Merge branch 'main' of https://github.com/biothings/biomedical_id_res…

…olver.js into dev
biothings · Mar 8, 2024 · 1925e24 · 1925e24
2 parents ce85aa5 + e375b08
commit 1925e24
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Showing 2 changed files with 25 additions and 14 deletions.
diff --git a/src/attrs.ts b/src/attrs.ts
@@ -117,9 +117,8 @@ function buildOneQuery(
   const returnFields = idReturnFields + attrReturnFields;
   const scopes = getInputScopes(metadata.mapping, prefix);
   debug(`inputs ${inputs}`);
-  const userAgent = `BTE/${process.env.NODE_ENV === 'production' ? 'prod' : 'dev'} Node/${process.version} ${
-    process.platform
-  }`;
+  const userAgent = `BTE/${process.env.NODE_ENV === 'production' ? 'prod' : 'dev'} Node/${process.version} ${process.platform
+    }`;
   return axios({
     method: 'post',
     url: metadata.url,
@@ -136,10 +135,17 @@ function buildOneQuery(
       'content-type': 'application/json',
       'User-Agent': userAgent,
     },
-  }).then((response) => getDBIDs(prefix, semanticType, response.data));
+  })
+    .then((response) => getDBIDs(prefix, semanticType, response.data))
+    .catch(() => undefined);
 }
 
-function buildQueries(metadata: MetaDataObject, prefix: string, inputs: string[], semanticType: string) {
+function buildQueries(
+  metadata: MetaDataObject,
+  prefix: string,
+  inputs: string[],
+  semanticType: string,
+): Promise<IndividualResolverOutput>[] {
   if (inputs.length > MAX_BIOTHINGS_INPUT_SIZE) {
     return _.chunk(inputs, MAX_BIOTHINGS_INPUT_SIZE).map((batch) =>
       buildOneQuery(metadata, prefix, batch, semanticType),
@@ -153,9 +159,9 @@ function getAPIMetaData(semanticType: string) {
   return APIMETA[semanticType];
 }
 
-function build(semanticType: string, curies: string[]) {
+function build(semanticType: string, curies: string[]): Promise<IndividualResolverOutput>[] {
   const grped = groupCuriesByPrefix(curies);
-  return Object.keys(grped).reduce((prev, current) => {
+  return Object.keys(grped).reduce((prev: Promise<IndividualResolverOutput>[], current) => {
     prev = [...prev, ...buildQueries(getAPIMetaData(semanticType), current, grped[current], semanticType)];
     return prev;
   }, []);
@@ -177,7 +183,7 @@ function getSupportedType(category: string): string {
 
 export async function _getAttributes(idsByType: object): Promise<any> {
   debug(`Adding attributes of ${JSON.stringify(idsByType)}`);
-  let promises = [];
+  let promises: Promise<IndividualResolverOutput>[] = [];
   for (const type in idsByType) {
     const ids = idsByType[type];
     const supportedType = getSupportedType(type);
@@ -190,9 +196,10 @@ export async function _getAttributes(idsByType: object): Promise<any> {
       }
     }
   }
-  let res: any = await Promise.all(promises);
+  let res: IndividualResolverOutput[] = await Promise.all(promises);
   let merged = {};
   res.forEach((res_obj) => {
+    if (typeof res_obj === 'undefined') return;
     merged = {
       ...merged,
       ...res_obj,

diff --git a/src/sri.ts b/src/sri.ts
@@ -19,7 +19,7 @@ axiosRetry(axios, {
 
 /** convert object of arrays into array of unique IDs */
 function combineInputs(userInput: ResolverInput): string[] {
-  const result = Object.keys(userInput).reduce(function(r, k) {
+  const result = Object.keys(userInput).reduce(function (r, k) {
     return r.concat(userInput[k]);
   }, []);
   return [...new Set(result)];
@@ -32,9 +32,9 @@ function combineInputs(userInput: ResolverInput): string[] {
 async function query(api_input: string[]) {
   const url = {
     dev: 'https://nodenormalization-sri.renci.org/get_normalized_nodes',
-    ci: 'https://nodenorm.ci.transltr.io/1.3/get_normalized_nodes',
-    test: 'https://nodenorm.test.transltr.io/1.3/get_normalized_nodes',
-    prod: 'https://nodenorm.transltr.io/1.3/get_normalized_nodes',
+    ci: 'https://nodenorm.ci.transltr.io/get_normalized_nodes',
+    test: 'https://nodenorm.test.transltr.io/get_normalized_nodes',
+    prod: 'https://nodenorm.transltr.io/get_normalized_nodes',
   }[process.env.INSTANCE_ENV ?? 'prod'];
 
   const chunked_input = _.chunk(api_input, 1000);
@@ -44,7 +44,11 @@ async function query(api_input: string[]) {
       `Node/${process.version} ${process.platform}`,
     ].join(' ');
     const axios_queries = chunked_input.map((input) => {
-      return axios.post(url, { curies: input }, { headers: { 'User-Agent': userAgent } });
+      return axios.post(
+        url,
+        { curies: input, conflate: true, drug_chemical_conflate: true },
+        { headers: { 'User-Agent': userAgent } },
+      );
     });
     //convert res array into single object with all curies
     let res = await Promise.all(axios_queries);