sequenceserver 3.1.1 → 3.1.3

checksums.yaml

@@ -1,7 +1,7 @@
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+  metadata.gz: cc2b537e7c30e2f882bbf34228d607b5cd51ee3b2b23de202bc472e6977638e6
+  data.tar.gz: 1d0a3c11b9d468fb5ad30df26fd58637f866afcbf3a00f7586244f4c65dca146
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+  data.tar.gz: 8260f22915cbfe511f9bd2a8b11a6f900478bde088162bc38aba49f22150936419f0b3e889f475ed391621e3804a7e7cffcd79dba4ef0988e7cc486a0a37c28c

data/lib/sequenceserver/api_errors.rb

@@ -52,6 +52,30 @@ module SequenceServer
     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)

data/lib/sequenceserver/blast/tasks.rb

@@ -6,7 +6,7 @@ module SequenceServer
 
       def self.to_h
         @to_h ||= ALGORITHMS.map do |algorithm|
-          help_text = `#{algorithm} -help`
+          help_text, = SequenceServer.sys("#{algorithm} -help", path: SequenceServer.config[:bin])
           [algorithm, extract_tasks(help_text)]
         end.to_h
       end

data/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

data/lib/sequenceserver/database.rb

@@ -37,8 +37,19 @@ module SequenceServer
     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 @@ module SequenceServer
     # 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

data/lib/sequenceserver/routes.rb

@@ -297,7 +297,7 @@ module SequenceServer
         error_data[:more_info] = error.backtrace.join("\n")
       end
 
-      if request.env['HTTP_ACCEPT'].to_s.include?('application/json')
+      if request.env['HTTP_ACCEPT'].to_s.include?('application/json') || request.path.end_with?('.json')
         status 422
         content_type :json
         error_data.to_json

data/lib/sequenceserver/sequence.rb

@@ -232,9 +232,8 @@ module SequenceServer
           )
         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?

data/lib/sequenceserver/version.rb

@@ -1,4 +1,4 @@
 # Define version number.
 module SequenceServer
-  VERSION = '3.1.1'.freeze
+  VERSION = '3.1.3'.freeze
 end

data/lib/sequenceserver.rb

@@ -8,7 +8,7 @@ Encoding.default_internal = 'UTF-8'
 # Top level module / namespace.
 module SequenceServer
   # The default version of BLAST that will be downloaded and configured for use.
-  BLAST_VERSION = '2.15.0+'.freeze
+  BLAST_VERSION = '2.16.0+'.freeze
 
