@js4cytoscape/ndex-client 0.5.0-alpha.9 → 0.6.0-alpha.2

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Files changed (30) hide show
  1. package/README.md +339 -13
  2. package/dist/.tsbuildinfo +1 -0
  3. package/dist/index.d.mts +1906 -0
  4. package/dist/index.d.ts +1906 -0
  5. package/dist/index.global.js +9 -0
  6. package/dist/index.global.js.map +1 -0
  7. package/dist/index.js +4 -0
  8. package/dist/index.js.map +1 -0
  9. package/dist/index.mjs +4 -0
  10. package/dist/index.mjs.map +1 -0
  11. package/package.json +80 -21
  12. package/src/CyNDEx.js.bak +178 -0
  13. package/src/NDEx.js +66 -13
  14. package/src/NDEx.js.bak +1107 -0
  15. package/src/index.ts +230 -0
  16. package/src/models/CX2Network.ts +423 -0
  17. package/src/services/AdminService.ts +10 -0
  18. package/src/services/CyNDExService.ts +338 -0
  19. package/src/services/FilesService.ts +234 -0
  20. package/src/services/HTTPService.ts +442 -0
  21. package/src/services/NetworkServiceV2.ts +427 -0
  22. package/src/services/NetworkServiceV3.ts +288 -0
  23. package/src/services/UnifiedNetworkService.ts +641 -0
  24. package/src/services/UserService.ts +233 -0
  25. package/src/services/WorkspaceService.ts +159 -0
  26. package/src/types/cytoscape.ts +81 -0
  27. package/src/types/index.ts +524 -0
  28. package/dist/ndexClient.common.js +0 -1057
  29. package/dist/ndexClient.js +0 -538
  30. package/src/index.js +0 -2
package/dist/index.mjs ADDED
@@ -0,0 +1,4 @@
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+ import U from'axios';/* NDEx Client Library - Modern TypeScript implementation */
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+ var A=(r=>(r.NONE="NONE",r.BASIC="BASIC",r.FULL="FULL",r))(A||{}),p=class extends Error{constructor(t,r,s,n){super(t);this.statusCode=r;this.errorCode=s;this.description=n;this.name="NDExError";}},k=class extends p{constructor(t,r){super(t,void 0,"NETWORK_ERROR");this.originalError=r;this.name="NDExNetworkError";}},N=class extends p{constructor(e="Authentication failed",t=401){super(e,t,"AUTH_ERROR"),this.name="NDExAuthError";}},C=class extends p{constructor(e="Resource not found",t=404){super(e,t,"NOT_FOUND"),this.name="NDExNotFoundError";}},P=class extends p{constructor(e,t=400){super(e,t,"VALIDATION_ERROR"),this.name="NDExValidationError";}},x=class extends p{constructor(e="Internal server error",t=500){super(e,t,"SERVER_ERROR"),this.name="NDExServerError";}};var g=class a{constructor(e){this.CXVersion="2.0";this.hasFragments=false;this.metaData=[];e&&Object.assign(this,e),this.ensureRequiredMetadata();}static createEmpty(){let e=new a;return e.nodes=[],e.edges=[],e.metaData=[{name:"nodes",elementCount:0},{name:"edges",elementCount:0}],e}static fromJSON(e){let t=typeof e=="string"?JSON.parse(e):e;return new a(t)}static fromNetworkSummary(e){let t=a.createEmpty();return t.networkAttributes=[{name:e.name},...e.description?[{description:e.description}]:[],...e.version?[{version:e.version}]:[]],e.properties&&Object.entries(e.properties).forEach(([r,s])=>{t.networkAttributes?.push({[r]:s.v});}),t}addNode(e,t){this.nodes||(this.nodes=[]);let r={id:e};return t&&(r.v=t),this.nodes.push(r),this.updateNodeCount(),r}addEdge(e,t,r,s){this.edges||(this.edges=[]);let n={id:e,s:t,t:r};return s&&(n.v=s),this.edges.push(n),this.updateEdgeCount(),n}addNodeAttribute(e,t,r){let s=this.nodes.find(n=>n.id===e);s&&(s.v||(s.v={}),s.v[t]=r);}addEdgeAttribute(e,t,r){let s=this.edges.find(n=>n.id===e);s&&(s.v||(s.v={}),s.v[t]=r);}setNodeCoordinates(e,t,r,s){this.nodes||(this.nodes=[]);let n=this.nodes.find(i=>i.id===e);n||(n={id:e},this.nodes.push(n),this.updateNodeCount()),n.x=t,n.y=r,s!==void 0&&(n.z=s);}getNode(e){return this.nodes?.find(t=>t.id===e)}getEdge(e){return this.edges?.find(t=>t.id===e)}getNodes(){return this.nodes||[]}getEdges(){return this.edges||[]}getNodeCount(){return this.nodes?.length||0}getEdgeCount(){return this.edges?.length||0}getNetworkName(){return this.networkAttributes?.find(e=>"name"in e)?.name}setNetworkName(e){this.networkAttributes||(this.networkAttributes=[]),this.networkAttributes=this.networkAttributes.filter(t=>!("name"in t)),this.networkAttributes.push({name:e});}getNetworkAttribute(e){return this.networkAttributes?.find(t=>e in t)?.[e]}setNetworkAttribute(e,t){this.networkAttributes||(this.networkAttributes=[]),this.networkAttributes=this.networkAttributes.filter(r=>!(e in r)),this.networkAttributes.push({[e]:t});}validate(){let e=[];return this.CXVersion||e.push("CXVersion is required"),this.hasFragments===void 0&&e.push("hasFragments is required"),(!this.metaData||this.metaData.length===0)&&e.push("metaData is required and must not be empty"),this.metaData?.forEach((t,r)=>{t.name||e.push(`metaData[${r}] is missing required 'name' field`);}),this.nodes&&this.nodes.forEach((t,r)=>{(t.id===void 0||t.id===null)&&e.push(`nodes[${r}] is missing required 'id' field`);}),this.edges&&this.edges.forEach((t,r)=>{if((t.id===void 0||t.id===null)&&e.push(`edges[${r}] is missing required 'id' field`),(t.s===void 0||t.s===null)&&e.push(`edges[${r}] is missing required 's' (source) field`),(t.t===void 0||t.t===null)&&e.push(`edges[${r}] is missing required 't' (target) field`),this.nodes&&t.s!==void 0&&t.t!==void 0){let s=this.nodes.some(i=>i.id===t.s),n=this.nodes.some(i=>i.id===t.t);s||e.push(`edges[${r}] references non-existent source node ${t.s}`),n||e.push(`edges[${r}] references non-existent target node ${t.t}`);}}),{isValid:e.length===0,errors:e}}toJSON(){return JSON.stringify(this,null,2)}clone(){return new a(JSON.parse(this.toJSON()))}getStatistics(){return {nodeCount:this.getNodeCount(),edgeCount:this.getEdgeCount(),hasCoordinates:!!(this.nodes&&this.nodes.some(e=>e.x!==void 0||e.y!==void 0||e.z!==void 0)),hasVisualProperties:!!(this.visualProperties&&(this.visualProperties.default||this.visualProperties.edgeMapping||this.visualProperties.nodeMapping))}}ensureRequiredMetadata(){this.metaData||(this.metaData=[]),this.nodes&&!this.metaData.find(e=>e.name==="nodes")&&this.metaData.push({name:"nodes",elementCount:this.nodes.length}),this.edges&&!this.metaData.find(e=>e.name==="edges")&&this.metaData.push({name:"edges",elementCount:this.edges.length});}updateNodeCount(){let e=this.metaData?.find(t=>t.name==="nodes");e&&(e.elementCount=this.nodes?.length||0);}updateEdgeCount(){let e=this.metaData?.find(t=>t.name==="edges");e&&(e.elementCount=this.edges?.length||0);}};var m=class{constructor(e){this.http=e;}async getRawCX1Network(e,t={}){let r=new URLSearchParams;t.accesskey&&r.append("accesskey",t.accesskey);let s=`network/${e}${r.toString()?`?${r.toString()}`:""}`;return this.http.get(s,{version:"v2",headers:{Accept:"application/json"}})}async getNetworkSummary(e,t={}){let r=new URLSearchParams;t.accesskey&&r.append("accesskey",t.accesskey);let s=`network/${e}/summary${r.toString()?`?${r.toString()}`:""}`;return this.http.get(s,{version:"v2"})}async copyNetwork(e){let t=`network/${e}/copy`;return this.http.post(t,{},{version:"v2"})}async searchNetworks(e,t,r,s){let n={};t!==void 0&&(n.start=t.toString()),r!==void 0&&(n.limit=r.toString());let i={searchString:e};return s!==void 0&&(s.permission!==void 0&&(i.permission=s.permission),s.includeGroups!==void 0&&(i.includeGroups=s.includeGroups),s.accountName!==void 0&&(i.accountName=s.accountName)),this.http.post("search/network",i,{version:"v2",params:n})}async createNetworkFromRawCX1(e,t={}){let n=(await this.http.post("network",e,{version:"v2",params:t})).split("/");return n[n.length-1]}async updateNetworkFromRawCX1(e,t){let r=`network/${e}`;return this.http.put(r,t,{version:"v2"})}async deleteNetwork(e){let t=`network/${e}`;return this.http.delete(t,{version:"v2"})}async getNetworkSummariesByUUIDs(e,t){let r=t?{accesskey:t}:void 0;return this.http.post("batch/network/summary",e,{version:"v2",params:r})}async getUserNetworks(e,t={}){let r=new URLSearchParams;t.start!==void 0&&r.append("start",t.start.toString()),t.size!==void 0&&r.append("size",t.size.toString());let s=`user/${e}/networks${r.toString()?`?${r.toString()}`:""}`;return this.http.get(s,{version:"v2"})}async setNetworkSystemProperties(e,t){let r=`networks/${e}/systemproperty`;return this.http.put(r,t,{version:"v2"})}async getNetworkPermissions(e){let t=`networks/${e}/permission`;return this.http.get(t,{version:"v2"})}async setNetworkPermissions(e,t){let r=`networks/${e}/permission`;return this.http.put(r,t,{version:"v2"})}async grantNetworkPermission(e,t,r){let s=`networks/${e}/permission`,n={memberUUID:t,permission:r};return this.http.post(s,n,{version:"v2"})}async revokeNetworkPermission(e,t){let r=`networks/${e}/permission`;return this.http.delete(r,{version:"v2",data:{memberUUID:t}})}async getNetworkProfile(e){let t=`networks/${e}/profile`;return this.http.get(t,{version:"v2"})}async setNetworkProfile(e,t){let r=`networks/${e}/profile`;return this.http.put(r,t,{version:"v2"})}async makeNetworkPublic(e){let t=`networks/${e}/systemproperty`,r={visibility:"PUBLIC"};return this.http.put(t,r,{version:"v2"})}async makeNetworkPrivate(e){let t=`networks/${e}/systemproperty`,r={visibility:"PRIVATE"};return this.http.put(t,r,{version:"v2"})}async getNetworkSample(e,t={}){let r=new URLSearchParams;t.accesskey&&r.append("accesskey",t.accesskey);let s=`networks/${e}/sample${r.toString()?`?${r.toString()}`:""}`;return this.http.get(s,{version:"v2"})}async getMetaData(e,t){let r=new URLSearchParams;t!==void 0&&r.append("accesskey",t);let s=`network/${e}/aspect${r.toString()?`?${r.toString()}`:""}`;return this.http.get(s,{version:"v2"})}async getAccessKey(e){let t=`networks/${e}/accesskey`;return this.http.get(t,{version:"v2"})}async updateAccessKey(e,t){let r=`networks/${e}/accesskey`;return this.http.put(r,{action:t},{version:"v2"})}};var h=class{constructor(e){this.http=e;}async getNetworkSummary(e,t={}){let r=new URLSearchParams;t.accesskey&&r.append("accesskey",t.accesskey);let s=`networks/${e}/summary${r.toString()?`?${r.toString()}`:""}`;return this.http.get(s,{version:"v3"})}async getRawCX2Network(e,t={}){let r=new URLSearchParams;t.accesskey&&r.append("accesskey",t.accesskey);let s=`networks/${e}${r.toString()?`?${r.toString()}`:""}`;return this.http.get(s,{version:"v3"})}async createNetworkDOI(e,t,r){let s=new URLSearchParams;s.append("key",t),s.append("email",r);let n=`networks/${e}/DOI?${s.toString()}`;return this.http.get(n,{version:"v3"})}async getAttributesOfSelectedNodes(e,t,r={}){let s=new URLSearchParams;r.accesskey&&s.append("accesskey",r.accesskey);let n={ids:t.ids,attributeNames:t.attributeNames},i=`search/networks/${e}/nodes${s.toString()?`?${s.toString()}`:""}`;return this.http.post(i,n,{version:"v3"})}async getNetworkSummariesV3ByUUIDs(e,t,r){let s={format:r===void 0?"FULL":r};return t!=null&&(s.accesskey=t),this.http.post("batch/networks/summary",e,{version:"v3",params:s})}async searchNetworks(e={}){let t=new URLSearchParams;e.searchString&&t.append("searchString",e.searchString),e.accountName&&t.append("accountName",e.accountName),e.permission&&t.append("permission",e.permission),e.includeGroups!==void 0&&t.append("includeGroups",e.includeGroups.toString()),e.admin&&t.append("admin",e.admin),e.start!==void 0&&t.append("start",e.start.toString()),e.size!==void 0&&t.append("size",e.size.toString()),e.source&&t.append("source",e.source);let r=`search/network${t.toString()?`?${t.toString()}`:""}`;return this.http.get(r,{version:"v3"})}async getNetworkAsCX2Object(e,t={}){let r=await this.getRawCX2Network(e,t);return new g(r)}async createNetworkFromCX2(e,t={}){let r="networks",s=e instanceof g?JSON.parse(e.toJSON()):e;return this.http.post(r,s,{version:"v3",params:t})}async updateNetworkCX2(e,t){let r=`networks/${e}`,s=t instanceof g?JSON.parse(t.toJSON()):t;return this.http.put(r,s,{version:"v3"})}async uploadNetworkFile(e,t={}){return this.http.uploadFile("networks/upload",e,{version:"v3",...t})}async getNetworkMetadata(e){let t=`networks/${e}/metadata`;return this.http.get(t,{version:"v3"})}async updateNetworkMetadata(e,t){let r=`networks/${e}/metadata`;return this.http.put(r,t,{version:"v3"})}async getNetworkAspect(e,t,r={}){let s=new URLSearchParams;r.accesskey&&s.append("accesskey",r.accesskey);let n=`networks/${e}/aspects/${t}${s.toString()?`?${s.toString()}`:""}`;return this.http.get(n,{version:"v3"})}};var f=class{constructor(e){this.http=e;this.v2Service=new m(e),this.v3Service=new h(e);}async getNetworkSummary(e,t={}){return this.v3Service.getNetworkSummary(e,t)}async getRawCX1Network(e,t={}){return this.v2Service.getRawCX1Network(e,t)}async getRawCX2Network(e,t={}){return this.v3Service.getRawCX2Network(e,t)}async deleteNetwork(e){return this.v2Service.deleteNetwork(e)}async createNetworkDOI(e,t,r){return this.v3Service.createNetworkDOI(e,t,r)}async getAttributesOfSelectedNodes(e,t,r={}){return this.v3Service.getAttributesOfSelectedNodes(e,t,r)}async neighborhoodQuery(e,t,r,s,n=false){let i={};r!==void 0&&r===true&&(i.save="true");let o={searchString:t,searchDepth:1};if(s!==void 0&&(s.searchDepth!==void 0&&(o.searchDepth=s.searchDepth),s.edgeLimit!==void 0&&(o.edgeLimit=s.edgeLimit),s.errorWhenLimitIsOver!==void 0&&(o.errorWhenLimitIsOver=s.errorWhenLimitIsOver),s.directOnly!==void 0&&(o.directOnly=s.directOnly),s.nodeIds!=null&&(o.nodeIds=s.nodeIds)),n){let c=`search/network/${e}/query`;return this.http.post(c,o,{version:"v3",params:i})}let d=`search/network/${e}/query`;return this.http.post(d,o,{version:"v2",params:i})}async interConnectQuery(e,t,r,s,n=false){let i={};r!==void 0&&r===true&&(i.save="true");let o={searchString:t};if(s!==void 0&&(s.edgeLimit!==void 0&&(o.edgeLimit=s.edgeLimit),s.errorWhenLimitIsOver!==void 0&&(o.errorWhenLimitIsOver=s.errorWhenLimitIsOver),s.nodeIds!=null&&(o.nodeIds=s.nodeIds)),n){let c=`search/networks/${e}/interconnectquery`;return this.http.post(c,o,{version:"v3",params:i})}let d=`search/network/${e}/interconnectquery`;return this.http.post(d,o,{version:"v2",params:i})}async getNetworkPermissionsByUUIDs(e){return this.http.post("batch/network/permission",e,{version:"v2"})}async exportNetworks(e){return this.http.post("batch/network/export",e,{version:"v2"})}async moveNetworks(e,t){if(!Array.isArray(e))throw new Error("Invalid networkIds - must be an array");let r="batch/networks/move",s={targetFolder:t,networks:e};return this.http.post(r,s,{version:"v3"})}async setNetworksVisibility(e,t){this.validateShareData(e);let r="batch/networks/visibility",s={items:e,visibility:t};return this.http.post(r,s,{version:"v3"})}async getRandomEdges(e,t,r){if(t<=0)throw new Error("Value of parameter limit has to be greater than 0.");let s={size:t.toString(),method:"random"};r!==void 0&&(s.accesskey=r);let n=`networks/${e}/aspects/edges`;return this.http.get(n,{version:"v3",params:s})}validateShareData(e){if(typeof e!="object"||e===null||e.files===void 0)throw new Error('Data must be an object with a "files" property');if(typeof e.files!="object"||e.files===null)throw new Error('The "files" property must be an object');let t=["NETWORK","FOLDER","SHORTCUT"];for(let[r,s]of Object.entries(e.files)){if(!/^[0-9a-f]{8}-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{12}$/i.test(r))throw new Error(`Invalid UUID format: ${r}`);if(!t.includes(s))throw new Error(`Invalid file type for ${r}: ${s}. Must be one of: ${t.join(", ")}`)}}async getAspectElements(e,t,r,s){let n={};r!==void 0&&(n.size=r.toString()),s!==void 0&&(n.accesskey=s);let i=`networks/${e}/aspects/${t}`;return this.http.get(i,{version:"v3",params:n})}async getFilteredEdges(e,t,r,s,n,i,o,d){let c={};n!==void 0&&(c.size=n.toString()),i!==void 0&&(c.order=i),d!==void 0&&(c.accesskey=d),o!==void 0&&(c.format=o);let u={name:t,value:r,operator:s},b=`search/networks/${e}/edges`;return this.http.post(b,u,{version:"v3",params:c})}async getCX2MetaData(e,t){let r={};t!==void 0&&(r.accesskey=t);let s=`networks/${e}/aspects`;return this.http.get(s,{version:"v3",params:r})}async createNetworkFromRawCX2(e,t={}){return this.v3.createNetworkFromCX2(e,t)}async updateNetworkFromRawCX2(e,t){let r=`networks/${e}`;return this.http.put(r,t,{version:"v3"})}get v2(){return this.v2Service}get v3(){return this.v3Service}};var y=class{constructor(e){this.http=e;}copyFile(e,t,r,s){let n={};return s!==void 0&&(n.accesskey=s),this.http.post("files/copy",{from_uuid:e,type:r,to_path:t},{params:n,version:"v3"})}getCount(){return this.http.get("files/count",{version:"v3"})}getTrash(){return this.http.get("files/trash",{version:"v3"})}emptyTrash(){return this.http.delete("files/trash",{version:"v3"})}permanentlyDeleteFile(e){return this.http.delete(`files/trash/${e}`,{version:"v3"})}restoreFile(e,t,r){return this.http.post("files/trash/restore",{networks:e,folders:t,shortcuts:r},{version:"v3"})}_validateShareData(e){if(typeof e!="object"||e===null||e.files===void 0)throw new Error('Data must be an object with a "files" property');if(typeof e.files!="object"||e.files===null)throw new Error('The "files" property must be an object');let t=["NETWORK","FOLDER","SHORTCUT"];for(let[r,s]of Object.entries(e.files)){if(!/^[0-9a-f]{8}-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{12}$/i.test(r))throw new Error(`Invalid UUID format: ${r}`);if(!t.includes(s))throw new Error(`Invalid file type for ${r}: ${s}. Must be one of: ${t.join(", ")}`)}}_validateMemberData(e){if(typeof e!="object"||e===null||e.members===void 0)throw new Error('Data must be an object with a "members" property');let t=["READ","WRITE"];for(let[r,s]of Object.entries(e.members)){if(!t.includes(s))throw new Error(`Invalid permission for ${r}: ${s}. Must be one of: ${t.join(", ")}`);if(typeof r!="string"||!