Merge branch 'master' into lis

Gemfile.lock

@@ -1,7 +1,7 @@
 PATH
   remote: .
   specs:
-    sequenceserver (3.1.1)
+    sequenceserver (3.1.2)
       json_pure (~> 2.6, >= 2.6.3)
       ox (~> 2.1, >= 2.1.1)
       rack_csrf (~> 2.7, >= 2.7.0)

lib/sequenceserver/api_errors.rb

@@ -52,6 +52,30 @@ def message
     end
   end
 
+  # InvalidParameterError is a more generic error class that can be
+  # raised when the frontend sends a request with an invalid parameter
+  class InvalidParameterError < ValidationError
+    attr_reader :more_info
+
+    def initialize(more_info)
+      super
+      @more_info = more_info
+    end
+
+    def http_status
+      422
+    end
+
+    def title
+      'Invalid parameter'
+    end
+
+    def message
+      "The action you're trying to perform is not possible because \
+        one of the provided parameters is invalid."
+    end
+  end
+
   # API errors have an http status, title, message, and additional information
   # like stacktrace or information from program output.
   APIError = Class.new(Error)

lib/sequenceserver/blast.rb

@@ -1,3 +1,9 @@
 require_relative 'blast/job'
 require_relative 'blast/report'
 require_relative 'blast/constants'
+
+module SequenceServer
+  module BLAST
+    VALID_SEQUENCE_ID = /\A[a-zA-Z0-9\-_.:*#|\[\]]+\z/
+  end
+end

lib/sequenceserver/database.rb

@@ -37,8 +37,19 @@ def initialize(*args)
     alias path name
 
     def retrieve(accession, coords = nil)
+      fail(
+        InvalidSequenceIdError,
+        "Invalid sequence id: #{accession}"
+      ) unless accession =~ SequenceServer::BLAST::VALID_SEQUENCE_ID
+
       cmd = "blastdbcmd -db #{name} -entry '#{accession}'"
+
       if coords
+        fail(
+          InvalidParameterError,
+          "Invalid range coordinates: #{coords}"
+        ) unless coords =~ /[0-9]+-[0-9]*/
+
         cmd << " -range #{coords}"
       end
       out, = sys(cmd, path: config[:bin])
@@ -52,6 +63,8 @@ def retrieve(accession, coords = nil)
     # Returns true if the database contains the given sequence id.
     # Returns false otherwise.
     def include?(id)
+      fail ArgumentError, "Invalid sequence id: #{id}" unless id =~ SequenceServer::BLAST::VALID_SEQUENCE_ID
+
       cmd = "blastdbcmd -entry '#{id}' -db #{name}"
       sys(cmd, path: config[:bin]) rescue false
     end

lib/sequenceserver/sequence.rb

@@ -232,9 +232,8 @@ def validate
           )
         end
 
-        valid_id_regex = /\A[a-zA-Z0-9-_.:*#|\[\]]+\z/
         invalid_sequence_ids = sequence_ids.reject do |id|
-          id =~ valid_id_regex
+          id =~ SequenceServer::BLAST::VALID_SEQUENCE_ID
         end
 
         unless invalid_sequence_ids.empty?

lib/sequenceserver/version.rb

@@ -1,4 +1,4 @@
 # Define version number.
 module SequenceServer
-  VERSION = '3.1.1'.freeze
+  VERSION = '3.1.2'.freeze
 end

package.json

@@ -13,8 +13,8 @@
     "watch-cloud": "webpack --watch --env=pluginsPath='../sequence_server_js_extensions' --env=targetEnv='cloud'",
     "test": "jest",
     "minify:css": "cleancss public/css/sequenceserver.css > public/css/sequenceserver.min.css && npx tailwindcss build -i ./public/css/app.css -o ./public/css/app.min.css --minify",
-    "build": "webpack && npm run minify:css",
-    "build-cloud": "webpack --env=pluginsPath='../sequence_server_js_extensions' --env=targetEnv='cloud' && npm run minify:css"
+    "build": "webpack --mode production && npm run minify:css",
+    "build-cloud": "webpack --mode production --env=pluginsPath='../sequence_server_js_extensions' --env=targetEnv='cloud' && npm run minify:css"
   },
   "dependencies": {
     "babel-plugin-transform-export-extensions": "^6.22.0",

