genevalidatorapp 2.1.0 → 2.1.1

checksums.yaml

@@ -1,7 +1,7 @@
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+  data.tar.gz: cc26578078bddb08c9eec2dcfbf4bf52688a25871f6e7e02c1ba83068a23ede3
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+  data.tar.gz: 8ac6ca88671374c76e57ab9e0b72318f1c42d45ce4bcb324b5be61dbeb5a70bc3d33a921a86eb3e8aa38b5e8d1b1182bc6937041ed6e9b91c13d75054b5702d6

data/.ruby-version

@@ -0,0 +1 @@
+2.2

data/genevalidatorapp.gemspec

@@ -7,7 +7,7 @@ Gem::Specification.new do |s|
   s.name          = 'genevalidatorapp'
   s.version       = GeneValidatorApp::VERSION
   s.authors       = ['Monica Dragan', 'Ismail Moghul', 'Anurag Priyam',
-                        'Yannick Wurm']
+                     'Yannick Wurm']
   s.email         = 'y.wurm@qmul.ac.uk'
   s.summary       = 'A Web App wrapper for GeneValidator.'
   s.description   = 'A Web App wrapper for GeneValidator, a program for' \
@@ -16,7 +16,6 @@ Gem::Specification.new do |s|
   s.license       = 'AGPL'
 
   s.files         = `git ls-files -z`.split("\x0")
-  s.executables   = s.files.grep(%r{^bin/}) { |f| File.basename(f) }
   s.test_files    = s.files.grep(%r{^(test|spec|features)/})
   s.require_paths = ['lib']
 

data/lib/genevalidatorapp/genevalidator.rb

@@ -211,7 +211,7 @@ module GeneValidatorApp
 
       def parse_output_json
         json_contents = File.read(output_json_file_path)
-        JSON.parse(json_contents)
+        JSON.parse(json_contents,symbolize_names: true)
       end
 
       def output_json_file_path

data/lib/genevalidatorapp/routes.rb

@@ -52,7 +52,7 @@ module GeneValidatorApp
       cross_origin # Required for the API to work...
       RunGeneValidator.init(request.url, params)
       @gv_results = RunGeneValidator.run
-      @json_results = @gv_results[:parsed_json]
+      @json_data_section = @gv_results[:parsed_json]
       if @params[:results_url]
         @gv_results[:results_url]
       elsif @params[:json_url]

data/lib/genevalidatorapp/version.rb

@@ -1,3 +1,3 @@
 module GeneValidatorApp
-  VERSION = '2.1.0'
+  VERSION = '2.1.1'
 end

