sequenceserver 2.0.0 → 2.1.0

data/lib/sequenceserver/sequence.rb

@@ -136,6 +136,7 @@ module SequenceServer
         # Returns a file name to use for the temporary file.
         def filename
           return @filename if @filename
+
           name = sequence_ids.first            if sequence_ids.length == 1
           name = "#{sequence_ids.length}_hits" if sequence_ids.length >= 2
           @filename = "sequenceserver-#{name}.fa"
@@ -182,14 +183,12 @@ module SequenceServer
         validate && run
       end
 
-      attr_reader :sequence_ids, :database_ids, :in_file
-
-      attr_reader :sequences
+      attr_reader :sequence_ids, :database_ids, :in_file, :sequences
 
-      def to_json
+      def to_json(*_args)
         {
           error_msgs: error_msgs,
-          sequences:  sequences.map(&:info)
+          sequences: sequences.map(&:info)
         }.to_json
       end
 
@@ -224,13 +223,15 @@ module SequenceServer
         ids = Database.ids
         return true if database_ids.is_a?(Array) && !database_ids.empty? &&
                        (ids & database_ids).length == database_ids.length
-        fail ArgumentError, 'Database id should be one of:' \
-                            " #{ids.join("\n")}."
+
+        fail DatabaseUnreachableError, 'Database id should be one of:' \
+                            " #{ids.join("\n")}"
       end
 
       # rubocop:disable Metrics/MethodLength
       def error_msgs
         return [] if sequences.length == sequence_ids.length
+
         [
           ['ERROR: incorrect number of sequences found.',
            <<~MSG

data/lib/sequenceserver/sys.rb

@@ -47,8 +47,8 @@ module SequenceServer
 
       # Execute the shell command, redirect stdout and stderr to the
       # temporary files.
-      exec("#{command} 1>#{temp_files[:stdout].path}" \
-           " 2>#{temp_files[:stderr].path}")
+      exec(command, out: temp_files[:stdout].path.to_s, \
+                    err: temp_files[:stderr].path.to_s)
     end
 
     # Wait for the termination of the child process.

data/lib/sequenceserver/version.rb

@@ -1,4 +1,4 @@
 # Define version number.
 module SequenceServer
-  VERSION = '2.0.0'.freeze
+  VERSION = '2.1.0'.freeze
 end

data/lib/sequenceserver/zip_file_generator.rb

@@ -0,0 +1,56 @@
+# Source: https://github.com/rubyzip/rubyzip/blob/9d891f7353e66052283562d3e252fe380bb4b199/samples/example_recursive.rb
+
+require 'zip'
+
+# This is a simple example which uses rubyzip to
+# recursively generate a zip file from the contents of
+# a specified directory. The directory itself is not
+# included in the archive, rather just its contents.
+#
+# Usage:
+#   directory_to_zip = "/tmp/input"
+#   output_file = "/tmp/out.zip"
+#   zf = ZipFileGenerator.new(directory_to_zip, output_file)
+#   zf.write()
+class ZipFileGenerator
+  # Initialize with the directory to zip and the location of the output archive.
+  def initialize(input_dir, output_file)
+    @input_dir = input_dir
+    @output_file = output_file
+  end
+
+  # Zip the input directory.
+  def write
+    entries = Dir.entries(@input_dir) - %w[. ..]
+
+    ::Zip::File.open(@output_file, ::Zip::File::CREATE) do |zipfile|
+      write_entries entries, '', zipfile
+    end
+  end
+
+  private
+
+  # A helper method to make the recursion work.
+  def write_entries(entries, path, zipfile)
+    entries.each do |e|
+      zipfile_path = path == '' ? e : File.join(path, e)
+      disk_file_path = File.join(@input_dir, zipfile_path)
+
+      if File.directory? disk_file_path
+        recursively_deflate_directory(disk_file_path, zipfile, zipfile_path)
+      else
+        put_into_archive(disk_file_path, zipfile, zipfile_path)
+      end
+    end
+  end
+
+  def recursively_deflate_directory(disk_file_path, zipfile, zipfile_path)
+    zipfile.mkdir zipfile_path
+    subdir = Dir.entries(disk_file_path) - %w[. ..]
+    write_entries subdir, zipfile_path, zipfile
+  end
+
+  def put_into_archive(disk_file_path, zipfile, zipfile_path)
+    zipfile.add(zipfile_path, disk_file_path)
+  end
+end

data/lib/sequenceserver.rb

@@ -24,6 +24,7 @@ module SequenceServer
   require 'sequenceserver/job_remover'
   require 'sequenceserver/exceptions'
   require 'sequenceserver/sys'
+  require 'sequenceserver/refinements'
 