   # Default location of configuration file.
   DEFAULT_CONFIG_FILE = '~/.sequenceserver.conf'.freeze

data/public/css/app.min.css

@@ -1 +1 @@
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#0000),var(--tw-shadow)}.shadow-2xl{--tw-shadow:0 25px 50px -12px #00000040;--tw-shadow-colored:0 25px 50px -12px var(--tw-shadow-color)}.shadow-lg{--tw-shadow:0 10px 15px -3px #0000001a,0 4px 6px -4px #0000001a;--tw-shadow-colored:0 10px 15px -3px var(--tw-shadow-color),0 4px 6px -4px var(--tw-shadow-color)}.shadow-lg,.shadow-sm{box-shadow:var(--tw-ring-offset-shadow,0 0 #0000),var(--tw-ring-shadow,0 0 #0000),var(--tw-shadow)}.shadow-sm{--tw-shadow:0 1px 2px 0 #0000000d;--tw-shadow-colored:0 1px 2px 0 var(--tw-shadow-color)}.shadow-xl{--tw-shadow:0 20px 25px -5px #0000001a,0 8px 10px -6px #0000001a;--tw-shadow-colored:0 20px 25px -5px var(--tw-shadow-color),0 8px 10px -6px var(--tw-shadow-color);box-shadow:var(--tw-ring-offset-shadow,0 0 #0000),var(--tw-ring-shadow,0 0 #0000),var(--tw-shadow)}.outline-none{outline:2px solid #0000;outline-offset:2px}.outline{outline-style:solid}.ring{--tw-ring-offset-shadow:var(--tw-ring-inset) 0 0 0 var(--tw-ring-offset-width) var(--tw-ring-offset-color);--tw-ring-shadow:var(--tw-ring-inset) 0 0 0 calc(3px + var(--tw-ring-offset-width)) var(--tw-ring-color);box-shadow:var(--tw-ring-offset-shadow),var(--tw-ring-shadow),var(--tw-shadow,0 0 #0000)}.ring-seqorange{--tw-ring-opacity:1;--tw-ring-color:rgb(199 79 19/var(--tw-ring-opacity))}.blur{--tw-blur:blur(8px);filter:var(--tw-blur) var(--tw-brightness) var(--tw-contrast) var(--tw-grayscale) var(--tw-hue-rotate) var(--tw-invert) var(--tw-saturate) var(--tw-sepia) var(--tw-drop-shadow)}.\!invert{--tw-invert:invert(100%)!important;filter:var(--tw-blur) var(--tw-brightness) var(--tw-contrast) var(--tw-grayscale) var(--tw-hue-rotate) var(--tw-invert) var(--tw-saturate) var(--tw-sepia) var(--tw-drop-shadow)!important}.invert{--tw-invert:invert(100%);filter:var(--tw-blur) var(--tw-brightness) var(--tw-contrast) var(--tw-grayscale) var(--tw-hue-rotate) var(--tw-invert) var(--tw-saturate) var(--tw-sepia) var(--tw-drop-shadow)}.\!filter{filter:var(--tw-blur) var(--tw-brightness) var(--tw-contrast) var(--tw-grayscale) var(--tw-hue-rotate) var(--tw-invert) var(--tw-saturate) var(--tw-sepia) var(--tw-drop-shadow)!important}.filter{filter:var(--tw-blur) var(--tw-brightness) var(--tw-contrast) var(--tw-grayscale) var(--tw-hue-rotate) var(--tw-invert) var(--tw-saturate) var(--tw-sepia) var(--tw-drop-shadow)}.\!transition{transition-property:color,background-color,border-color,fill,stroke,opacity,box-shadow,transform,filter,-webkit-text-decoration-color,-webkit-backdrop-filter!important;transition-property:color,background-color,border-color,text-decoration-color,fill,stroke,opacity,box-shadow,transform,filter,backdrop-filter!important;transition-property:color,background-color,border-color,text-decoration-color,fill,stroke,opacity,box-shadow,transform,filter,backdrop-filter,-webkit-text-decoration-color,-webkit-backdrop-filter!important;transition-timing-function:cubic-bezier(.4,0,.2,1)!important;transition-duration:.15s!important}.transition{transition-property:color,background-color,border-color,fill,stroke,opacity,box-shadow,transform,filter,-webkit-text-decoration-color,-webkit-backdrop-filter;transition-property:color,background-color,border-color,text-decoration-color,fill,stroke,opacity,box-shadow,transform,filter,backdrop-filter;transition-property:color,background-color,border-color,text-decoration-color,fill,stroke,opacity,box-shadow,transform,filter,backdrop-filter,-webkit-text-decoration-color,-webkit-backdrop-filter;transition-timing-function:cubic-bezier(.4,0,.2,1);transition-duration:.15s}.transition-all{transition-property:all;transition-timing-function:cubic-bezier(.4,0,.2,1);transition-duration:.15s}.transition-opacity{transition-property:opacity;transition-timing-function:cubic-bezier(.4,0,.2,1);transition-duration:.15s}.tooltip{position:absolute;z-index:1070;display:block;font-family:Helvetica Neue,Helvetica,Arial,sans-serif;font-style:normal;font-weight:400;line-height:1.42857143;line-break:auto;text-align:left;text-align:start;text-decoration:none;text-shadow:none;text-transform:none;letter-spacing:normal;word-break:normal;word-spacing:normal;word-wrap:normal;white-space:normal;font-size:12px;filter:alpha(opacity=0);opacity:0}.tooltip.in{filter:alpha(opacity=90);opacity:.9}.tooltip.top{padding:5px 0;margin-top:-3px}.tooltip.right{padding:0 5px;margin-left:3px}.tooltip.bottom{padding:5px 