@abi-software/mapintegratedvuer 0.7.1-demo.0 → 0.7.2-vue3.0-alpha.0

package/src/mixins/DynamicMarkerMixin.js

@@ -1,88 +1,88 @@
-
-import markerZoomLevels from "../components/markerZoomLevelsHardCoded.js";
-import { mapStores } from 'pinia';
-import { useSettingsStore } from '../stores/settings';
-
-
-/*
-* Function to check markers visibility at the given zoom level.
-* I have modified it to make sure the marker is displayed
-* if the uberon is not present in the hardcoded zoom-level list.
-*/
-const checkMarkersAtZoomLevel = (flatmapImp, markers, zoomLevel) => {
-  if (markers) {
-    markers.forEach(id => {
-      let foundInArray = false;
-      // First check if uberon is in the list, check for zoom level
-      // if true. Note: markerZoomLevels is imported.
-      for (let i = 0; i < markerZoomLevels.length; i++) {
-        if (markerZoomLevels[i].id === id) {
-          foundInArray = true;
-          if (zoomLevel >= markerZoomLevels[i].showAtZoom) {
-            flatmapImp.addMarker(id, {className: "standard-marker"});
-          }
-          break;
-        }
-      }
-      // Did not match, add it regardless so we do not lose any
-      // markers.
-      if (!foundInArray) {
-        flatmapImp.addMarker(id, {className: "standard-marker"});
-      }
-    });
-  }
-};
-  
-/* eslint-disable no-alert, no-console */
-export default {
-  computed: {
-    ...mapStores(useSettingsStore),
-  },
-  methods: {
-    flatmapPanZoomCallback: function (payload) {
-      if (this.mouseHovered) {
-        const result = {
-          paneIndex: this.entry.id,
-          eventType: "panZoom",
-          payload: payload,
-          type: this.entry.type,
-        };
-        this.flatmapMarkerZoomUpdate(false, undefined);
-        this.$emit("resource-selected", result);
-      }
-    },
-        /**
-     * Function used for updating the flatmap markers.
-     * It will only update the markers if zoom level has changed or
-     * the force flag is true.
-     */
-    flatmapMarkerZoomUpdate(force, flatmap) {
-      if (!this.flatmapReady) return;
-
-      let flatmapImp = flatmap;
-      if (!flatmapImp)
-        flatmapImp = this.getFlatmapImp();
-
-      if (flatmapImp) {
-        let currentZoom = flatmapImp.getZoom()["zoom"];
-        if (force || this.zoomLevel !== currentZoom) {
-          this.zoomLevel = currentZoom;
-          flatmapImp.clearMarkers();
-          let markers = this.settingsStore.markers;
-          checkMarkersAtZoomLevel(flatmapImp, markers, this.zoomLevel);
-          if (this.entry.type === "MultiFlatmap") {
-            this.restoreFeaturedMarkers(flatmapImp);
-          }
-        }
-      }
-    },
-    flatmapReadyForMarkerUpdates: function (flatmap) {
-      if (flatmap) {
-        flatmap.enablePanZoomEvents(true); // Use zoom events for dynamic markers
-        this.flatmapReady = true;
-        const flatmapImp = flatmap.mapImp;
-        this.flatmapMarkerZoomUpdate(true, flatmapImp);
-      }
-    },
-  }
-}
+
+import markerZoomLevels from "../components/markerZoomLevelsHardCoded.js";
+import { mapStores } from 'pinia';
+import { useSettingsStore } from '../stores/settings';
+
+
+/*
+* Function to check markers visibility at the given zoom level.
+* I have modified it to make sure the marker is displayed
+* if the uberon is not present in the hardcoded zoom-level list.
+*/
+const checkMarkersAtZoomLevel = (flatmapImp, markers, zoomLevel) => {
+  if (markers) {
+    markers.forEach(id => {
+      let foundInArray = false;
+      // First check if uberon is in the list, check for zoom level
+      // if true. Note: markerZoomLevels is imported.
+      for (let i = 0; i < markerZoomLevels.length; i++) {
+        if (markerZoomLevels[i].id === id) {
+          foundInArray = true;
+          if (zoomLevel >= markerZoomLevels[i].showAtZoom) {
+            flatmapImp.addMarker(id, {className: "standard-marker"});
+          }
+          break;
+        }
+      }
+      // Did not match, add it regardless so we do not lose any
+      // markers.
+      if (!foundInArray) {
+        flatmapImp.addMarker(id, {className: "standard-marker"});
+      }
+    });
+  }
+};
+  
+/* eslint-disable no-alert, no-console */
+export default {
+  computed: {
+    ...mapStores(useSettingsStore),
+  },
+  methods: {
+    flatmapPanZoomCallback: function (payload) {
+      if (this.mouseHovered) {
+        const result = {
+          paneIndex: this.entry.id,
+          eventType: "panZoom",
+          payload: payload,
+          type: this.entry.type,
+        };
+        this.flatmapMarkerZoomUpdate(false, undefined);
+        this.$emit("resource-selected", result);
+      }
+    },
+        /**
+     * Function used for updating the flatmap markers.
+     * It will only update the markers if zoom level has changed or
+     * the force flag is true.
+     */
+    flatmapMarkerZoomUpdate(force, flatmap) {
+      if (!this.flatmapReady) return;
+
+      let flatmapImp = flatmap;
+      if (!flatmapImp)
+        flatmapImp = this.getFlatmapImp();
+
+      if (flatmapImp) {
+        let currentZoom = flatmapImp.getZoom()["zoom"];
+        if (force || this.zoomLevel !== currentZoom) {
+          this.zoomLevel = currentZoom;
+          flatmapImp.clearMarkers();
+          let markers = this.settingsStore.markers;
+          checkMarkersAtZoomLevel(flatmapImp, markers, this.zoomLevel);
+          if (this.entry.type === "MultiFlatmap") {
+            this.restoreFeaturedMarkers(flatmapImp);
+          }
+        }
+      }
+    },
+    flatmapReadyForMarkerUpdates: function (flatmap) {
+      if (flatmap) {
+        flatmap.enablePanZoomEvents(true); // Use zoom events for dynamic markers
+        this.flatmapReady = true;
+        const flatmapImp = flatmap.mapImp;
+        this.flatmapMarkerZoomUpdate(true, flatmapImp);
+      }
+    },
+  }
+}

