jbrowse-plugin-msaview 2.0.2 → 2.0.4

package/src/utils/msa.ts

@@ -98,6 +98,7 @@ async function wait({
   algorithm: string
   onProgress: (arg: string) => void
 }) {
+  // eslint-disable-next-line @typescript-eslint/no-unnecessary-condition
   while (true) {
     for (let i = 0; i < 10; i++) {
       await timeout(1000)
@@ -107,6 +108,8 @@ async function wait({
 
     if (result === 'FINISHED') {
       break
+    } else if (result.includes('FAILURE')) {
+      throw new Error(`Failed to run: jobId ${jobId}`)
     }
   }
 }

package/src/utils/ncbiBlast.ts

@@ -23,15 +23,26 @@ export async function queryBlast({
   })
   onRid(rid)
   await waitForRid({ rid, onProgress })
-  const ret = await jsonfetch(
+  const ret = (await jsonfetch(
     `${BLAST_URL}?CMD=Get&RID=${rid}&FORMAT_TYPE=JSON2_S&FORMAT_OBJECT=Alignment`,
-  )
-  const hits = ret.BlastOutput2[0].report.results.search.hits as {
-    description: { accession: string; id: string; sciname: string }[]
-    hsps: { hseq: string }[]
-  }[]
-
-  return { rid, hits }
+  )) as {
+    BlastOutput2: {
+      report: {
+        results: {
+          search: {
+            hits: {
+              description: { accession: string; id: string; sciname: string }[]
+              hsps: { hseq: string }[]
+            }[]
+          }
+        }
+      }
+    }[]
+  }
+  return {
+    rid,
+    hits: ret.BlastOutput2[0]?.report.results.search.hits ?? [],
+  }
 }
 
 async function initialQuery({
@@ -62,8 +73,8 @@ async function initialQuery({
   // the initial submission/query to the BLAST "REST API" does not return JSON
   // as a response (e.g. FORMAT_TYPE=JSON does not work), so the RID is
   // literally parsed from the text of the HTML that is returned
-  const rid = res.match(/^    RID = (.*$)/m)?.[1]
-  const rtoe = res.match(/^    RTOE = (.*$)/m)?.[1]
+  const rid = /^ {4}RID = (.*$)/m.exec(res)?.[1]
+  const rtoe = /^ {4}RTOE = (.*$)/m.exec(res)?.[1]
 
   if (!rid) {
     throw new Error('Failed to get RID from BLAST request')
@@ -78,6 +89,7 @@ async function waitForRid({
   rid: string
   onProgress: (arg: string) => void
 }) {
+  // eslint-disable-next-line @typescript-eslint/no-unnecessary-condition
   while (true) {
     const iter = 20
     for (let i = 0; i < iter; i++) {