Allow selecting nr or nr_clustered_seq

GMOD · Jan 29, 2024 · 8656751 · 8656751
1 parent 9124cce
commit 8656751
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Showing 3 changed files with 62 additions and 52 deletions.
diff --git a/src/LaunchMsaView/components/NCBIBlastPanel.tsx b/src/LaunchMsaView/components/NCBIBlastPanel.tsx
@@ -57,7 +57,7 @@ const NcbiBlastPanel = observer(function ({
   const [error, setError] = useState<unknown>()
   const [rid, setRid] = useState<string>()
   const [progress, setProgress] = useState('')
-  const database = 'nr_cluster_seq'
+  const [database, setDatabase] = useState('nr_clustered_seq')
   const program = 'blastp'
 
   const options = getTranscriptFeatures(feature)
@@ -76,6 +76,7 @@ const NcbiBlastPanel = observer(function ({
       : ''
 
   const e = error || error2
+  const databaseOptions = ['nr', 'nr_clustered_seq']
   return (
     <DialogContent className={classes.dialogContent}>
       {e ? <ErrorMessage error={e} /> : null}
@@ -89,22 +90,34 @@ const NcbiBlastPanel = observer(function ({
         </Typography>
       ) : null}
 
-      <Typography>
-        Querying {database} with {program}:
-      </Typography>
-
-      <TextField
-        value={userSelection}
-        onChange={event => setUserSelection(event.target.value)}
-        label="Choose isoform to BLAST"
-        select
-      >
-        {options.map(val => (
-          <MenuItem value={getId(val)} key={val.id()}>
-            {getGeneDisplayName(feature)} - {getTranscriptDisplayName(val)}
-          </MenuItem>
-        ))}
-      </TextField>
+      <div>
+        <TextField
+          value={database}
+          onChange={event => setDatabase(event.target.value)}
+          label="BLAST database"
+          select
+        >
+          {databaseOptions.map(val => (
+            <MenuItem value={val} key={val}>
+              {val}
+            </MenuItem>
+          ))}
+        </TextField>
+      </div>
+      <div>
+        <TextField
+          value={userSelection}
+          onChange={event => setUserSelection(event.target.value)}
+          label="Choose isoform to BLAST"
+          select
+        >
+          {options.map(val => (
+            <MenuItem value={getId(val)} key={val.id()}>
+              {getGeneDisplayName(feature)} - {getTranscriptDisplayName(val)}
+            </MenuItem>
+          ))}
+        </TextField>
+      </div>
 
       <TextField
         variant="outlined"
@@ -134,8 +147,6 @@ const NcbiBlastPanel = observer(function ({
             ;(async () => {
               try {
                 setError(undefined)
-                setRid(undefined)
-
                 const res = await queryBlast({
                   query: protein,
                   database,

diff --git a/src/LaunchMsaView/components/useFeatureSequence.ts b/src/LaunchMsaView/components/useFeatureSequence.ts
@@ -28,7 +28,6 @@ export function useFeatureSequence({
   const [sequence, setSequence] = useState<SeqState | ErrorState>()
   const [error, setError] = useState<unknown>()
   useEffect(() => {
-    console.log('here')
     if (view) {
       const { assemblyManager, rpcManager } = getSession(view)
       const [assemblyName] = view?.assemblyNames || []

diff --git a/yarn.lock b/yarn.lock
@@ -1268,27 +1268,27 @@
   dependencies:
     "@floating-ui/utils" "^0.2.1"
 
-"@floating-ui/dom@^1.6.0":
-  version "1.6.0"
-  resolved "https://registry.yarnpkg.com/@floating-ui/dom/-/dom-1.6.0.tgz#282f31c5c7d2aaef3999e09f2c06280a020364d1"
-  integrity sha512-SZ0BEXzsaaS6THZfZJUcAobbZTD+MvfGM42bxgeg0Tnkp4/an/avqwAXiVLsFtIBZtfsx3Ymvwx0+KnnhdA/9g==
+"@floating-ui/dom@^1.6.1":
+  version "1.6.1"
+  resolved "https://registry.yarnpkg.com/@floating-ui/dom/-/dom-1.6.1.tgz#d552e8444f77f2d88534372369b3771dc3a2fa5d"
+  integrity sha512-iA8qE43/H5iGozC3W0YSnVSW42Vh522yyM1gj+BqRwVsTNOyr231PsXDaV04yT39PsO0QL2QpbI/M0ZaLUQgRQ==
   dependencies:
     "@floating-ui/core" "^1.6.0"
     "@floating-ui/utils" "^0.2.1"
 
