@abi-software/flatmapvuer 1.6.2-beta.4 → 1.6.2

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@abi-software/flatmapvuer",
-  "version": "1.6.2-beta.4",
+  "version": "1.6.2",
   "license": "Apache-2.0",
   "files": [
     "dist/*",
@@ -43,8 +43,8 @@
     "./src/*": "./src/*"
   },
   "dependencies": {
-    "@abi-software/flatmap-viewer": "^3.2.8",
-    "@abi-software/map-utilities": "^1.2.2-beta.3",
+    "@abi-software/flatmap-viewer": "^3.2.10",
+    "@abi-software/map-utilities": "^1.2.1",
     "@abi-software/sparc-annotation": "0.3.2",
     "@abi-software/svg-sprite": "^1.0.1",
     "@element-plus/icons-vue": "^2.3.1",

package/src/components/FlatmapVuer.vue

@@ -152,6 +152,7 @@ Please use `const` to assign meaningful names to them...
           class: '.maplibregl-canvas',
         }"
         :toolbarOptions="toolbarOptions"
+        :drawnType="drawnType"
         :activeDrawTool="activeDrawTool"
         :activeDrawMode="activeDrawMode"
         :newlyDrawnEntry="drawnCreatedEvent"
@@ -259,7 +260,7 @@ Please use `const` to assign meaningful names to them...
           <div
             class="pathway-location"
             :class="{ open: drawerOpen, close: !drawerOpen }"
-            v-show="!disableUI && requiresDrawer"
+            v-show="!disableUI"
           >
             <div
               class="pathway-container"
@@ -269,27 +270,27 @@ Please use `const` to assign meaningful names to them...
             >
               <svg-legends v-if="!isFC" class="svg-legends-container" />
               <template v-if="showStarInLegend">
-                <el-popover
-                  content="Location of the featured dataset"
-                  placement="right"
-                  :teleported="true"
-                  trigger="manual"
-                  width="max-content"
-                  :offset="-10"
-                  popper-class="flatmap-popper flatmap-teleport-popper"
-                  :visible="hoverVisibilities[9].value"
-                  ref="featuredMarkerPopover"
-                >
-                  <template #reference>
-                    <div
-                      v-popover:featuredMarkerPopover
-                      class="yellow-star-legend"
-                      v-html="yellowstar"
-                      @mouseover="showTooltip(9)"
-                      @mouseout="hideTooltip(9)"
-                    ></div>
-                  </template>
-                </el-popover>
+              <el-popover
+                content="Location of the featured dataset"
+                placement="right"
+                :teleported="true"
+                trigger="manual"
+                width="max-content"
+                :offset="-10"
+                popper-class="flatmap-popper flatmap-teleport-popper"
+                :visible="hoverVisibilities[9].value"
+                ref="featuredMarkerPopover"
+              >
+                <template #reference>
+                  <div
+                    v-popover:featuredMarkerPopover
+                    class="yellow-star-legend"
+                    v-html="yellowstar"
+                    @mouseover="showTooltip(9)"
+                    @mouseout="hideTooltip(9)"
+                  ></div>
+                </template>
+              </el-popover>
               </template>
               <!-- The line below places the yellowstar svg on the left, and the text "Featured markers on the right" with css so they are both centered in the div -->
               <el-popover
@@ -453,22 +454,44 @@ Please use `const` to assign meaningful names to them...
