Merge pull request #23 from mboudet/test

Fix async annotation + add back config file
gogepp · May 2, 2023 · 89ee954 · 89ee954
2 parents 017cc9d + a045efd
commit 89ee954
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Showing 17 changed files with 242 additions and 49 deletions.
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -5,6 +5,24 @@ All notable changes to this project will be documented in this file.
 The format is based on [Keep a Changelog](http://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.html)
 
+## [0.4.3] 2023-05-02
+
+### Fixed
+
+- Fixed Protein domains view in gene list
+- Removed remaining console.log in Eggnog
+- Fixed display for blast/diamond when there is no data
+- Fixed typo in Show more / Show less for diamond
+- Fixed async annotation add
+
+### Added
+
+- Added back config file option at startup (see config.json.template)
+- Added config option to disable login (and registration) (*disable_user_login* key)
+- Added config option to disable registrations (*disable_user_registration* key)
+- Added config option to hide blast link (*disable_blast* key)
+- Added config option to redirect blast link to custom external link (*blast_link* key)
+
 ## [0.4.2] 2023-04-13
 
 ### Fixed

diff --git a/cli/genoboo.js b/cli/genoboo.js
@@ -1,6 +1,7 @@
 #!/usr/bin/env node
 /* eslint-disable no-underscore-dangle, no-console */
 
+const fs = require('fs');
 const commander = require('commander');
 const { Tail } = require('tail');
 const { spawn, execFileSync } = require('child_process');
@@ -151,6 +152,7 @@ function startMongoDaemon(
 
 async function startGeneNoteBook(cmd) {
   const {
+    config,
     port,
     rootUrl,
     mongoUrl,
@@ -160,11 +162,22 @@ async function startGeneNoteBook(cmd) {
     dbCacheSizeGB,
     storagePath
   } = cmd.opts();
+
   const PORT = parseInt(port, 10) || 3000;
   const ROOT_URL = rootUrl || `http://localhost:${PORT}`;
   const STORAGE_PATH = storagePath || 'assets/app/uploads';
   const opts = { PORT, ROOT_URL, GNB_VERSION: pkginfo.version, STORAGE_PATH };
 
+  if (config && fs.existsSync(config)) {
+    try {
+      const METEOR_SETTINGS = fs.readFileSync(config, 'utf8');
+      Object.assign(opts, { METEOR_SETTINGS });
+   } catch (error) {
+      logger.error(`Cannot read ${config}: `)
+      logger.error(error)
+   }
+  }
+
   if (mongoUrl) {
     if (dbPath) {
       throw new Error('--db-path and --mongo-url are mutually exclusive');
@@ -200,6 +213,10 @@ program
   .command('run')
   .description('Run a GeneNoteBook server')
   .usage('[options]')
+  .option(
+    '--config [config]',
+    'Path to an optional json config file. To be available client-side, options must be under a "public" key.'
+  )
   .option(
     '--port [port]',
     'Web server port on which to serve GeneNoteBook. Default: 3000'

diff --git a/config.json.template b/config.json.template
@@ -0,0 +1,8 @@
+{
+  "public":{
+    "disable_blast": false,
+    "disable_user_login": false,
+    "disable_user_registration": false,
+    "blast_link": ""
+  }
+}
diff --git a/imports/api/genomes/annotation/parser/annotationParserGff3.js b/imports/api/genomes/annotation/parser/annotationParserGff3.js
@@ -589,7 +589,7 @@ class AnnotationProcessor {
     });
 
     if (this.geneBulkOperation.length > 0) {
-      this.geneBulkOperation.execute();
+      return this.geneBulkOperation.execute();
     }
   };
 }

diff --git a/imports/api/jobqueue/process-annotation.js b/imports/api/jobqueue/process-annotation.js
@@ -64,12 +64,12 @@ jobQueue.processJobs(
           parser.abort();
         }
       },
-      complete(result) {
+      complete: async function(result) {
         if (result.meta.aborted === true) {
           job.fail();
         } else {
           try {
-            lineProcessor.lastAnnotation();
+            await lineProcessor.lastAnnotation();
             const nAnnotation = lineProcessor.getNumberAnnotation();
             job.done({ nInserted: nAnnotation });
           } catch (err) {

diff --git a/imports/startup/server/useraccounts-configuration.js b/imports/startup/server/useraccounts-configuration.js
@@ -20,6 +20,10 @@ Accounts.onCreateUser((options, user) => {
   return user;
 });
 
