feat: LitVar for SeqVars (#421)

src/api/litvar/client.ts

@@ -0,0 +1,70 @@
+import { urlConfig } from '../../lib/urlConfig'
+import type { SearchResult } from './types'
+
+/**
+ * Client for the LitVar API.
+ */
+export class LitVarClient {
+  /** API base URL to use in this client instance. */
+  private apiBaseUrl: string
+
+  /**
+   * @param apiBaseUrl
+   *            API base to the backend, excluding trailing `/`.
+   *            The default is declared in '@/lib/urlConfig`.
+   */
+  constructor(apiBaseUrl?: string) {
+    if (apiBaseUrl !== undefined || urlConfig.baseUrlLitVar !== undefined) {
+      // @ts-ignore
+      this.apiBaseUrl = apiBaseUrl ?? urlConfig.baseUrlLitVar
+    } else {
+      throw new Error('Configuration error: API base URL not configured')
+    }
+  }
+
+  /**
+   * Perform search for the given HGNC symbol.
+   *
+   * @param hgncSymbol HGNC symbol to search for.
+   * @returns Promise for the search results.
+   * @throws Error if the search fails.
+   */
+  async performSearch(seqVar: string): Promise<{ [key: string]: SearchResult }> {
+    const url = `${this.apiBaseUrl}/${seqVar}`
+    const searchRes = await fetch(url, {
+      method: 'GET'
+    })
+    if (!searchRes.ok) {
+      throw new Error(`Error running LitVar search: ${searchRes.statusText}`)
+    }
+    const searchData = await searchRes.json()
+
+    // Then, extract PMID list and retrieve biocjson for the PMIDs
+    // const pmids: string[] = searchData!.results!.map((doc: any) => doc.pmid)
+    // const exportRes = await fetch(
+    //   `${this.apiBaseUrl}/publications/export/biocjson` + `?pmids=${pmids.join(',')}`
+    // )
+    // if (!exportRes.ok) {
+    //   throw new Error(`Error running LitVar export: ${exportRes.statusText}`)
+    // }
+    // const exportDataText = await exportRes.text()
+    // const exportDataLines = exportDataText.split(/\n/)
+
+    // // Zip search results and exports into searchResults
+    // const searchaResults: { [key: string]: SearchResult } = {}
+    // for (const searchDataRecord of searchData.results) {
+    //   searchResults[searchDataRecord.pmid] = {
+    //     searchResult: searchDataRecord,
+    //     abstract: undefined
+    //   }
+    // }
+    // for (const exportDataLine of exportDataLines) {
+    //   if (exportDataLine) {
+    //     const exportData = JSON.parse(exportDataLine)
+    //     searchResults[exportData.pmid].abstract = exportData
+    //   }
+    // }
+
+    return searchData
+  }
+}

src/api/litvar/index.ts

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+export * from './client'
+export * from './types'

src/api/litvar/types.ts

@@ -0,0 +1,2 @@
+/** Interface for search result entry plus PubMed abstract. */
+export interface SearchResult {}