/^[0-9a-f]{8}-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{12}$/i.test(r))throw new Error(`Invalid UUID format: ${r}`)}}updateMember(e,t){return this._validateShareData({files:e}),this._validateMemberData({members:t}),this.http.post("files/sharing/members",{files:e,members:t},{version:"v3"})}listMembers(e){return this.http.get("files/sharing/members/list",{params:e,version:"v3"})}transferOwnership(e,t){return this._validateShareData({files:e}),this.http.post("files/sharing/transfer_ownership",{files:e,new_owner:t},{version:"v3"})}listShares(e){let t={};return e!==void 0&&(t.limit=e),this.http.post("files/sharing/list",t,{version:"v3"})}share(e){return this._validateShareData({files:e}),this.http.post("files/sharing/share",{files:e},{version:"v3"})}unshare(e){return this._validateShareData({files:e}),this.http.post("files/sharing/unshare",{files:e},{version:"v3"})}getFolders(e){let t={};return e!==void 0&&(t.limit=e),this.http.get("files/folders",{params:t,version:"v3"})}createFolder(e,t){return this.http.post("files/folders",{name:e,parent:t},{version:"v3"})}getFolder(e,t){let r={};return t!==void 0&&(r.accesskey=t),this.http.get(`files/folders/${e}`,{params:r,version:"v3"})}updateFolder(e,t,r){return this.http.put(`files/folders/${e}`,{name:t,parent:r},{version:"v3"})}deleteFolder(e){return this.http.delete(`files/folders/${e}`,{version:"v3"})}getFolderCount(e,t){let r={};return t!==void 0&&(r.accesskey=t),this.http.get(`files/folders/${e}/count`,{params:r,version:"v3"})}getFolderList(e,t,r,s){let n={};return t!==void 0&&(n.accesskey=t),r!==void 0&&(n.format=r),s!==void 0&&(n.type=s),this.http.get(`files/folders/${e}/list`,{params:n,version:"v3"})}getShortcuts(e){let t={};return e!==void 0&&(t.limit=e),this.http.get("files/shortcuts",{params:t,version:"v3"})}createShortcut(e,t,r,s){return this.http.post("files/shortcuts",{name:e,parent:t,target:r,targetType:s},{version:"v3"})}getShortcut(e,t){let r={};return t!==void 0&&(r.accesskey=t),this.http.get(`files/shortcuts/${e}`,{params:r,version:"v3"})}updateShortcut(e,t,r,s,n){return this.http.put(`files/shortcuts/${e}`,{name:t,parent:r,target:s,targetType:n},{version:"v3"})}deleteShortcut(e){return this.http.delete(`files/shortcuts/${e}`,{version:"v3"})}};var l=class{constructor(e){this.http=e;}async createCyWebWorkspace(e){return this.http.post("workspaces",e,{version:"v3"})}async getCyWebWorkspace(e){let t=`workspaces/${e}`;return this.http.get(t,{version:"v3"})}async deleteCyWebWorkspace(e){let t=`workspaces/${e}`;return this.http.delete(t,{version:"v3"})}async updateCyWebWorkspace(e,t){let r=`workspaces/${e}`;return this.http.put(r,t,{version:"v3"})}async updateCyWebWorkspaceName(e,t){let r=`workspaces/${e}/name`;return this.http.put(r,{name:t},{version:"v3"})}async updateCyWebWorkspaceNetworks(e,t){let r=`workspaces/${e}/networkids`;return this.http.put(r,t,{version:"v3"})}async getUserCyWebWorkspaces(){let t=`users/${(await this.http.get("user",{params:{valid:true}})).externalId}/workspaces`;return this.http.get(t,{version:"v3"})}};var v=class{constructor(e){this.http=e;}async authenticate(){let e=this.http.getAuthType();if(!e)throw new Error("Authentication parameters are missing in NDEx client.");if(e==="basic"){let t="user",r={valid:true};return this.http.get(t,{params:r})}else if(e==="oauth"){let t=this.http.getIdToken();if(!t)throw new Error("OAuth ID token is missing.");let r="users/signin",s={idToken:t};return this.http.post(r,s,{version:"v3"})}throw new Error(`Unsupported authentication type: ${e}`)}async getCurrentUser(){if(!this.http.getAuthType())throw new Error("Authentication parameters are missing in NDEx client.");let t="user",r={valid:true};return this.http.get(t,{params:r})}async updateCurrentUser(e){if(!e.externalId)throw new Error("User uuid is required in 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URLSearchParams;e&&t.append("format",e);let r=`admin/status${t.toString()?`?${t.toString()}`:""}`;return this.httpService.get(r)}hasAuthInfo(){let e=this.httpService.getConfig().auth;return e?e.type==="basic"?!!e.username&&!!e.password:e.type==="oauth"?!!e.idToken:false:false}updateConfig(e){this.httpService.updateConfig(e);}getConfig(){return this.httpService.getConfig()}get http(){return this.httpService}get v2(){return {networks:this.networks.v2}}get v3(){return {networks:this.networks.v3}}},le=E;
3
+ export{w as AdminService,g as CX2Network,S as CyNDEx,S as CyNDExService,y as FilesService,N as NDExAuthError,D as NDExClient,p as NDExError,k as NDExNetworkError,C as NDExNotFoundError,x as NDExServerError,P as NDExValidationError,A as NetworkIndexLevel,m as NetworkServiceV2,h as NetworkServiceV3,f as UnifiedNetworkService,v as UserService,l as WorkspaceService,le as version};//# sourceMappingURL=index.mjs.map
4
+ //# sourceMappingURL=index.mjs.map
package/dist/index.mjs.map ADDED
@@ -0,0 +1 @@
1
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* Core type definitions for NDEx Client Library\n * Pragmatic TypeScript types allowing flexibility with any types where needed\n */\n\n// Export Cytoscape-related types\nexport * from './cytoscape';\n\n// ============================================================================\n// Authentication Types\n// ============================================================================\n\nexport interface BasicAuth {\n type: 'basic';\n username: string;\n password: string;\n}\n\nexport interface OAuthAuth {\n type: 'oauth';\n idToken: string; // ID token from OAuth provider\n}\n\nexport interface NDExAuthResponse {\n token?: string;\n userId?: string;\n userName?: string;\n isAdmin?: boolean;\n permissions?: string[];\n expirationTime?: number;\n}\n\nexport interface NDExUser {\n externalId: string;\n userName: string;\n firstName?: string;\n lastName?: string;\n emailAddress?: string;\n website?: string;\n description?: string;\n image?: string;\n isIndividual?: boolean;\n isVerified?: boolean;\n creationTime?: number;\n modificationTime?: number;\n}\n\n// ============================================================================\n// Network Types\n// ============================================================================\n\nexport interface CX1MetaDataItem {\n name: string;\n elementCount: number;\n version: string;\n idCounter?: number;\n [key: string]: any; // Allow any additional properties\n}\n\nexport interface CX1MetaDataResponse {\n metaData: CX1MetaDataItem[];\n}\n\nexport interface CX1NetworkProperty {\n predicateString: string;\n value: string;\n dataType?: 'string' | 'integer' | 'double' | 'boolean' | 'list_of_string';\n}\n\nexport interface CX2NetworkProperties {\n [key: string]: {\n t: string; // type\n v: any; // value\n };\n}\n\nexport enum NetworkIndexLevel {\n NONE = 'NONE',\n BASIC = 'BASIC',\n FULL = 'FULL'\n}\n\nexport interface NetworkSummaryV2 {\n externalId: string;\n name: string;\n description?: string;\n nodeCount: number;\n edgeCount: number;\n visibility: 'PUBLIC' | 'PRIVATE';\n owner: string;\n ownerUUID: string;\n creationTime: number;\n modificationTime: number;\n version?: string;\n properties?: CX1NetworkProperty[]; // V2 uses CX1 array format\n isReadOnly: boolean;\n isValid: boolean;\n warnings?: string[];\n hasLayout: boolean;\n hasSample: boolean;\n \n // Additional attributes for both V2 and V3\n updatedBy: string; // username who modified this network last\n errorMessage?: string;\n cxFormat?: string;\n cxFileSize?: number; // File size in bytes\n cx2FileSize?: number; // File size in bytes\n isShowcase?: boolean;\n isCompleted?: boolean;\n doi?: string;\n isCertified?: boolean;\n indexLevel?: NetworkIndexLevel;\n parentDirUUID?: string;\n showInTrash?: boolean;\n subnetworkIds?: string[];\n reference?: string;\n organism?: string;\n disease?: string;\n tissue?: string;\n networkType?: string[];\n rightsHolder?: string;\n rights?: string;\n sourceFormat?: string;\n}\n\n/**\n * NetworkSummaryV3 - Network summary for NDEx API v3\n * \n * Extends NetworkSummaryV2 but uses CX2-style properties format instead of CX1 format.\n * The main difference is in how network properties are structured:\n * \n * | Aspect | NetworkSummaryV2 | NetworkSummaryV3 |\n * |--------|------------------|------------------|\n * | **Properties Format** | `CX1NetworkProperty[]` (array) | `CX2NetworkProperties` (object) |\n * | **Structure** | CX1-style array of property objects | CX2-style key-value map |\n * | **Example** | `[{predicateString: \"name\", value: \"My Network\"}]` | `{name: {t: \"string\", v: \"My Network\"}}` |\n * \n * @example\n * ```typescript\n * // V2 properties format (array of objects)\n * const v2Summary: NetworkSummaryV2 = {\n * externalId: \"12345\",\n * name: \"Sample Network\",\n * properties: [\n * { predicateString: \"description\", value: \"A sample network\", dataType: \"string\" },\n * { predicateString: \"nodeCount\", value: \"100\", dataType: \"integer\" }\n * ]\n * };\n * \n * // V3 properties format (object map)\n * const v3Summary: NetworkSummaryV3 = {\n * externalId: \"12345\", \n * name: \"Sample Network\",\n * properties: {\n * description: { t: \"string\", v: \"A sample network\" },\n * nodeCount: { t: \"integer\", v: 100 }\n * }\n * };\n * ```\n */\nexport interface NetworkSummaryV3 extends Omit<NetworkSummaryV2, 'properties'> {\n properties?: CX2NetworkProperties; // V3 uses CX2 object/map format\n // V3-specific additional attributes can be added here as needed\n}\n\n\nexport interface NetworkPermission {\n uuid: string;\n permission: 'READ' | 'WRITE' | 'ADMIN';\n memberUUID: string;\n memberAccountName?: string;\n resourceUUID: string;\n}\n\n// NetworkSet interface removed - deprecated in NDEx v3, replaced by folders with network shortcuts\n\n// ============================================================================\n// CX2 Network Types\n// ============================================================================\n\nexport interface CX2Network {\n CXVersion: string;\n hasFragments: boolean;\n metaData: CX2MetaData[];\n attributeDeclarations?: CX2AttributeDeclarations;\n networkAttributes?: CX2NetworkAttribute[];\n nodes?: CX2Node[];\n edges?: CX2Edge[];\n nodeBypass?: CX2NodeBypass[];\n edgeBypass?: CX2EdgeBypass[];\n visualProperties?: CX2VisualProperty;\n status?: CX2Status[];\n}\n\nexport interface CX2MetaData {\n name: string;\n elementCount?: number;\n}\n\nexport interface CX2AttributeDeclarations {\n [aspectName: string]: {\n [attributeName: string]: {\n d: string; // datatype\n a?: string; // alias\n v?: any; // default value\n };\n };\n}\n\nexport interface CX2AttributeSpec {\n d: string; // data type\n v?: any; // default value\n s?: boolean; // is single\n}\n\nexport interface CX2NetworkAttribute {\n [key: string]: any;\n}\n\nexport interface CX2Node {\n id: number;\n x?: number; // x coordinate\n y?: number; // y coordinate \n z?: number; // z coordinate (optional)\n v?: Record<string, any>; // attributes\n}\n\nexport interface CX2Edge {\n id: number;\n s: number; // source node id\n t: number; // target node id\n v?: Record<string, any>; // attributes\n}\n\nexport interface CX1Edge {\n // CX1 edge structure varies - can be any array structure\n [key: string]: any;\n}\n\nexport interface CX2NodeBypass {\n id: number; // node id\n v: VisualPropertyTable; // visual properties\n}\n\nexport interface CX2EdgeBypass {\n id: number; // edge id\n v: VisualPropertyTable; // visual properties\n}\n\n// ============================================================================\n// CX2 Visual Property Types - Based on server-side CxVisualProperty class\n// ============================================================================\n\n/**\n * Visual Property Mapping Types\n */\nexport type VPMappingType = 'DISCRETE' | 'CONTINUOUS' | 'PASSTHROUGH';\n\n/**\n * Mapping Definition for visual property mappings\n * Note: Using flexible typing for mapping definitions as they vary by type\n */\nexport interface MappingDefinition {\n mapppingList?: Array<Record<string, any>>; // Note: server has typo \"mapppingList\"\n [key: string]: any; // Allow other mapping definition properties\n}\n\n/**\n * Visual Property Mapping structure\n */\nexport interface VisualPropertyMapping {\n type: VPMappingType;\n definition: MappingDefinition;\n}\n\n/**\n * Visual Property Table - holds visual property values\n * Equivalent to server-side VisualPropertyTable class\n */\nexport interface VisualPropertyTable {\n [visualPropertyName: string]: any; // Maps visual property names to their values\n}\n\n/**\n * Table Column Visual Style - for individual visual properties\n */\nexport interface TableColumnVisualStyle {\n default?: any; // Default value for the visual property\n mapping?: VisualPropertyMapping; // Optional mapping definition\n}\n\n/**\n * Default Visual Properties structure\n */\nexport interface DefaultVisualProperties {\n edge?: VisualPropertyTable; // Default edge visual properties\n network?: Record<string, any>; // Default network visual properties \n node?: VisualPropertyTable; // Default node visual properties\n}\n\n/**\n * CX2 Visual Property - Main visual properties aspect\n * Equivalent to server-side CxVisualProperty class\n */\nexport interface CX2VisualProperty {\n default?: DefaultVisualProperties; // Default visual properties\n edgeMapping?: Record<string, VisualPropertyMapping>; // Edge visual property mappings\n nodeMapping?: Record<string, VisualPropertyMapping>; // Node visual property mappings\n}\n\nexport interface CX2Status {\n error?: string;\n success?: boolean;\n}\n\n// ============================================================================\n// Search Types\n// ============================================================================\n\nexport interface SearchResult {\n numFound: number;\n start: number;\n networks: NetworkSummaryV2[] | NetworkSummaryV3[];\n}\n\nexport interface SearchParameters {\n searchString?: string;\n accountName?: string;\n permission?: string;\n includeGroups?: boolean;\n admin?: string;\n start?: number;\n size?: number;\n source?: string;\n}\n\n// ============================================================================\n// File/Export Types\n// ============================================================================\n\nexport interface ExportFormat {\n format: 'CX' | 'CX2' | 'XGMML' | 'SIF' | 'GRAPHML';\n version?: string;\n}\n\nexport interface ExportRequest {\n networkUUID: string;\n format: ExportFormat;\n accesskey?: string;\n}\n\n// ============================================================================\n// Task/Status Types\n// ============================================================================\n\nexport interface Task {\n externalId: string;\n taskType: string;\n status: 'submitted' | 'processing' | 'completed' | 'failed';\n progress?: number;\n message?: string;\n resource?: string;\n startTime?: number;\n finishTime?: number;\n attributes?: Record<string, any>;\n}\n\n// ============================================================================\n// API Configuration Types\n// ============================================================================\n\nexport interface NDExClientConfig {\n baseURL?: string;\n timeout?: number;\n retries?: number;\n retryDelay?: number;\n debug?: boolean;\n headers?: Record<string, string>;\n auth?: BasicAuth | OAuthAuth; // Simplified to 2 authentication options\n}\n\nexport interface APIResponse<T = any> {\n data?: T;\n errorCode?: string;\n message?: string;\n description?: string;\n stackTrace?: string;\n timeStamp?: number;\n}\n\nexport interface APIError {\n errorCode: string;\n message: string;\n description?: string;\n stackTrace?: string;\n timeStamp?: number;\n}\n\n// ============================================================================\n// Service Types\n// ============================================================================\n\n\n/**\n * Base error class for all NDEx API errors\n */\nexport class NDExError extends Error {\n constructor(\n message: string,\n public statusCode?: number,\n public errorCode?: string,\n public description?: string\n ) {\n super(message);\n this.name = 'NDExError';\n }\n}\n\n/**\n * Error thrown when network or request fails\n */\nexport class NDExNetworkError extends NDExError {\n constructor(message: string, public originalError?: Error) {\n super(message, undefined, 'NETWORK_ERROR');\n this.name = 'NDExNetworkError';\n }\n}\n\n/**\n * Error thrown when authentication fails\n */\nexport class NDExAuthError extends NDExError {\n constructor(message: string = 'Authentication failed', statusCode: number = 401) {\n super(message, statusCode, 'AUTH_ERROR');\n this.name = 'NDExAuthError';\n }\n}\n\n/**\n * Error thrown when requested resource is not found\n */\nexport class NDExNotFoundError extends NDExError {\n constructor(message: string = 'Resource not found', statusCode: number = 404) {\n super(message, statusCode, 'NOT_FOUND');\n this.name = 'NDExNotFoundError';\n }\n}\n\n/**\n * Error thrown when request validation fails\n */\nexport class NDExValidationError extends NDExError {\n constructor(message: string, statusCode: number = 400) {\n super(message, statusCode, 'VALIDATION_ERROR');\n this.name = 'NDExValidationError';\n }\n}\n\n/**\n * Error thrown when server encounters an internal error\n */\nexport class NDExServerError extends NDExError {\n constructor(message: string = 'Internal server error', statusCode: number = 500) {\n super(message, statusCode, 'SERVER_ERROR');\n this.name = 'NDExServerError';\n }\n}\n\n// ============================================================================\n// Utility Types\n// ============================================================================\n\nexport type UUID = string;\nexport type Timestamp = number;\n\n// Allow flexible typing for gradual migration\nexport type NDExAny = any;\n\n// Common parameter types\nexport interface PaginationParams {\n start?: number;\n size?: number;\n}\n\nexport interface AccessParams {\n accesskey?: string;\n}\n\n// ============================================================================\n// Workspace Types\n// ============================================================================\n\n/**\n * CyWeb workspace object structure\n */\nexport interface CyWebWorkspace {\n externalId?: string;\n name: string;\n description?: string;\n networkIds?: string[];\n [key: string]: any; // Allow additional properties\n}\n\n/**\n * Network access key response structure\n */\nexport interface AccessKeyResponse {\n accessKey: string | null;\n}\n\n/**\n * Valid actions for updating access keys\n */\nexport type AccessKeyAction = 'enable' | 'disable';\n\n/**\n * NDEx object update status - returned from network creation and update operations\n * Corresponds to server-side NdexObjectUpdateStatus class\n */\nexport interface NDExObjectUpdateStatus {\n uuid: string;\n modificationTime: number; // Timestamp in milliseconds\n}\n\n","import { \n CX2Network as CX2NetworkType,\n CX2MetaData,\n CX2Node,\n CX2Edge,\n CX2AttributeDeclarations,\n CX2NetworkAttribute,\n CX2NodeBypass,\n CX2EdgeBypass,\n CX2VisualProperty,\n NetworkSummaryV3\n} from '../types';\n\n/**\n * CX2Network - Modern representation of CX2 format networks\n * Provides utilities for creating, manipulating, and validating CX2 networks\n */\nexport class CX2Network implements CX2NetworkType {\n CXVersion: string = '2.0';\n hasFragments: boolean = false;\n metaData: CX2MetaData[] = [];\n attributeDeclarations?: CX2AttributeDeclarations;\n networkAttributes?: CX2NetworkAttribute[];\n nodes?: CX2Node[];\n edges?: CX2Edge[];\n nodeBypass?: CX2NodeBypass[];\n edgeBypass?: CX2EdgeBypass[];\n visualProperties?: CX2VisualProperty;\n status?: any[];\n\n constructor(data?: Partial<CX2NetworkType>) {\n if (data) {\n Object.assign(this, data);\n }\n \n // Ensure required metadata is present\n this.ensureRequiredMetadata();\n }\n\n /**\n * Create a new empty CX2Network\n */\n static createEmpty(): CX2Network {\n const network = new CX2Network();\n network.nodes = [];\n network.edges = [];\n network.metaData = [\n {\n name: 'nodes',\n elementCount: 0\n },\n {\n name: 'edges',\n elementCount: 0\n },\n ];\n return network;\n }\n\n /**\n * Create CX2Network from raw JSON data\n */\n static fromJSON(json: string | object): CX2Network {\n const data = typeof json === 'string' ? JSON.parse(json) : json;\n return new CX2Network(data);\n }\n\n /**\n * Create CX2Network from NetworkSummary (for compatibility)\n */\n static fromNetworkSummary(summary: NetworkSummaryV3): CX2Network {\n const network = CX2Network.createEmpty();\n \n network.networkAttributes = [\n { name: summary.name },\n ...