Merge pull request #23 from biothings/workflow-id

Use correct workflow id conditionally
biothings · Apr 12, 2024 · 4b89202 · 4b89202
2 parents 13f2834 + 6eb4390
commit 4b89202
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Showing 5 changed files with 34 additions and 25 deletions.
diff --git a/src/controllers/async/asyncquery.ts b/src/controllers/async/asyncquery.ts
@@ -194,7 +194,7 @@ export async function asyncqueryResponse(
  status: "Failed",
  schema_version: global.SCHEMA_VERSION,
  biolink_version: global.BIOLINK_VERSION,
- workflow: [{ id: "lookup" }],
+ workflow: [{ id: handler.options.teamName || handler.options.smartAPIID ? "lookup" : "lookup_and_score" }],
  description: (e as Error).toString(),
  trace: process.env.NODE_ENV === "production" ? undefined : (e as Error).stack,
  logs: handler.logs,

diff --git a/src/controllers/async/asyncquery_queue.ts b/src/controllers/async/asyncquery_queue.ts
@@ -55,26 +55,35 @@ export function getQueryQueue(name: string): BullQueue {
  }
 
  global.queryQueue[name] = new Queue(name, process.env.REDIS_HOST ?? "redis://127.0.0.1:6379", details)
- .on("error", function(error) {
+ .on("error", function (error) {
  console.log("err", error);
  })
- .on("failed", async function(job: BullJob, error) {
+ .on("failed", async function (job: BullJob, error) {
  debug(`Async job ${job.id} failed with error ${error.message}`);
  try {
  job.data.abortController.abort();
  } catch (error) {
  debug(error);
  }
  if (job.data.callback_url) {
- const logs: TrapiLog[] = await global.queryQueue[name]?.getJobLogs(job.id)?.logs?.map((log: string) => JSON.parse(log));
+ const logs: TrapiLog[] = await global.queryQueue[name]
+ ?.getJobLogs(job.id)
+ ?.logs?.map((log: string) => JSON.parse(log));
  try {
  await axios({
  method: "post",
  url: job.data.callback_url,
  data: {
  schema_version: global.SCHEMA_VERSION,
  biolink_version: global.BIOLINK_VERSION,
- workflow: [{ id: "lookup" }],
+ workflow: [
+ {
+ id:
+ job.data.route.includes(":smartapi_id") || job.data.route.includes(":team_name")
+ ? "lookup"
+ : "lookup_and_score",
+ },
+ ],
  logs: logs,
  message: {
  query_graph: job.data.queryGraph,

diff --git a/src/controllers/cron/update_local_smartapi.ts b/src/controllers/cron/update_local_smartapi.ts
@@ -217,7 +217,7 @@ function getPredicatesFromGraphData(predicate_endpoint: string, data) {
 
  const addNewPredicates = edge => {
  if (edge.knowledge_types && Array.isArray(edge.knowledge_types)) {
- if (!edge.knowledge_types.includes("lookup")) {
+ if (!(edge.knowledge_types.includes("lookup"))) {
  return;
  }
  }

diff --git a/src/controllers/meta_knowledge_graph.ts b/src/controllers/meta_knowledge_graph.ts
@@ -171,21 +171,21 @@ export default class MetaKnowledgeGraphHandler {
  object: output,
  qualifiers: pred.qualifiers
  ? Object.entries(pred.qualifiers).map(([qual, val]) => {
-  if (!Array.isArray(val)) {
-  const [type_id, value] = this._modifyQualifierData(qual, val);
-  return { qualifier_type_id: type_id, applicable_values: [value] };
-  } else {
-  let type_id = this._modifyPredicate(qual);
-  let values = [];
-  val.forEach(curVal => {
-  const [_, value] = this._modifyQualifierData(qual, curVal);
-  values.push(value);
-  });
-  return { qualifier_type_id: type_id, applicable_values: values };
-  }
-  })
+ if (!Array.isArray(val)) {
+ const [type_id, value] = this._modifyQualifierData(qual, val);
+ return { qualifier_type_id: type_id, applicable_values: [value] };
+ } else {
+ let type_id = this._modifyPredicate(qual);
+ let values = [];
+ val.forEach(curVal => {
+ const [_, value] = this._modifyQualifierData(qual, curVal);
+ values.push(value);
+ });
+ return { qualifier_type_id: type_id, applicable_values: values };
+ }
+ })
  : undefined,
- knowledge_types: ["lookup"],
+ knowledge_types: this.smartAPIID || this.teamName ? ["lookup"] : ["lookup_and_score"],
  };
  knowledge_graph.edges.push(edge);
  edges[`${input}-${pred.predicate}-${output}`] = edge;
@@ -222,9 +222,9 @@ export default class MetaKnowledgeGraphHandler {
  object,
  qualifiers: qualifiers
  ? Object.entries(qualifiers).map(([qual, val]) => {
-  const [type_id, value] = this._modifyQualifierData(qual, val);
-  return { qualifier_type_id: type_id, applicable_values: [value] };
-  })
+ const [type_id, value] = this._modifyQualifierData(qual, val);
+ return { qualifier_type_id: type_id, applicable_values: [value] };
+ })
  : undefined,
  knowledge_types: ["inferred"],
  };

diff --git a/src/utils/common.ts b/src/utils/common.ts
@@ -31,7 +31,8 @@ export function validateWorkflow(workflow: TrapiWorkflow[] | unknown) {
  if (workflow === undefined) {
  return;
  }
- if (!Array.isArray(workflow) || workflow.length !== 1 || workflow[0].id !== "lookup") {
+
+ if (!Array.isArray(workflow) || workflow.length !== 1 || !["lookup", "lookup_and_score"].includes(workflow[0].id)) {
  throw new WorkflowError("BTE doesn't handle the operations specified in the workflow field.");
  }
 }
@@ -63,4 +64,3 @@ export function filterForLogLevel(logs: TrapiLog[], logLevel: string) {
 export function methodNotAllowed(_req: Request, res: Response, _next: NextFunction) {
  res.status(405).send();
 }
-