public/sequenceserver-report.min.js.LICENSE.txt

@@ -0,0 +1,233 @@
+/*!
+     * jQuery Browser Plugin v0.0.6
+     * https://github.com/gabceb/jquery-browser-plugin
+     *
+     * Original jquery-browser code Copyright 2005, 2013 jQuery Foundation, Inc. and other contributors
+     * http://jquery.org/license
+     *
+     * Modifications Copyright 2013 Gabriel Cebrian
+     * https://github.com/gabceb
+     *
+     * Released under the MIT license
+     *
+     * Date: 2013-07-29T17:23:27-07:00
+     */
+
+/*!
+     * jQuery Color Animations v2.1.2
+     * https://github.com/jquery/jquery-color
+     *
+     * Copyright 2014 jQuery Foundation and other contributors
+     * Released under the MIT license.
+     * http://jquery.org/license
+     *
+     * Date: Wed Jan 16 08:47:09 2013 -0600
+     */
+
+/*!
+     * jQuery UI Autocomplete 1.11.4
+     * http://jqueryui.com
+     *
+     * Copyright jQuery Foundation and other contributors
+     * Released under the MIT license.
+     * http://jquery.org/license
+     *
+     * http://api.jqueryui.com/autocomplete/
+     */
+
+/*!
+     * jQuery UI Button 1.11.4
+     * http://jqueryui.com
+     *
+     * Copyright jQuery Foundation and other contributors
+     * Released under the MIT license.
+     * http://jquery.org/license
+     *
+     * http://api.jqueryui.com/button/
+     */
+
+/*!
+     * jQuery UI Core 1.11.4
+     * http://jqueryui.com
+     *
+     * Copyright jQuery Foundation and other contributors
+     * Released under the MIT license.
+     * http://jquery.org/license
+     *
+     * http://api.jqueryui.com/category/ui-core/
+     */
+
+/*!
+     * jQuery UI Datepicker 1.11.4
+     * http://jqueryui.com
+     *
+     * Copyright jQuery Foundation and other contributors
+     * Released under the MIT license.
+     * http://jquery.org/license
+     *
+     * http://api.jqueryui.com/datepicker/
+     */
+
+/*!
+     * jQuery UI Draggable 1.11.4
+     * http://jqueryui.com
+     *
+     * Copyright jQuery Foundation and other contributors
+     * Released under the MIT license.
+     * http://jquery.org/license
+     *
+     * http://api.jqueryui.com/draggable/
+     */
+
+/*!
+     * jQuery UI Droppable 1.11.4
+     * http://jqueryui.com
+     *
+     * Copyright jQuery Foundation and other contributors
+     * Released under the MIT license.
+     * http://jquery.org/license
+     *
+     * http://api.jqueryui.com/droppable/
+     */
+
+/*!
+     * jQuery UI Mouse 1.11.4
+     * http://jqueryui.com
+     *
+     * Copyright jQuery Foundation and other contributors
+     * Released under the MIT license.
+     * http://jquery.org/license
+     *
+     * http://api.jqueryui.com/mouse/
+     */
+
+/*!
+     * jQuery UI Position 1.11.4
+     * http://jqueryui.com
+     *
+     * Copyright jQuery Foundation and other contributors
+     * Released under the MIT license.
+     * http://jquery.org/license
+     *
+     * http://api.jqueryui.com/position/
+     */
+
+/*!
+     * jQuery UI Resizable 1.11.4
+     * http://jqueryui.com
+     *
+     * Copyright jQuery Foundation and other contributors
+     * Released under the MIT license.
+     * http://jquery.org/license
+     *
+     * http://api.jqueryui.com/resizable/