               </template>
             </div>
             <el-row class="viewing-mode-description">
-              {{ modeDescription }}
+              {{ viewingModes[viewingMode] }}
             </el-row>
           </el-row>
           <template v-if="viewingMode === 'Annotation' && userInformation">
-            <el-row class="backgroundText">Annotations From</el-row>
+            <el-row class="backgroundText">Drawn By*</el-row>
+            <el-row class="backgroundControl">
+              <el-select
+                :teleported="false"
+                v-model="drawnType"
+                placeholder="Select"
+                class="select-box"
+                popper-class="flatmap_dropdown"
+                @change="setDrawnType"
+              >
+                <el-option
+                  v-for="item in drawnTypes"
+                  :key="item"
+                  :label="item"
+                  :value="item"
+                >
+                  <el-row>
+                    <el-col :span="12">{{ item }}</el-col>
+                  </el-row>
+                </el-option>
+              </el-select>
+            </el-row>
+            <el-row class="backgroundText">Annotated By*</el-row>
             <el-row class="backgroundControl">
               <el-select
                 :teleported="false"
-                v-model="annotationFrom"
+                v-model="annotatedType"
                 placeholder="Select"
                 class="select-box"
                 popper-class="flatmap_dropdown"
-                @change="setAnnotationFrom"
+                @change="setAnnotatedType"
               >
                 <el-option
-                  v-for="item in annotatedSource"
+                  v-for="item in annotatedTypes"
                   :key="item"
                   :label="item"
                   :value="item"
@@ -645,24 +668,20 @@ const centroid = (geometry) => {
   let featureGeometry = { lng: 0, lat: 0, }
   let coordinates
   if (geometry.type === "Polygon") {
-    if (geometry.coordinates.length) {
-      coordinates = geometry.coordinates[0]
-    }
+    coordinates = geometry.coordinates[0]
   } else {
     coordinates = geometry.coordinates
   }
-  if (coordinates) {    
-    if (!(geometry.type === 'Point')) {
-      coordinates.map((coor) => {
-        featureGeometry.lng += parseFloat(coor[0])
-        featureGeometry.lat += parseFloat(coor[1])
-      })
-      featureGeometry.lng = featureGeometry.lng / coordinates.length
-      featureGeometry.lat = featureGeometry.lat / coordinates.length
-    } else {
-      featureGeometry.lng += parseFloat(coordinates[0])
-      featureGeometry.lat += parseFloat(coordinates[1])
-    }
+  if (!(geometry.type === 'Point')) {
+    coordinates.map((coor) => {
+      featureGeometry.lng += parseFloat(coor[0])
+      featureGeometry.lat += parseFloat(coor[1])
+    })
+    featureGeometry.lng = featureGeometry.lng / coordinates.length
+    featureGeometry.lat = featureGeometry.lat / coordinates.length
+  } else {
+    featureGeometry.lng += parseFloat(coordinates[0])
+    featureGeometry.lat += parseFloat(coordinates[1])
   }
   return featureGeometry
 }
@@ -754,7 +773,6 @@ export default {
       if (this.annotationSidebar) this.$emit("annotation-close")
       this.closeTooltip()
       this.annotationEventCallback({}, { type: 'aborted' })
-      this.initialiseDrawing()
     },
     /**
      * @public
@@ -830,19 +848,21 @@ export default {
      * @arg {String} `name`
      */
     toolbarEvent: function (type, name) {
-      if (this.isValidDrawnCreated) return;
       this.manualAbortedOnClose()
       this.doubleClickedFeature = false
-      // Deselect any feature when draw mode/tool is changed
-      this.changeAnnotationDrawMode({ mode: 'simple_select' })
+      this.connectionEntry = {}
       if (type === 'mode') {
+        // Deselect any feature when draw mode is changed
+        this.changeAnnotationDrawMode({ mode: 'simple_select' })
         this.activeDrawMode = name
       } else if (type === 'tool') {
-        // Remove any unsubmitted drawn
-        this.cancelDrawnFeature()
         if (name) {
           const tool = name.replace(/[A-Z]/g, letter => `_${letter.toLowerCase()}`)
           this.changeAnnotationDrawMode({ mode: `draw${tool}` })
+          this.initialiseDrawing()
+        } else {
+          this.changeAnnotationDrawMode({ mode: 'simple_select' })
+          this.cancelDrawnFeature()
         }
         this.activeDrawTool = name
       }
@@ -865,7 +885,8 @@ export default {
           }
           this.doubleClickedFeature = false
         }
-      } else if (this.activeDrawMode === 'Delete') {
+      }
+      if (this.activeDrawMode === 'Delete') {
         this.changeAnnotationDrawMode({
           mode: 'simple_select',
           options: { featureIds: [data.feature.feature.id] }
@@ -951,12 +972,9 @@ export default {
       ) {
         this.featureAnnotationSubmitted = true
         this.mapImp.commitAnnotationEvent(this.annotationEntry)
-        if (annotation.body.comment === "Position Updated") {
-          this.annotationEntry.positionUpdated = false
-        } else if (this.annotationEntry.type === 'deleted') {
+        if (this.annotationEntry.type === 'deleted') {
           if (this.annotationSidebar) this.$emit("annotation-close")
           this.closeTooltip()
-          // Only delete need, keep the annotation tooltip/sidebar open if created/updated
           this.annotationEntry = {}
         }
         this.addAnnotationFeature()
@@ -997,6 +1015,12 @@ export default {
       let drawnFeatures = await this.annotator.drawnFeatures(this.userToken, this.serverURL, annotatedItemIds)
       // The annotator has `resource` and `features` fields
       if ('resource' in drawnFeatures) drawnFeatures = drawnFeatures.features
+      // Use to switch the displayed feature type
+      if (this.drawnType !== 'All tools') {
+        drawnFeatures = drawnFeatures.filter((feature) => {
+          return feature.geometry.type === this.drawnType
+        })
+      }
       return drawnFeatures
     },
     /**
@@ -1005,22 +1029,22 @@ export default {
      */
     addAnnotationFeature: async function () {
       if (this.mapImp) {
-        if (!this.featureAnnotationSubmitted) {
-          this.clearAnnotationFeature()
-          this.loading = true
-        }
-        const userId = this.annotationFrom === 'Anyone' ?
