From f3d9323d79cb64b669c206f54fd9db1ae4178a70 Mon Sep 17 00:00:00 2001
From: Colin <colin.diesh@gmail.com>
Date: Thu, 19 Sep 2024 09:48:04 -0400
Subject: [PATCH] Fix plaintext indexing desktop

---
 packages/text-indexing/src/TextIndexing.ts    | 36 +++++++++++++++++--
 .../jbrowse-desktop/src/indexJobsModel.ts     |  1 +
 2 files changed, 34 insertions(+), 3 deletions(-)

diff --git a/packages/text-indexing/src/TextIndexing.ts b/packages/text-indexing/src/TextIndexing.ts
index b0f3573cc8..25d940ab9c 100644
--- a/packages/text-indexing/src/TextIndexing.ts
+++ b/packages/text-indexing/src/TextIndexing.ts
@@ -215,7 +215,22 @@ async function* indexFiles({
       indexingAttributes: attributesToIndex = idx1,
     } = textSearching || {}
     let myTotalBytes: number | undefined
-    if (type === 'Gff3TabixAdapter' || type === 'Gff3Adapter') {
+    if (type === 'Gff3Adapter') {
+      yield* indexGff3({
+        config: track,
+        attributesToIndex,
+        inLocation: getLoc('gffLocation', track),
+        outDir,
+        featureTypesToExclude,
+        onStart: totalBytes => {
+          myTotalBytes = totalBytes
+        },
+        onUpdate: progressBytes => {
+          statusCallback(`${progressBytes}/${myTotalBytes}`)
+        },
+      })
+    }
+    if (type === 'Gff3TabixAdapter') {
       yield* indexGff3({
         config: track,
         attributesToIndex,
@@ -229,7 +244,20 @@ async function* indexFiles({
           statusCallback(`${progressBytes}/${myTotalBytes}`)
         },
       })
-    } else if (type === 'VcfTabixAdapter' || type === 'VcfAdapter') {
+    } else if (type === 'VcfAdapter') {
+      yield* indexVcf({
+        config: track,
+        attributesToIndex,
+        inLocation: getLoc('vcfLocation', track),
+        outDir,
+        onStart: totalBytes => {
+          myTotalBytes = totalBytes
+        },
+        onUpdate: progressBytes => {
+          statusCallback(`${progressBytes}/${myTotalBytes}`)
+        },
+      })
+    } else if (type === 'VcfTabixAdapter') {
       yield* indexVcf({
         config: track,
         attributesToIndex,
@@ -252,7 +280,9 @@ function getLoc(attr: string, config: Track) {
     | { uri: string; localPath: string }
     | undefined
   if (!elt) {
-    throw new Error('none')
+    throw new Error(
+      `can't get find ${attr} from ${config.adapter} for text indexing`,
+    )
   }
   return elt.uri || elt.localPath
 }
diff --git a/products/jbrowse-desktop/src/indexJobsModel.ts b/products/jbrowse-desktop/src/indexJobsModel.ts
index eb3c7b0f0c..02196dd7a5 100644
--- a/products/jbrowse-desktop/src/indexJobsModel.ts
+++ b/products/jbrowse-desktop/src/indexJobsModel.ts
@@ -313,6 +313,7 @@ export default function jobsModelFactory(_pluginManager: PluginManager) {
             }
           }
         } catch (e) {
+          console.error(e)
           if (isAbortException(e)) {
             self.session?.notify('Cancelled job', 'info')
           } else {