sequenceserver 2.2.0 → 3.0

data/views/layout.erb

@@ -6,12 +6,8 @@
   <meta name="viewport" content="width=device-width, initial-scale=1">
 
   <title>SequenceServer: Custom BLAST Server</title>
-  <meta name="author" content="Anurag Priyam">
-  <meta name="author" content="Ben J. Woodcroft">
-  <meta name="author" content="Vivek Rai">
-  <meta name="author" content="Cedric Wurm">
-  <meta name="author" content="Yannick Wurm">
-  <meta name="description" content="Custom BLAST server provided by SequenceServer (https://www.sequenceserver.com)"/>
+  <meta name="author" content="Pragmatic Genomics Ltd">
+  <meta name="description" content="Custom BLAST server provided by SequenceServer (https://sequenceserver.com)"/>
 
   <!-- CSS -->
   <% if settings.production? || settings.test? %>
@@ -38,7 +34,7 @@
         <li>
           <a
             target="_blank"
-            href="https://www.sequenceserver.com/#support">
+            href="https://sequenceserver.com/support">
             <i class="fa fa-comment-o"></i>
             &nbsp;Help &amp; Support
           </a>
@@ -90,16 +86,17 @@
               "SequenceServer: Local BLAST with bespoke html interface.",
               "Set up custom BLAST interface with SequenceServer.",
               "Easy BLASTing with SequenceServer.",
-              "Run BLAST locally with Sequenceserver.",
               "BLAST against a custom, local database with SequenceServer.",
-              "Run BLAST locally on Mac OSX with SequenceServer.",
-              "Run BLAST locally on Ubuntu with SequenceServer.",
-              "Run BLAST locally on Linux with SequenceServer."
+  	      "Cloud BLAST custom genome.",
+	      "NCBI BLAST alternative.",
+	      "BLAST private transcriptome assembly in the Cloud.",
+	      "Cloud server for comparative genomics, oligos, crisp, primers and more."
             ][rand(19)]
           %>
         </em></a>
       </p>
-      <%= File.read(File.join(settings.root, '../website-extras/footer.html')) if File.exist?(File.join(settings.root, '../website-extras/footer.html')) %>
+      <% footer_path = File.join(settings.root, '../website-extras/footer.html.erb') %>
+      <%= erb :'../../website-extras/footer.html', locals: { path_prefix: root_path_prefix } if File.exist?(footer_path) %>
     </div> <!-- /container -->
   </div>
 

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: sequenceserver
 version: !ruby/object:Gem::Version
-  version: 2.2.0
+  version: '3.0'
 platform: ruby
 authors:
 - Queen Mary University of London
@@ -9,7 +9,7 @@ authors:
 autorequire:
 bindir: bin
 cert_chain: []
-date: 2023-10-05 00:00:00.000000000 Z
+date: 2024-02-13 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: json_pure
@@ -51,6 +51,20 @@ dependencies:
     - - ">="
       - !ruby/object:Gem::Version
         version: 2.1.1
+- !ruby/object:Gem::Dependency
+  name: rackup
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
 - !ruby/object:Gem::Dependency
   name: rest-client
   requirement: !ruby/object:Gem::Requirement
@@ -97,20 +111,14 @@ dependencies:
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '2.0'
-    - - ">="
-      - !ruby/object:Gem::Version
-        version: 2.0.0
+        version: '4.0'
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '2.0'
-    - - ">="
-      - !ruby/object:Gem::Version
-        version: 2.0.0
+        version: '4.0'
 - !ruby/object:Gem::Dependency
   name: slop
   requirement: !ruby/object:Gem::Requirement
@@ -211,20 +219,14 @@ dependencies:
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '1.0'
-    - - ">="
-      - !ruby/object:Gem::Version
-        version: 1.0.0
+        version: '2.1'
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '1.0'
-    - - ">="
-      - !ruby/object:Gem::Version
-        version: 1.0.0
+        version: '2.1'
 - !ruby/object:Gem::Dependency
   name: rspec
   requirement: !ruby/object:Gem::Requirement
@@ -271,20 +273,20 @@ dependencies:
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: 4.10.0
+        version: 4.15.0
     - - ">="
       - !ruby/object:Gem::Version
-        version: 4.10.0
+        version: 4.15.0
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: 4.10.0
+        version: 4.15.0
     - - ">="
       - !ruby/object:Gem::Version
-        version: 4.10.0
+        version: 4.15.0
 - !ruby/object:Gem::Dependency
   name: simplecov
   requirement: !ruby/object:Gem::Requirement
@@ -322,6 +324,7 @@ files:
 - lib/sequenceserver/api_errors.rb
 - lib/sequenceserver/blast.rb
 - lib/sequenceserver/blast/constants.rb
+- lib/sequenceserver/blast/error.rb
 - lib/sequenceserver/blast/formatter.rb
 - lib/sequenceserver/blast/hit.rb
 - lib/sequenceserver/blast/hsp.rb
@@ -336,6 +339,7 @@ files:
 - lib/sequenceserver/job_remover.rb
 - lib/sequenceserver/links.rb
 - lib/sequenceserver/logger.rb
+- lib/sequenceserver/makeblastdb-modified-with-cache.rb
 - lib/sequenceserver/makeblastdb.rb
 - lib/sequenceserver/pool.rb
 - lib/sequenceserver/refinements.rb
@@ -346,6 +350,7 @@ files:
 - lib/sequenceserver/sys.rb
 - lib/sequenceserver/version.rb
 - lib/sequenceserver/zip_file_generator.rb
+- public/404.html
 - public/SequenceServer_logo.png
 - public/config.js
 - public/css/fonts.css
@@ -377,6 +382,7 @@ files:
 - public/js/download_fasta.js
 - public/js/error_modal.js
 - public/js/exporter.js
+- public/js/fastq_to_fasta.js
 - public/js/form.js
 - public/js/grapher.js
 - public/js/hit.js
@@ -387,6 +393,9 @@ files:
 - public/js/kablammo/alignment_viewer.js
 - public/js/length_distribution.js
 - public/js/mailto.js
+- public/js/null_plugins/download_links.js
+- public/js/null_plugins/hit_buttons.js
+- public/js/null_plugins/report_plugins.js
 - public/js/options.js
 - public/js/query.js
 - public/js/report.js
@@ -3521,7 +3530,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
     - !ruby/object:Gem::Version
       version: '0'
 requirements: []
-rubygems_version: 3.4.13
+rubygems_version: 3.4.10
 signing_key:
 specification_version: 4
 summary: BLAST search made easy!