feat: add in metadata key value searching to samples table

phac-nml · Oct 3, 2024 · 864fa3e · 864fa3e
1 parent c21f739
commit 864fa3e
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Showing 9 changed files with 117 additions and 9 deletions.
diff --git a/Gemfile b/Gemfile
@@ -68,6 +68,9 @@ gem 'pagy', '~> 9.0.5' # omit patch digit
 # Ransack
 gem 'ransack', '~> 4.2.1'
 
+# Search Syntax
+gem 'search_syntax'
+
 # Use Active Storage variants [https://guides.rubyonrails.org/active_storage_overview.html#transforming-images]
 # gem "image_processing", "~> 1.2"
 

diff --git a/Gemfile.lock b/Gemfile.lock
@@ -417,6 +417,7 @@ GEM
       ast (~> 2.4.1)
       racc
     pg (1.5.7)
+    polyglot (0.3.5)
     prettier_print (1.2.1)
     psych (5.1.2)
       stringio
@@ -536,6 +537,8 @@ GEM
       nokogiri (>= 1.13.10)
       rexml
     rubyzip (2.3.2)
+    search_syntax (0.1.3)
+      treetop (~> 1.6)
     securerandom (0.3.1)
     signet (0.19.0)
       addressable (~> 2.8)
@@ -603,6 +606,8 @@ GEM
     timecop (0.9.10)
     timeout (0.4.1)
     trailblazer-option (0.1.2)
+    treetop (1.6.12)
+      polyglot (~> 0.3)
     turbo-rails (2.0.6)
       actionpack (>= 6.0.0)
       activejob (>= 6.0.0)
@@ -707,6 +712,7 @@ DEPENDENCIES
   rubocop
   rubocop-graphql
   rubocop-rails
+  search_syntax
   simplecov
   solargraph
   sprockets-rails

diff --git a/app/controllers/groups/samples_controller.rb b/app/controllers/groups/samples_controller.rb
@@ -7,7 +7,7 @@ class SamplesController < Groups::ApplicationController
     include Storable
 
     before_action :group, :current_page
-    before_action :process_samples, only: %i[index search]
+    before_action :process_samples, only: %i[index search select]
     include Sortable
 
     def index
@@ -25,10 +25,7 @@ def select
 
       respond_to do |format|
         format.turbo_stream do
-          if params[:select].present?
-            @q = authorized_samples.ransack(search_params)
-            @selected_sample_ids = @q.result.select(:id).pluck(:id)
-          end
+          @selected_sample_ids = @q.result.select(:id).pluck(:id) if params[:select].present?
         end
       end
     end
@@ -75,8 +72,11 @@ def process_samples
       authorize! @group, to: :sample_listing?
       @search_params = search_params
       set_metadata_fields
-
-      @q = authorized_samples.ransack(@search_params)
+      query_parser = Irida::SearchSyntax::Ransack.new(text: :name_or_puid_cont,
+                                                      # params: { project: 'project_namespace_puid' },
+                                                      metadata_fields: @fields)
+      parsed_params = query_parser.parse(@search_params.fetch(:name_or_puid_cont, nil))
+      @q = authorized_samples.ransack(@search_params.except(:name_or_puid_cont).merge(parsed_params))
     end
 
     def search_params

diff --git a/app/controllers/projects/samples_controller.rb b/app/controllers/projects/samples_controller.rb
@@ -144,7 +144,9 @@ def process_samples
       @search_params = search_params
 
       set_metadata_fields
-      @q = load_samples.ransack(@search_params)
+      query_parser = Irida::SearchSyntax::Ransack.new(text: :name_or_puid_cont, metadata_fields: @fields)
+      parsed_params = query_parser.parse(@search_params.fetch(:name_or_puid_cont, nil))
+      @q = load_samples.ransack(@search_params.except(:name_or_puid_cont).merge(parsed_params))
     end
 
     def search_params

diff --git a/app/models/sample.rb b/app/models/sample.rb
@@ -36,6 +36,7 @@ def self.ransackable_attributes(_auth_object = nil)
   end
 
   def self.ransackable_associations(_auth_object = nil)
+    #%w[project]
     %w[]
   end
 

diff --git a/app/views/groups/samples/index.html.erb b/app/views/groups/samples/index.html.erb
@@ -110,6 +110,7 @@
                 <%= viral_icon(name: "magnifying_glass", classes: "h-5 w-5") %>
               </div>
               <%= f.search_field :name_or_puid_cont,
+                             value: @search_params[:name_or_puid_cont],
                              "data-action": "filters#submit",
                              class:
                                "block w-full p-2.5 pl-10 text-sm text-slate-900 border border-slate-300 rounded-lg bg-slate-50 focus:ring-primary-500 focus:border-primary-500 dark:bg-slate-700 dark:border-slate-600 dark:placeholder-slate-400 dark:text-white dark:focus:ring-primary-500 dark:focus:border-primary-500",