+     */
+
+/*!
+     * jQuery UI Spinner 1.11.4
+     * http://jqueryui.com
+     *
+     * Copyright jQuery Foundation and other contributors
+     * Released under the MIT license.
+     * http://jquery.org/license
+     *
+     * http://api.jqueryui.com/spinner/
+     */
+
+/*!
+     * jQuery UI Tabs 1.11.4
+     * http://jqueryui.com
+     *
+     * Copyright jQuery Foundation and other contributors
+     * Released under the MIT license.
+     * http://jquery.org/license
+     *
+     * http://api.jqueryui.com/tabs/
+     */
+
+/*!
+     * jQuery UI Widget 1.11.4
+     * http://jqueryui.com
+     *
+     * Copyright jQuery Foundation and other contributors
+     * Released under the MIT license.
+     * http://jquery.org/license
+     *
+     * http://api.jqueryui.com/jQuery.widget/
+     */
+
+/*!
+ * Sizzle CSS Selector Engine v2.2.1
+ * http://sizzlejs.com/
+ *
+ * Copyright jQuery Foundation and other contributors
+ * Released under the MIT license
+ * http://jquery.org/license
+ *
+ * Date: 2015-10-17
+ */
+
+/*!
+ * jQuery JavaScript Library v2.2.4
+ * http://jquery.com/
+ *
+ * Includes Sizzle.js
+ * http://sizzlejs.com/
+ *
+ * Copyright jQuery Foundation and other contributors
+ * Released under the MIT license
+ * http://jquery.org/license
+ *
+ * Date: 2016-05-20T17:23Z
+ */
+
+/*! jQuery UI - v1.11.4 - 2021-01-29
+* http://jqueryui.com
+* Includes: core.js, widget.js, mouse.js, position.js, draggable.js, droppable.js, resizable.js, selectable.js, sortable.js, accordion.js, autocomplete.js, button.js, datepicker.js, dialog.js, menu.js, progressbar.js, selectmenu.js, slider.js, spinner.js, tabs.js, tooltip.js, effect.js, effect-blind.js, effect-bounce.js, effect-clip.js, effect-drop.js, effect-explode.js, effect-fade.js, effect-fold.js, effect-highlight.js, effect-puff.js, effect-pulsate.js, effect-scale.js, effect-shake.js, effect-size.js, effect-slide.js, effect-transfer.js
+* Copyright jQuery Foundation and other contributors; Licensed MIT */
+
+/**
+ * @license React
+ * react-dom.development.js
+ *
+ * Copyright (c) Facebook, Inc. and its affiliates.
+ *
+ * This source code is licensed under the MIT license found in the
+ * LICENSE file in the root directory of this source tree.
+ */
+
+/**
+ * @license React
+ * react-jsx-runtime.development.js
+ *
+ * Copyright (c) Facebook, Inc. and its affiliates.
+ *
+ * This source code is licensed under the MIT license found in the
+ * LICENSE file in the root directory of this source tree.
+ */
+
+/**
+ * @license React
+ * scheduler.development.js
+ *
+ * Copyright (c) Facebook, Inc. and its affiliates.
+ *
+ * This source code is licensed under the MIT license found in the
+ * LICENSE file in the root directory of this source tree.
+ */
+
+/**
+ * Checks if an event is supported in the current execution environment.
+ *
+ * NOTE: This will not work correctly for non-generic events such as `change`,
+ * `reset`, `load`, `error`, and `select`.
+ *
+ * Borrows from Modernizr.
+ *
+ * @param {string} eventNameSuffix Event name, e.g. "click".
+ * @return {boolean} True if the event is supported.
+ * @internal
+ * @license Modernizr 3.0.0pre (Custom Build) | MIT
+ */
+
+/** @preserve http://github.com/easeway/js-class */