Merge pull request #744 from tadast/tt/advanced-params

Refresh options UI

Author: yannickwurm

babel.config.js

@@ -7,4 +7,4 @@ module.exports = {
         '@babel/plugin-proposal-class-properties',
         '@babel/plugin-syntax-dynamic-import',
     ],
-};
+};

jest.config.js

@@ -44,11 +44,12 @@ module.exports = {
         'circos$': '<rootDir>/public/js/tests/mocks/circos.js',
         'grapher': '<rootDir>/public/js/grapher.js',
         'histogram': '<rootDir>/public/js/null_plugins/grapher/histogram.js',
-        'query_stats': '<rootDir>/public/js/null_plugins/query_stats.js'
+        'query_stats': '<rootDir>/public/js/null_plugins/query_stats.js',
+        '^options$': '<rootDir>/public/js/options.js'
     },
     watchPlugins: [
         'jest-watch-typeahead/filename',
         'jest-watch-typeahead/testname'
     ],
-    resetMocks: true
+    resetMocks: true,
 };

jest_scripts/babelTransform.js

@@ -12,6 +12,8 @@ const hasJsxRuntime = (() => {
         return false;
     }
 })();
+
+
 module.exports = babelJest.createTransformer({
     presets: [
         [

lib/sequenceserver/blast/tasks.rb

@@ -0,0 +1,38 @@
+module SequenceServer
+  module BLAST
+    # Shells out to each blast algorithm to get the help text and then parses it to extract the tasks.
+    module Tasks
+      ALGORITHMS = %w[blastn blastp blastx tblastn tblastx].freeze
+
+      def self.to_h
+        @to_h ||= ALGORITHMS.map do |algorithm|
+          help_text = `#{algorithm} -help`
+          [algorithm, extract_tasks(help_text)]
+        end.to_h
+      end
+
+      def self.extract_tasks(help_text)
+        lines = help_text.split("\n")
+
+        # Find task help paragraph start
+        task_line_index = lines.find_index { |line| line =~ /^\W-task/ }
+        return [] unless task_line_index.to_i.positive?
+
+        lines.slice!(0...task_line_index)
+
+        # Find the end of task help paragraph
+        next_option_line_index = lines.find_index { |line| line =~ /^\W-/ && !line.include?('-task') }
+        lines.slice!(next_option_line_index..-1)
+
+        extract_tasks_from_paragraph(lines)
+      end
+
+      def self.extract_tasks_from_paragraph(paragraph_lines)
+        as_one_liner = paragraph_lines.map(&:strip).join(' ')
+        as_one_liner.split('Permissible values:').last.split('>').first.split(' ').map do |task|
+          task.strip.gsub("'", '')
+        end.reject(&:empty?)
+      end
+    end
+  end
+end

lib/sequenceserver/config.rb

@@ -22,7 +22,7 @@ def initialize(data = {})
 
       return unless @upgraded
 
-      logger.info 'You are using old configuration syntax. ' \
+      logger.warn 'You are using old configuration syntax. ' \
                   'Run `sequenceserver -s` to update your config file syntax.'
     end
 
@@ -69,20 +69,7 @@ def normalize(data)
         @upgrade = true
       end
 
-      # Old config files may have an options hash with array values. We turn the
-      # array values into a hash. The logic is simple: If the array value is the
-      # same as default, we give it the key 'default', otherwise we give it the
-      # key 'custom'
-      data[:options]&.each do |key, val|
-        next if val.is_a? Hash
-
-        data[:options][key] = if val == defaults[:options][key][:default]
-                                { default: val }
-                              else
-                                { custom: val }
-                              end
-        @upgraded = true
-      end
+      data[:options] = convert_deprecated_options(data[:options]) if data[:options]
 
       data
     end
@@ -112,19 +99,34 @@ def defaults
         databases_widget: 'classic',
         options: {
           blastn: {
-            default: ['-task blastn', '-evalue 1e-5']
+            default: {
+              description: nil,
+              attributes: ['-task blastn', '-evalue 1e-5']
+            }
           },
           blastp: {
-            default: ['-evalue 1e-5']
+            default: {
+              description: nil,
+              attributes: ['-evalue 1e-5']
+            }
           },
           blastx: {
-            default: ['-evalue 1e-5']
+            default: {
+              description: nil,
+              attributes: ['-evalue 1e-5']
+            }
           },
           tblastx: {
-            default: ['-evalue 1e-5']
+            default: {
+              description: nil,
+              attributes: ['-evalue 1e-5']
+            }
           },
           tblastn: {
-            default: ['-evalue 1e-5']
+            default: {
+              description: nil,
+              attributes: ['-evalue 1e-5']
+            }
           }
         },
         num_threads: 1,
@@ -137,5 +139,37 @@ def defaults
         optimistic: false # Faster, but does not perform DB compatibility checks
       }
     end
+
+    def convert_deprecated_options(options)
+      options.each do |blast_algo, algo_config|
+        if algo_config.is_a?(Array)
+          # Very old config files may have a single array with CLI args.
+          # e.g. { blastn: ['-task blastn', '-evalue 1e-5'] }
+          # Convert the array values into a single hash naming it 'default' if
+          # the values match SequenceServer defaults.
+          options[blast_algo] = if algo_config == defaults.dig(:options, blast_algo, :default, :attributes)
+                                  { default: { attributes: algo_config } }
+                                else
+                                  { custom: { attributes: algo_config } }
+                                end
+          @upgraded = true
+        elsif algo_config.is_a?(Hash)
+          # v3.0.1 and older config files contain a flatter structure
+          # with an array instead of 'description' and 'attributes' keys.
+          # e.g. { blastn: { default: ['-task blastn', '-evalue 1e-5'] }
+          algo_config.each do |config_name, config|
+            next unless config.is_a?(Array)
+
+            options[blast_algo][config_name] = {
+              description: nil,
+              attributes: config
+            }
+            @upgraded = true
+          end
+        end
+      end
+
+      options
+    end
   end
 end

lib/sequenceserver/routes.rb

@@ -5,6 +5,7 @@
 
 require 'sequenceserver/job'
 require 'sequenceserver/blast'
+require 'sequenceserver/blast/tasks'
 require 'sequenceserver/report'
 require 'sequenceserver/database'
 require 'sequenceserver/sequence'
@@ -85,7 +86,8 @@ class Routes < Sinatra::Base
       searchdata = {
         query: Database.retrieve(params[:query]),
         database: Database.all,
-        options: SequenceServer.config[:options]
+        options: SequenceServer.config[:options],
+        blastTaskMap: SequenceServer::BLAST::Tasks.to_h
       }
 
       searchdata.update(tree: Database.tree) if SequenceServer.config[:databases_widget] == 'tree'