(summary.description ? [{ description: summary.description }] : []),\n ...(summary.version ? [{ version: summary.version }] : []),\n ];\n\n // Add properties as network attributes\n if (summary.properties) {\n Object.entries(summary.properties).forEach(([key, value]) => {\n network.networkAttributes?.push({\n [key]: (value as { t: string; v: any }).v\n });\n });\n }\n\n return network;\n }\n\n /**\n * Add a node to the network\n */\n addNode(id: number, attributes?: Record<string, any>): CX2Node {\n if (!this.nodes) {\n this.nodes = [];\n }\n\n const node: CX2Node = { id };\n if (attributes) {\n node.v = attributes;\n }\n\n this.nodes.push(node);\n this.updateNodeCount();\n return node;\n }\n\n /**\n * Add an edge to the network\n */\n addEdge(id: number, sourceId: number, targetId: number, attributes?: Record<string, any>): CX2Edge {\n if (!this.edges) {\n this.edges = [];\n }\n\n const edge: CX2Edge = {\n id,\n s: sourceId,\n t: targetId,\n };\n\n if (attributes) {\n edge.v = attributes;\n }\n\n this.edges.push(edge);\n this.updateEdgeCount();\n return edge;\n }\n\n /**\n * Add an individual node attribute\n */\n addNodeAttribute(nodeId: number, attributeName: string, value: any): void {\n\n //find the nodes with the given ID\n const node = this.nodes.find(n => n.id === nodeId);\n //set the node attribute\n if (node) {\n if (!node.v) {\n node.v = {};\n }\n node.v[attributeName] = value;\n }\n\n }\n\n /**\n * Add edge attributes (bulk)\n */\n addEdgeAttribute(edgeId: number, attributeName: string, value: any): void {\n //similar to addNodeAttribute\n const edge = this.edges.find(e => e.id === edgeId);\n if (edge) {\n if (!edge.v) {\n edge.v = {};\n }\n edge.v[attributeName] = value;\n }\n\n \n }\n\n /**\n * Set node coordinates\n */\n setNodeCoordinates(nodeId: number, x: number, y: number, z?: number): void {\n if (!this.nodes) {\n this.nodes = [];\n }\n\n // Find the node and update its coordinates directly\n let node = this.nodes.find(n => n.id === nodeId);\n \n if (!node) {\n // Create new node if it doesn't exist\n node = { id: nodeId };\n this.nodes.push(node);\n this.updateNodeCount();\n }\n\n // Set coordinates directly on the node\n node.x = x;\n node.y = y;\n if (z !== undefined) {\n node.z = z;\n }\n }\n\n /**\n * Get node by ID\n */\n getNode(id: number): CX2Node | undefined {\n return this.nodes?.find(node => node.id === id);\n }\n\n /**\n * Get edge by ID\n */\n getEdge(id: number): CX2Edge | undefined {\n return this.edges?.find(edge => edge.id === id);\n }\n\n /**\n * Get all nodes\n */\n getNodes(): CX2Node[] {\n return this.nodes || [];\n }\n\n /**\n * Get all edges\n */\n getEdges(): CX2Edge[] {\n return this.edges || [];\n }\n\n /**\n * Get node count\n */\n getNodeCount(): number {\n return this.nodes?.length || 0;\n }\n\n /**\n * Get edge count\n */\n getEdgeCount(): number {\n return this.edges?.length || 0;\n }\n\n /**\n * Get network name from attributes\n */\n getNetworkName(): string | undefined {\n return this.networkAttributes?.find(attr => 'name' in attr)?.name;\n }\n\n /**\n * Set network name\n */\n setNetworkName(name: string): void {\n if (!this.networkAttributes) {\n this.networkAttributes = [];\n }\n\n // Remove existing name attribute\n this.networkAttributes = this.networkAttributes.filter(attr => !('name' in attr));\n \n // Add new name\n this.networkAttributes.push({ name });\n }\n\n /**\n * Get network attribute by key\n */\n getNetworkAttribute(key: string): any {\n return this.networkAttributes?.find(attr => key in attr)?.[key];\n }\n\n /**\n * Set network attribute\n */\n setNetworkAttribute(key: string, value: any): void {\n if (!this.networkAttributes) {\n this.networkAttributes = [];\n }\n\n // Remove existing attribute with same key\n this.networkAttributes = this.networkAttributes.filter(attr => !(key in attr));\n \n // Add new attribute\n this.networkAttributes.push({ [key]: value });\n }\n\n /**\n * Validate the CX2 network structure\n */\n validate(): { isValid: boolean; errors: string[] } {\n const errors: string[] = [];\n\n // Check required fields\n if (!this.CXVersion) {\n errors.push('CXVersion is required');\n }\n\n if (this.hasFragments === undefined) {\n errors.push('hasFragments is required');\n }\n\n if (!this.metaData || this.metaData.length === 0) {\n errors.push('metaData is required and must not be empty');\n }\n\n // Validate metadata\n this.metaData?.forEach((meta, index) => {\n if (!meta.name) {\n errors.push(`metaData[${index}] is missing required 'name' field`);\n }\n });\n\n // Validate nodes\n if (this.nodes) {\n this.nodes.forEach((node, index) => {\n if (node.id === undefined || node.id === null) {\n errors.push(`nodes[${index}] is missing required 'id' field`);\n }\n });\n }\n\n // Validate edges\n if (this.edges) {\n this.edges.forEach((edge, index) => {\n if (edge.id === undefined || edge.id === null) {\n errors.push(`edges[${index}] is missing required 'id' field`);\n }\n if (edge.s === undefined || edge.s === null) {\n errors.push(`edges[${index}] is missing required 's' (source) field`);\n }\n if (edge.t === undefined || edge.t === null) {\n errors.push(`edges[${index}] is missing required 't' (target) field`);\n }\n\n // Check if source and target nodes exist\n if (this.nodes && edge.s !== undefined && edge.t !== undefined) {\n const sourceExists = this.nodes.some(node => node.id === edge.s);\n const targetExists = this.nodes.some(node => node.id === edge.t);\n \n if (!sourceExists) {\n errors.push(`edges[${index}] references non-existent source node ${edge.s}`);\n }\n if (!targetExists) {\n errors.push(`edges[${index}] references non-existent target node ${edge.t}`);\n }\n }\n });\n }\n\n return {\n isValid: errors.length === 0,\n errors,\n };\n }\n\n /**\n * Convert to JSON string\n */\n toJSON(): string {\n return JSON.stringify(this, null, 2);\n }\n\n /**\n * Create a deep copy of the network\n */\n clone(): CX2Network {\n return new CX2Network(JSON.parse(this.toJSON()));\n }\n\n /**\n * Get basic statistics about the network\n */\n getStatistics() {\n return {\n nodeCount: this.getNodeCount(),\n edgeCount: this.getEdgeCount(),\n hasCoordinates: Boolean(this.nodes && this.nodes.some(node => \n node.x !== undefined || node.y !== undefined || node.z !== undefined\n )),\n hasVisualProperties: Boolean(this.visualProperties && (\n this.visualProperties.default || \n this.visualProperties.edgeMapping || \n this.visualProperties.nodeMapping\n ))\n };\n }\n\n /**\n * Ensure required metadata is present\n */\n private ensureRequiredMetadata(): void {\n if (!this.metaData) {\n this.metaData = [];\n }\n\n // Ensure nodes metadata exists\n if (this.nodes && !this.metaData.find(m => m.name === 'nodes')) {\n this.metaData.push({\n name: 'nodes',\n elementCount: this.nodes.length\n });\n }\n\n // Ensure edges metadata exists \n if (this.edges && !this.metaData.find(m => m.name === 'edges')) {\n this.metaData.push({\n name: 'edges',\n elementCount: this.edges.length\n });\n }\n }\n\n /**\n * Update node count in metadata\n */\n private updateNodeCount(): void {\n const nodesMeta = this.metaData?.find(m => m.name === 'nodes');\n if (nodesMeta) {\n nodesMeta.elementCount = this.nodes?.length || 0;\n }\n }\n\n /**\n * Update edge count in metadata\n */\n private updateEdgeCount(): void {\n const edgesMeta = this.metaData?.find(m => m.name === 'edges');\n if (edgesMeta) {\n edgesMeta.elementCount = this.edges?.length || 0;\n }\n }\n}\n","import { HTTPService } from './HTTPService';\nimport { \n NetworkSummaryV2, \n NetworkPermission, \n PaginationParams,\n AccessParams,\n CX1MetaDataResponse,\n AccessKeyResponse,\n AccessKeyAction\n} from '../types';\n\n/**\n * NetworkServiceV2 - NDEx API v2 network operations\n * Handles legacy v2 endpoints with modern TypeScript interface\n */\nexport class NetworkServiceV2 {\n constructor(private http: HTTPService) {}\n\n /**\n * Get raw network in CX1 format\n * \n * Returns raw CX1 data as an array of aspects. This data may contain fragmented aspects\n * that need to be assembled into a complete CX1 network model for proper usage.\n * For a fully assembled network object, consider using getNetworkAsCX2Object() instead.\n * \n * @param networkUUID - The UUID of the network to retrieve\n * @param options - Access options including optional access key\n * @returns Promise resolving to raw CX1 data as an array of aspects\n */\n async getRawCX1Network(\n networkUUID: string, \n options: AccessParams = {}\n ): Promise<any[]> {\n const params = new URLSearchParams();\n if (options.accesskey) {\n params.append('accesskey', options.accesskey);\n }\n\n const endpoint = `network/${networkUUID}${params.toString() ? `?${params.toString()}` : ''}`;\n return this.http.get<any[]>(endpoint, { \n version: 'v2',\n headers: { 'Accept': 'application/json' }\n });\n }\n\n /**\n * Get network summary by UUID\n */\n async getNetworkSummary(\n networkUUID: string, \n options: AccessParams = {}\n ): Promise<NetworkSummaryV2> {\n const params = new URLSearchParams();\n if (options.accesskey) {\n params.append('accesskey', options.accesskey);\n }\n\n const endpoint = `network/${networkUUID}/summary${params.toString() ? `?${params.toString()}` : ''}`;\n return this.http.get<NetworkSummaryV2>(endpoint, { version: 'v2' });\n }\n\n /**\n * Copy network\n * \n * Creates a copy of an existing network using the server's copy endpoint.\n * The copied network will have the same content but will be assigned a new UUID\n * and will be owned by the authenticated user.\n * \n * @param networkUUID - The UUID of the network to copy\n * @returns Promise resolving to the URL of the cloned CX1 network\n */\n async copyNetwork(networkUUID: string): Promise<string> {\n const endpoint = `network/${networkUUID}/copy`;\n return this.http.post<string>(endpoint, {}, { \n version: 'v2'\n });\n }\n\n\n /**\n * Search networks (migrated from original NDEx.js)\n * \n * Searches networks using POST request with search parameters in the request body.\n * This implementation matches the original NDEx.js searchNetworks function.\n * \n * @param searchTerms - Search string to find networks\n * @param start - Starting offset for pagination (optional)\n * @param size - Maximum number of results to return (optional)\n * @param optionalParameters - Additional search filters\n * @param optionalParameters.permission - Filter by permission level\n * @param optionalParameters.includeGroups - Whether to include group networks\n * @param optionalParameters.accountName - Filter by account name\n * @returns Promise resolving to search results\n */\n async searchNetworks(\n searchTerms: string,\n start?: number,\n size?: number,\n optionalParameters?: {\n permission?: string;\n includeGroups?: boolean;\n accountName?: string;\n }\n ): Promise<any> {\n const params: Record<string, string> = {};\n\n if (start !== undefined) {\n params.start = start.toString();\n }\n if (size !== undefined) {\n params.limit = size.toString();\n }\n\n const data: Record<string, any> = { searchString: searchTerms };\n\n if (optionalParameters !== undefined) {\n if (optionalParameters.permission !== undefined) {\n data.permission = optionalParameters.permission;\n }\n if (optionalParameters.includeGroups !== undefined) {\n data.includeGroups = optionalParameters.includeGroups;\n }\n if (optionalParameters.accountName !== undefined) {\n data.accountName = optionalParameters.accountName;\n }\n }\n\n const endpoint = 'search/network';\n return this.http.post<any>(endpoint, data, { \n version: 'v2',\n params \n });\n }\n\n \n\n /**\n * Create new network from raw CX1 data\n * \n * Creates a new network in NDEx from raw CX1 network data. This method handles\n * the server response parsing to extract the network UUID from the location header.\n * \n * @param rawCX - Raw CX1 network data as an array of aspects\n * @param options - Optional options for network creation (visibility settings)\n * @returns Promise resolving to the UUID string of the newly created network\n */\n async createNetworkFromRawCX1(\n rawCX: any[],\n options: { visibility?: 'PUBLIC' | 'PRIVATE' } = {}\n ): Promise<string> {\n const endpoint = 'network';\n const response = await this.http.post<string>(endpoint, rawCX, { \n version: 'v2',\n params: options\n });\n\n // Extract UUID from response URL (e.g., \"/v2/network/12345\" -> \"12345\")\n const uuidr = response.split('/');\n const uuid = uuidr[uuidr.length - 1];\n \n return uuid;\n }\n\n\n /**\n * Update network from raw CX1 data\n * \n * Updates an existing network in NDEx with new raw CX1 network data.\n * This completely replaces the network content with the provided CX1 data.\n * Uses the legacy v2 endpoint format from the original NDEx.js implementation.\n * \n * @param networkUUID - The UUID of the network to update\n * @param rawCX - Raw CX1 network data as an array of aspects\n * @returns Promise resolving when the update is complete\n */\n async updateNetworkFromRawCX1(\n networkUUID: string,\n rawCX: any[]\n ): Promise<void> {\n const endpoint = `network/${networkUUID}`;\n return this.http.put<void>(endpoint, rawCX, { version: 'v2' });\n }\n\n /**\n * Delete network\n */\n async deleteNetwork(networkUUID: string): Promise<void> {\n const endpoint = `network/${networkUUID}`;\n return this.http.delete<void>(endpoint, { version: 'v2' });\n }\n\n /**\n * Get network summaries by UUIDs (migrated from original NDEx.js)\n * \n * Retrieves network summaries for multiple networks in a single batch request.\n * Uses the V2 API batch endpoint for efficient bulk operations.\n * \n * @param uuidList - Array of network UUIDs to retrieve summaries for\n * @param accessKey - Optional access key for private networks\n * @returns Promise resolving to array of network summaries\n */\n async getNetworkSummariesByUUIDs(\n uuidList: string[], \n accessKey?: string\n ): Promise<NetworkSummaryV2[]> {\n const params = accessKey ? { accesskey: accessKey } : undefined;\n\n const endpoint = 'batch/network/summary';\n return this.http.post<NetworkSummaryV2[]>(endpoint, uuidList, { \n version: 'v2',\n params \n });\n }\n\n// The following functions need to be either reviewed or removed.\n\n\n /**\n * Get user's networks\n */\n async getUserNetworks(\n accountName: string, \n options: PaginationParams = {}\n ): Promise<NetworkSummaryV2[]> {\n const params = new URLSearchParams();\n if (options.start !== undefined) {\n params.append('start', options.start.toString());\n }\n if (options.size !== undefined) {\n params.append('size', options.size.toString());\n }\n\n const endpoint = `user/${accountName}/networks${params.toString() ? `?