-          undefined : this.userInformation.orcid ?
-            this.userInformation.orcid : '0000-0000-0000-0000'
-        const participated = this.annotationFrom === 'Anyone' ?
-          undefined : this.annotationFrom === 'Me' ?
-            true : false
-        const drawnFeatures = await this.fetchDrawnFeatures(userId, participated)
-        this.existDrawnFeatures = drawnFeatures
-        this.loading = false
-        if (!this.featureAnnotationSubmitted) {
-          for (const feature of drawnFeatures) {
-            this.mapImp.addAnnotationFeature(feature)
+        if (!this.featureAnnotationSubmitted) this.clearAnnotationFeature()
+        if (this.drawnType !== 'None') {
+          if (!this.featureAnnotationSubmitted) this.loading = true
+          const userId = this.annotatedType === 'Anyone' ?
+            undefined : this.userInformation.orcid ?
+              this.userInformation.orcid : '0000-0000-0000-0000'
+          const participated = this.annotatedType === 'Anyone' ?
+            undefined : this.annotatedType === 'Me' ?
+              true : false
+          const drawnFeatures = await this.fetchDrawnFeatures(userId, participated)
+          this.existDrawnFeatures = drawnFeatures
+          this.loading = false
+          if (!this.featureAnnotationSubmitted) {
+            for (const feature of drawnFeatures) {
+              this.mapImp.addAnnotationFeature(feature)
+            }
           }
         }
       }
@@ -1038,13 +1062,26 @@ export default {
         this.$el.querySelector('.maplibregl-ctrl-group').style.display = 'none'
       }
     },
+    /**
+     * @public
+     * Function to switch the type of annotation.
+     * @arg {Boolean} `flag`
+     */
+    setDrawnType: function (flag) {
+      this.drawnType = flag
+      if (this.mapImp) {
+        this.manualAbortedOnClose()
+        this.addAnnotationFeature()
+        this.initialiseDrawing()
+      }
+    },
     /**
      * @public
      * Function to switch the type of person who annotated.
      * @arg {Boolean} `flag`
      */
-    setAnnotationFrom: function (flag) {
-      this.annotationFrom = flag
+    setAnnotatedType: function (flag) {
+      this.annotatedType = flag
       if (this.mapImp) {
         this.manualAbortedOnClose()
         this.addAnnotationFeature()
@@ -1552,7 +1589,7 @@ export default {
         this.annotationEntry = {}
       } else if (data.type === 'modeChanged') {
         if (data.feature.mode === 'direct_select') this.doubleClickedFeature = true
-        if (this.annotationSidebar && data.feature.mode === 'simple_select' && this.activeDrawMode === 'Deleted') {
+        if (this.annotationSidebar && data.feature.mode === 'simple_select') {
           this.annotationEventCallback({}, { type: 'aborted' })
         }
       } else if (data.type === 'selectionChanged') {
@@ -1570,15 +1607,6 @@ export default {
               this.connectionEntry = drawnFeature.connection
             }
             this.annotationDrawModeEvent(payload)
-          } else {
-            if (this.annotationSidebar && this.previousEditEvent.type === 'updated') {
-              this.annotationEntry = {
-                ...this.previousEditEvent,
-                resourceId: this.serverURL
-              }
-              this.annotationEventCallback({}, { type: 'aborted' })
-            }
-            this.previousEditEvent = {}
           }
         }
       } else {
@@ -1596,7 +1624,6 @@ export default {
         if (data.type === 'created') this.drawnCreatedEvent = payload
         else this.checkAndCreatePopups(payload)
       }
-      if (data.type === 'updated') this.previousEditEvent = data
       if (data.type === 'deleted') this.previousDeletedEvent = data
       else this.previousDeletedEvent = {}
     },
@@ -1843,8 +1870,12 @@ export default {
           if (data.feature.featureId && data.feature.models) {
             this.displayTooltip(data.feature.models)
           } else if (data.feature.feature) {
-            // in drawing or edit/delete mode is on or valid drawn
-            if (this.activeDrawTool || this.activeDrawMode || this.isValidDrawnCreated) {
+            // in drawing or edit/delete mode is on or has connectivity
+            if (
+              this.activeDrawTool ||
+              this.activeDrawMode ||
+              Object.keys(this.connectionEntry).length > 0
+            ) {
               this.featureAnnotationSubmitted = false
               this.annotationEntry.featureId = data.feature.feature.id
               if (this.activeDrawTool) {
@@ -2011,11 +2042,7 @@ export default {
             isPathwayContainer(parentElement) ||
             isPathwayContainer(nextElementSibling)
           ) {
-            if (this.requiresDrawer) {
-              this.drawerOpen = true;
