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cytoscape · Dec 17, 2024 · 90f6ed5 · 90f6ed5
1 parent 33e46b9
commit 90f6ed5
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diff --git a/src/components/ToolBar/FileUpload.tsx b/src/components/ToolBar/FileUpload.tsx
@@ -48,10  48,10 @@ import { useNetworkSummaryStore } from '../../store/NetworkSummaryStore'
 import { generateUniqueName } from '../../utils/network-utils'
 import { VisualStyleOptions } from '../../models/VisualStyleModel/VisualStyleOptions'
 import { useUiStateStore } from '../../store/UiStateStore'
-import { Aspect } from '../../models/CxModel/Cx2/Aspect'
 import { getOptionalAspects } from '../../utils/cx-utils'
 import { useOpaqueAspectStore } from '../../store/OpaqueAspectStore'
 import { useMessageStore } from '../../store/MessageStore'
 import { OpaqueAspects } from '../../models/OpaqueAspectModel'
 
 interface FileUploadProps {
   show: boolean
@@ -66,7  66,7 @@ export function FileUpload(props: FileUploadProps) {
     visualStyle: VisualStyle
     networkView: NetworkView
     visualStyleOptions: VisualStyleOptions
-    otherAspects: Aspect[]
     otherAspects: OpaqueAspects[]
   }
 
   const setCurrentNetworkId = useWorkspaceStore(
@@ -117,7  117,7 @@ export function FileUpload(props: FileUploadProps) {
     const visualStyleOptions: VisualStyleOptions =
       VisualStyleFn.createVisualStyleOptionsFromCx(cxData)
 
-    const otherAspects: Aspect[] = getOptionalAspects(cxData)
     const otherAspects: OpaqueAspects[] = getOptionalAspects(cxData)
 
     return {
       network,

diff --git a/src/models/NetworkWithViewModel/NetworkWithView.ts b/src/models/NetworkWithViewModel/NetworkWithView.ts
@@ -3,6  3,7 @@ import { Table } from '../TableModel'
 import { NetworkView } from '../ViewModel'
 import { VisualStyle } from '../VisualStyleModel'
 import { VisualStyleOptions } from '../VisualStyleModel/VisualStyleOptions'
 import { OpaqueAspects } from '../OpaqueAspectModel'
 
 /**
  * An utility interface to hold all the data needed to build a network view
@@ -15,5  16,5 @@ export interface NetworkWithView {
   visualStyle: VisualStyle
   networkViews: NetworkView[]
   visualStyleOptions?: VisualStyleOptions
-  otherAspects?: any[] // All other optional aspects found in the CX2 stream
   otherAspects?: OpaqueAspects[] // All other optional aspects found in the CX2 stream
 }
diff --git a/src/models/VisualStyleModel/impl/cxVisualPropertyConverter.ts b/src/models/VisualStyleModel/impl/cxVisualPropertyConverter.ts
@@ -107,14  107,15 @@ export const convertPassthroughMappingToCX = (
   vs: VisualStyle,
   vp: VisualProperty<VisualPropertyValueType>,
   mapping: PassthroughMappingFunction,
   isNameInTable: boolean,
 ): CXPassthroughMappingFunction => {
   const { attribute } = mapping
 
   return {
     type: 'PASSTHROUGH',
     definition: {
       attribute,
-      type:mapping.attributeType
       ...(isNameInTable ? {} : { type: mapping.attributeType }),
     },
   }
 }
@@ -123,6  124,7 @@ export const convertDiscreteMappingToCX = (
   vs: VisualStyle,
   vp: VisualProperty<VisualPropertyValueType>,
   mapping: DiscreteMappingFunction,
   isNameInTable: boolean,
 ): CXDiscreteMappingFunction<CXVisualPropertyValue> => {
   const { vpValueMap, attribute } = mapping
 