${params.toString()}` : ''}`;\n return this.http.get<NetworkSummaryV2[]>(endpoint, { version: 'v2' });\n }\n\n\n /**\n * Set network system properties\n */\n async setNetworkSystemProperties(\n networkUUID: string, \n properties: Record<string, any>\n ): Promise<void> {\n const endpoint = `networks/${networkUUID}/systemproperty`;\n return this.http.put<void>(endpoint, properties, { version: 'v2' });\n }\n\n /**\n * Get network permissions\n */\n async getNetworkPermissions(networkUUID: string): Promise<NetworkPermission[]> {\n const endpoint = `networks/${networkUUID}/permission`;\n return this.http.get<NetworkPermission[]>(endpoint, { version: 'v2' });\n }\n\n /**\n * Set network permissions\n */\n async setNetworkPermissions(\n networkUUID: string, \n permissions: NetworkPermission[]\n ): Promise<void> {\n const endpoint = `networks/${networkUUID}/permission`;\n return this.http.put<void>(endpoint, permissions, { version: 'v2' });\n }\n\n /**\n * Grant network permission to user\n */\n async grantNetworkPermission(\n networkUUID: string, \n userUUID: string, \n permission: 'READ' | 'WRITE' | 'ADMIN'\n ): Promise<void> {\n const endpoint = `networks/${networkUUID}/permission`;\n const permissionData = {\n memberUUID: userUUID,\n permission: permission\n };\n return this.http.post<void>(endpoint, permissionData, { version: 'v2' });\n }\n\n /**\n * Revoke network permission from user\n */\n async revokeNetworkPermission(\n networkUUID: string, \n userUUID: string\n ): Promise<void> {\n const endpoint = `networks/${networkUUID}/permission`;\n return this.http.delete<void>(endpoint, { \n version: 'v2',\n data: { memberUUID: userUUID }\n });\n }\n\n /**\n * Get network profile (additional metadata)\n */\n async getNetworkProfile(networkUUID: string): Promise<any> {\n const endpoint = `networks/${networkUUID}/profile`;\n return this.http.get<any>(endpoint, { version: 'v2' });\n }\n\n /**\n * Set network profile\n */\n async setNetworkProfile(\n networkUUID: string, \n profile: any\n ): Promise<void> {\n const endpoint = `networks/${networkUUID}/profile`;\n return this.http.put<void>(endpoint, profile, { version: 'v2' });\n }\n\n /**\n * Make network public\n */\n async makeNetworkPublic(networkUUID: string): Promise<void> {\n const endpoint = `networks/${networkUUID}/systemproperty`;\n const properties = { visibility: 'PUBLIC' };\n return this.http.put<void>(endpoint, properties, { version: 'v2' });\n }\n\n /**\n * Make network private\n */\n async makeNetworkPrivate(networkUUID: string): Promise<void> {\n const endpoint = `networks/${networkUUID}/systemproperty`;\n const properties = { visibility: 'PRIVATE' };\n return this.http.put<void>(endpoint, properties, { version: 'v2' });\n }\n\n /**\n * Get network sample (if available)\n */\n async getNetworkSample(\n networkUUID: string, \n options: AccessParams = {}\n ): Promise<any[]> {\n const params = new URLSearchParams();\n if (options.accesskey) {\n params.append('accesskey', options.accesskey);\n }\n\n const endpoint = `networks/${networkUUID}/sample${params.toString() ? `?${params.toString()}` : ''}`;\n return this.http.get<any[]>(endpoint, { version: 'v2' });\n }\n\n /**\n * Get network metadata (migrated from original NDEx.js)\n * \n * Retrieves metadata information about network aspects including element counts,\n * versions, and ID counters for each aspect in the network. This provides\n * an overview of the network's structure and content organization.\n * \n * @param networkUUID - The UUID of the network to get metadata for\n * @param accessKey - Optional access key for private networks\n * @returns Promise resolving to metadata containing aspect information\n * @example\n * ```typescript\n * const metadata = await networkService.getMetaData('network-uuid');\n * // Returns: { metaData: [{ name: 'nodes', elementCount: 330, version: '1.0' }, ...] }\n * ```\n */\n async getMetaData(\n networkUUID: string, \n accessKey?: string\n ): Promise<CX1MetaDataResponse> {\n const params = new URLSearchParams();\n if (accessKey !== undefined) {\n params.append('accesskey', accessKey);\n }\n\n const endpoint = `network/${networkUUID}/aspect${params.toString() ? `?${params.toString()}` : ''}`;\n return this.http.get<CX1MetaDataResponse>(endpoint, { version: 'v2' });\n }\n\n /**\n * Get network access key (migrated from original NDEx.js)\n * \n * Retrieves the current access key for a network. Access keys allow\n * users to share private networks without requiring individual permissions.\n * \n * @param networkUUID - The UUID of the network to get access key for\n * @returns Promise resolving to access key response object\n * \n * @example\n * ```typescript\n * const response = await networkService.getAccessKey('network-uuid');\n * console.log(response.accessKey); // \"acialdfeoa03430023\" or null\n * ```\n */\n async getAccessKey(networkUUID: string): Promise<AccessKeyResponse> {\n const endpoint = `networks/${networkUUID}/accesskey`;\n return this.http.get<AccessKeyResponse>(endpoint, { version: 'v2' });\n }\n\n /**\n * Update network access key (migrated from original NDEx.js)\n * \n * Enables or disables the access key for a network. When enabled, creates\n * a new access key that can be shared. When disabled, invalidates the\n * current access key.\n * \n * @param networkUUID - The UUID of the network to update access key for\n * @param action - Action to perform: 'enable' creates/updates key, 'disable' removes it\n * @returns Promise resolving to access key response (accessKey will be null when disabled)\n * \n * @example\n * ```typescript\n * // Enable access key\n * const enabled = await networkService.updateAccessKey('network-uuid', 'enable');\n * console.log(enabled.accessKey); // \"new-access-key-string\"\n * \n * // Disable access key \n * const disabled = await networkService.updateAccessKey('network-uuid', 'disable');\n * console.log(disabled.accessKey); // null\n * ```\n */\n async updateAccessKey(networkUUID: string, action: AccessKeyAction): Promise<AccessKeyResponse> {\n const endpoint = `networks/${networkUUID}/accesskey`;\n return this.http.put<AccessKeyResponse>(endpoint, { action }, { version: 'v2' });\n }\n\n}\n","import { HTTPService } from './HTTPService';\nimport { \n NetworkSummaryV3, \n SearchResult, \n SearchParameters, \n PaginationParams,\n AccessParams,\n CX2Network as CX2NetworkType,\n NDExObjectUpdateStatus\n} from '../types';\nimport { CX2Network } from '../models/CX2Network';\n\n/**\n * NetworkServiceV3 - NDEx API v3 network operations\n * Handles modern v3 endpoints with native CX2 support\n */\nexport class NetworkServiceV3 {\n constructor(private http: HTTPService) {}\n\n /**\n * Get network summary by UUID\n */\n async getNetworkSummary(\n networkUUID: string, \n options: AccessParams = {}\n ): Promise<NetworkSummaryV3> {\n const params = new URLSearchParams();\n if (options.accesskey) {\n params.append('accesskey', options.accesskey);\n }\n\n const endpoint = `networks/${networkUUID}/summary${params.toString() ? `?${params.toString()}` : ''}`;\n return this.http.get<NetworkSummaryV3>(endpoint, { version: 'v3' });\n }\n\n\n /**\n * Get raw network in CX2 format (native V3)\n * \n * Returns raw CX2 data which may contain fragmented aspects that need to be assembled\n * into a complete CX2 network model for proper usage. The returned data follows the\n * CX2 specification but may have aspects split across multiple fragments.\n * For a fully assembled network object with utility methods, use getNetworkAsCX2Object() instead.\n * \n * @param networkUUID - The UUID of the network to retrieve\n * @param options - Access options including optional access key \n * @returns Promise resolving to raw CX2 network data that may be fragmented\n */\n async getRawCX2Network(\n networkUUID: string, \n options: AccessParams = {}\n ): Promise<CX2NetworkType> {\n const params = new URLSearchParams();\n if (options.accesskey) {\n params.append('accesskey', options.accesskey);\n }\n\n const endpoint = `networks/${networkUUID}${params.toString() ? `?${params.toString()}` : ''}`;\n return this.http.get<CX2NetworkType>(endpoint, { version: 'v3' });\n }\n\n\n /**\n * Create network DOI\n * \n * @param networkUUID - The UUID of the network to create a DOI for\n * @param key - DOI creation key\n * @param email - Email address for DOI registration\n * @returns Promise resolving to a confirmation message string from the server\n */\n async createNetworkDOI(\n networkUUID: string, \n key: string, \n email: string\n ): Promise<string> {\n const params = new URLSearchParams();\n params.append('key', key);\n params.append('email', email);\n\n const endpoint = `networks/${networkUUID}/DOI?${params.toString()}`;\n return this.http.get<string>(endpoint, { version: 'v3' });\n }\n\n /**\n * Get attributes of selected nodes\n * \n * Retrieves specific attributes for a set of nodes in a network. The server will return\n * a 404 error if the network has no attributes on nodes.\n * \n * @param networkUUID - The UUID of the network\n * @param nodeSelection - Object containing node IDs and attribute names to retrieve\n * @param nodeSelection.ids - Array of node IDs (long numbers) to get attributes for\n * @param nodeSelection.attributeNames - Array of attribute names to retrieve\n * @param options - Access options including optional access key\n * @returns Promise resolving to a JSON object where keys are stringified node IDs\n * and values are the selected attributes for that node\n * @throws {404} When the network has no attributes on nodes\n */\n async getAttributesOfSelectedNodes(\n networkUUID: string,\n nodeSelection: { ids: number[]; attributeNames: string[] },\n options: AccessParams = {}\n ): Promise<Record<string, any>> {\n const params = new URLSearchParams();\n if (options.accesskey) {\n params.append('accesskey', options.accesskey);\n }\n\n const data = {\n ids: nodeSelection.ids,\n attributeNames: nodeSelection.attributeNames\n };\n\n const endpoint = `search/networks/${networkUUID}/nodes${params.toString() ? `?${params.toString()}` : ''}`;\n return this.http.post<Record<string, any>>(endpoint, data, { version: 'v3' });\n }\n\n /**\n * Get network summaries by UUIDs using V3 API (migrated from original NDEx.js)\n * \n * Retrieves network summaries for multiple networks in a single batch request using V3 API.\n * Uses the V3 API batch endpoint with format parameter support.\n * \n * @param uuidList - Array of network UUIDs to retrieve summaries for\n * @param accessKey - Optional access key for private networks\n * @param format - Summary format (\"FULL\" by default, can be \"BASIC\" or other supported formats)\n * @returns Promise resolving to array of V3 network summaries\n */\n async getNetworkSummariesV3ByUUIDs(\n uuidList: string[], \n accessKey?: string,\n format?: string\n ): Promise<NetworkSummaryV3[]> {\n const params: Record<string, string> = { \n format: format === undefined ? 'FULL' : format \n };\n\n if (accessKey != null) {\n params.accesskey = accessKey;\n }\n\n const endpoint = 'batch/networks/summary';\n return this.http.post<NetworkSummaryV3[]>(endpoint, uuidList, { \n version: 'v3',\n params \n });\n }\n\n\n\n// following functions need to be reviewed or removed.\n\n /**\n * Search networks with V3 enhanced features\n */\n async searchNetworks(searchParams: SearchParameters = {}): Promise<SearchResult> {\n const params = new URLSearchParams();\n \n if (searchParams.searchString) {\n params.append('searchString', searchParams.searchString);\n }\n if (searchParams.accountName) {\n params.append('accountName', searchParams.accountName);\n }\n if (searchParams.permission) {\n params.append('permission', searchParams.permission);\n }\n if (searchParams.includeGroups !== undefined) {\n params.append('includeGroups', searchParams.includeGroups.toString());\n }\n if (searchParams.admin) {\n params.append('admin', searchParams.admin);\n }\n if (searchParams.start !== undefined) {\n params.append('start', searchParams.start.toString());\n }\n if (searchParams.size !== undefined) {\n params.append('size', searchParams.size.toString());\n }\n if (searchParams.source) {\n params.append('source', searchParams.source);\n }\n\n const endpoint = `search/network${params.toString() ? `?${params.toString()}` : ''}`;\n return this.http.get<SearchResult>(endpoint, { version: 'v3' });\n }\n /**\n * Get network as CX2Network object with utilities\n */\n async getNetworkAsCX2Object(\n networkUUID: string, \n options: AccessParams = {}\n ): Promise<CX2Network> {\n const cx2Data = await this.getRawCX2Network(networkUUID, options);\n return new CX2Network(cx2Data);\n }\n\n /**\n * Create new network from CX2\n */\n async createNetworkFromCX2(\n cx2Data: CX2NetworkType | CX2Network, \n options: { visibility?: 'PUBLIC' | 'PRIVATE'; folderId?: string } = {}\n ): Promise<NDExObjectUpdateStatus> {\n const endpoint = 'networks';\n \n // Convert CX2Network object to plain object if needed\n const data = cx2Data instanceof CX2Network ? JSON.parse(cx2Data.toJSON()) : cx2Data;\n \n return this.http.post<NDExObjectUpdateStatus>(endpoint, data, { \n version: 'v3',\n params: options\n });\n }\n\n /**\n * Update network with CX2 data\n */\n async updateNetworkCX2(\n networkUUID: string, \n cx2Data: CX2NetworkType | CX2Network\n ): Promise<NDExObjectUpdateStatus> {\n const endpoint = `networks/${networkUUID}`;\n \n // Convert CX2Network object to plain object if needed\n const data = cx2Data instanceof CX2Network ? JSON.parse(cx2Data.toJSON()) : cx2Data;\n \n return this.http.put<NDExObjectUpdateStatus>(endpoint, data, { version: 'v3' });\n }\n\n /**\n * Upload network file (CX2, CX, or other formats)\n */\n async uploadNetworkFile(\n file: File | Blob | string,\n options: {\n filename?: string;\n visibility?: 'PUBLIC' | 'PRIVATE';\n name?: string;\n onProgress?: (progress: number) => void;\n } = {}\n ): Promise<{ uuid: string }> {\n return this.http.uploadFile<{ uuid: string }>('networks/upload', file, {\n version: 'v3',\n ...options,\n });\n }\n\n /**\n * Get network metadata (V3 enhanced)\n */\n async getNetworkMetadata(networkUUID: string): Promise<any> {\n const endpoint = `networks/${networkUUID}/metadata`;\n return this.http.get<any>(endpoint, { version: 'v3' });\n }\n\n /**\n * Update network metadata\n */\n async updateNetworkMetadata(\n networkUUID: string, \n metadata: Record<string, any>\n ): Promise<void> {\n const endpoint = `networks/${networkUUID}/metadata`;\n return this.http.put<void>(endpoint, metadata, { version: 'v3' });\n }\n\n \n\n /**\n * Get network aspect (specific CX2 aspect)\n */\n async getNetworkAspect(\n networkUUID: string, \n aspectName: string,\n options: AccessParams = {}\n ): Promise<any> {\n const params = new URLSearchParams();\n if (options.accesskey) {\n params.append('accesskey', options.accesskey);\n }\n\n const endpoint = `networks/${networkUUID}/aspects/${aspectName}${params.toString() ? `?${params.toString()}` : ''}`;\n return this.http.get<any>(endpoint, { version: 'v3' });\n }\n\n\n}\n","import { HTTPService } from './HTTPService';\nimport { NetworkServiceV2 } from './NetworkServiceV2';\nimport { NetworkServiceV3 } from './NetworkServiceV3';\nimport { \n NetworkSummaryV3,\n PaginationParams,\n AccessParams,\n CX2Network as CX2NetworkType,\n CX2Edge,\n CX1Edge,\n CX2MetaData,\n NetworkPermission,\n NDExObjectUpdateStatus\n} from '../types';\nimport { CX2Network } from '../models/CX2Network';\n\n/**\n * UnifiedNetworkService - Provides access to both V2/V3 network services\n * Allows individual function calls to choose between v2 and v3 APIs\n */\nexport class UnifiedNetworkService {\n private v2Service: NetworkServiceV2;\n private v3Service: NetworkServiceV3;\n\n constructor(private http: HTTPService) {\n this.v2Service = new NetworkServiceV2(http);\n this.v3Service = new NetworkServiceV3(http);\n }\n\n /**\n * Get network summary using specified API version\n */\n async getNetworkSummary(\n networkUUID: string, \n options: AccessParams = {}\n ): Promise<NetworkSummaryV3> {\n return this.v3Service.getNetworkSummary(networkUUID, options);\n }\n\n /**\n * Search networks using specified API version\n * NOTE: This method is temporarily commented out as the V2 searchNetworks \n * signature has been migrated from NDEx.js and needs separate integration\n */\n // async searchNetworks(\n // searchParams: SearchParameters & { useV3?: boolean } = {}\n // ): Promise<SearchResult> {\n // const { useV3, ...params } = searchParams;\n // \n // if (useV3) {\n // return this.v3Service.searchNetworks(params);\n // }\n // \n // return this.v2Service.searchNetworks(params);\n // }\n\n\n /**\n * Get network in CX1 format (V2 API)\n */\n async getRawCX1Network(\n networkUUID: string,\n options: AccessParams = {}\n ): Promise<any[]> {\n return this.v2Service.getRawCX1Network(networkUUID, options);\n }\n\n /**\n * Get network in CX2 format (V3 API)\n */\n async getRawCX2Network(\n networkUUID: string,\n options: AccessParams = {}\n ): Promise<CX2NetworkType> {\n return this.v3Service.getRawCX2Network(networkUUID, options);\n }\n\n \n \n /**\n * Delete network\n */\n async deleteNetwork(networkUUID: string): Promise<void> {\n return this.v2Service.deleteNetwork(networkUUID);\n }\n\n\n /**\n * Create network DOI\n * \n * @param networkUUID - The UUID of the network to create a DOI for\n * @param key - DOI creation key\n * @param email - Email address for DOI registration\n * @returns Promise resolving to a confirmation message string from the server\n */\n async createNetworkDOI(\n networkUUID: string, \n key: string, \n email: string\n ): Promise<string> {\n return this.v3Service.createNetworkDOI(networkUUID, key, email);\n }\n\n /**\n * Get attributes of selected nodes\n * \n * Retrieves specific attributes for a set of nodes in a network. The server will return\n * a 404 error if the network has no attributes on nodes.\n * \n * @param networkUUID - The UUID of the network\n * @param nodeSelection - Object containing node IDs and attribute names to retrieve\n * @param nodeSelection.ids - Array of node IDs (long numbers) to get attributes for\n * @param nodeSelection.attributeNames - Array of attribute names to retrieve\n * @param options - Access options including optional access key\n * @returns Promise resolving to a JSON object where keys are stringified node IDs\n * and values are the selected attributes for that node\n * @throws {404} When the network has no attributes on nodes\n */\n async getAttributesOfSelectedNodes(\n networkUUID: string,\n nodeSelection: { ids: number[]; attributeNames: string[] },\n options: AccessParams = {}\n ): Promise<Record<string, any>> {\n return this.v3Service.getAttributesOfSelectedNodes(networkUUID, nodeSelection, options);\n }\n\n /**\n * Neighborhood query (migrated from original NDEx.js)\n * \n * Performs a neighborhood search within a network, returning nodes and edges\n * within the specified search depth from nodes matching the search terms.