@abi-software/mapintegratedvuer 1.16.2 → 1.16.3-simulation.0

package/src/services/mapping.js

@@ -0,0 +1,69 @@
+import readXlsxFile from 'read-excel-file'
+
+const BASE_URL =
+  'https://raw.githubusercontent.com/hsorby/fc-feature-mapping/main/'
+const INDEX_FILE = 'mapping_index.json'
+
+export class MappingService {
+  // Find the correct Excel file for the current Flatmap
+  static async getMappingIndex() {
+    try {
+      // Fetch the master index
+      const response = await fetch(`${BASE_URL}${INDEX_FILE}`)
+      if (!response.ok) throw new Error('Failed to fetch index')
+
+      const index = await response.json()
+
+      return index || null
+    } catch (e) {
+      console.error('Error finding map mapping:', e)
+      return null
+    }
+  }
+
+  // Fetch and Parse the Excel file
+  static async loadMapping(index) {
+    const flatmapMap = new Map()
+
+    for (const entry in index) {
+      try {
+        const filename = index[entry]
+
+        const response = await fetch(`${BASE_URL}${filename}`)
+        if (!response.ok) throw new Error(`Failed to fetch ${filename}`)
+
+        // Get the binary data
+        const blob = await response.blob()
+
+        // Parse with read-excel-file
+        // rows is an array of arrays: [ ["Header1", "Header2"], ["Row1Col1", "Row1Col2"] ]
+        const rows = await readXlsxFile(blob)
+
+        // Remove header row
+        const headers = rows.shift()
+        const nameIndex = headers.indexOf('Name')
+        const componentIndex = headers.indexOf('Component')
+        const flatmapIdIndex = headers.indexOf('Flatmap ID')
+
+        // Convert to a Lookup Map for fast access
+        // Assuming Column 0 = FlatmapID, Column 1 = Component, Column 2 = Variable
+        const lookup = new Map()
+
+        rows.forEach((row) => {
+          const flatmapId = row[flatmapIdIndex]
+          const component = row[componentIndex]
+          const variable = row[nameIndex]
+
+          if (flatmapId && component && variable) {
+            lookup.set(flatmapId, { component, variable })
+          }
+        })
+        flatmapMap.set(entry, lookup)
+      } catch (e) {
+        console.error('Error parsing mapping file:', e)
+      }
+    }
+
+    return flatmapMap
+  }
+}

package/src/stores/entries.js

@@ -1,6 +1,6 @@
 import { defineStore } from 'pinia';
 import { initialDefaultState } from "../components/scripts/utilities";
-import { getKnowledgeSourceFromProvenance } from '@abi-software/flatmapvuer/src/services/flatmapKnowledge.js';
+import { getKnowledgeSourceFromProvenance } from '@abi-software/flatmapvuer';
 
 /* eslint-disable no-alert, no-console */
 

package/src/stores/mapping.js

@@ -0,0 +1,29 @@
+import { defineStore } from 'pinia'
+import { MappingService } from '../services/mapping'
+
+export const useMappingStore = defineStore('mapping', {
+  state: () => ({
+    elementMap: new Map(),
+  }),
+
+  actions: {
+    async initializeMapping() {
+      this.elementMap.clear()
+
+      // Find which file to load
+      const index = await MappingService.getMappingIndex()
+
+      if (index) {
+        // Parse and store
+        this.elementMap = await MappingService.loadMapping(index)
+      } else {
+        console.warn('No index found.')
+      }
+    },
+
+    // Helper to get data for a specific element ID
+    mapToCellMLIdentifiers(flatmapUuid, flatmapElementId) {
+      return this.elementMap.get(flatmapUuid)?.get(flatmapElementId) || { component: undefined, variable: undefined }
+    },
+  },
+})