@@ -134,14  136,15 @@ export const convertDiscreteMappingToCX = (
         v: value,
         vp: vpToCX(vp.name, vpValue),
       })),
-      type:mapping.attributeType
       ...(isNameInTable ? {} : { type: mapping.attributeType }),
     },
   }
 }
 export const convertContinuousMappingToCX = (
   vs: VisualStyle,
   vp: VisualProperty<VisualPropertyValueType>,
   mapping: ContinuousMappingFunction,
   isNameInTable: boolean,
 ): CXContinuousMappingFunction<CXVisualPropertyValue> => {
   const { min, max, controlPoints, attribute, ltMinVpValue, gtMaxVpValue } =
     mapping
@@ -183,7  186,7 @@ export const convertContinuousMappingToCX = (
         },
       ],
       attribute,
-      type:mapping.attributeType // must be number type
       ...(isNameInTable ? {} : { type: mapping.attributeType }),
     },
   }
 }

diff --git a/src/store/io/exportCX.ts b/src/store/io/exportCX.ts
@@ -15,6  15,7 @@ import VisualStyleFn, {
   VisualPropertyName,
   VisualProperty,
   VisualPropertyValueType,
   NodeVisualPropertyName,
 } from '../../models/VisualStyleModel'
 
 import { translateEdgeIdToCX } from '../../models/NetworkModel/impl/CyNetwork'
@@ -96,6  97,12 @@ export const exportNetworkToCx2 = (
   ): { [key: CXVPName]: CXVisualMappingFunction<CXVisualPropertyValue> } => {
     const { name, mapping } = vp
     const cxVPName = vpNameToCXName(name)
     const attributeName = mapping?.attribute
     // whether attributeName is in nodeTable or edgeTable
     let isNameInTable = false
     if(attributeName){
       isNameInTable = Object.values(NodeVisualPropertyName).includes(name as NodeVisualPropertyName) ? nodeTable.columns.map((col)=>col.name).includes(attributeName) : edgeTable.columns.map((col)=>col.name).includes(attributeName)  
     }
 
     if (mapping != null) {
       switch (mapping.type) {
@@ -104,6  111,7 @@ export const exportNetworkToCx2 = (
             vs,
             vp,
             mapping as ContinuousMappingFunction,
             isNameInTable
           )
           mappings[cxVPName] = convertedMapping
           break
@@ -113,6  121,7 @@ export const exportNetworkToCx2 = (
             vs,
             vp,
             mapping as DiscreteMappingFunction,
             isNameInTable
           )
           mappings[cxVPName] = convertedMapping
           break
@@ -122,6  131,7 @@ export const exportNetworkToCx2 = (
             vs,
             vp,
             mapping as PassthroughMappingFunction,
             isNameInTable
           )
           mappings[cxVPName] = convertedMapping
           break

diff --git a/src/store/persist/db.ts b/src/store/persist/db.ts
@@ -697,6  697,12 @@ export const deleteServiceAppFromDb = async (url: string): Promise<void> => {
   })
 }
 
 // opaque aspects
 export interface OpaqueAspectsDB {
   id: IdType
   aspects: Record<string, any[]>
 }
 
 export const putOpaqueAspectsToDb = async (
   networkId: IdType,
   aspects: Record<string, any[]>,
@@ -708,7  714,7 @@ export const putOpaqueAspectsToDb = async (
 
 export const getOpaqueAspectsFromDb = async (
   networkId: IdType,
-): Promise< any[] | undefined> => {
 ): Promise< OpaqueAspectsDB | undefined> => {
   return await db.opaqueAspects.get({ id: networkId })
 }
 

diff --git a/src/utils/CachedData.ts b/src/utils/CachedData.ts
@@ -3,6  3,7 @@ import { Table } from '../models/TableModel'
 import { NetworkView } from '../models/ViewModel'
 import { VisualStyle } from '../models/VisualStyleModel'
 import { VisualStyleOptions } from '../models/VisualStyleModel/VisualStyleOptions'
 import { OpaqueAspects } from '../models/OpaqueAspectModel'
 
 export interface CachedData {
   network?: Network
@@ -11,5  12,5 @@ export interface CachedData {
   visualStyle?: VisualStyle
   networkViews?: NetworkView[]
   visualStyleOptions?: VisualStyleOptions
-  otherAspects?: any[]
   otherAspects?: OpaqueAspects[]
 }
diff --git a/src/utils/cx-utils.ts b/src/utils/cx-utils.ts
@@ -11,6  11,7 @@ import {
   getVisualStyleFromDb,
   getUiStateFromDb,
   getOpaqueAspectsFromDb,
   OpaqueAspectsDB,
 } from '../store/persist/db'
 import { CachedData } from './CachedData'
 import { createNetworkAttributesFromCx } from '../models/TableModel/impl/NetworkAttributesImpl'
@@ -20,6  21,7 @@ import { NetworkWithView } from '../models/NetworkWithViewModel'
 import { VisualStyleOptions } from '../models/VisualStyleModel/VisualStyleOptions'
 import { Ui } from '../models/UiModel'
 import { IdType } from '../models/IdType'
 import { OpaqueAspects } from '../models/OpaqueAspectModel'
 