   # The singleton methods defined below constitute the "runtime" environment of
   # SequenceServer.

data/public/config.js

@@ -1,147 +1,153 @@
 System.config({
-    defaultJSExtensions: true,
-    transpiler: 'babel',
-    babelOptions: {
-        'optional': [
-            'runtime',
-            'optimisation.modules.system'
-        ],
-        'blacklist': [
-            'strict'
-        ]
-    },
-    paths: {
-        'github:*': 'vendor/github/*',
-        'npm:*': 'vendor/npm/*'
-    },
+  defaultJSExtensions: true,
+  transpiler: "babel",
+  babelOptions: {
+    "optional": [
+      "runtime",
+      "optimisation.modules.system"
+    ],
+    "blacklist": [
+      "strict"
+    ]
+  },
+  paths: {
+    "github:*": "vendor/github/*",
+    "npm:*": "vendor/npm/*"
+  },
 
-    map: {
-        'babel': 'npm:babel-core@5.8.23',
-        'babel-runtime': 'npm:babel-runtime@5.8.20',
-        'bootstrap': 'github:twbs/bootstrap@3.3.5',
-        'core-js': 'npm:core-js@1.1.2',
-        'd3': 'github:mbostock/d3@3.5.6',
-        'font-awesome': 'npm:font-awesome@4.4.0',
-        'jquery': 'github:components/jquery@2.1.4',
-        'jquery-ui': 'github:components/jqueryui@1.11.4',
-        'nicgirault/circosJs': 'github:nicgirault/circosJs@1.7.0',
-        'react': 'npm:react@0.13.3',
-        'underscore': 'npm:underscore@1.8.3',
-        'vakata/jstree': 'github:vakata/jstree@3.3.8',
-        'webshim': 'npm:webshim@1.15.8',
-        'github:components/jqueryui@1.11.4': {
-            'jquery': 'github:components/jquery@2.1.4'
-        },
-        'github:jspm/nodelibs-buffer@0.1.0': {
-            'buffer': 'npm:buffer@3.4.3'
-        },
-        'github:jspm/nodelibs-events@0.1.1': {
-            'events': 'npm:events@1.0.2'
-        },
-        'github:jspm/nodelibs-path@0.1.0': {
-            'path-browserify': 'npm:path-browserify@0.0.0'
-        },
-        'github:jspm/nodelibs-process@0.1.1': {
-            'process': 'npm:process@0.10.1'
-        },
-        'github:jspm/nodelibs-stream@0.1.0': {
-            'stream-browserify': 'npm:stream-browserify@1.0.0'
-        },
-        'github:jspm/nodelibs-util@0.1.0': {
-            'util': 'npm:util@0.10.3'
-        },
-        'github:twbs/bootstrap@3.3.5': {
-            'jquery': 'github:components/jquery@2.1.4'
-        },
-        'npm:amdefine@1.0.0': {
-            'fs': 'github:jspm/nodelibs-fs@0.1.2',
-            'module': 'github:jspm/nodelibs-module@0.1.0',
-            'path': 'github:jspm/nodelibs-path@0.1.0',
-            'process': 'github:jspm/nodelibs-process@0.1.1'
-        },
-        'npm:babel-runtime@5.8.20': {
-            'process': 'github:jspm/nodelibs-process@0.1.1'
-        },
-        'npm:buffer@3.4.3': {
-            'base64-js': 'npm:base64-js@0.0.8',
-            'ieee754': 'npm:ieee754@1.1.6',
-            'is-array': 'npm:is-array@1.0.1'
-        },
-        'npm:core-js@1.1.2': {
-            'fs': 'github:jspm/nodelibs-fs@0.1.2',
-            'process': 'github:jspm/nodelibs-process@0.1.1',
-            'systemjs-json': 'github:systemjs/plugin-json@0.1.0'
-        },
-        'npm:core-util-is@1.0.1': {
-            'buffer': 'github:jspm/nodelibs-buffer@0.1.0'
-        },
-        'npm:envify@3.4.0': {
-            'jstransform': 'npm:jstransform@10.1.0',
-            'process': 'github:jspm/nodelibs-process@0.1.1',
-            'through': 'npm:through@2.3.8'
-        },
-        'npm:esprima-fb@13001.1001.0-dev-harmony-fb': {
-            'fs': 'github:jspm/nodelibs-fs@0.1.2',
-            'process': 'github:jspm/nodelibs-process@0.1.1'
-        },
-        'npm:font-awesome@4.4.0': {
-            'css': 'github:systemjs/plugin-css@0.1.15'