\n * Can return either raw CX1 or CX2 format based on outputCX2 parameter.\n * \n * @param networkUUID - The UUID of the network to search\n * @param searchTerms - Search string to find starting nodes\n * @param saveResult - Whether to save the query result as a new network\n * @param parameters - Additional query parameters\n * @param parameters.searchDepth - How many hops to search (default: 1)\n * @param parameters.edgeLimit - Maximum number of edges to return\n * @param parameters.errorWhenLimitIsOver - Throw error if edge limit exceeded\n * @param parameters.directOnly - Only include direct connections\n * @param parameters.nodeIds - Specific node IDs to start search from\n * @param outputCX2 - If true, return CX2 format via V3 API; if false, return CX1 format via V2 API\n * @returns Promise resolving to raw CX1 or CX2 network data\n */\n async neighborhoodQuery(\n networkUUID: string,\n searchTerms: string,\n saveResult?: boolean,\n parameters?: {\n searchDepth?: number;\n edgeLimit?: number;\n errorWhenLimitIsOver?: boolean;\n directOnly?: boolean;\n nodeIds?: number[];\n },\n outputCX2: boolean = false\n ): Promise<any[] | CX2NetworkType> {\n const params: Record<string, string> = {};\n\n if (saveResult !== undefined && saveResult === true) {\n params.save = 'true';\n }\n\n const data: Record<string, any> = {\n searchString: searchTerms,\n searchDepth: 1\n };\n\n if (parameters !== undefined) {\n if (parameters.searchDepth !== undefined) {\n data.searchDepth = parameters.searchDepth;\n }\n if (parameters.edgeLimit !== undefined) {\n data.edgeLimit = parameters.edgeLimit;\n }\n if (parameters.errorWhenLimitIsOver !== undefined) {\n data.errorWhenLimitIsOver = parameters.errorWhenLimitIsOver;\n }\n if (parameters.directOnly !== undefined) {\n data.directOnly = parameters.directOnly;\n }\n if (parameters.nodeIds != null) {\n data.nodeIds = parameters.nodeIds;\n }\n }\n\n if (outputCX2) {\n const endpoint = `search/network/${networkUUID}/query`;\n return this.http.post<CX2NetworkType>(endpoint, data, { \n version: 'v3',\n params \n });\n }\n\n const endpoint = `search/network/${networkUUID}/query`;\n return this.http.post<any[]>(endpoint, data, { \n version: 'v2',\n params \n });\n }\n\n /**\n * Interconnect query (migrated from original NDEx.js)\n * \n * Finds connections between nodes matching the search terms within a network.\n * Returns the interconnected subnetwork as either raw CX1 or CX2 format.\n * Can return either raw CX1 or CX2 format based on outputCX2 parameter.\n * \n * @param networkUUID - The UUID of the network to search\n * @param searchTerms - Search string to find nodes to interconnect\n * @param saveResult - Whether to save the query result as a new network\n * @param parameters - Additional query parameters\n * @param parameters.edgeLimit - Maximum number of edges to return\n * @param parameters.errorWhenLimitIsOver - Throw error if edge limit exceeded\n * @param parameters.nodeIds - Specific node IDs to find connections between\n * @param outputCX2 - If true, return CX2 format via V3 API; if false, return CX1 format via V2 API\n * @returns Promise resolving to raw CX1 or CX2 network data\n */\n async interConnectQuery(\n networkUUID: string,\n searchTerms: string,\n saveResult?: boolean,\n parameters?: {\n edgeLimit?: number;\n errorWhenLimitIsOver?: boolean;\n nodeIds?: number[];\n },\n outputCX2: boolean = false\n ): Promise<any[] | CX2NetworkType> {\n const params: Record<string, string> = {};\n\n if (saveResult !== undefined && saveResult === true) {\n params.save = 'true';\n }\n\n const data: Record<string, any> = { searchString: searchTerms };\n\n if (parameters !== undefined) {\n if (parameters.edgeLimit !== undefined) {\n data.edgeLimit = parameters.edgeLimit;\n }\n if (parameters.errorWhenLimitIsOver !== undefined) {\n data.errorWhenLimitIsOver = parameters.errorWhenLimitIsOver;\n }\n if (parameters.nodeIds != null) {\n data.nodeIds = parameters.nodeIds;\n }\n }\n\n if (outputCX2) {\n const endpoint = `search/networks/${networkUUID}/interconnectquery`;\n return this.http.post<CX2NetworkType>(endpoint, data, { \n version: 'v3',\n params \n });\n }\n\n const endpoint = `search/network/${networkUUID}/interconnectquery`;\n return this.http.post<any[]>(endpoint, data, { \n version: 'v2',\n params \n });\n }\n\n /**\n * Get network permissions by UUIDs (migrated from original NDEx.js)\n * \n * Retrieves network permissions for multiple networks in a single batch request.\n * Uses the V2 API batch endpoint to efficiently get permission information.\n * \n * @param uuidList - Array of network UUIDs to retrieve permissions for\n * @returns Promise resolving to permission information for the specified networks\n */\n async getNetworkPermissionsByUUIDs(uuidList: string[]): Promise<any[]> {\n const endpoint = 'batch/network/permission';\n return this.http.post<any[]>(endpoint, uuidList, { version: 'v2' });\n }\n\n /**\n * Export networks (migrated from original NDEx.js)\n * \n * Creates an export job for networks using the V2 batch export endpoint.\n * This allows exporting multiple networks in various formats.\n * \n * @param exportJob - Export job configuration specifying networks and format\n * @returns Promise resolving to export job result\n */\n async exportNetworks(exportJob: any): Promise<any> {\n const endpoint = 'batch/network/export';\n return this.http.post<any>(endpoint, exportJob, { version: 'v2' });\n }\n\n /**\n * Move networks to folder (migrated from original NDEx.js)\n * \n * Moves multiple networks to a specified folder using the V3 API.\n * This is a V3-specific feature for organizing networks in folders.\n * \n * @param networkIds - Array of network IDs to move\n * @param folderId - Target folder ID to move networks to\n * @returns Promise resolving when networks are moved\n */\n async moveNetworks(networkIds: string[], folderId: string): Promise<any> {\n if (!Array.isArray(networkIds)) {\n throw new Error('Invalid networkIds - must be an array');\n }\n\n const endpoint = 'batch/networks/move';\n const data = {\n targetFolder: folderId,\n networks: networkIds\n };\n\n return this.http.post<any>(endpoint, data, { version: 'v3' });\n }\n\n /**\n * Set networks visibility (migrated from original NDEx.js)\n * \n * Changes visibility settings for multiple networks using the V3 API.\n * Requires proper file validation to ensure data integrity.\n * \n * @param files - Object containing files with their types (must have 'files' property)\n * @param visibility - Visibility setting (e.g., 'PUBLIC', 'PRIVATE')\n * @returns Promise resolving when visibility is updated\n */\n async setNetworksVisibility(\n files: { files: Record<string, 'NETWORK' | 'FOLDER' | 'SHORTCUT'> },\n visibility: string\n ): Promise<any> {\n this.validateShareData(files);\n\n const endpoint = 'batch/networks/visibility';\n const data = {\n items: files,\n visibility: visibility\n };\n\n return this.http.post<any>(endpoint, data, { version: 'v3' });\n }\n\n /**\n * Get random edges from network (migrated from original NDEx.js)\n * \n * Retrieves a random sample of edges from a network using the V3 API.\n * This is useful for previewing large networks or sampling edge data.\n * \n * @param networkUUID - The UUID of the network to get edges from\n * @param limit - Number of random edges to retrieve (must be greater than 0)\n * @param accessKey - Optional access key for private networks\n * @returns Promise resolving to array of CX2Edge objects\n * @throws Error if limit is less than or equal to 0\n */\n async getRandomEdges(\n networkUUID: string, \n limit: number, \n accessKey?: string\n ): Promise<CX2Edge[]> {\n if (limit <= 0) {\n throw new Error(\"Value of parameter limit has to be greater than 0.\");\n }\n\n const params: Record<string, string> = {\n size: limit.toString(),\n method: \"random\"\n };\n\n if (accessKey !== undefined) {\n params.accesskey = accessKey;\n }\n\n const endpoint = `networks/${networkUUID}/aspects/edges`;\n return this.http.get<CX2Edge[]>(endpoint, { \n version: 'v3',\n params \n });\n }\n\n /**\n * Validate share data format (helper method for file operations)\n * \n * Validates the structure and content of file data used in sharing operations.\n * Ensures proper UUID format and valid file types.\n * \n * @param data - Data object to validate (must contain 'files' property)\n * @throws Error if validation fails\n */\n private validateShareData(data: any): void {\n // Check if data is an object and has files property\n if (typeof data !== 'object' || data === null || data.files === undefined) {\n throw new Error('Data must be an object with a \"files\" property');\n }\n \n // Check if files is an object\n if (typeof data.files !== 'object' || data.files === null) {\n throw new Error('The \"files\" property must be an object');\n }\n \n // Check each key-value pair in files\n const validValues = ['NETWORK', 'FOLDER', 'SHORTCUT'];\n \n for (const [uuid, fileType] of Object.entries(data.files)) {\n // Validate UUID format (basic validation)\n if (!/^[0-9a-f]{8}-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{12}$/i.test(uuid)) {\n throw new Error(`Invalid UUID format: ${uuid}`);\n }\n \n // Validate file type\n if (!validValues.includes(fileType as string)) {\n throw new Error(`Invalid file type for ${uuid}: ${fileType}. Must be one of: ${validValues.join(', ')}`);\n }\n }\n }\n\n /**\n * Get aspect elements (migrated from original NDEx.js)\n * \n * Retrieves elements from a specific aspect of a network using the V3 API.\n * This function can be used to get nodes, edges, or other aspect data\n * with optional size limiting and access key support for private networks.\n * \n * @param networkUUID - The UUID of the network to get aspect elements from\n * @param aspectName - Name of the aspect to retrieve (e.g., 'nodes', 'edges', 'networkAttributes')\n * @param limit - Optional maximum number of elements to return\n * @param accessKey - Optional access key for private networks\n * @returns Promise resolving to array of aspect elements\n * @example\n * ```typescript\n * // Get first 100 nodes from a network\n * const nodes = await client.networks.getAspectElements('network-uuid', 'nodes', 100);\n * \n * // Get all edges from a network\n * const edges = await client.networks.getAspectElements('network-uuid', 'edges');\n * ```\n */\n async getAspectElements(\n networkUUID: string,\n aspectName: string,\n limit?: number,\n accessKey?: string\n ): Promise<any[]> {\n const params: Record<string, string> = {};\n\n if (limit !== undefined) {\n params.size = limit.toString();\n }\n\n if (accessKey !== undefined) {\n params.accesskey = accessKey;\n }\n\n const endpoint = `networks/${networkUUID}/aspects/${aspectName}`;\n return this.http.get<any[]>(endpoint, { \n version: 'v3',\n params \n });\n }\n\n /**\n * Get filtered edges (migrated from original NDEx.js)\n * \n * Retrieves edges from a network that match specific filtering criteria on a column value.\n * The function supports both CX1 and CX2 formats based on the format parameter, with CX2 \n * being the default format used by the server.\n * \n * @param networkUUID - The UUID of the network to get filtered edges from\n * @param columnName - Name of the edge attribute column to filter on\n * @param valueString - Value to filter by (converted to string for comparison)\n * @param operator - Filtering operation: '>' | '<' | '=' | '!='\n * @param limit - Optional maximum number of edges to return (default: -1 = all matching edges)\n * @param order - Optional sort order for edges before applying limit: 'asc' | 'desc' (default: 'desc')\n * @param format - Optional output format: 'cx' | 'cx2' (default: 'cx2')\n * @param accessKey - Optional access key for private networks\n * @returns Promise resolving to array of edges in the specified format\n * \n * @example\n * ```typescript\n * // Get edges with weight > 0.5 in CX2 format (default)\n * const cx2Edges = await client.networks.getFilteredEdges(\n * 'network-uuid', 'weight', '0.5', '>'\n * );\n * \n * // Get top 10 edges with highest score in CX1 format\n * const cx1Edges = await client.networks.getFilteredEdges(\n * 'network-uuid', 'score', '0', '>', 10, 'desc', 'cx'\n * );\n * \n * // Get edges where interaction equals 'pp'\n * const ppEdges = await client.networks.getFilteredEdges(\n * 'network-uuid', 'interaction', 'pp', '=', undefined, undefined, 'cx2'\n * );\n * ```\n */\n async getFilteredEdges(\n networkUUID: string,\n columnName: string,\n valueString: string,\n operator: '>' | '<' | '=' | '!=',\n limit?: number,\n order?: 'asc' | 'desc',\n format?: 'cx' | 'cx2',\n accessKey?: string\n ): Promise<CX2Edge[] | CX1Edge[]> {\n const params: Record<string, string> = {};\n\n if (limit !== undefined) {\n params.size = limit.toString();\n }\n\n if (order !== undefined) {\n params.order = order;\n }\n\n if (accessKey !== undefined) {\n params.accesskey = accessKey;\n }\n\n if (format !== undefined) {\n params.format = format;\n }\n\n const data = {\n name: columnName,\n value: valueString,\n operator: operator\n };\n\n const endpoint = `search/networks/${networkUUID}/edges`;\n return this.http.post<CX2Edge[] | CX1Edge[]>(endpoint, data, { \n version: 'v3',\n params \n });\n }\n\n /**\n * Get CX2 metadata (migrated from original NDEx.js)\n * \n * Retrieves metadata information for all aspects in a CX2 network format.\n * This function provides aspect metadata including element counts for each\n * aspect in the network using the V3 API.\n * \n * @param networkUUID - The UUID of the network to get CX2 metadata for\n * @param accessKey - Optional access key for private networks\n * @returns Promise resolving to array of CX2MetaData objects\n * \n * @example\n * ```typescript\n * // Get CX2 metadata for a network\n * const metaData = await client.networks.getCX2MetaData('network-uuid');\n * console.log(metaData); // [{ name: 'nodes', elementCount: 100 }, { name: 'edges', elementCount: 150 }]\n * \n * // Get CX2 metadata for a private network\n * const privateMetaData = await client.networks.getCX2MetaData('private-network-uuid', 'access-key');\n * ```\n */\n async getCX2MetaData(\n networkUUID: string,\n accessKey?: string\n ): Promise<CX2MetaData[]> {\n const params: Record<string, string> = {};\n\n if (accessKey !== undefined) {\n params.accesskey = accessKey;\n }\n\n const endpoint = `networks/${networkUUID}/aspects`;\n return this.http.get<CX2MetaData[]>(endpoint, { \n version: 'v3',\n params \n });\n }\n\n /**\n * Create network from raw CX2 data (migrated from original NDEx.js)\n * \n * Creates a new network on NDEx from raw CX2 data using the V3 API.\n * This function delegates to the NetworkServiceV3 implementation.\n * \n * @param cx2Data - Raw CX2 network data as an object or CX2Network instance\n * @param options - Creation options including visibility and folderId\n * @param options.visibility - Network visibility: 'PUBLIC' or 'PRIVATE' (default: 'PRIVATE')\n * @param options.folderId - UUID of the folder to create the network in. If omitted, network is created in user's home directory\n * @returns Promise resolving to NDExObjectUpdateStatus with uuid and modificationTime\n * \n * @example\n * ```typescript\n * // Create private network from raw CX2 data in user's home directory\n * const result = await client.networks.createNetworkFromRawCX2(cx2Data);\n * console.log(result.uuid); // \"12345678-1234-1234-1234-123456789abc\"\n * \n * // Create public network from raw CX2 data in a specific folder\n * const publicResult = await client.networks.createNetworkFromRawCX2(cx2Data, { \n * visibility: 'PUBLIC', \n * folderId: '87654321-4321-4321-4321-876543210fed'\n * });\n * console.log(publicResult.uuid);\n * ```\n */\n async createNetworkFromRawCX2(\n cx2Data: CX2NetworkType | CX2Network,\n options: { visibility?: 'PUBLIC' | 'PRIVATE'; folderId?: string } = {}\n ): Promise<NDExObjectUpdateStatus> {\n return this.v3.createNetworkFromCX2(cx2Data, options);\n }\n\n /**\n * Update network from raw CX2 data (migrated from original NDEx.js)\n * \n * Updates an existing network with new raw CX2 data using the V3 API.\n * This function replaces the entire network content with the provided CX2 data.\n * \n * @param networkUUID - The UUID of the network to update\n * @param rawCX2 - Raw CX2 network data as an object or CX2Network instance\n * @returns Promise resolving when the network update is complete\n * \n * @example\n * ```typescript\n * // Update existing network with new CX2 data\n * await client.networks.updateNetworkFromRawCX2('network-uuid', updatedCx2Data);\n * ```\n */\n async updateNetworkFromRawCX2(\n networkUUID: string,\n rawCX2: CX2NetworkType | any\n ): Promise<void> {\n const endpoint = `networks/${networkUUID}`;\n return this.http.put<void>(endpoint, rawCX2, { version: 'v3' });\n }\n\n /**\n * Access to underlying service instances for advanced usage\n */\n get v2(): NetworkServiceV2 {\n return this.v2Service;\n }\n\n get v3(): NetworkServiceV3 {\n return this.v3Service;\n }\n}\n","import { HTTPService } from './HTTPService';\n\n// Type definitions for better type safety\ninterface ShareData {\n files: Record<string, 'NETWORK' | 'FOLDER' | 'SHORTCUT'>;\n}\n\ninterface MemberData {\n members: Record<string, 'READ' | 'WRITE'>;\n}\n\ninterface UpdateMemberRequest {\n files: ShareData['files'];\n members: MemberData['members'];\n}\n\ninterface TransferOwnershipRequest {\n files: ShareData['files'];\n new_owner: string;\n}\n\n/**\n * FilesService - NDEx file operations and task management\n * Handles file uploads, downloads, exports, and asynchronous task tracking\n */\nexport class FilesService {\n constructor(private http: HTTPService) {}\n\n /**\n * Copy a file to a different location\n * @param fromUuid - Source file UUID\n * @param toPath - Target path\n * @param type - File type (NETWORK, FOLDER, SHORTCUT)\n * @param accessKey - Optional access key for protected files\n */\n copyFile(fromUuid: string, toPath: string, type: string, accessKey?: string): Promise<any> {\n let parameters: Record<string, any> = {};\n\n if (accessKey !