 /**
  *
@@ -73,7  75,10 @@ export const getCachedData = async (id: string): Promise<CachedData> => {
       uiState?.visualStyleOptions ?? {}
     // Fall back to an empty object if the visual style options are not found
     const visualStyleOptions: VisualStyleOptions = vsOptions[id] ?? {}
-    const otherAspects:  any[] | undefined = await getOpaqueAspectsFromDb(id) 
     const opaqueAspects: OpaqueAspectsDB|undefined = await getOpaqueAspectsFromDb(id)
     const otherAspects: OpaqueAspects[] = opaqueAspects
       ? Object.entries(opaqueAspects.aspects).map(([key, value]) => ({ [key]: value }))
       : []
     return {
       network,
       visualStyle,
@@ -109,7  114,7 @@ export const createDataFromCx = async (
   )
   const visualStyleOptions: VisualStyleOptions =
     VisualStyleFn.createVisualStyleOptionsFromCx(cxData)
-  const otherAspects: Aspect[] = getOptionalAspects(cxData)
   const otherAspects: OpaqueAspects[] = getOptionalAspects(cxData)
 
   return {
     network,
@@ -132,8  137,8 @@ const CoreAspectTagValueSet = new Set<string>(
  * @param cx2
  * @returns Array of optional Aspects
  */
-export const getOptionalAspects = (cx2: Cx2): Aspect[] => {
-  const optionalAspects: Aspect[] = []
 export const getOptionalAspects = (cx2: Cx2): OpaqueAspects[] => {
   const optionalAspects: OpaqueAspects[] = []
   for (const entry of cx2) {
     if (entry !== undefined) {
       const key = Object.keys(entry)[0]
@@ -142,7  147,7 @@ export const getOptionalAspects = (cx2: Cx2): Aspect[] => {
         key !== 'status' &&
         key !== 'CXVersion'
       ) {
-        optionalAspects.push(entry as Aspect)
         optionalAspects.push(entry as OpaqueAspects)
       }
     }
   }

diff --git a/src/utils/ndex-utils.ts b/src/utils/ndex-utils.ts
@@ -15,7  15,6 @@ import { exportNetworkToCx2 } from '../store/io/exportCX'
 import { TableRecord } from '../models/StoreModel/TableStoreModel'
 import { useNdexNetwork } from '../store/hooks/useNdexNetwork'
 import { OpaqueAspects } from '../models/OpaqueAspectModel'
-import { Aspect } from '../models/CxModel/Cx2/Aspect'
 import { ndexSummaryFetcher } from '../store/hooks/useNdexNetworkSummary'
 
 export const ndexDuplicateKeyErrorMessage =
@@ -145,6  144,9 @@ export const saveNetworkToNDEx = async (
   )
   await ndexClient.updateNetworkFromRawCX2(networkId, cx)
   const ndexSummary = await ndexClient.getNetworkSummary(networkId)
   if(ndexSummary.completed === false || ndexSummary.errorMessage){
     throw new Error('The network is rejected by NDEx')
   }
   const newNdexModificationTime = ndexSummary.modificationTime
   updateSummary(networkId, {
     modificationTime: newNdexModificationTime,
@@ -195,11  197,12 @@ export const saveAllNetworks = async (
 
       if (res.otherAspects) {
         opaqueAspect = res.otherAspects.reduce(
-          (acc: OpaqueAspects, aspect: Aspect) => {
           (acc: OpaqueAspects, aspect: OpaqueAspects) => {
             const [aspectName, aspectData] = Object.entries(aspect)[0]
             acc[aspectName] = aspectData
             return acc
           },
-          {},
           {} as OpaqueAspects,
         )
       } else {
         opaqueAspect = {}