-            } else {
-              this.helpModeActiveIndex += 1;
-            }
+            this.drawerOpen = true;
           }
         } else {
           // skip the unavailable tooltips
@@ -2147,7 +2174,8 @@ export default {
         !this.disableUI && (
           (
             this.viewingMode === 'Annotation' &&
-            !this.annotationSidebar
+            !this.annotationSidebar &&
+            this.userInformation
           ) ||
           (
             this.viewingMode === 'Exploration' &&
@@ -2161,6 +2189,7 @@ export default {
           this.mapImp.showPopup(featureId, this.$refs.tooltip.$el, options);
           this.popUpCssHacks();
         });
+
       }
     },
     hasTooltipEntry: function () {
@@ -2454,7 +2483,7 @@ export default {
           }
         }
 
-        let promise1 = this.mapManagerRef.loadMap(
+        let promise1 = this.mapManager.loadMap(
           identifier,
           this.$refs.display,
           this.eventCallback(),
@@ -2539,6 +2568,7 @@ export default {
       this.addResizeButtonToMinimap()
       this.loading = false
       this.computePathControlsMaximumHeight()
+      this.drawerOpen = true;
       this.mapResize()
       this.handleMapClick();
       this.setInitMapState();
@@ -2801,14 +2831,6 @@ export default {
       type: Object,
       default: undefined,
     },
-    /**
-     * Flatmap's Map Manager to use as single Map Manager
-     * if the FlatmapVuer is loaded from MultiFlatmapVuer.
-     */
-    mapManager: {
-      type: Object,
-      default: undefined,
-    },
     /**
      * Specify the endpoint of the flatmap server.
      */
@@ -2856,7 +2878,7 @@ export default {
   data: function () {
     return {
       sensor: null,
-      mapManagerRef: undefined,
+      mapManager: undefined,
       flatmapQueries: undefined,
       annotationEntry: {},
       //tooltip display has to be set to false until it is rendered
@@ -2920,10 +2942,12 @@ export default {
       viewingModes: {
         'Exploration': 'Find relevant research and view detail of neural pathways by selecting a pathway to view its connections and data sources',
         'Neuron Connection': 'Discover Neuron connections by selecting a neuron and viewing its associated network connections',
-        'Annotation': ['View feature annotations', 'Add, comment on and view feature annotations']
+        'Annotation': 'View internal identifiers of features'
       },
-      annotationFrom: 'Anyone',
-      annotatedSource: ['Anyone', 'Me', 'Others'],
+      drawnType: 'All tools',
+      drawnTypes: ['All tools', 'Point', 'LineString', 'Polygon', 'None'],
+      annotatedType: 'Anyone',
+      annotatedTypes: ['Anyone', 'Me', 'Others'],
       openMapRef: undefined,
       backgroundIconRef: undefined,
       toolbarOptions: [
@@ -2940,7 +2964,6 @@ export default {
       activeDrawTool: undefined,
       featureAnnotationSubmitted: false,
       drawnCreatedEvent: {},
-      previousEditEvent: {},
       previousDeletedEvent: {},
       connectionEntry: {},
       existDrawnFeatures: [], // Store all exist drawn features
@@ -2975,37 +2998,6 @@ export default {
     isValidDrawnCreated: function () {
       return Object.keys(this.drawnCreatedEvent).length > 0
     },
-    requiresDrawer: function() {
-      if (this.loading) {
-        this.drawerOpen = false
-        return false
-      }
-      if (!this.isFC) {
-        this.drawerOpen = true
-        return true
-      } else {
-        if ((this.systems?.length > 0) ||
-          (this.containsAlert && this.alertOptions) ||
-          (this.pathways?.length > 0) ||
-          (this.taxonConnectivity?.length > 0)
-        ) {
-          this.drawerOpen = true
-          return true
-        }
-      }
-      this.drawerOpen = false
-      return true
-    },
-    modeDescription: function () {
-      let description = this.viewingModes[this.viewingMode]
-      if (this.viewingMode === 'Annotation') {
-        if (this.userInformation) {
-          return description[1]
-        }
-        return description[0]
-      }
-      return description
-    },
   },
   watch: {
     entry: function () {
@@ -3027,7 +3019,7 @@ export default {
     state: {
       handler: function (state, oldVal) {
         if (state !== oldVal) {
-          if (this.mapManagerRef) {
+          if (this.mapManager) {
             this.setState(state)
           } else {
             //this component has not been mounted yet
@@ -3096,22 +3088,11 @@ export default {
       }
     }
   },
-  created: function () {
-    if (this.mapManager) {
-      this.mapManagerRef = this.mapManager;
-    } else {
-      this.mapManagerRef = markRaw(new flatmap.MapManager(this.flatmapAPI));
-      /**
-       * The event emitted after a new mapManager is loaded.