data/views/results.slim

@@ -1,7 +1,24 @@
 h4 Overview
 #overview.text-left
+  span
+    strong BLAST Database Used: 
+    = @params[:database]
+    br
+    strong BLAST E-Value Used: 
+    | 10<sup>-5</sup>
+  br
   #overview_text
-  button#overview_btn.btn.btn-primary.btn-sm data-toggle="button" onclick="GV.toggleOverviewBtn();" data-overviewjson="/GeneValidator/#{@gv_results[:unique_id]}/output/html_files/json/overview.json"
+  button#overview_btn.btn.btn-primary.btn-sm style="margin-bottom:10px" data-toggle="button" onclick="GV.toggleOverviewBtn();" data-overviewjson="/GeneValidator/#{@gv_results[:unique_id]}/output/html_files/json/overview.json"
+  br
+
+  - output_dir = "/GeneValidator/#{@gv_results[:unique_id]}/output/"
+  - csv_file = File.join(output_dir, 'input_file_results.csv')
+  - json_file = File.join(output_dir, 'input_file_results.json')
+  - summary_file = File.join(output_dir, 'input_file_summary.csv')
+  a.btn.btn-primary.btn-sm target="_blank" download="" style="margin-right:10px;" href="#{uri(csv_file)}" CSV Output File
+  a.btn.btn-primary.btn-sm target="_blank" download="" style="margin-right:10px;" href="#{uri(json_file)}" JSON Output File
+  a.btn.btn-primary.btn-sm target="_blank" download="" style="margin-right:10px;" href="#{uri(summary_file)}" Summary CSV Output File
+
 br/
 hr/
 h4#results_header Results
@@ -18,37 +35,35 @@ table#sortable_table.table.table-striped.table-collapsed.table-bordered.table-co
         | No. Hits 
         span data-placement="top" data-toggle="tooltip" title=("Number of non-identical hits found by BLAST.")
           i.fa.fa-question-circle
-      - @json_results[0]['validations'].each do |_short_header, item|
-        th.sorter-false
-          b= item['header']
-          |  &nbsp;
-          - if item['header'] == "Length Cluster" || item['header'] == "Gene Merge" || item['header'] == "Main ORF" || item['header'] == "Missing/Extra Sequences"
-            span data-placement="top" data-toggle="tooltip" title=("Charts available for this validation")
-              i.fa.fa-bar-chart-o.chartIcon
-            |  &nbsp;
-            span data-placement="top" data-toggle="tooltip" title="#{item['description']}"
-              i.fa.fa-question-circle
-          - else
-            span data-placement="top" data-toggle="tooltip" title="#{item['description']}"
+      - @json_data_section[0][:validations].each do |_short_header, item|
+          th.sorter-false
+            strong
+              = item[:header]
+            |  
+            - if item[:header] == "Length Cluster" || item[:header] == "Gene Merge" || item[:header] == "Main ORF" || item[:header] == "Missing/Extra Sequences"
+              span data-placement="top" data-toggle="tooltip" title=("Charts available for this validation")
+                i.fa.fa-bar-chart-o.chartIcon
+            |  
+            span data-placement="top" data-toggle="tooltip" title="#{item[:description]}"
               i.fa.fa-question-circle
       th.sorter-false.chart-column
   tbody
-    - @json_results.each do |query|
-      - json_file = "/GeneValidator/#{@gv_results[:unique_id]}/output/html_files/json/input_file_#{query['idx']}.json"
-      tr data-jsonfile="#{uri(json_file)}" data-target="toggle#{query['idx']}"
-        td title="idx" = query['idx']
-        td data-score="#{query['overall_score']}"
+    - @json_data_section.each do |row|
+      - json_file = "/GeneValidator/#{@gv_results[:unique_id]}/output/html_files/json/input_file_#{row[:idx]}.json"
+      tr data-jsonfile="#{uri(json_file)}" data-target="toggle#{row[:idx]}"
+        td title="idx" = row[:idx]
+        td data-score="#{row[:overall_score]}"
           .ratings
             .empty-stars
-            .full-stars style=("width:#{query['overall_score']}%;")
-        td title="Definition" = query['definition']
-        td title=("No. Hits") = query['no_hits']
-        - query['validations'].each do |_short_header, item|
-          td class="#{item['status']}" title="#{item['header']}"
-            == item['print'].gsub(/\s/, '&nbsp;').gsub(';&nbsp;', '; ')
-        - if query['validations'].select{|_short_header, item| item['graphs'] != nil}.map{|_short_header, item| item['graphs'].length}.inject(0){|r, e| r+e } != 0
+            .full-stars style=("width:#{row[:overall_score]}%;")
+        td title="Definition" = row[:definition]
+        td title=("No. Hits") = row[:no_hits]
+        - row[:validations].each do |_short_header, item|
+          td class="#{item[:status]}" title="#{item[:header]}"
+            == item[:print].gsub(' ', '&nbsp;').gsub(';&nbsp;', '; ')
+        - if row[:validations].select { |_short_header, item| item[:graphs] != nil }.map{ |_short_header, item| item[:graphs].length }.inject(0) { |r, e| r + e } != 0
           td
             button.plot_btn.btn.btn-default title=("Show plots")
               i.fa.fa-bar-chart-o
         - else
-          td
+          td

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: genevalidatorapp
 version: !ruby/object:Gem::Version
-  version: 2.1.0
+  version: 2.1.1
 platform: ruby
 authors:
 - Monica Dragan
@@ -124,6 +124,7 @@ extensions: []
 extra_rdoc_files: []
 files:
 - ".gitignore"
+- ".ruby-version"
 - ".travis.yml"
 - Gemfile
 - LICENSE.txt