0;margin-top:3px}.tooltip.left{padding:0 5px;margin-left:-3px}.tooltip.top .tooltip-arrow{bottom:0;left:50%;margin-left:-5px;border-width:5px 5px 0;border-top-color:#000}.tooltip.top-left .tooltip-arrow{right:5px}.tooltip.top-left .tooltip-arrow,.tooltip.top-right .tooltip-arrow{bottom:0;margin-bottom:-5px;border-width:5px 5px 0;border-top-color:#000}.tooltip.top-right .tooltip-arrow{left:5px}.tooltip.right .tooltip-arrow{top:50%;left:0;margin-top:-5px;border-width:5px 5px 5px 0;border-right-color:#000}.tooltip.left .tooltip-arrow{top:50%;right:0;margin-top:-5px;border-width:5px 0 5px 5px;border-left-color:#000}.tooltip.bottom .tooltip-arrow{top:0;left:50%;margin-left:-5px;border-width:0 5px 5px;border-bottom-color:#000}.tooltip.bottom-left .tooltip-arrow{top:0;right:5px;margin-top:-5px;border-width:0 5px 5px;border-bottom-color:#000}.tooltip.bottom-right .tooltip-arrow{top:0;left:5px;margin-top:-5px;border-width:0 5px 5px;border-bottom-color:#000}.tooltip-inner{max-width:200px;padding:3px 8px;color:#fff;text-align:center;background-color:#000;border-radius:4px}.tooltip-arrow{position:absolute;width:0;height:0;border-color:#0000;border-style:solid}.hover\:bg-blue-400:hover{--tw-bg-opacity:1;background-color:rgb(96 165 250/var(--tw-bg-opacity))}.hover\:bg-gray-200:hover{--tw-bg-opacity:1;background-color:rgb(229 231 235/var(--tw-bg-opacity))}.hover\:bg-gray-300:hover{--tw-bg-opacity:1;background-color:rgb(209 213 219/var(--tw-bg-opacity))}.hover\:bg-red-600:hover{--tw-bg-opacity:1;background-color:rgb(220 38 38/var(--tw-bg-opacity))}.hover\:bg-seqorange:hover{--tw-bg-opacity:1;background-color:rgb(199 79 19/var(--tw-bg-opacity))}.hover\:bg-sky-400:hover{--tw-bg-opacity:1;background-color:rgb(56 189 248/var(--tw-bg-opacity))}.hover\:bg-sky-500:hover{--tw-bg-opacity:1;background-color:rgb(14 165 233/var(--tw-bg-opacity))}.hover\:bg-yellow-100:hover{--tw-bg-opacity:1;background-color:rgb(254 249 195/var(--tw-bg-opacity))}.hover\:font-bold:hover{font-weight:700}.hover\:text-white:hover{--tw-text-opacity:1;color:rgb(255 255 255/var(--tw-text-opacity))}.focus\:outline-none:focus{outline:2px solid #0000;outline-offset:2px}.focus\:ring-1:focus{--tw-ring-offset-shadow:var(--tw-ring-inset) 0 0 0 var(--tw-ring-offset-width) var(--tw-ring-offset-color);--tw-ring-shadow:var(--tw-ring-inset) 0 0 0 calc(1px + var(--tw-ring-offset-width)) var(--tw-ring-color)}.focus\:ring-1:focus,.focus\:ring-2:focus{box-shadow:var(--tw-ring-offset-shadow),var(--tw-ring-shadow),var(--tw-shadow,0 0 #0000)}.focus\:ring-2:focus{--tw-ring-offset-shadow:var(--tw-ring-inset) 0 0 0 var(--tw-ring-offset-width) var(--tw-ring-offset-color);--tw-ring-shadow:var(--tw-ring-inset) 0 0 0 calc(2px + var(--tw-ring-offset-width)) var(--tw-ring-color)}.focus\:ring-seqorange:focus{--tw-ring-opacity:1;--tw-ring-color:rgb(199 79 19/var(--tw-ring-opacity))}.focus\:ring-offset-2:focus{--tw-ring-offset-width:2px}.group:hover .group-hover\:visible{visibility:visible}@media (min-width:640px){.sm\:my-8{margin-top:2rem;margin-bottom:2rem}.sm\:ml-3{margin-left:.75rem}.sm\:block{display:block}.sm\:inline-block{display:inline-block}.sm\:flex{display:flex}.sm\:h-screen{height:100vh}.sm\:w-auto{width:auto}.sm\:w-full{width:100%}.sm\:max-w-screen-md{max-width:768px}.sm\:flex-row-reverse{flex-direction:row-reverse}.sm\:items-center{align-items:center}.sm\:p-0{padding:0}.sm\:p-6{padding:1.5rem}.sm\:px-6{padding-left:1.5rem;padding-right:1.5rem}.sm\:pb-4{padding-bottom:1rem}.sm\:align-middle{vertical-align:middle}.sm\:text-sm{font-size:.875rem;line-height:1.25rem}}@media (min-width:768px){.md\:my-2{margin-top:.5rem;margin-bottom:.5rem}.md\:flex{display:flex}.md\:w-auto{width:auto}.md\:grid-cols-2{grid-template-columns:repeat(2,minmax(0,1fr))}.md\:space-x-4>:not([hidden])~:not([hidden]){--tw-space-x-reverse:0;margin-right:calc(1rem*var(--tw-space-x-reverse));margin-left:calc(1rem*(1 - var(--tw-space-x-reverse)))}}@media (min-width:1024px){.lg\:px-8{padding-left:2rem;padding-right:2rem}}

data/public/css/sequenceserver.css

@@ -232,20 +232,6 @@ a.disabled:hover,
   text-transform: uppercase;
 }
 
-/**
- * Use monospace font.
- */
-.text-monospace {
-  font-family:
-    "SFMono-Regular",
-    Consolas,
-    "Liberation Mono",
-    Menlo,
-    Courier,
-    monospace;
-  font-size: 12px;
-}
-
 /**
  * Make text bold.
  */
@@ -459,10 +445,6 @@ td.nowrap-ellipsis {
   padding-left: 0;
 }
 
-.footer a:first-child {
-  vertical-align: super;
-}
-
 /* higlight when hit is selected */
 .glow {
   border-left: 2px solid #c74f14;