== undefined) {\n parameters['accesskey'] = accessKey;\n }\n return this.http.post('files/copy', {from_uuid: fromUuid, type: type, to_path: toPath}, {params: parameters, version: 'v3'});\n }\n\n /** Get file count statistics for the current user */\n getCount(): Promise<any> {\n return this.http.get('files/count', {version: 'v3'});\n }\n\n /** Get files in the trash for the current user */\n getTrash(): Promise<any> {\n return this.http.get('files/trash', {version: 'v3'});\n }\n\n /** Permanently delete all files in trash */\n emptyTrash(): Promise<any> {\n return this.http.delete('files/trash', {version: 'v3'});\n }\n\n /**\n * Permanently delete a file from trash\n * @param fileId - File UUID to permanently delete\n */\n permanentlyDeleteFile(fileId: string): Promise<any> {\n return this.http.delete(`files/trash/${fileId}`, { version: 'v3' });\n }\n\n /**\n * Restore files from trash\n * @param networkIds - Array of network UUIDs to restore\n * @param folderIds - Array of folder UUIDs to restore \n * @param shortcutIds - Array of shortcut UUIDs to restore\n */\n restoreFile(networkIds: string[], folderIds: string[], shortcutIds: string[]): Promise<any> {\n return this.http.post('files/trash/restore', {networks: networkIds, folders: folderIds, shortcuts: shortcutIds}, {version: 'v3'});\n }\n\n private _validateShareData(data: any): void {\n // Check if data is an object and has files property\n if (typeof data !== 'object' || data === null || data.files === undefined) {\n throw new Error('Data must be an object with a \"files\" property');\n }\n \n // Check if files is an object\n if (typeof data.files !== 'object' || data.files === null) {\n throw new Error('The \"files\" property must be an object');\n }\n \n // Check each key-value pair in files\n const validValues = ['NETWORK', 'FOLDER', 'SHORTCUT'];\n \n for (const [uuid, fileType] of Object.entries(data.files)) {\n // Validate UUID format (basic validation)\n if (!/^[0-9a-f]{8}-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{12}$/i.test(uuid)) {\n throw new Error(`Invalid UUID format: ${uuid}`);\n }\n \n // Validate file type\n if (!validValues.includes(fileType as string)) {\n throw new Error(`Invalid file type for ${uuid}: ${fileType}. Must be one of: ${validValues.join(', ')}`);\n }\n }\n }\n\n private _validateMemberData(data: any): void {\n if (typeof data !== 'object' || data === null || data.members === undefined) {\n throw new Error('Data must be an object with a \"members\" property');\n }\n const validValues = ['READ', 'WRITE'];\n for (const [uuid, permission] of Object.entries(data.members)) {\n if (!validValues.includes(permission as string)) {\n throw new Error(`Invalid permission for ${uuid}: ${permission}. Must be one of: ${validValues.join(', ')}`);\n }\n if (typeof uuid !== 'string' || !/^[0-9a-f]{8}-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{12}$/i.test(uuid)) {\n throw new Error(`Invalid UUID format: ${uuid}`);\n }\n }\n }\n\n updateMember(files: ShareData['files'], members: MemberData['members']): Promise<any> {\n this._validateShareData({ files });\n this._validateMemberData({ members });\n return this.http.post('files/sharing/members', { files, members }, { version: 'v3' });\n }\n\n listMembers(files: any): Promise<any> {\n return this.http.get('files/sharing/members/list', {params: files, version: 'v3'});\n }\n\n transferOwnership(files: ShareData['files'], newOwner: string): Promise<any> {\n this._validateShareData({ files });\n return this.http.post('files/sharing/transfer_ownership', { files, new_owner: newOwner }, { version: 'v3' });\n }\n\n listShares(limit?: number): Promise<any> {\n const parameters: Record<string, any> = {};\n if (limit !== undefined) {\n parameters['limit'] = limit;\n }\n return this.http.post('files/sharing/list', parameters, { version: 'v3' });\n }\n \n share(files: ShareData['files']): Promise<any> {\n this._validateShareData({ files });\n return this.http.post('files/sharing/share', { files }, { version: 'v3' });\n }\n\n unshare(files: ShareData['files']): Promise<any> {\n this._validateShareData({ files });\n return this.http.post('files/sharing/unshare', { files }, { version: 'v3' });\n }\n\n // Folder operations\n getFolders(limit?: number): Promise<any> {\n let parameters: Record<string, any> = {};\n\n if (limit !== undefined) {\n parameters['limit'] = limit;\n }\n return this.http.get('files/folders', {params: parameters, version: 'v3'});\n }\n \n createFolder(name: string, parentFolderId?: string): Promise<any> {\n return this.http.post('files/folders', { name: name, parent: parentFolderId }, { version: 'v3' });\n }\n\n getFolder(folderId: string, accessKey?: string): Promise<any> {\n const parameters: Record<string, any> = {};\n if (accessKey !== undefined) {\n parameters['accesskey'] = accessKey;\n }\n return this.http.get(`files/folders/${folderId}`, { params: parameters, version: 'v3' });\n }\n\n updateFolder(folderId: string, name: string, parentFolderId?: string): Promise<any> {\n return this.http.put(`files/folders/${folderId}`, { name: name, parent: parentFolderId }, { version: 'v3' });\n }\n\n deleteFolder(folderId: string): Promise<any> {\n return this.http.delete(`files/folders/${folderId}`, { version: 'v3' });\n }\n\n getFolderCount(folderId: string, accessKey?: string): Promise<any> {\n const parameters: Record<string, any> = {};\n if (accessKey !== undefined) {\n parameters['accesskey'] = accessKey;\n }\n return this.http.get(`files/folders/${folderId}/count`, { params: parameters, version: 'v3' });\n }\n\n getFolderList(folderId: string, accessKey?: string, format?: string, type?: string): Promise<any> {\n const parameters: Record<string, any> = {};\n if (accessKey !== undefined) {\n parameters['accesskey'] = accessKey;\n }\n if (format !== undefined) {\n parameters['format'] = format;\n }\n if (type !== undefined) {\n parameters['type'] = type;\n }\n return this.http.get(`files/folders/${folderId}/list`, { params: parameters, version: 'v3' });\n }\n\n // Shortcut operations\n getShortcuts(limit?: number): Promise<any> {\n let parameters: Record<string, any> = {};\n\n if (limit !== undefined) {\n parameters['limit'] = limit;\n }\n return this.http.get('files/shortcuts', {params: parameters, version: 'v3'});\n }\n\n createShortcut(name: string, parentFolderId?: string, targetId?: string, targetType?: string): Promise<any> {\n return this.http.post('files/shortcuts', { name: name, parent: parentFolderId, target: targetId, targetType }, { version: 'v3' });\n }\n\n getShortcut(shortcutId: string, accessKey?: string): Promise<any> {\n const parameters: Record<string, any> = {};\n if (accessKey !== undefined) {\n parameters['accesskey'] = accessKey;\n }\n return this.http.get(`files/shortcuts/${shortcutId}`, { params: parameters, version: 'v3' });\n }\n \n updateShortcut(shortcutId: string, name: string, parentFolderId?: string, targetId?: string, targetType?: string): Promise<any> {\n return this.http.put(`files/shortcuts/${shortcutId}`, { name: name, parent: parentFolderId, target: targetId, targetType }, { version: 'v3' });\n }\n\n deleteShortcut(shortcutId: string): Promise<any> {\n return this.http.delete(`files/shortcuts/${shortcutId}`, { version: 'v3' });\n }\n}\n","import { HTTPService } from './HTTPService';\nimport { CyWebWorkspace } from '../types';\n\n/**\n * WorkspaceService - NDEx CyWeb workspace operations\n * \n * Provides methods for managing CyWeb workspaces including creation, retrieval,\n * updates, and deletion of workspaces and their associated networks.\n * All workspace operations use the V3 API.\n */\nexport class WorkspaceService {\n constructor(private http: HTTPService) {}\n\n /**\n * Create a new CyWeb workspace (migrated from original NDEx.js)\n * \n * Creates a new workspace with the specified workspace data.\n * \n * @param workspace - The workspace object to create\n * @returns Promise resolving to the response from the server (typically contains workspace location)\n * \n * @example\n * ```typescript\n * const workspaceData = {\n * name: \"My Workspace\",\n * description: \"A sample workspace\",\n * networkIds: []\n * };\n * const response = await client.workspace.createCyWebWorkspace(workspaceData);\n * ```\n */\n async createCyWebWorkspace(workspace: CyWebWorkspace): Promise<string> {\n const endpoint = 'workspaces';\n return this.http.post<string>(endpoint, workspace, { version: 'v3' });\n }\n\n /**\n * Get a CyWeb workspace by ID (migrated from original NDEx.js)\n * \n * Retrieves a workspace and its details by workspace ID.\n * \n * @param workspaceId - The UUID of the workspace to retrieve\n * @returns Promise resolving to the workspace object\n * \n * @example\n * ```typescript\n * const workspace = await client.workspace.getCyWebWorkspace('workspace-uuid');\n * console.log(workspace.name);\n * ```\n */\n async getCyWebWorkspace(workspaceId: string): Promise<CyWebWorkspace> {\n const endpoint = `workspaces/${workspaceId}`;\n return this.http.get<CyWebWorkspace>(endpoint, { version: 'v3' });\n }\n\n /**\n * Delete a CyWeb workspace (migrated from original NDEx.js)\n * \n * Deletes the specified workspace permanently.\n * \n * @param workspaceId - The UUID of the workspace to delete\n * @returns Promise resolving when the workspace is deleted\n * \n * @example\n * ```typescript\n * await client.workspace.deleteCyWebWorkspace('workspace-uuid');\n * ```\n */\n async deleteCyWebWorkspace(workspaceId: string): Promise<void> {\n const endpoint = `workspaces/${workspaceId}`;\n return this.http.delete<void>(endpoint, { version: 'v3' });\n }\n\n /**\n * Update a CyWeb workspace (migrated from original NDEx.js)\n * \n * Updates a workspace with new data, replacing the entire workspace object.\n * \n * @param workspaceId - The UUID of the workspace to update\n * @param workspaceObj - The updated workspace object\n * @returns Promise resolving when the workspace is updated\n * \n * @example\n * ```typescript\n * const updatedWorkspace = {\n * name: \"Updated Workspace Name\",\n * description: \"Updated description\",\n * networkIds: [\"network-uuid-1\", \"network-uuid-2\"]\n * };\n * await client.workspace.updateCyWebWorkspace('workspace-uuid', updatedWorkspace);\n * ```\n */\n async updateCyWebWorkspace(workspaceId: string, workspaceObj: CyWebWorkspace): Promise<void> {\n const endpoint = `workspaces/${workspaceId}`;\n return this.http.put<void>(endpoint, workspaceObj, { version: 'v3' });\n }\n\n /**\n * Update CyWeb workspace name (migrated from original NDEx.js)\n * \n * Updates only the name of a workspace.\n * \n * @param workspaceId - The UUID of the workspace to update\n * @param newName - The new name for the workspace\n * @returns Promise resolving when the workspace name is updated\n * \n * @example\n * ```typescript\n * await client.workspace.updateCyWebWorkspaceName('workspace-uuid', 'New Workspace Name');\n * ```\n */\n async updateCyWebWorkspaceName(workspaceId: string, newName: string): Promise<void> {\n const endpoint = `workspaces/${workspaceId}/name`;\n return this.http.put<void>(endpoint, { name: newName }, { version: 'v3' });\n }\n\n /**\n * Update CyWeb workspace networks (migrated from original NDEx.js)\n * \n * Updates the list of network IDs associated with a workspace.\n * \n * @param workspaceId - The UUID of the workspace to update\n * @param networkIds - Array of network UUIDs to associate with the workspace\n * @returns Promise resolving when the workspace networks are updated\n * \n * @example\n * ```typescript\n * const networkIds = ['network-uuid-1', 'network-uuid-2', 'network-uuid-3'];\n * await client.workspace.updateCyWebWorkspaceNetworks('workspace-uuid', networkIds);\n * ```\n */\n async updateCyWebWorkspaceNetworks(workspaceId: string, networkIds: string[]): Promise<void> {\n const endpoint = `workspaces/${workspaceId}/networkids`;\n return this.http.put<void>(endpoint, networkIds, { version: 'v3' });\n }\n\n /**\n * Get user's CyWeb workspaces (migrated from original NDEx.js)\n * \n * Retrieves all workspaces belonging to the currently authenticated user.\n * Requires authentication.\n * \n * @returns Promise resolving to array of workspace objects\n * \n * @example\n * ```typescript\n * const workspaces = await client.workspace.getUserCyWebWorkspaces();\n * workspaces.forEach(workspace => {\n * console.log(`Workspace: ${workspace.name}`);\n * });\n * ```\n */\n async getUserCyWebWorkspaces(): Promise<CyWebWorkspace[]> {\n // First get the current user to get their externalId\n const user = await this.http.get<any>('user', { params: { valid: true } });\n const endpoint = `users/${user.externalId}/workspaces`;\n return this.http.get<CyWebWorkspace[]>(endpoint, { version: 'v3' });\n }\n}\n","import { HTTPService } from './HTTPService';\nimport { \n NDExUser,\n PaginationParams,\n NetworkSummaryV2\n} from '../types';\n\n/**\n * UserService - NDEx user-related operations\n * Handles authentication, user management, and user workspace operations\n */\nexport class UserService {\n constructor(private http: HTTPService) {}\n\n // ============================================================================\n // Authentication Methods\n // ============================================================================\n\n /**\n * Get authenticated user (equivalent to getSignedInUser from legacy client)\n * Returns the current signed-in user object from NDEx server\n * \n * For basic authentication: Gets the current user using the /user endpoint\n * For OAuth authentication: Uses the /users/signin endpoint with ID token\n * \n * @returns The authenticated user object\n * @note When authenticating with OAuth ID token, if a user with matching email \n * doesn't exist on the server, this function will automatically create \n * that user and return the newly created user object.\n */\n async authenticate(): Promise<NDExUser> {\n const authType = this.http.getAuthType();\n if (!authType) {\n throw new Error('Authentication parameters are missing in NDEx client.');\n }\n \n if (authType === 'basic') {\n // For basic auth, use the standard user endpoint with valid parameter\n const endpoint = 'user';\n const params = { valid: true };\n return this.http.get<NDExUser>(endpoint, { params });\n } else if (authType === 'oauth') {\n // For OAuth, use the signin endpoint with ID token (v3 API)\n const idToken = this.http.getIdToken();\n if (!idToken) {\n throw new Error('OAuth ID token is missing.');\n }\n \n const endpoint = 'users/signin';\n const data = { idToken };\n return this.http.post<NDExUser>(endpoint, data, { version: 'v3' });\n }\n \n throw new Error(`Unsupported authentication type: ${authType}`);\n }\n\n /**\n * Get current user profile (equivalent to getSignedInUser from legacy client)\n * Returns the current signed-in user object from NDEx server\n * \n * Uses the /user endpoint with {valid: true} parameter for both basic and OAuth authentication.\n * Unlike authenticate(), this function will NOT automatically create a user account for OAuth.\n * If the OAuth ID token doesn't match an existing user, it will return an unauthorized error.\n * \n * @returns The current user object\n * @note This function requires existing authentication and will not create new users\n */\n async getCurrentUser(): Promise<NDExUser> {\n const authType = this.http.getAuthType();\n if (!authType) {\n throw new Error('Authentication parameters are missing in NDEx client.');\n }\n \n const endpoint = 'user';\n const params = { valid: true };\n return this.http.get<NDExUser>(endpoint, { params });\n }\n\n /**\n * Update current user profile\n * Uses the UUID from the userUpdate object and server validates against authenticated user\n */\n async updateCurrentUser(userUpdate: Partial<NDExUser>): Promise<void> {\n if (!userUpdate.externalId) {\n throw new Error('User uuid is required in userUpdate object');\n }\n\n const endpoint = `user/${userUpdate.externalId}`;\n return this.http.put<void>(endpoint, userUpdate);\n }\n\n\n /**\n * Request password reset\n */\n async requestPasswordReset(email: string): Promise<void> {\n const endpoint = 'user/forgot-password';\n return this.http.post<void>(endpoint, { email });\n }\n\n /**\n * Reset password with user UUID (server validates UUID matches authenticated user)\n * @param userUUID - User UUID (must match authenticated user)\n * @param newPassword - New password as plain text\n */\n async resetPassword(userUUID: string, newPassword: string): Promise<void> {\n const endpoint = `user/${userUUID}/password`;\n const config: any = {\n headers: {\n 'Content-Type': 'text/plain' // Send password as plain text\n }\n };\n \n return this.http.put<void>(endpoint, newPassword, config);\n }\n\n // ============================================================================\n // User Management Methods\n // ============================================================================\n\n /**\n * Get user by UUID\n */\n async getUser(userUUID: string): Promise<NDExUser> {\n const endpoint = `user/${userUUID}`;\n return this.http.get<NDExUser>(endpoint);\n }\n\n /**\n * Get user by account name or email (matches server getUserByAccountNameOrAuthenticatUser)\n * @param searchBy - Search criteria - either by username OR by email, but not both\n * @returns User object matching the search criteria\n * @note If both username and email are provided, only username will be used\n */\n async getUserByNameOrEmail(searchBy: \n | { username: string }\n | { email: string }\n ): Promise<NDExUser> {\n const params = new URLSearchParams();\n \n if ('username' in searchBy) {\n params.append('username', searchBy.username);\n } else if ('email' in searchBy) {\n params.append('email', searchBy.email);\n }\n\n const endpoint = `user?