+Accounts.validateLoginAttempt(attempt => {
+  return !Meteor.settings.public.disable_user_login === true
+})
+
 Accounts.onLogout(({ user }) => {
   logger.debug('logout', { user });
   if (user) {
@@ -46,3 +50,7 @@ Meteor.users.allow({
     return false;
   },
 });
+
+Accounts.config({
+    forbidClientAccountCreation: Meteor.settings.public.disable_user_registration === true
+});
diff --git a/imports/ui/blast/SubmitBlast.jsx b/imports/ui/blast/SubmitBlast.jsx
@@ -366,7 +366,38 @@ function SubmitBlast({ genomes }) {
     return <Redirect to={{ pathname: redirect, from: 'blast' }} />;
   }
 
+
+  if (Meteor.settings.public.disable_blast === true || Meteor.settings.public.blast_link){
+    let blastLink
+    if (Meteor.settings.public.blast_link){
+      blastLink = (
+        <p>You can access an external blast interface <a href={Meteor.settings.public.blast_link} target="_blank" style={{color: "#485fc7"}}>here</a></p>
+      )
+    }
+    return (
+      <div className="hero is-small is-light is-bold">
+      <div className="hero-body">
+        <form className="container" id="blast">
+          <header className="has-background-light">
+            <h4 className="title is-size-4 has-text-weight-light">
+              BLAST search
+            </h4>
+          </header>
+          <div className="card">
+            <div className="card-content">
+              <p> GeneNoteBook blast interface is currently disabled. </p>
+              {blastLink}
+            </div>
+          </div>
+        </form>
+      </div>
+      </div>
+    )
+  }
+
   return (
+    <div className="hero is-small is-light is-bold">
+    <div className="hero-body">
     <form className="container" id="blast">
       <div className="card">
         <header className="has-background-light">
@@ -408,6 +439,8 @@ function SubmitBlast({ genomes }) {
         </div>
       </div>
     </form>
+    </div>
+    </div>
   );
 }
 

diff --git a/imports/ui/landingpage/LandingPage.jsx b/imports/ui/landingpage/LandingPage.jsx
@@ -101,10 +101,14 @@ function NoGenomes() {
         <article className="message is-info" role="alert">
           <div className="message-body">
             No public genomes are available.&nbsp;
-            {/*<Link to="/login">
-              Sign in
-            </Link>
-            &nbsp;to access private data.*/}
+            {! Meteor.settings.public.disable_user_login && (
+              <>
+              <Link to="/login">
+                Sign in
+              </Link>
+              &nbsp;to access private data.
+              </> 
+            )}
           </div>
         </article>
       )
@@ -120,6 +124,23 @@ const withConditionalRendering = compose(
 const StatsWithDataTracker = withConditionalRendering(Stats);
 
 function LandingPage() {
+  const block = Meteor.settings.public.disable_blast ? 6 : 4
+
+  let blastLink = (
+    <Link to="/blast" className="button is-light is-link is-fullwidth">
+      <span className="icon-database" aria-hidden="true" />&nbsp;Blast
+    </Link>
+  )
+
+  if (Meteor.settings.public.blast_link){
+    blastLink = (
+      <a target="_blank" href={Meteor.settings.public.blast_link} className="button is-light is-link is-fullwidth">
+        <span className="icon-database" aria-hidden="true" />&nbsp;Blast
+      </a>
+    )
+  }
+
+
   return (
     <>
       <section className="hero is-small is-light is-bold">
@@ -136,16 +157,18 @@ function LandingPage() {
           !Meteor.userId()
           && (
           <div className="buttons are-small" role="group">
-            {/*
+            {! (Meteor.settings.public.disable_user_login === true || Meteor.settings.public.disable_user_registration === true) && ( 
             <Link to="/register" className="button is-success">
               <span className="icon-user-add" aria-hidden="true" />
               &nbsp;Create account
             </Link>
+            )}
+            {! Meteor.settings.public.disable_user_login === true && (
             <Link to="/login" className="button is-link">
               <span className="icon-login" aria-hidden="true" />
               &nbsp;Sign in
             </Link>
-            */}
+            )}
             <a href="http://genenotebook.github.io/" className="button is-dark is-outlined">
               <span className="icon-github" aria-hidden="true" />
               &nbsp;About GeneNotebook
@@ -160,7 +183,7 @@ function LandingPage() {
         <div className="hero-body">
           <div className="columns">
 
-            <div className="column is-4">
+            <div className={"column is-" + block}>
               <div className="card">
                 <div className="card-content">
                   <div className="media">
@@ -191,7 +214,7 @@ function LandingPage() {
               </div>
             </div>
 
-            <div className="column is-4">
+            <div className={"column is-" + block}>
               <div className="card">
                 <div className="card-content">
                   <div className="media">
@@ -223,7 +246,9 @@ function LandingPage() {
               </div>
             </div>
 
