Merge pull request #114 from biothings/parallel-creative

allow sri queries to be aborted
biothings · Oct 11, 2024 · 3761d62 · 3761d62
2 parents 8c1f094 + 8aaaf09
commit 3761d62
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Showing 4 changed files with 21 additions and 17 deletions.
diff --git a/package.json b/package.json
@@ -53,7 +53,7 @@
     "@commitlint/cli": "^17.8.1",
     "@commitlint/config-conventional": "^11.0.0",
     "axios-retry": "^3.8.0",
-    "axios": "^0.21.4",
+    "axios": "^1.7.2",
     "biolink-model": "workspace:../biolink-model",
     "debug": "^4.3.4",
     "husky": "^8.0.3",

diff --git a/src/attrs.ts b/src/attrs.ts
@@ -108,6 +108,7 @@ function buildOneQuery(
   prefix: string,
   inputs: string[],
   semanticType: string,
+  abortSignal?: AbortSignal
 ): Promise<IndividualResolverOutput> {
   const idReturnFields = getReturnFields(metadata.mapping);
   let attrReturnFields = '';
@@ -135,8 +136,9 @@ function buildOneQuery(
       'content-type': 'application/json',
       'User-Agent': userAgent,
     },
+    signal: abortSignal,
   })
-    .then((response) => getDBIDs(prefix, semanticType, response.data))
+    .then((response) => getDBIDs(prefix, semanticType, response.data as any))
     .catch(() => undefined);
 }
 
@@ -145,24 +147,25 @@ function buildQueries(
   prefix: string,
   inputs: string[],
   semanticType: string,
+  abortSignal?: AbortSignal
 ): Promise<IndividualResolverOutput>[] {
   if (inputs.length > MAX_BIOTHINGS_INPUT_SIZE) {
     return _.chunk(inputs, MAX_BIOTHINGS_INPUT_SIZE).map((batch) =>
-      buildOneQuery(metadata, prefix, batch, semanticType),
+      buildOneQuery(metadata, prefix, batch, semanticType, abortSignal),
     );
   } else {
-    return [buildOneQuery(metadata, prefix, inputs, semanticType)];
+    return [buildOneQuery(metadata, prefix, inputs, semanticType, abortSignal)];
   }
 }
 
 function getAPIMetaData(semanticType: string) {
   return APIMETA[semanticType];
 }
 
-function build(semanticType: string, curies: string[]): Promise<IndividualResolverOutput>[] {
+function build(semanticType: string, curies: string[], abortSignal?: AbortSignal): Promise<IndividualResolverOutput>[] {
   const grped = groupCuriesByPrefix(curies);
   return Object.keys(grped).reduce((prev: Promise<IndividualResolverOutput>[], current) => {
-    prev = [...prev, ...buildQueries(getAPIMetaData(semanticType), current, grped[current], semanticType)];
+    prev = [...prev, ...buildQueries(getAPIMetaData(semanticType), current, grped[current], semanticType, abortSignal)];
     return prev;
   }, []);
 }
@@ -181,7 +184,7 @@ function getSupportedType(category: string): string {
   return '';
 }
 
-export async function _getAttributes(idsByType: object): Promise<any> {
+export async function _getAttributes(idsByType: object, abortSignal?: AbortSignal): Promise<any> {
   debug(`Adding attributes of ${JSON.stringify(idsByType)}`);
   let promises: Promise<IndividualResolverOutput>[] = [];
   for (const type in idsByType) {
@@ -190,7 +193,7 @@ export async function _getAttributes(idsByType: object): Promise<any> {
     if (ids) {
       if (supportedType) {
         debug(`Processing attributes of: ${JSON.stringify(type)}`);
-        promises = [...promises, ...build(supportedType, ids)];
+        promises = [...promises, ...build(supportedType, ids, abortSignal)];
       } else {
         debug(`Cannot get attributes of type: ${JSON.stringify(type)}`);
       }

diff --git a/src/index.ts b/src/index.ts
@@ -34,12 +34,12 @@ export class Resolver implements IResolver {
   }
 }
 
-export async function resolveSRI(userInput: ResolverInput): Promise<SRIResolverOutput> {
-  return await _resolveSRI(userInput);
+export async function resolveSRI(userInput: ResolverInput, abortSignal?: AbortSignal): Promise<SRIResolverOutput> {
+  return await _resolveSRI(userInput, abortSignal);
 }
 
-export async function getAttributes(idsByType: object): Promise<any> {
-  return await _getAttributes(idsByType);
+export async function getAttributes(idsByType: object, abortSignal?: AbortSignal): Promise<any> {
+  return await _getAttributes(idsByType, abortSignal);
 }
 
 export const METADATA = APIMETA;

diff --git a/src/sri.ts b/src/sri.ts
@@ -29,7 +29,7 @@ function combineInputs(userInput: ResolverInput): string[] {
  * input: array of curies
  * handles querying and batching of inputs
  */
-async function query(api_input: string[]) {
+async function query(api_input: string[], abortSignal?: AbortSignal) {
   const url = {
     dev: 'https://nodenormalization-sri.renci.org/get_normalized_nodes',
     ci: 'https://nodenorm.ci.transltr.io/get_normalized_nodes',
@@ -47,7 +47,7 @@ async function query(api_input: string[]) {
       return axios.post(
         url,
         { curies: input, conflate: true, drug_chemical_conflate: true },
-        { headers: { 'User-Agent': userAgent } },
+        { headers: { 'User-Agent': userAgent }, signal: abortSignal },
       );
     });
     //convert res array into single object with all curies
@@ -57,7 +57,8 @@ async function query(api_input: string[]) {
     });
     return Object.assign({}, ...res);
   } catch (err) {
-    throw new SRINodeNormFailure(`SRI resolver failed: ${err.message}`);
+    // throw new SRINodeNormFailure(`SRI resolver failed: ${err.message}`);
+    return Object.fromEntries(api_input.map((curie) => [curie, null]));
   }
 }
 
@@ -135,10 +136,10 @@ function mapInputSemanticTypes(originalInput: ResolverInput, result: SRIResolver
   return result;
 }
 
-export async function _resolveSRI(userInput: ResolverInput): Promise<SRIResolverOutput> {
+export async function _resolveSRI(userInput: ResolverInput, abortSignal?: AbortSignal): Promise<SRIResolverOutput> {
   const uniqueInputIDs = combineInputs(userInput);
 
-  let queryResults = await query(uniqueInputIDs);
+  let queryResults = await query(uniqueInputIDs, abortSignal);
 
   queryResults = transformResults(queryResults);