${params.toString()}`;\n return this.http.get<NDExUser>(endpoint);\n }\n\n /**\n * Get multiple users by their UUIDs (batch operation)\n * @param uuidList - Array of user UUIDs to fetch\n * @returns Array of user objects corresponding to the provided UUIDs\n */\n async getUsersByUUIDs(uuidList: string[]): Promise<NDExUser[]> {\n const endpoint = 'batch/user';\n return this.http.post<NDExUser[]>(endpoint, uuidList);\n }\n\n /**\n * Search users (equivalent to searchUsers from legacy client)\n * @param searchTerms - Search string to find users\n * @param start - Starting offset for pagination (optional)\n * @param size - Maximum number of results to return (optional)\n * @returns Array of users matching the search criteria\n */\n async searchUsers(\n searchTerms: string, \n start?: number, \n size?: number\n ): Promise<NDExUser[]> {\n const params: Record<string, string> = {};\n \n if (start !== undefined) {\n params.start = start.toString();\n }\n if (size !== undefined) {\n params.limit = size.toString();\n }\n\n const data = { searchString: searchTerms };\n const endpoint = 'search/user';\n \n return this.http.post<NDExUser[]>(endpoint, data, { params });\n }\n\n\n // ============================================================================\n // User Network Methods\n // ============================================================================\n\n /**\n * Get networks for a user's account page (equivalent to getAccountPageNetworks from legacy client)\n * \n * @param userUUID - User UUID to get networks for\n * @param offset - Starting offset for pagination (optional)\n * @param limit - Maximum number of networks to return (optional)\n * @returns Array of V2 network summaries for the specified user\n * @note This function requires authentication. The auth attribute must be set in the client configuration.\n */\n async getAccountPageNetworks(\n userUUID: string,\n offset?: number, \n limit?: number\n ): Promise<NetworkSummaryV2[]> {\n // Build parameters for the network summary request\n const params: Record<string, string> = {};\n if (offset !== undefined) {\n params.offset = offset.toString();\n }\n if (limit !== undefined) {\n params.limit = limit.toString();\n }\n\n // Get network summaries for the user\n const endpoint = `user/${userUUID}/networksummary`;\n return this.http.get<NetworkSummaryV2[]>(endpoint, { params });\n }\n\n\n\n /**\n * Delete user account (server validates userid matches authenticated user)\n * @param userUUID - User UUID to delete (must match authenticated user)\n * @note This function requires authentication. The auth attribute must be set in the client configuration.\n * @note The userUUID parameter must be the UUID of the currently authenticated user. The server will validate this.\n */\n async deleteUserAccount(userUUID: string): Promise<void> {\n const endpoint = `user/${userUUID}`;\n return this.http.delete<void>(endpoint);\n }\n}\n","import { HTTPService } from './HTTPService';\n\n/**\n * AdminService - NDEx admin operations\n * Handles system administration and user management for admin users\n */\nexport class AdminService {\n constructor(private http: HTTPService) {}\n\n}\n","import axios, { AxiosInstance } from 'axios';\nimport {\n CyNDExConfig,\n CyNDExAuthConfig,\n NDExImportParams,\n NDExExportParams,\n CytoscapeNetworkSummary,\n CyNDExStatusResponse,\n CX2ImportParams\n} from '../types/cytoscape';\n\n/**\n * CyNDEx Service - Cytoscape-NDEx Bridge\n * \n * Provides seamless integration between Cytoscape desktop application and NDEx,\n * enabling import/export of networks with support for CX and CX2 formats.\n * \n * This service communicates with Cytoscape via its REST API and handles NDEx\n * authentication parameters that are passed to Cytoscape for NDEx operations.\n * \n * @example\n * ```typescript\n * // Basic usage\n * const cyNDEx = new CyNDExService();\n * \n * // Configure NDEx server\n * cyNDEx.setNDExBaseURL('https://www.ndexbio.org');\n * \n * // Set authentication\n * cyNDEx.setBasicAuth('username', 'password');\n * // or\n * cyNDEx.setAuthToken('oauth-id-token');\n * \n * // Import network from NDEx to Cytoscape\n * await cyNDEx.postNDExNetworkToCytoscape('network-uuid', 'access-key');\n * \n * // Export network from Cytoscape to NDEx\n * await cyNDEx.postCytoscapeNetworkToNDEx('current');\n * \n * // Import CX2 data to Cytoscape\n * await cyNDEx.postCX2NetworkToCytoscape(cx2String, 'My Network', 'My Collection');\n * ```\n */\nexport class CyNDExService {\n private _port: number;\n private cyRestBaseURL: string;\n private ndexBaseURL: string;\n private authConfig?: CyNDExAuthConfig;\n private axiosInstance: AxiosInstance;\n\n /**\n * Create a new CyNDEx service instance\n * \n * @param port - Port number for Cytoscape REST API (default: 1234)\n * @param config - Optional configuration object\n */\n constructor(port: number = 1234, config?: CyNDExConfig) {\n this._port = port;\n this.cyRestBaseURL = config?.cyRestBaseURL || 'http://127.0.0.1';\n this.ndexBaseURL = config?.ndexBaseURL || 'https://www.ndexbio.org';\n\n // Create axios instance for Cytoscape REST API calls\n this.axiosInstance = axios.create({\n baseURL: this.cyRestURL(),\n timeout: 30000,\n headers: {\n 'Content-Type': 'application/json'\n }\n });\n }\n\n /**\n * Get the port number for Cytoscape REST API\n */\n get port(): number {\n return this._port;\n }\n\n /**\n * Get the base URL for Cytoscape REST API\n */\n static get cyRestBaseURL(): string {\n return 'http://127.0.0.1';\n }\n\n /**\n * Set NDEx server base URL\n * \n * @param ndexBaseURL - Complete base URL for NDEx server (e.g., 'https://www.ndexbio.org')\n * Must include protocol (https:// or http://)\n * \n * @example\n * ```typescript\n * cyNDEx.setNDExBaseURL('https://www.ndexbio.org');\n * cyNDEx.setNDExBaseURL('https://test.ndexbio.org');\n * ```\n */\n setNDExBaseURL(ndexBaseURL: string): void {\n if (ndexBaseURL?.trim()) {\n this.ndexBaseURL = ndexBaseURL.trim();\n }\n }\n\n /**\n * Get the current NDEx server base URL\n * \n * @returns Complete NDEx server base URL\n */\n getNDExBaseURL(): string {\n return this.ndexBaseURL;\n }\n\n\n /**\n * Set basic authentication credentials for NDEx operations\n * \n * @param username - NDEx username\n * @param password - NDEx password\n */\n setBasicAuth(username: string, password: string): void {\n if (username?.trim() && password) {\n this.authConfig = {\n type: 'basic',\n username: username.trim(),\n password: password\n };\n }\n }\n\n /**\n * Set OAuth ID token for NDEx operations\n * \n * @param idToken - OAuth ID token from authentication provider\n */\n setAuthToken(idToken: string): void {\n if (idToken?.trim()) {\n this.authConfig = {\n type: 'oauth',\n idToken: idToken.trim()\n };\n }\n }\n\n /**\n * Clear authentication credentials\n */\n clearAuth(): void {\n this.authConfig = undefined;\n }\n\n /**\n * Get the complete Cytoscape REST API URL\n * \n * @returns Complete URL for Cytoscape REST API\n */\n cyRestURL(): string {\n return `${this.cyRestBaseURL}:${this._port}`;\n }\n\n /**\n * Get authorization fields for NDEx operations\n * These are passed as parameters to Cytoscape for NDEx authentication\n * \n * @private\n * @returns Authorization parameters object\n */\n private getAuthFields(): Record<string, string> {\n if (!this.authConfig) return {};\n\n switch (this.authConfig.type) {\n case 'basic':\n return {\n username: this.authConfig.username!,\n password: this.authConfig.password!\n };\n case 'oauth':\n return {\n idToken: this.authConfig.idToken!\n };\n default:\n return {};\n }\n }\n\n /**\n * Perform HTTP GET request to Cytoscape REST API\n * \n * @private\n * @param url - Endpoint URL (relative to base URL)\n * @returns Promise resolving to response data\n */\n private async _httpGet<T = any>(url: string): Promise<T> {\n const response = await this.axiosInstance.get<T>(url);\n return response.data;\n }\n\n /**\n * Perform HTTP POST request to Cytoscape REST API\n * \n * @private\n * @param url - Endpoint URL (relative to base URL)\n * @param params - Optional query parameters\n * @param data - Optional request body data\n * @returns Promise resolving to response data\n */\n private async _httpPost<T = any>(url: string, params?: any, data?: any): Promise<T> {\n const response = await this.axiosInstance.post<T>(url, data, { params });\n return response.data;\n }\n\n /**\n * Perform HTTP PUT request to Cytoscape REST API\n * \n * @private\n * @param url - Endpoint URL (relative to base URL)\n * @param params - Optional query parameters\n * @param data - Optional request body data\n * @returns Promise resolving to response data\n */\n private async _httpPut<T = any>(url: string, params?: any, data?: any): Promise<T> {\n const response = await this.axiosInstance.put<T>(url, data, { params });\n return response.data;\n }\n\n // =============================================================================\n // Public API Methods - Maintain exact same signatures as original CyNDEx.js\n // =============================================================================\n\n /**\n * Get CyNDEx plugin status from Cytoscape\n * \n * @returns Promise resolving to CyNDEx status information\n */\n async getCyNDExStatus(): Promise<CyNDExStatusResponse> {\n return this._httpGet<CyNDExStatusResponse>('/cyndex2/v1');\n }\n\n /**\n * Get network summary information from Cytoscape\n * \n * @param suid - Network SUID or 'current' for current network (default: 'current')\n * @returns Promise resolving to network summary\n */\n async getCytoscapeNetworkSummary(suid: string = 'current'): Promise<CytoscapeNetworkSummary> {\n return this._httpGet<CytoscapeNetworkSummary>(`/cyndex2/v1/networks/${suid}`);\n }\n\n /**\n * Import network from NDEx to Cytoscape\n * \n * @param uuid - NDEx network UUID\n * @param accessKey - Optional access key for private networks\n * @param createView - Whether to create a network view (default: undefined)\n * @returns Promise resolving to import result\n */\n async postNDExNetworkToCytoscape(\n uuid: string, \n accessKey?: string, \n createView?: boolean\n ): Promise<any> {\n const importParams: NDExImportParams = {\n serverUrl: `${this.ndexBaseURL}/v2`,\n uuid: uuid,\n accessKey: accessKey,\n createView: createView,\n ...this.getAuthFields()\n };\n\n return this._httpPost('/cyndex2/v1/networks', undefined, importParams);\n }\n\n /**\n * Import CX network data to Cytoscape\n * \n * @param cx - CX format network data\n * @returns Promise resolving to import result\n */\n async postCXNetworkToCytoscape(cx: any): Promise<any> {\n return this._httpPost('/cyndex2/v1/networks/cx', undefined, cx);\n }\n\n /**\n * Import CX2 network data to Cytoscape\n * \n * @param cx2_string - CX2 format network data as string\n * @param title - Network title\n * @param collection_name - Collection name\n * @returns Promise resolving to import result\n */\n async postCX2NetworkToCytoscape(\n cx2_string: string, \n title: string, \n collection_name: string\n ): Promise<any> {\n const params: CX2ImportParams = {\n format: 'cx2',\n collection: collection_name,\n title: title\n };\n\n return this._httpPost('/v1/networks', params, cx2_string);\n }\n\n /**\n * Export network from Cytoscape to NDEx (create new network)\n * \n * @param suid - Network SUID or 'current' for current network (default: 'current')\n * @returns Promise resolving to export result\n */\n async postCytoscapeNetworkToNDEx(suid: string = 'current'): Promise<any> {\n const saveParams: NDExExportParams = {\n serverUrl: `${this.ndexBaseURL}/v2`,\n ...this.getAuthFields()\n };\n\n return this._httpPost(`/cyndex2/v1/networks/${suid}`, undefined, saveParams);\n }\n\n /**\n * Update existing network in NDEx with data from Cytoscape\n * \n * @param suid - Network SUID or 'current' for current network (default: 'current')\n * @param uuid - Target NDEx network UUID to update\n * @returns Promise resolving to update result\n */\n async putCytoscapeNetworkInNDEx(suid: string = 'current', uuid: string): Promise<any> {\n const saveParams: NDExExportParams = {\n serverUrl: `${this.ndexBaseURL}/v2`,\n uuid: uuid,\n ...this.getAuthFields()\n };\n\n return this._httpPut(`/cyndex2/v1/networks/${suid}`, undefined, saveParams);\n }\n}\n\n// Export both as named export and default for backward compatibility\nexport default CyNDExService;","{\n \"name\": \"@js4cytoscape/ndex-client\",\n \"version\": \"0.6.0-alpha.2\",\n \"description\": \"NDEx client library - Modern TypeScript implementation\",\n \"repository\": {\n \"type\": \"git\",\n \"url\": \"git+https://github.com/cytoscape/js4cytoscape.git\"\n },\n \"bugs\": {\n \"url\": \"https://github.com/cytoscape/js4cytoscape/issues\"\n },\n \"homepage\": \"https://github.com/cytoscape/js4cytoscape\",\n \"main\": \"./dist/index.js\",\n \"module\": \"./dist/index.mjs\",\n \"umd\": \"./dist/index.umd.js\",\n \"types\": \"./dist/index.d.ts\",\n \"exports\": {\n \".\": {\n \"types\": \"./dist/index.d.ts\",\n \"import\": \"./dist/index.mjs\",\n \"require\": \"./dist/index.js\"\n }\n },\n \"files\": [\n \"dist\",\n \"src\",\n \"README.md\",\n \"LICENSE\"\n ],\n \"scripts\": {\n \"dev\": \"tsup --watch\",\n \"build\": \"tsup\",\n \"build:docs\": \"typedoc\",\n \"docs:api\": \"npm run build:docs\",\n \"docs:site\": \"cd docs-root/guide && npm install && npm run build\",\n \"docs:serve\": \"cd docs-root/guide && npm run start\",\n \"docs:build\": \"npm run docs:api && npm run docs:site\",\n \"docs:clean\": \"rimraf docs-root/api docs-root/guide/build\",\n \"test\": \"npm run test:unit\",\n \"test:unit\": \"jest --config jest.unit.config.js\",\n \"test:integration\": \"jest --config jest.integration.config.js\",\n \"test:all\": \"npm run test:unit && npm run test:integration\",\n \"test:watch\": \"npm run test:unit -- --watch\",\n \"test:coverage\": \"npm run test:unit -- --coverage\",\n \"test:ci\": \"npm run test:all -- --coverage\",\n \"debug:integration\": \"node --inspect-brk ./node_modules/.bin/jest --config jest.integration.config.js --runInBand --no-cache\",\n \"debug:unit\": \"node --inspect-brk ./node_modules/.bin/jest --config jest.unit.config.js --runInBand --no-cache\",\n \"debug:client\": \"node --inspect-brk debug-response.js\",\n \"lint\": \"eslint src __tests__ --ext .ts,.js --fix\",\n \"format\": \"prettier --write \\\"src/**/*.{ts,js}\\\" \\\"__tests__/**/*.{ts,js}\\\"\",\n \"type-check\": \"tsc --noEmit\",\n \"clean\": \"rimraf dist coverage\",\n \"prepare\": \"npm run build\",\n \"changeset\": \"changeset\",\n \"release\": \"changeset publish\"\n },\n \"author\": \"Jing Chen\",\n \"license\": \"MIT\",\n \"engines\": {\n \"node\": \">=16.0.0\"\n },\n \"keywords\": [\n \"ndex\",\n \"network\",\n \"cytoscape\",\n \"bioinformatics\",\n \"graph\",\n \"cx2\",\n \"typescript\"\n ],\n \"dependencies\": {\n \"axios\": \"^1.11.0\"\n },\n \"devDependencies\": {\n \"@changesets/cli\": \"^2.27.1\",\n \"@types/jest\": \"^29.5.12\",\n \"@types/node\": \"^20.11.25\",\n \"@typescript-eslint/eslint-plugin\": \"^7.1.1\",\n \"@typescript-eslint/parser\": \"^7.1.1\",\n \"eslint\": \"^8.57.0\",\n \"eslint-config-prettier\": \"^9.1.0\",\n \"eslint-plugin-prettier\": \"^5.1.3\",\n \"glob\": \"^7.2.0\",\n \"jest\": \"^29.7.0\",\n \"jest-environment-jsdom\": \"^29.7.0\",\n \"nock\": \"^13.5.4\",\n \"prettier\": \"^3.2.5\",\n \"rimraf\": \"^5.0.5\",\n \"ts-jest\": \"^29.1.2\",\n \"tsup\": \"^8.0.2\",\n \"typedoc\": \"^0.28.12\",\n \"typedoc-material-theme\": \"^1.4.0\",\n \"typedoc-plugin-markdown\": \"^4.8.1\",\n \"typescript\": \"^5.4.2\"\n },\n \"peerDependencies\": {\n \"cytoscape\": \"^3.0.0\"\n },\n \"peerDependenciesMeta\": {\n \"cytoscape\": {\n \"optional\": true\n }\n }\n}\n","import axios, { AxiosInstance, AxiosRequestConfig, AxiosResponse } from 'axios';\nimport { \n NDExClientConfig, \n APIResponse, \n APIError, \n BasicAuth, \n OAuthAuth,\n NDExError,\n NDExNetworkError,\n NDExAuthError,\n NDExNotFoundError,\n NDExValidationError,\n NDExServerError\n} from '../types';\nimport { version } from '../../package.json';\n\n/**\n * HTTPService - Core HTTP client for NDEx API communication\n * Handles v2/v3 endpoint routing, authentication, and error handling\n * \n * @note User-Agent header is set to 'NDEx-JS-Client/${version}' but only works in Node.js.\n * Browsers will ignore custom User-Agent headers for security reasons.