-       * This mapManager can be used to create new flatmaps.
-       */
-      this.$emit('mapmanager-loaded', this.mapManagerRef);
-    }
-  },
   mounted: function () {
     this.openMapRef = shallowRef(this.$refs.openMapRef)
     this.backgroundIconRef = shallowRef(this.$refs.backgroundIconRef)
     this.tooltipWait.length = this.hoverVisibilities.length
+    this.mapManager = markRaw(new flatmap.MapManager(this.flatmapAPI))
     this.flatmapQueries = markRaw(new FlatmapQueries())
     this.flatmapQueries.initialise(this.flatmapAPI)
     if (this.state) {
@@ -3208,7 +3189,6 @@ export default {
 
 .svg-legends-container {
   width: 70%;
-  min-width:183px;
   height: auto;
   position: relative;
   max-height: 140px;

package/src/components/MultiFlatmapVuer.vue

@@ -83,7 +83,6 @@
       :displayMinimap="displayMinimap"
       :showStarInLegend="showStarInLegend"
       style="height: 100%"
-      :mapManager="mapManagerRef"
       :flatmapAPI="flatmapAPI"
       :sparcAPI="sparcAPI"
     />
@@ -125,9 +124,6 @@ export default {
     Popover,
     FlatmapVuer,
   },
-  created: function () {
-    this.loadMapManager();
-  },
   mounted: function () {
     this.initialise()
     EventBus.on('onActionClick', (action) => {
@@ -223,23 +219,6 @@ export default {
         }
       })
     },
-    /**
-     * Function to load `mapManager` to create flatmap.
-     */
-    loadMapManager: function () {
-      if (!this.mapManagerRef) {
-        if (this.mapManager) {
-          this.mapManagerRef = this.mapManager;
-        } else {
-          this.mapManagerRef = markRaw(new flatmap.MapManager(this.flatmapAPI));
-          /**
-           * The event emitted after a new mapManager is loaded.
-           * This mapManager can be used to create new flatmaps.
-           */
-          this.$emit('mapmanager-loaded', this.mapManagerRef);
-        }
-      }
-    },
     /**
      * @public
      * Function to emit ``resource-selected`` event with provided ``resource``.
@@ -431,11 +410,12 @@ export default {
             //uuid is in the state but should be checked if it is the latest map
             //for that taxon
             return new Promise(() => {
+              const mapManager = new flatmap.MapManager(this.flatmapAPI)
               //mapManager.findMap_ is an async function so we need to wrap this with a promise
               const identifier = { taxon: mapState.entry }
               if (mapState.biologicalSex)
                 identifier['biologicalSex'] = mapState.biologicalSex
-              this.mapManagerRef
+              mapManager
                 .findMap_(identifier)
                 .then((map) => {
                   if (map.uuid !== mapState.uuid) {
@@ -481,9 +461,6 @@ export default {
      */
     setState: function (state) {
       if (state) {
-        // Update undefined mapManagerRef for setState happens before created event
-        this.loadMapManager();
-
         //Update state if required
         this.updateState(state).then((currentState) => {
           this.initialise().then(() => {
@@ -719,14 +696,6 @@ export default {
       type: Object,
       default: undefined,
     },
-    /**
-     * Flatmap's Map Manager to use as single Map Manager
-     * when the value is provided.
-     */
-    mapManager: {
-      type: Object,
-      default: undefined,
-    },
     /**
      * Specify the endpoint of the flatmap server.
      */
@@ -770,7 +739,6 @@ export default {
       requireInitialisation: true,
       resolveList: markRaw([]),
       initialised: false,
-      mapManagerRef: undefined,
     }
   },
   watch: {