-        },
-        'npm:inherits@2.0.1': {
-            'util': 'github:jspm/nodelibs-util@0.1.0'
-        },
-        'npm:jstransform@10.1.0': {
-            'base62': 'npm:base62@0.1.1',
-            'buffer': 'github:jspm/nodelibs-buffer@0.1.0',
-            'esprima-fb': 'npm:esprima-fb@13001.1001.0-dev-harmony-fb',
-            'fs': 'github:jspm/nodelibs-fs@0.1.2',
-            'process': 'github:jspm/nodelibs-process@0.1.1',
-            'source-map': 'npm:source-map@0.1.31'
-        },
-        'npm:path-browserify@0.0.0': {
-            'process': 'github:jspm/nodelibs-process@0.1.1'
-        },
-        'npm:react@0.13.3': {
-            'buffer': 'github:jspm/nodelibs-buffer@0.1.0',
-            'envify': 'npm:envify@3.4.0',
-            'process': 'github:jspm/nodelibs-process@0.1.1'
-        },
-        'npm:readable-stream@1.1.13': {
-            'buffer': 'github:jspm/nodelibs-buffer@0.1.0',
-            'core-util-is': 'npm:core-util-is@1.0.1',
-            'events': 'github:jspm/nodelibs-events@0.1.1',
-            'inherits': 'npm:inherits@2.0.1',
-            'isarray': 'npm:isarray@0.0.1',
-            'process': 'github:jspm/nodelibs-process@0.1.1',
-            'stream-browserify': 'npm:stream-browserify@1.0.0',
-            'string_decoder': 'npm:string_decoder@0.10.31'
-        },
-        'npm:source-map@0.1.31': {
-            'amdefine': 'npm:amdefine@1.0.0',
-            'fs': 'github:jspm/nodelibs-fs@0.1.2',
-            'path': 'github:jspm/nodelibs-path@0.1.0',
-            'process': 'github:jspm/nodelibs-process@0.1.1'
-        },
-        'npm:stream-browserify@1.0.0': {
-            'events': 'github:jspm/nodelibs-events@0.1.1',
-            'inherits': 'npm:inherits@2.0.1',
-            'readable-stream': 'npm:readable-stream@1.1.13'
-        },
-        'npm:string_decoder@0.10.31': {
-            'buffer': 'github:jspm/nodelibs-buffer@0.1.0'
-        },
-        'npm:through@2.3.8': {
-            'process': 'github:jspm/nodelibs-process@0.1.1',
-            'stream': 'github:jspm/nodelibs-stream@0.1.0'
-        },
-        'npm:util@0.10.3': {
-            'inherits': 'npm:inherits@2.0.1',
-            'process': 'github:jspm/nodelibs-process@0.1.1'
-        },
-        'npm:webshim@1.15.8': {
-            'fs': 'github:jspm/nodelibs-fs@0.1.2',
-            'path': 'github:jspm/nodelibs-path@0.1.0',
-            'process': 'github:jspm/nodelibs-process@0.1.1'
-        }
+  map: {
+    "babel": "npm:babel-core@5.8.23",
+    "babel-runtime": "npm:babel-runtime@5.8.20",
+    "bootstrap": "github:twbs/bootstrap@3.3.5",
+    "core-js": "npm:core-js@1.1.2",
+    "d3": "github:mbostock/d3@3.5.6",
+    "font-awesome": "npm:font-awesome@4.4.0",
+    "jquery": "github:components/jquery@2.1.4",
+    "jquery-ui": "github:components/jqueryui@1.11.4",
+    "nicgirault/circosJs": "github:nicgirault/circosJs@1.7.0",
+    "react": "npm:react@18.0.0",
+    "react-dom": "npm:react-dom@18.0.0",
+    "underscore": "npm:underscore@1.8.3",
+    "vakata/jstree": "github:vakata/jstree@3.3.8",
+    "webshim": "npm:webshim@1.15.8",
+    "github:components/jqueryui@1.11.4": {
+      "jquery": "github:components/jquery@2.1.4"
+    },
+    "github:jspm/nodelibs-assert@0.1.0": {
+      "assert": "npm:assert@1.5.0"
+    },
+    "github:jspm/nodelibs-buffer@0.1.1": {
+      "buffer": "npm:buffer@5.7.1"
+    },
+    "github:jspm/nodelibs-events@0.1.1": {
+      "events": "npm:events@1.0.2"
+    },
+    "github:jspm/nodelibs-path@0.1.0": {
+      "path-browserify": "npm:path-browserify@0.0.0"
+    },
+    "github:jspm/nodelibs-process@0.1.2": {
+      "process": "npm:process@0.11.10"
+    },