-"@floating-ui/react-dom@^2.0.6", "@floating-ui/react-dom@^2.0.7":
-  version "2.0.7"
-  resolved "https://registry.yarnpkg.com/@floating-ui/react-dom/-/react-dom-2.0.7.tgz#873e0a55a25d8ddbbccd159d6ab4a4b98eb05494"
-  integrity sha512-B5GJxKUyPcGsvE1vua+Abvw0t6zVMyTbtG+Jk7BoI4hfc5Ahv50dstRIAn0nS0274kR9gnKwxIXyGA8EzBZJrA==
+"@floating-ui/react-dom@^2.0.6", "@floating-ui/react-dom@^2.0.8":
+  version "2.0.8"
+  resolved "https://registry.yarnpkg.com/@floating-ui/react-dom/-/react-dom-2.0.8.tgz#afc24f9756d1b433e1fe0d047c24bd4d9cefaa5d"
+  integrity sha512-HOdqOt3R3OGeTKidaLvJKcgg75S6tibQ3Tif4eyd91QnIJWr0NLvoXFpJA/j8HqkFSL68GDca9AuyWEHlhyClw==
   dependencies:
-    "@floating-ui/dom" "^1.6.0"
+    "@floating-ui/dom" "^1.6.1"
 
 "@floating-ui/react@^0.26.3":
-  version "0.26.7"
-  resolved "https://registry.yarnpkg.com/@floating-ui/react/-/react-0.26.7.tgz#0565521962402e4fb87a6f47bdd724ea5d74b207"
-  integrity sha512-0uMI9IBJBPPt8N+8uRg4gazJvQReWTu/fVUHHLfAOuy1WB6f242jtjWm52hLJG8nzuZVuU+2crW4lJbJQoqeIA==
+  version "0.26.8"
+  resolved "https://registry.yarnpkg.com/@floating-ui/react/-/react-0.26.8.tgz#9f8dc9d21aa35456ccc32b536d853d365ce8b9d9"
+  integrity sha512-fOZb8BnJBrVohGPZ8RthDM5cHD9SnBKgY/U7LFXHhuwafSZD7TVmCX67+ezkkwxFbWpQGTEbgcjuHUDRonGy1g==
   dependencies:
-    "@floating-ui/react-dom" "^2.0.7"
+    "@floating-ui/react-dom" "^2.0.8"
     "@floating-ui/utils" "^0.2.1"
     tabbable "^6.0.1"
 
@@ -1752,9 +1752,9 @@
   integrity sha512-5+fP8P8MFNC+AyZCDxrB2pkZFPGzqQWUzpSeuuVLvm8VMcorNYavBqoFcxK8bQz4Qsbn4oUEEem4wDLfcysGHA==
 
 "@types/node@*", "@types/node@^20.8.6":
-  version "20.11.7"
-  resolved "https://registry.yarnpkg.com/@types/node/-/node-20.11.7.tgz#cb49aedd758c978c30806d0c38b520ed2a3df6e0"
-  integrity sha512-GPmeN1C3XAyV5uybAf4cMLWT9fDWcmQhZVtMFu7OR32WjrqGG+Wnk2V1d0bmtUyE/Zy1QJ9BxyiTih9z8Oks8A==
+  version "20.11.10"
+  resolved "https://registry.yarnpkg.com/@types/node/-/node-20.11.10.tgz#6c3de8974d65c362f82ee29db6b5adf4205462f9"
+  integrity sha512-rZEfe/hJSGYmdfX9tvcPMYeYPW2sNl50nsw4jZmRcaG0HIAb0WYEpsB05GOb53vjqpyE9GUhlDQ4jLSoB5q9kg==
   dependencies:
     undici-types "~5.26.4"
 
@@ -2243,12 +2243,12 @@ browserify-sign@^4.0.0:
     safe-buffer "^5.2.1"
 
 browserslist@^4.22.2:
-  version "4.22.2"
-  resolved "https://registry.yarnpkg.com/browserslist/-/browserslist-4.22.2.tgz#704c4943072bd81ea18997f3bd2180e89c77874b"
-  integrity sha512-0UgcrvQmBDvZHFGdYUehrCNIazki7/lUP3kkoi/r3YB2amZbFM9J43ZRkJTXBUZK4gmx56+Sqk9+Vs9mwZx9+A==
+  version "4.22.3"
+  resolved "https://registry.yarnpkg.com/browserslist/-/browserslist-4.22.3.tgz#299d11b7e947a6b843981392721169e27d60c5a6"
+  integrity sha512-UAp55yfwNv0klWNapjs/ktHoguxuQNGnOzxYmfnXIS+8AsRDZkSDxg7R1AX3GKzn078SBI5dzwzj/Yx0Or0e3A==
   dependencies:
-    caniuse-lite "^1.0.30001565"
-    electron-to-chromium "^1.4.601"
+    caniuse-lite "^1.0.30001580"
+    electron-to-chromium "^1.4.648"
     node-releases "^2.0.14"
     update-browserslist-db "^1.0.13"
 
