sequenceserver 3.1.1 → 3.1.2

checksums.yaml

@@ -1,7 +1,7 @@
 ---
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+  data.tar.gz: 3a5fa2dce619076a5e0b626981c2bb95ffc544ae8b920942b2979cabe4869120e549f494cbd15a02bf10e265bb303f8988264824839ea934f80797e280b8045a

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.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/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 = '3.1.2'.freeze
 end

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: sequenceserver
 version: !ruby/object:Gem::Version
-  version: 3.1.1
+  version: 3.1.2
 platform: ruby
 authors:
 - Queen Mary University of London
@@ -9,7 +9,7 @@ authors:
 autorequire:
 bindir: bin
 cert_chain: []
-date: 2024-07-02 00:00:00.000000000 Z
+date: 2024-07-04 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: json_pure