feat: add UShER tree field to open data

chaoran-chen · chaoran-chen · commit 946d02594f10 · 2025-07-16T16:13:46.000+02:00
diff --git a/src/main/kotlin/org/genspectrum/ingest/proc/JoinSC2NextstrainOpenData.kt b/src/main/kotlin/org/genspectrum/ingest/proc/JoinSC2NextstrainOpenData.kt
@@ -72,6 +72,7 @@ fun joinSC2NextstrainOpenData(
             aminoAcidInsertions,
         )
         clean(joined)
+        addUsherTreeField(joined)
         if (joined.metadata["strain"] == null) {
             continue
         }
@@ -216,3 +217,7 @@ private fun clean(entry: MutableEntry) {
         metadata["nextcladeDatasetVersion"] = null
     }
 }
+
+fun addUsherTreeField(joined: MutableEntry) {
+    joined.metadata["usherTree"] = joined.metadata["genbankAccessionRev"]
+}

Original file line number	Diff line number	Diff line change
`@@ -72,6 +72,7 @@ fun joinSC2NextstrainOpenData(`
`72`	`72`	`aminoAcidInsertions,`
`73`	`73`	`)`
`74`	`74`	`clean(joined)`
	`75`	`+ addUsherTreeField(joined)`
`75`	`76`	`if (joined.metadata["strain"] == null) {`
`76`	`77`	`continue`
`77`	`78`	`}`
`@@ -216,3 +217,7 @@ private fun clean(entry: MutableEntry) {`
`216`	`217`	`metadata["nextcladeDatasetVersion"] = null`
`217`	`218`	`}`
`218`	`219`	`}`
	`220`	`+`
	`221`	`+fun addUsherTreeField(joined: MutableEntry) {`
	`222`	`+ joined.metadata["usherTree"] = joined.metadata["genbankAccessionRev"]`
	`223`	`+}`