getInteractiveAction(result, action);
-      }
       if (returnedAction) EventBus.emit("PopoverActionClick", returnedAction);
       if (fireResourceSelected) this.$emit("resource-selected", result);
     },

package/vite.bundle-build.js

@@ -12,11 +12,12 @@ export default defineConfig((configEnv) => {
       fileName: "mapintegratedvuer",
     },
     rollupOptions: {
-      external: ["vue", "pinia"],
+      external: ["vue", "pinia", "@abi-software/simulationvuer"],
       output: {
         globals: {
           vue: "Vue",
           pinia: "pinia",
+          "@abi-software/simulationvuer": "simulationvuer",
         },
       },
     },

package/dist/Plot-C_rKnKaZ.js

@@ -1,24 +0,0 @@
-import { C as o } from "./plotvuer-X4h-Lj3L.js";
-import { C as a } from "./ContentMixin-DG--521q.js";
-import { resolveComponent as r, openBlock as n, createBlock as s } from "vue";
-import { _ as m } from "./index-BbKW1iaX.js";
-const p = {
-  name: "Plot",
-  mixins: [a],
-  components: {
-    PlotVuer: o
-  }
-};
-function l(e, c, u, d, i, f) {
-  const t = r("PlotVuer");
-  return n(), s(t, {
-    "data-source": e.entry.resource.dataSource,
-    metadata: e.entry.resource.metadata,
-    "supplemental-data": e.entry.resource.supplementalData,
-    style: { overflow: "hidden" }
-  }, null, 8, ["data-source", "metadata", "supplemental-data"]);
-}
-const $ = /* @__PURE__ */ m(p, [["render", l]]);
-export {
-  $ as default
-};