package/src/mixins/RetrieveContextCardMixin.js

@@ -0,0 +1,82 @@
+
+/* eslint-disable no-alert, no-console */
+export default {
+  // Note that the setting store is included in MapContent.vue
+  methods: {
+    retrieveContextCardFromUrl: async function (url) {
+      // split the url to get the datasetId
+      const [datasetId, basePath, scaffoldPath, s3uri] = this.splitInfoFromUrl(url);
+
+      // get the context file from scicrunch
+      const sciResults = await this.getContextFileFromScicrunch(datasetId, scaffoldPath);
+      if (!sciResults.success){
+        return {} // return empty object if no context file is found (the empty object will be added to the entry)
+      }
+
+      // return the context file
+      const fullPath = basePath + sciResults.contextFile + s3uri;
+      return {
+        s3uri: sciResults.s3uri,
+        contextCardUrl: fullPath,
+      }
+    },
+    splitInfoFromUrl: function (url) {
+      // example url: "https://mapcore-demo.org/current/sparc-api-v2/s3-resource/221/3/files/derivative/Scaffolds/mouse_colon_metadata.json",
+      // find the part after 's3-resource' 
+      let s3path = url.split('s3-resource')[1];
+      let basePath = url.split('files/')[0] + 'files/' // This gives us the base path for our relative path we will get from scicrunch
+      let scaffoldPath = url.split('files/')[1].split('?')[0] // This gives us the relative path to the file we want to get from scicrunch
+      let s3uri = '?' + url.split('?')[1] // This gives us the full path to the file we want to get from scicrunch
+
+      // split the url by '/'
+      const parts = s3path.split('/');
+      // remove the first part
+      parts.shift();
+      // return the parts
+      const datasetId = parts[0];
+
+      return [datasetId, basePath, scaffoldPath, s3uri];
+    },
+    getContextFileFromScicrunch: async function (datasetId, scaffoldPath) {
+      // get the context file from scicrunch
+      let results = await fetch(`${this.settingsStore.sparcApi}/dataset_info/using_multiple_discoverIds/?discoverIds=${datasetId}`)
+        .then(response => response.json())
+        .then(data => {
+          // get the context file
+          if (data.numberOfHits === 1) { // chgeck if there is only one hit
+            const contextFile = data.results[0]['abi-contextual-information']
+
+            // check if there is only one context file 
+            if ( contextFile && contextFile.length === 1) {
+              return {
+                success: true,
+                contextFile: contextFile[0], 
+                s3uri: data.results[0]['s3uri']
+              }
+            }
+
+            // If there are multiple context files, find the one that matches the scaffold path
+            else if (contextFile && contextFile.length > 1) {
+              let search = this.findContextInforForFilePath(data.results[0]['abi-context-file'], scaffoldPath);
+              if (search) {
+                return {
+                  success: true,
+                  contextFile: search, 
+                  s3uri: data.results[0]['s3uri']
+                }
+              }
+            }
+          }
+          return {success: false};
+        }).catch(error => {
+          console.error('Error:', error);
+          return {success: false};
+        });
+      return results;
+    },
+    findContextInforForFilePath: function (dataciteInfo, filePath) {
+      let result = dataciteInfo.find((info) => info.datacite.isDerivedFrom.path.includes(filePath))
+      return result?.dataset?.path
+    }
+  }
+}