package/src/stores/settings.js

@@ -12,7 +12,6 @@ export const useSettingsStore = defineStore('settings', {
       algoliaId: undefined,
       pennsieveApi: undefined,
       flatmapAPI: undefined,
-      nlLinkPrefix: undefined,
       mapManager: undefined,
       rootUrl: undefined,
       facets: { species: [], gender: [], organ: [] },
@@ -114,9 +113,6 @@ export const useSettingsStore = defineStore('settings', {
     updateMapManager(mapManager) {
       this.mapManager = mapManager;
     },
-    updateNLLinkPrefix(nlLinkPrefix) {
-      this.nlLinkPrefix = nlLinkPrefix;
-    },
     updateRootUrl(rootUrl) {
       this.rootUrl = rootUrl;
     },

package/src/stores/simulationPlotStore.js

@@ -0,0 +1,104 @@
+import { defineStore } from 'pinia'
+import { ref } from 'vue'
+import EventBus from '../components/EventBus'
+
+const BASE_Z_INDEX = 100
+
+export const useSimulationPlotStore = defineStore('simulationPlots', () => {
+  const windows = ref([])
+  const zStack = ref([])
+  const simulationEntries = ref({})
+
+  function initListeners() {
+    EventBus.on('simulation-response', handleSimulationResponse)
+    EventBus.on('simulation-ready', handleSimulationReady)
+  }
+
+  function cleanupListeners() {
+    EventBus.off('simulation-response', handleSimulationResponse)
+    EventBus.off('simulation-ready', handleSimulationReady)
+  }
+
+  function removeWindow(windowId) {
+    const targetWindow = windows.value.find(win => win.id === windowId)
+    if (!targetWindow) return
+    windows.value = windows.value.filter((win) => win.id !== windowId)
+    zStack.value = zStack.value.filter((stackId) => stackId !== windowId)
+    EventBus.emit('plot-window-closed', { id: targetWindow.id})
+  }
+
+  function refreshZIndices() {
+    windows.value.forEach((win) => {
+      // Find where this window sits in the stack
+      const stackIndex = zStack.value.indexOf(win.id)
+
+      // If found, assign zIndex. If not (error case), keep it low.
+      if (stackIndex !== -1) {
+        win.zIndex = BASE_Z_INDEX + stackIndex
+      }
+    })
+  }
+
+  function bringToFront(windowId) {
+    const stackIndex = zStack.value.indexOf(windowId)
+    if (stackIndex === -1) return // Should not happen
+
+    zStack.value.splice(stackIndex, 1)
+
+    zStack.value.push(windowId)
+
+    refreshZIndices()
+  }
+
+  function handleSimulationReady(data) {
+    simulationEntries.value[data.resourceId] = { ready: data.ready }
+  }
+
+  function requestSimulation(data) {
+    if (data.protocol === null || !simulationEntries.value[data.protocol?.resource]?.ready) return
+
+    let targetWindow = windows.value.find(win => win.id === data.windowId)
+    if (!targetWindow) {
+      targetWindow = {
+        id: data.windowId,
+        ownerId: data.ownerId,
+        data: null,
+        zIndex: BASE_Z_INDEX,
+        x: data.position.x + data.offset.left,
+        y: data.position.y + data.offset.top,
+      }
+      windows.value.push(targetWindow)
+      zStack.value.push(targetWindow.id)
+      refreshZIndices()
+    } else {
+      bringToFront(targetWindow.id)
+    }
+
+    EventBus.emit('simulation-data-request', {
+      id: 'nz.ac.auckland.simulation-data-request',
+      version: '0.1.0',
+      payload: data,
+    })
+  }
+
+  function handleSimulationResponse(response) {
+    if (response.id !== 'nz.ac.auckland.simulation-data-response') return
+    const targetWindow = windows.value.find(win => win.id === response.payload.windowId)
+
+    if (targetWindow) {
+      targetWindow.data = response.payload.data
+    } else {
+      console.warn('Received simulation response for unknown window ID:', response.payload.windowId)
+    }
+  }
+
+  return {
+    windows,
+    bringToFront,
+    cleanupListeners,
+    handleSimulationResponse,
+    requestSimulation,
+    initListeners,
+    removeWindow,
+  }
+})