@@ -2286,10 +2286,10 @@ callsites@^3.0.0:
   resolved "https://registry.yarnpkg.com/callsites/-/callsites-3.1.0.tgz#b3630abd8943432f54b3f0519238e33cd7df2f73"
   integrity sha512-P8BjAsXvZS+VIDUI11hHCQEv74YT67YUi5JJFNWIqL235sBmjX4+qx9Muvls5ivyNENctx46xQLQ3aTuE7ssaQ==
 
-caniuse-lite@^1.0.30001565:
-  version "1.0.30001580"
-  resolved "https://registry.yarnpkg.com/caniuse-lite/-/caniuse-lite-1.0.30001580.tgz#e3c76bc6fe020d9007647044278954ff8cd17d1e"
-  integrity sha512-mtj5ur2FFPZcCEpXFy8ADXbDACuNFXg6mxVDqp7tqooX6l3zwm+d8EPoeOSIFRDvHs8qu7/SLFOGniULkcH2iA==
+caniuse-lite@^1.0.30001580:
+  version "1.0.30001581"
+  resolved "https://registry.yarnpkg.com/caniuse-lite/-/caniuse-lite-1.0.30001581.tgz#0dfd4db9e94edbdca67d57348ebc070dece279f4"
+  integrity sha512-whlTkwhqV2tUmP3oYhtNfaWGYHDdS3JYFQBKXxcUR9qqPWsRhFHhoISO2Xnl/g0xyKzht9mI1LZpiNWfMzHixQ==
 
 canvas-sequencer@^3.1.0:
   version "3.1.0"
@@ -2643,10 +2643,10 @@ eastasianwidth@^0.2.0:
   resolved "https://registry.yarnpkg.com/eastasianwidth/-/eastasianwidth-0.2.0.tgz#696ce2ec0aa0e6ea93a397ffcf24aa7840c827cb"
   integrity sha512-I88TYZWc9XiYHRQ4/3c5rjjfgkjhLyW2luGIheGERbNQ6OY7yTybanSpDXZa8y7VUP9YmDcYa+eyq4ca7iLqWA==
 
-electron-to-chromium@^1.4.601:
-  version "1.4.647"
-  resolved "https://registry.yarnpkg.com/electron-to-chromium/-/electron-to-chromium-1.4.647.tgz#3c8d4815e5ed2fbdd37f4ab7333cd9f8fc56d53a"
-  integrity sha512-Z/fTNGwc45WrYQhPaEcz5tAJuZZ8G7S/DBnhS6Kgp4BxnS40Z/HqlJ0hHg3Z79IGVzuVartIlTcjw/cQbPLgOw==
+electron-to-chromium@^1.4.648:
+  version "1.4.648"
+  resolved "https://registry.yarnpkg.com/electron-to-chromium/-/electron-to-chromium-1.4.648.tgz#c7b46c9010752c37bb4322739d6d2dd82354fbe4"
+  integrity sha512-EmFMarXeqJp9cUKu/QEciEApn0S/xRcpZWuAm32U7NgoZCimjsilKXHRO9saeEW55eHZagIDg6XTUOv32w9pjg==
 
 elliptic@^6.5.3, elliptic@^6.5.4:
   version "6.5.4"
@@ -3024,9 +3024,9 @@ fast-levenshtein@^2.0.6:
   integrity sha512-DCXu6Ifhqcks7TZKY3Hxp3y6qphY5SJZmrWMDrKcERSOXWQdMhU9Ig/PYrzyw/ul9jOIyh0N4M0tbC5hodg8dw==
 
 fastq@^1.6.0:
-  version "1.16.0"
-  resolved "https://registry.yarnpkg.com/fastq/-/fastq-1.16.0.tgz#83b9a9375692db77a822df081edb6a9cf6839320"
-  integrity sha512-ifCoaXsDrsdkWTtiNJX5uzHDsrck5TzfKKDcuFFTIrrc/BS076qgEIfoIy1VeZqViznfKiysPYTh/QeHtnIsYA==
+  version "1.17.0"
+  resolved "https://registry.yarnpkg.com/fastq/-/fastq-1.17.0.tgz#ca5e1a90b5e68f97fc8b61330d5819b82f5fab03"
+  integrity sha512-zGygtijUMT7jnk3h26kUms3BkSDp4IfIKjmnqI2tvx6nuBfiF1UqOxbnLfzdv+apBy+53oaImsKtMw/xYbW+1w==
   dependencies:
     reusify "^1.0.4"