package/src/mixins/S3Bucket.vue

@@ -1,37 +1,37 @@
-<script>
-export default {
-  name: "S3Bucket",
-  data() {
-    return {
-      s3Bucket: undefined,
-      s3Prefix: "",
-    };
-  },
-  methods: {
-    updateS3Bucket: function(s3uri) {
-      this.s3Bucket = undefined;
-      if (s3uri) {
-        const substring = s3uri.split("//")[1];
-        if (substring) {
-          this.s3Bucket = substring.split("/")[0];
-          const n = substring.indexOf('/');
-          this.s3Prefix = substring.substring(n + 1);
-          return;
-        }
-      }
-    },
-    getS3Args: function() {
-      if (this.s3Bucket) {
-        return `?s3BucketName=${this.s3Bucket}`
-      }
-      return "";
-    },
-    getS3Prefix: function() {
-      return this.s3Prefix;
-    }
-  },
-
-};
-</script>
-
-
+<script>
+export default {
+  name: "S3Bucket",
+  data() {
+    return {
+      s3Bucket: undefined,
+      s3Prefix: "",
+    };
+  },
+  methods: {
+    updateS3Bucket: function(s3uri) {
+      this.s3Bucket = undefined;
+      if (s3uri) {
+        const substring = s3uri.split("//")[1];
+        if (substring) {
+          this.s3Bucket = substring.split("/")[0];
+          const n = substring.indexOf('/');
+          this.s3Prefix = substring.substring(n + 1);
+          return;
+        }
+      }
+    },
+    getS3Args: function() {
+      if (this.s3Bucket) {
+        return `?s3BucketName=${this.s3Bucket}`
+      }
+      return "";
+    },
+    getS3Prefix: function() {
+      return this.s3Prefix;
+    }
+  },
+
+};
+</script>
+
+

package/src/stores/entries.js

@@ -1,40 +1,40 @@
-import { defineStore } from 'pinia';
-import { initialDefaultState } from "../components/scripts/utilities";
-
-/* eslint-disable no-alert, no-console */
-
-export const useEntriesStore = defineStore('entries', {
-  state: () => {
-    return initialDefaultState();
-  },
-  getters: {
-    findIndexOfId: (state) => id => {
-      for (let i = 0; i < state.entries.length; i++) {
-        if (state.entries[i].id == id) {
-          return i;
-        }
-      }
-      return -1;
-    },
-  },
-  actions: {
-    addNewEntry(entry) {
-      this.entries.push(entry);
-    },
-    destroyEntry(index) {
-      if (index > -1) {
-        this.entries.splice(index, 1);
-      }
-    },
-    setAll(newEntries) {
-      this.entries = [];
-      Object.assign(this.entries, newEntries);
-    },
-    updateViewForEntry( {id, viewUrl}) {
-      // Update the scaffold with a view url
-      const entry = this.entries.find(entry => entry.id === id);
-      entry.viewUrl = viewUrl;
-    },
-
-  }
-});
+import { defineStore } from 'pinia';
+import { initialDefaultState } from "../components/scripts/utilities";
+
+/* eslint-disable no-alert, no-console */
+
+export const useEntriesStore = defineStore('entries', {
+  state: () => {
+    return initialDefaultState();
+  },
+  getters: {
+    findIndexOfId: (state) => id => {
+      for (let i = 0; i < state.entries.length; i++) {
+        if (state.entries[i].id == id) {
+          return i;
+        }
+      }
+      return -1;
+    },
+  },
+  actions: {
+    addNewEntry(entry) {
+      this.entries.push(entry);
+    },
+    destroyEntry(index) {
+      if (index > -1) {
+        this.entries.splice(index, 1);
+      }
+    },
+    setAll(newEntries) {
+      this.entries = [];
+      Object.assign(this.entries, newEntries);
+    },
+    updateViewForEntry( {id, viewUrl}) {
+      // Update the scaffold with a view url
+      const entry = this.entries.find(entry => entry.id === id);
+      entry.viewUrl = viewUrl;
+    },
+
+  }
+});

package/src/stores/index.js

@@ -1,16 +1,24 @@
-import Vue from 'vue';
-import Vuex from 'vuex';
-import entries from './modules/entries';
-import settings from './modules/settings';
-import splitFlow from './modules/splitFlow';
-Vue.use(Vuex);
-
-export const store = new Vuex.Store({
-  modules: {
-    entries,
-    splitFlow,
-    settings,
-  }
-});
-
-export default store;
+import { defineStore } from 'pinia'
+
+/**
+ * Activate the store when run the application individually.
+ * If the store exist in parent application, 
+ * instead of creating a new store it will access the parent main store.
+ */
+export const useMainStore = defineStore('main', {
+  state: () => ({
+    userProfile: {
+      token: ''
+    },
+  }),
+  getters: {
+    userToken(state) {
+      return state.userProfile.token
+    },
+  },
+  actions: {
+    setUserToken(value) {
+      this.userProfile.token = value
+    },
+  }
+})