+    "github:jspm/nodelibs-stream@0.1.0": {
+      "stream-browserify": "npm:stream-browserify@1.0.0"
+    },
+    "github:jspm/nodelibs-util@0.1.0": {
+      "util": "npm:util@0.10.3"
+    },
+    "github:jspm/nodelibs-vm@0.1.0": {
+      "vm-browserify": "npm:vm-browserify@0.0.4"
+    },
+    "github:twbs/bootstrap@3.3.5": {
+      "jquery": "github:components/jquery@2.1.4"
+    },
+    "npm:assert@1.5.0": {
+      "assert": "github:jspm/nodelibs-assert@0.1.0",
+      "buffer": "github:jspm/nodelibs-buffer@0.1.1",
+      "object-assign": "npm:object-assign@4.1.1",
+      "process": "github:jspm/nodelibs-process@0.1.2",
+      "util": "npm:util@0.10.3"
+    },
+    "npm:babel-runtime@5.8.20": {
+      "process": "github:jspm/nodelibs-process@0.1.2"
+    },
+    "npm:buffer@5.7.1": {
+      "base64-js": "npm:base64-js@1.5.1",
+      "ieee754": "npm:ieee754@1.2.1"
+    },
+    "npm:core-js@1.1.2": {
+      "fs": "github:jspm/nodelibs-fs@0.1.2",
+      "process": "github:jspm/nodelibs-process@0.1.2",
+      "systemjs-json": "github:systemjs/plugin-json@0.1.0"
+    },
+    "npm:core-util-is@1.0.3": {
+      "buffer": "github:jspm/nodelibs-buffer@0.1.1"
+    },
+    "npm:font-awesome@4.4.0": {
+      "css": "github:systemjs/plugin-css@0.1.15"
+    },
+    "npm:inherits@2.0.1": {
+      "util": "github:jspm/nodelibs-util@0.1.0"
+    },
+    "npm:loose-envify@1.4.0": {
+      "fs": "github:jspm/nodelibs-fs@0.1.2",
+      "js-tokens": "npm:js-tokens@4.0.0",
+      "process": "github:jspm/nodelibs-process@0.1.2",
+      "stream": "github:jspm/nodelibs-stream@0.1.0",
+      "util": "github:jspm/nodelibs-util@0.1.0"
+    },
+    "npm:path-browserify@0.0.0": {
+      "process": "github:jspm/nodelibs-process@0.1.2"
+    },
+    "npm:process@0.11.10": {
+      "assert": "github:jspm/nodelibs-assert@0.1.0",
+      "fs": "github:jspm/nodelibs-fs@0.1.2",
+      "vm": "github:jspm/nodelibs-vm@0.1.0"
+    },
+    "npm:react-dom@18.0.0": {
+      "buffer": "github:jspm/nodelibs-buffer@0.1.1",
+      "loose-envify": "npm:loose-envify@1.4.0",
+      "process": "github:jspm/nodelibs-process@0.1.2",
+      "react": "npm:react@18.0.0",
+      "scheduler": "npm:scheduler@0.21.0",
+      "stream": "github:jspm/nodelibs-stream@0.1.0"
+    },
+    "npm:react@18.0.0": {
+      "loose-envify": "npm:loose-envify@1.4.0",
+      "process": "github:jspm/nodelibs-process@0.1.2"
+    },
+    "npm:readable-stream@1.1.14": {
+      "buffer": "github:jspm/nodelibs-buffer@0.1.1",
+      "core-util-is": "npm:core-util-is@1.0.3",
+      "events": "github:jspm/nodelibs-events@0.1.1",
+      "inherits": "npm:inherits@2.0.1",
+      "isarray": "npm:isarray@0.0.1",
+      "process": "github:jspm/nodelibs-process@0.1.2",
+      "stream-browserify": "npm:stream-browserify@1.0.0",
+      "string_decoder": "npm:string_decoder@0.10.31"
+    },
+    "npm:scheduler@0.21.0": {
+      "loose-envify": "npm:loose-envify@1.4.0",
+      "process": "github:jspm/nodelibs-process@0.1.2"
+    },
+    "npm:stream-browserify@1.0.0": {
+      "events": "github:jspm/nodelibs-events@0.1.1",
+      "inherits": "npm:inherits@2.0.1",
+      "readable-stream": "npm:readable-stream@1.1.14"
+    },
+    "npm:string_decoder@0.10.31": {
+      "buffer": "github:jspm/nodelibs-buffer@0.1.1"
+    },
+    "npm:util@0.10.3": {
+      "inherits": "npm:inherits@2.0.1",
+      "process": "github:jspm/nodelibs-process@0.1.2"
+    },
+    "npm:vm-browserify@0.0.4": {
+      "indexof": "npm:indexof@0.0.1"
+    },
+    "npm:webshim@1.15.8": {
+      "fs": "github:jspm/nodelibs-fs@0.1.2",
+      "path": "github:jspm/nodelibs-path@0.1.0",
+      "process": "github:jspm/nodelibs-process@0.1.2"
     }
+  }
 });