diff --git a/app/views/projects/samples/index.html.erb b/app/views/projects/samples/index.html.erb
@@ -57,7 +57,7 @@
                 },
                 class:
                   "flex items-center px-4 py-2 bg-slate-100 text-slate-600 dark:bg-slate-600 dark:text-slate-300
-                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    border-slate-100 dark:border-slate-600 pointer-events-none cursor-not-allowed",
+                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            border-slate-100 dark:border-slate-600 pointer-events-none cursor-not-allowed",
               ) %>
             <% else %>
               <% dropdown.with_item(
@@ -167,6 +167,7 @@
                 <%= viral_icon(name: "magnifying_glass", classes: "h-5 w-5") %>
               </div>
               <%= f.search_field :name_or_puid_cont,
+                             value: @search_params[:name_or_puid_cont],
                              "data-action": "filters#submit",
                              class:
                                "block w-full p-2.5 pl-10 text-sm text-slate-900 border border-slate-300 rounded-lg bg-slate-50 focus:ring-primary-500 focus:border-primary-500 dark:bg-slate-700 dark:border-slate-600 dark:placeholder-slate-400 dark:text-white dark:focus:ring-primary-500 dark:focus:border-primary-500",

diff --git a/lib/irida/search_syntax/ransack.rb b/lib/irida/search_syntax/ransack.rb
@@ -0,0 +1,23 @@
+# frozen_string_literal: true
+
+require_relative 'ransack_transformer'
+
+module Irida
+  module SearchSyntax
+    # IRIDA Next specific Ransack search syntax parser that supports metadata_fields
+    class Ransack
+      def initialize(text:, params: [], metadata_fields: [], sort: nil)
+        @transformer = RansackTransformer.new(text:, params:, metadata_fields:, sort:)
+        @parser = ::SearchSyntax::Parser.new
+      end
+
+      def parse_with_errors(text)
+        @transformer.transform_with_errors(@parser.parse(text || '').value)
+      end
+
+      def parse(text)
+        parse_with_errors(text)[0]
+      end
+    end
+  end
+end
diff --git a/lib/irida/search_syntax/ransack_transformer.rb b/lib/irida/search_syntax/ransack_transformer.rb
@@ -0,0 +1,71 @@
+module Irida
+  module SearchSyntax
+    # IRIDA Next specific RansackTransformer that supoorts metadata_fields
+    class RansackTransformer < ::SearchSyntax::RansackTransformer
+      def initialize(text:, params:, metadata_fields:, sort: nil)
+        super(text:, params:, sort:)
+        @metadata_fields = metadata_fields
+      end
+
+      def transform_with_errors(ast) # rubocop:disable Metrics/AbcSize,Metrics/CyclomaticComplexity,Metrics/MethodLength,Metrics/PerceivedComplexity
+        errors = []
+        result = {}
+
+        if @allowed_params.length.positive? || @metadata_fields.length.positive?
+          ast = ast.filter do |node| # rubocop:disable Metrics/BlockLength
+            if node[:type] != :param
+              true
+            elsif node[:name] == @sort
+              result[:s] = transform_sort_param(node[:value])
+              false
+            elsif @allowed_params.include?(node[:name])
+              key = name_with_predicate(node)
+              if result.key?(key)
+                errors.push(::SearchSyntax::DuplicateParamError.new(
+                              name: node[:name],
+                              start: node[:start],
+                              finish: node[:finish]
+                            ))
+              else
+                result[key] = node[:value]
+              end
+              false
+            elsif @metadata_fields.include?(node[:name])
+              key = 'metadata_jcont'
+              search_value = {}
+              search_value = JSON.parse(result[key]) if result.key?(key)
+              if search_value.key?(node[:name])
+                errors.push(::SearchSyntax::DuplicateParamError.new(
+                              name: node[:name],
+                              start: node[:start],
+                              finish: node[:finish]
+                            ))
+              else
+                search_value[node[:name]] = node[:value]
+                result[key] = JSON.generate(search_value)
+              end
+              false
+            else
+              errors.push(::SearchSyntax::UnknownParamError.new(
+                            name: node[:name],
+                            start: node[:start],
+                            finish: node[:finish],
+                            did_you_mean: @spell_checker.correct(node[:name])
+                          ))
+              true
+            end
+          end
+        end
+
+        previous = -1
+        result[@text] = ast.map do |node|
+          separator = previous == node[:start] || previous == -1 ? '' : ' '
+          previous = node[:finish]
+          separator + node[:raw]
+        end.join
+
+        [result, errors]
+      end
+    end
+  end
+end