-            <div className="column is-4">
+           {!Meteor.settings.public.disable_blast && (
+
+            <div className={"column is-" + block}>
               <div className="card">
                 <div className="card-content">
                   <div className="media">
@@ -244,15 +269,13 @@ function LandingPage() {
                   <div className="content">
                     BLAST your protein or DNA sequence to genome annotations.
                   </div>
-                  <div className="content">
-                    <Link to="/blast" className="button is-light is-link is-fullwidth">
-                      <span className="icon-database" aria-hidden="true" />
-              &nbsp;Blast
-                    </Link>
+                  <div className="content"> 
+                    {blastLink}
                   </div>
                 </div>
               </div>
             </div>
+           )}
           </div>
         </div>
       </section>

diff --git a/imports/ui/main/Header.jsx b/imports/ui/main/Header.jsx
@@ -62,12 +62,12 @@ const LoggedInButtonWithTracker = withTracker(adminTracker)(LoggedInButton);
 function LoggedOutButton() {
   return (
     <div className="navbar-item">
-      {/*
+      {! Meteor.settings.public.disable_user_login === true && (
       <Link to="/login" className="button is-small is-link" id="signin">
         <span className="icon-login" aria-hidden="true" />
       &nbsp;Sign in
       </Link>
-     */}
+     )}
     </div> 
   );
 }
@@ -83,6 +83,17 @@ function NavBar() {
   const [show, setShow] = useState(false);
   const activeText = show ? 'is-active' : '';
   const urlPrefix = Meteor.absoluteUrl();
+
+  let blastLink = (
+    <NavLink to="/blast" className="navbar-item" activeClassName="active">
+      Blast
+    </NavLink>
+  )
+
+  if (Meteor.settings.public.blast_link){
+    blastLink = (<a target="_blank" href={Meteor.settings.public.blast_link} className="navbar-item" activeClassName="active">Blast</a>)
+  }
+
   return (
     <nav className="navbar is-white" role="navigation">
       <div className="navbar-brand">
@@ -113,9 +124,9 @@ function NavBar() {
           <NavLink id="gene-link" to="/genes" className="navbar-item" activeClassName="active">
             Genes
           </NavLink>
-          <NavLink to="/blast" className="navbar-item" activeClassName="active">
-            Blast
-          </NavLink>
+          {! Meteor.settings.public.disable_blast && (
+            blastLink
+          )}
           <SearchBar />
         </div>
         <div className="navbar-end">

diff --git a/imports/ui/main/Login.jsx b/imports/ui/main/Login.jsx
@@ -28,11 +28,35 @@ export default function Login({ location }) {
   if (redirect) {
     return <Redirect to={redirectTo} />;
   }
+
+  if (Meteor.settings.public.disable_user_login === true){
+    return (
+      <div className="hero is-small is-light is-bold">
+      <div className="hero-body">
+        <div className="container is-centered has-text-centered">
+          <div className="card column is-4 is-offset-4 login-form">
+            <div className="card-image">
+              <figure className="image is-96x96">
+                <img className="is-rounded" src="logo.svg" alt="" />
+              </figure>
+            </div>
+            <div className="card-content">
+              <div className="content">
+                Login is currently disabled
+              </div>
+            </div>
+          </div>
+        </div>
+      </div>
+      </div>    
+    )
+  }
+
   return (
     <div className="hero is-small is-light is-bold">
       <div className="hero-body">
-        <div className="container columns is-centered has-text-centered">
-          <form className="card column is-4 login-form" onSubmit={handleSubmit}>
+        <div className="container is-centered has-text-centered">
+          <form className="card column is-4 is-offset-4 login-form" onSubmit={handleSubmit}>
             <div className="card-image">
               <figure className="image is-96x96">
                 <img className="is-rounded" src="logo.svg" alt="" />
@@ -85,12 +109,14 @@ export default function Login({ location }) {
                     Sign in
                   </button>
                 </div>
-
+
+                { ! Meteor.settings.public.disable_user_registration === true && (
                 <footer className="card-footer">
                   <Link to="/register" id="new-account">
                     Create new account
                   </Link>
                 </footer>
+                )}
               </div>
             </div>
           </form>
-Original file line number
+Diff line change
@@ Expand Up / @@ -589,7 +589,7 @@ class AnnotationProcessor { @@
         });
         if (this.geneBulkOperation.length > 0) {
-          this.geneBulkOperation.execute();
+          return this.geneBulkOperation.execute();
         }
       };
     }
@@ Expand Down @@