data/public/css/sequenceserver.css

@@ -344,6 +344,15 @@ td.nowrap-ellipsis {
   font-size: 18px;
 }
 
+.modal-error {
+  color: red;
+  font-size: 18px;
+  border: 1px solid red;
+  padding: 0.5em;
+  margin-top: 0.5em;
+  margin-bottom: 0.5em;
+}
+
 .biojs-vis-sequence pre {
   margin: 0 0;
   border: none;
@@ -443,7 +452,8 @@ input[type=checkbox] {
   margin-top: 0;
 }
 
-.sidebar li a {
+.sidebar li a,
+.sidebar li button {
   padding: 3px 2px;
 }
 
@@ -515,12 +525,14 @@ input[type=checkbox] {
 }
 
 .hsp {
-  padding: 1px 0 1px 2px;
+  padding: 1px 0 20px 2px;
 }
 
 .hsp-stats {
-  font-size: 12px;
+  font-size: 13px;
+  letter-spacing: 0.7px;
   color: #5f5f5f;
+  font-weight: 600;
 }
 
 .hsp-lines {
@@ -583,6 +595,10 @@ input[type=checkbox] {
   cursor: pointer;
 }
 
+.sharing-panel a {
+  cursor: pointer;
+}
+
 /* CSS class for logo */
 .logo {
   width: 205.05px;
@@ -621,3 +637,28 @@ input[type=checkbox] {
 .hit-header {
   display: table-cell;
 }
+
+
+/** For advanced params dropdown **/
+.input-group-btn {
+  vertical-align: top;
+}
+#advanced-params-dropdown {
+  padding: 0;
+}
+#advanced-params-dropdown li {
+  padding: 10px;
+  cursor: pointer;
+  letter-spacing: 1px;
+}
+
+.share-url-component input[type="text"] {
+  width: 100%;
+}
+
+.share-url-component .actions {
+  padding-top: 1em;
+  padding-bottom: 1em;
+  display: flex;
+  justify-content: space-between;
+}