\n * @internal\n */\nexport class HTTPService {\n private axiosInstance: AxiosInstance;\n private config: NDExClientConfig;\n\n constructor(config: NDExClientConfig = {}) {\n this.config = {\n baseURL: 'https://www.ndexbio.org',\n timeout: 30000,\n retries: 3,\n retryDelay: 1000,\n debug: false,\n ...config,\n };\n\n // Create headers object\n const headers: Record<string, string> = {\n 'Content-Type': 'application/json',\n ...this.config.headers,\n ...this.getAuthHeaders(),\n };\n\n // Only set User-Agent in Node.js environments (not in browsers)\n if (typeof window === 'undefined') {\n headers['User-Agent'] = `NDEx-JS-Client/${version}`;\n }\n\n this.axiosInstance = axios.create({\n baseURL: this.config.baseURL,\n timeout: this.config.timeout,\n headers,\n });\n\n this.setupInterceptors();\n }\n\n /**\n * Get authentication headers based on config.auth\n */\n private getAuthHeaders(): Record<string, string> {\n if (!this.config.auth) {\n return {};\n }\n\n if (this.config.auth.type === 'basic') {\n // Basic authentication: encode username:password in base64\n const credentials = btoa(`${this.config.auth.username}:${this.config.auth.password}`);\n return {\n 'Authorization': `Basic ${credentials}`,\n };\n } else if (this.config.auth.type === 'oauth') {\n // OAuth Bearer token\n return {\n 'Authorization': `Bearer ${this.config.auth.idToken}`,\n };\n }\n\n return {};\n }\n\n /**\n * Build API endpoint URL with version routing\n */\n private buildUrl(endpoint: string, version: 'v2' | 'v3' = 'v2'): string {\n const cleanEndpoint = endpoint.startsWith('/') ? endpoint.slice(1) : endpoint;\n return `/${version}/${cleanEndpoint}`;\n }\n\n /**\n * Generic GET request with intelligent version routing\n */\n async get<T = any>(\n endpoint: string,\n config?: AxiosRequestConfig & { version?: 'v2' | 'v3' }\n ): Promise<T> {\n const { version, ...axiosConfig } = config || {};\n const url = this.buildUrl(endpoint, version);\n\n try {\n const response = await this.axiosInstance.get<APIResponse<T>>(url, axiosConfig);\n return this.handleResponse<T>(response);\n } catch (error) {\n this.handleError(error);\n }\n }\n\n /**\n * Generic POST request with intelligent version routing\n */\n async post<T = any>(\n endpoint: string,\n data?: any,\n config?: AxiosRequestConfig & { version?: 'v2' | 'v3' }\n ): Promise<T> {\n const { version, ...axiosConfig } = config || {};\n const url = this.buildUrl(endpoint, version);\n\n try {\n const response = await this.axiosInstance.post<APIResponse<T>>(url, data, axiosConfig);\n return this.handleResponse<T>(response);\n } catch (error) {\n this.handleError(error);\n }\n }\n\n /**\n * Generic PUT request with intelligent version routing\n */\n async put<T = any>(\n endpoint: string,\n data?: any,\n config?: AxiosRequestConfig & { version?: 'v2' | 'v3' }\n ): Promise<T> {\n const { version, ...axiosConfig } = config || {};\n const url = this.buildUrl(endpoint, version);\n\n try {\n const response = await this.axiosInstance.put<APIResponse<T>>(url, data, axiosConfig);\n return this.handleResponse<T>(response);\n } catch (error) {\n this.handleError(error);\n }\n }\n\n /**\n * Generic DELETE request with intelligent version routing\n */\n async delete<T = any>(\n endpoint: string,\n config?: AxiosRequestConfig & { version?: 'v2' | 'v3' }\n ): Promise<T> {\n const { version, ...axiosConfig } = config || {};\n const url = this.buildUrl(endpoint, version);\n\n try {\n const response = await this.axiosInstance.delete<APIResponse<T>>(url, axiosConfig);\n return this.handleResponse<T>(response);\n } catch (error) {\n this.handleError(error);\n }\n }\n\n\n /*\n * Upload a file to the NDEx API with progress tracking support\n * \n * This method handles file uploads using multipart/form-data encoding and supports\n * various input types for maximum flexibility across different environments.\n * \n * @template T - The expected response type from the API\n * @param endpoint - API endpoint path (e.g., 'networks' for network upload)\n * @param file - File data to upload. Supports multiple input types:\n * - `File` (browser): HTML5 File object from file input or drag-and-drop\n * - `Blob` (browser): Binary data as Blob object\n * - `Buffer` (Node.js): Binary data as Buffer for server-side uploads\n * - `string`: Text content that will be converted to Blob (useful for CX/CX2 JSON)\n * @param options - Upload configuration options\n *\n * @param options.contentType - MIME type for string content (default: 'application/json')\n * @param options.onProgress - Progress callback that receives percentage (0-100)\n * Called periodically during upload with current progress\n * @param options.version - API version to use ('v2' or 'v3', defaults to 'v2')\n * \n * @returns Promise resolving to upload result\n * \n * @example\n * ```typescript\n * // Upload a File object from file input (browser)\n * const fileInput = document.getElementById('file') as HTMLInputElement;\n * const file = fileInput.files[0];\n * const result = await httpService.uploadFile('networks', file, {\n * filename: 'my-network.cx2',\n * onProgress: (progress) => console.log(`Upload: ${progress}%`),\n * version: 'v3'\n * });\n * \n * // Upload CX2 network data as string\n * const cx2Data = JSON.stringify({ CXVersion: '2.0', networks: [...] });\n * const result = await httpService.uploadFile('networks', cx2Data, {\n * filename: 'network.cx2',\n * contentType: 'application/json',\n * version: 'v3'\n * });\n * \n * // Upload with progress tracking\n * const result = await httpService.uploadFile('networks', file, {\n * onProgress: (progress) => {\n * progressBar.style.width = `${progress}%`;\n * console.log(`Uploading: ${progress}%`);\n * }\n * });\n * ```\n * \n * @throws Will throw NDExError on network errors,\n * server errors, or invalid file data\n * \n * @note The Content-Type header is automatically set to 'multipart/form-data'\n * and Axios will handle the boundary parameter automatically\n */\n async uploadFile<T = any>(\n endpoint: string,\n file: File | Blob | Buffer | string,\n options: {\n contentType?: string;\n onProgress?: (progress: number) => void;\n version?: 'v2' | 'v3';\n } = {}\n ): Promise<T> {\n const { version, onProgress, contentType, ...config } = options;\n const url = this.buildUrl(endpoint, version);\n\n const formData = new FormData();\n \n if (file instanceof File) {\n formData.append('file', file, file.name);\n } else if (file instanceof Blob) {\n formData.append('file', file, 'file.cx2');\n } else if (typeof file === 'string') {\n const blob = new Blob([file], { type: contentType || 'application/json' });\n formData.append('file', blob,'file.cx2');\n } else {\n // Buffer (Node.js environment)\n formData.append('file', file as any, 'file.cx2');\n }\n\n try {\n const response = await this.axiosInstance.post<APIResponse<T>>(url, formData, {\n headers: {\n 'Content-Type': 'multipart/form-data',\n },\n onUploadProgress: onProgress ? (progressEvent) => {\n const progress = Math.round((progressEvent.loaded * 100) / (progressEvent.total || 1));\n onProgress(progress);\n } : undefined,\n ...config,\n });\n\n return this.handleResponse<T>(response);\n } catch (error) {\n this.handleError(error);\n }\n }\n\n /**\n * Setup axios interceptors for debugging and retry logic\n */\n private setupInterceptors(): void {\n // Request interceptor for debugging\n this.axiosInstance.interceptors.request.use(\n (config) => {\n if (this.config.debug) {\n console.log('NDEx API Request:', {\n method: config.method?.toUpperCase(),\n url: config.url,\n headers: config.headers,\n });\n }\n return config;\n },\n (error) => {\n if (this.config.debug) {\n console.error('NDEx API Request Error:', error);\n }\n return Promise.reject(error);\n }\n );\n\n // Response interceptor for debugging\n this.axiosInstance.interceptors.response.use(\n (response) => {\n if (this.config.debug) {\n console.log('NDEx API Response:', {\n status: response.status,\n url: response.config.url,\n data: response.data,\n });\n }\n return response;\n },\n (error) => {\n if (this.config.debug) {\n console.error('NDEx API Response Error:', error.response?.data || error.message);\n }\n return Promise.reject(error);\n }\n );\n }\n\n /**\n * Handle successful API responses\n */\n private handleResponse<T>(response: AxiosResponse<any>): T {\n // Handle different response formats from NDEx API\n if (response.data && typeof response.data === 'object') {\n if ('errorCode' in response.data) {\n // NDEx error format - throw appropriate error\n this.throwNDExError(\n response.data.message || 'Unknown error occurred',\n response.status,\n response.data.errorCode || 'UNKNOWN_ERROR',\n response.data.description\n );\n }\n }\n\n // Handle wrapped vs direct responses\n const data = response.data && typeof response.data === 'object' && 'data' in response.data \n ? response.data.data \n : response.data;\n\n return data as T;\n }\n\n /**\n * Handle API errors by throwing appropriate NDEx error types\n */\n private handleError(error: any): never {\n if (error.response) {\n // Server responded with error status\n const message = error.response.data?.message || error.message;\n const errorCode = error.response.data?.errorCode || `HTTP_${error.response.status}`;\n const description = error.response.data?.description;\n \n this.throwNDExError(message, error.response.status, errorCode, description);\n } else if (error.request) {\n // Request made but no response received\n throw new NDExNetworkError('Network error - no response received', error);\n } else {\n // Something else happened\n throw new NDExError(error.message || 'Unknown error occurred', undefined, 'CLIENT_ERROR', error.toString());\n }\n }\n\n /**\n * Throw appropriate NDEx error based on status code\n */\n private throwNDExError(message: string, statusCode: number, errorCode: string, description?: string): never {\n switch (statusCode) {\n case 400:\n throw new NDExValidationError(message, statusCode);\n case 401:\n case 403:\n throw new NDExAuthError(message, statusCode);\n case 404:\n throw new NDExNotFoundError(message, statusCode);\n case 500:\n case 502:\n case 503:\n case 504:\n throw new NDExServerError(message, statusCode);\n default:\n throw new NDExError(message, statusCode, errorCode, description);\n }\n }\n\n /**\n * Update client configuration\n */\n updateConfig(newConfig: Partial<NDExClientConfig>): void {\n this.config = { ...this.config, ...newConfig };\n \n if (newConfig.baseURL) {\n this.axiosInstance.defaults.baseURL = newConfig.baseURL;\n }\n \n if (newConfig.timeout) {\n this.axiosInstance.defaults.timeout = newConfig.timeout;\n }\n\n if (newConfig.headers) {\n Object.assign(this.axiosInstance.defaults.headers, newConfig.headers);\n }\n\n // Update auth headers if auth config changed\n if ('auth' in newConfig) {\n const authHeaders = this.getAuthHeaders();\n \n // Clear existing authorization header first\n delete this.axiosInstance.defaults.headers.common['Authorization'];\n \n // Set new auth headers\n Object.assign(this.axiosInstance.defaults.headers.common, authHeaders);\n }\n }\n\n /**\n * Get current configuration\n */\n getConfig(): NDExClientConfig {\n return { ...this.config };\n }\n\n /**\n * Get current authentication type\n * @returns The type of authentication configured ('basic' | 'oauth'), or undefined if no auth is configured\n */\n getAuthType(): 'basic' | 'oauth' | undefined {\n return this.config.auth?.type;\n }\n\n /**\n * Get ID token from OAuth authentication\n * @returns The ID token if OAuth auth is configured, undefined otherwise\n */\n getIdToken(): string | undefined {\n return this.config.auth?.type === 'oauth' ? this.config.auth.idToken : undefined;\n }\n\n /**\n * Set ID token for OAuth authentication\n * Creates OAuth auth configuration if no auth is currently configured\n * @param idToken - The ID token to set\n */\n setIdToken(idToken: string): void {\n this.updateConfig({\n auth: { type: 'oauth', idToken }\n });\n }\n}\n","/**\n * NDEx Client Library - Modern TypeScript Implementation\n * \n * A comprehensive, modern TypeScript client for the NDEx (Network Data Exchange) API.\n * Supports both v2 and v3 APIs with intelligent version routing, native CX2 format support,\n * and provides a clean, type-safe interface for network operations.\n */\n\n// Core Types\nexport * from './types';\n\n// Models\nexport { CX2Network } from './models/CX2Network';\n\n// Core Services\nexport { NetworkServiceV2 } from './services/NetworkServiceV2';\nexport { NetworkServiceV3 } from './services/NetworkServiceV3';\nexport { UnifiedNetworkService } from './services/UnifiedNetworkService';\nexport { FilesService } from './services/FilesService';\nexport { WorkspaceService } from './services/WorkspaceService';\nexport { UserService } from './services/UserService';\nexport { AdminService } from './services/AdminService';\nexport { CyNDExService } from './services/CyNDExService';\n\n// Backward compatibility alias\nexport { CyNDExService as CyNDEx } from './services/CyNDExService';\n\n// Legacy compatibility exports - temporarily commented out for test setup\n// TODO: Fix ES module compatibility for NDEx.js and CyNDEx.js\n// export { default as NDEx } from './NDEx.js';\n// export { default as CyNDEx } from './CyNDEx.js';\n\n// Main Client Class\nimport { HTTPService } from './services/HTTPService';\nimport { UnifiedNetworkService } from './services/UnifiedNetworkService';\nimport { FilesService } from './services/FilesService';\nimport { WorkspaceService } from './services/WorkspaceService';\nimport { UserService } from './services/UserService';\nimport { AdminService } from './services/AdminService';\nimport { NDExClientConfig, BasicAuth, OAuthAuth } from './types';\n\n/**\n * NDExClient - Main client class for NDEx API operations\n * \n * Provides a unified interface for all NDEx operations with intelligent\n * version routing between v2 and v3 APIs.\n * \n * @example\n * ```typescript\n * // Basic usage\n * const client = new NDExClient({\n * baseURL: 'https://www.ndexbio.org',\n * debug: true\n * });\n * \n * // Authenticate\n * await client.user.authenticate({ username: 'user', password: 'pass' });\n * \n * // Search networks\n * const results = await client.networks.searchNetworks({ searchString: 'pathway' });\n * \n * // Get network as CX2\n * const network = await client.networks.getNetworkAsCX2Object('network-uuid');\n * \n * // User operations\n * const profile = await client.user.getCurrentUser();\n * \n * // Admin operations (requires admin privileges)\n * const stats = await client.admin.getSystemStats();\n * ```\n */\nexport class NDExClient {\n private httpService: HTTPService;\n \n /** Network operations with intelligent v2/v3 routing */\n public readonly networks: UnifiedNetworkService;\n \n /** File upload/download and task management */\n public readonly files: FilesService;\n \n /** Workspace operations (deprecated - most functionality moved to other services) */\n public readonly workspace: WorkspaceService;\n \n /** User authentication and management */\n public readonly user: UserService;\n \n /** System administration operations */\n public readonly admin: AdminService;\n\n constructor(config: NDExClientConfig = {}) {\n this.httpService = new HTTPService(config);\n this.networks = new UnifiedNetworkService(this.httpService);\n this.files = new FilesService(this.httpService);\n this.workspace = new WorkspaceService(this.httpService);\n this.user = new UserService(this.httpService);\n this.admin = new AdminService(this.httpService);\n }\n\n\n /**\n * Clear authentication\n */\n logout(): void {\n this.httpService.updateConfig({ auth: undefined });\n }\n\n /**\n * Get server status information\n * Can be called by authenticated or anonymous users.\n * @param format - Optional format parameter. Use 'full' for detailed information including properties and importers/exporters\n * @returns Server status including network/user counts and optional server details\n */\n async getServerStatus(format?: 'full'): Promise<{\n message: string;\n properties?: {\n ServerVersion: string;\n Build: string;\n ServerResultLimit: string;\n ImporterExporters: Array<{\n importer: boolean;\n exporter: boolean;\n fileExtension: string;\n name: string;\n description: string;\n }>;\n };\n networkCount: number;\n userCount: number;\n groupCount?: number;\n }> {\n const params = new URLSearchParams();\n if (format) {\n params.append('format', format);\n }\n\n const endpoint = `admin/status${params.toString() ? `?${params.toString()}` : ''}`;\n return this.httpService.get(endpoint);\n }\n\n /**\n * Check if client has valid authentication information configured\n * @returns true if auth is a valid BasicAuth or OAuthAuth object, false otherwise\n */\n hasAuthInfo(): boolean {\n const auth = this.httpService.getConfig().auth;\n if (!auth) return false;\n \n // Check for BasicAuth structure\n if (auth.type === 'basic') {\n return !!(auth as BasicAuth).username && !!(auth as BasicAuth).password;\n }\n \n // Check for OAuthAuth structure \n if (auth.type === 'oauth') {\n return !!(auth as OAuthAuth).idToken;\n }\n \n return false;\n }\n\n /**\n * Update client configuration\n */\n updateConfig(config: Partial<NDExClientConfig>): void {\n this.httpService.updateConfig(config);\n }\n\n /**\n * Get current client configuration\n */\n getConfig(): NDExClientConfig {\n return this.httpService.getConfig();\n }\n\n\n /**\n * Access to low-level HTTP service for advanced usage\n */\n get http(): HTTPService {\n return this.httpService;\n }\n\n /**\n * Access to version-specific network services for advanced usage\n */\n get v2() {\n return {\n networks: this.networks.v2,\n };\n }\n\n get v3() {\n return {\n networks: this.networks.v3,\n };\n }\n\n}\n\n// Main export - New modern client (named export for better tree-shaking)\n// Users should import as: import { NDExClient } from '@js4cytoscape/ndex-client'\n\n// Version information - imported from package.json to ensure consistency\nimport { version as packageVersion } from '../package.json';\n\n/**\n * Library version string imported from package.json\n * \n * Provides programmatic access to the current library version for:\n * - Runtime version checking and validation\n * - Debugging and error reporting\n * - Logging and telemetry\n * - Version-dependent feature detection\n * \n * @example\n * ```typescript\n * import { NDExClient, version } from '@js4cytoscape/ndex-client';\n * \n * console.log(`Using NDEx Client v${version}`);\n * \n * // In error reports\n * const errorReport = {\n * error: err.message,\n * libraryVersion: version,\n * timestamp: new Date().toISOString()\n * };\n * ```\n */\nexport const version = packageVersion;\n\n"]}