linting cleanups

bin/fetch-categories.rb

@@ -6,7 +6,7 @@
 
 # Get the list of toolcats
 def fetch_toolcats(server)
-  uri = URI.parse("#{server}")
+  uri = URI.parse(server.to_s)
   request = Net::HTTP::Get.new(uri)
   req_options = {
     use_ssl: uri.scheme == 'https',
@@ -45,16 +45,11 @@ def fetch_toolcats(server)
   values = [eu, org, aus].compact
   # values = [org].compact
 
-
   # Majority answer wins
   # set that value to toolcats[k]
   # If there is no majority, pick one.
   # print("#{k} - #{values.length} => #{values.uniq.compact.length}\n")
-  if values.length.positive?
-    toolcats[k] = values.max_by { |v| v['count'] }
-  else
-    toolcats[k] = nil
-  end
+  toolcats[k] = (values.max_by { |v| v['count'] } if values.length.positive?)
 end
 
 # Write the list to a file

bin/lint.rb

@@ -1110,7 +1110,9 @@ def self.enumerate_symlinks
   end
 
   def self.enumerate_lintable
-    enumerate_type(/bib$/) + enumerate_type(/md$/) + enumerate_type(/md$/, root_dir: 'faqs') + enumerate_type(/md$/, root_dir: 'news')
+    enumerate_type(/bib$/) + enumerate_type(/md$/) + enumerate_type(/md$/,
+                                                                    root_dir: 'faqs') + enumerate_type(/md$/,
+                                                                                                       root_dir: 'news')
   end
 
   def self.enumerate_all

bin/workflow-test.rb

@@ -1,16 +1,17 @@
 #!/usr/bin/env ruby
 # frozen_string_literal: true
+
 require './_plugins/gtn/usegalaxy'
 
 require 'open3'
 require 'json'
 
-GALAXIES = Gtn::Usegalaxy.servers.select{|s| s[:id] == "eu"}.map do |server|
+GALAXIES = Gtn::Usegalaxy.servers.select { |s| s[:id] == 'eu' }.to_h do |server|
   [
     server[:id],
     { url: server[:url], key: ENV.fetch("GALAXY_#{server[:id].upcase}_KEY", 'NONE') }
   ]
-end.to_h
+end
 
 def test_workflow(workflow_file, galaxy_id)
   directory = File.dirname(workflow_file)

bin/workflows-fetch.rb

@@ -5,18 +5,16 @@
 require 'yaml'
 require './_plugins/gtn/usegalaxy'
 
-
 def request(url)
   uri = URI.parse(url)
   request = Net::HTTP::Get.new(uri)
   request['Accept'] = 'application/json'
   req_options = {
     use_ssl: uri.scheme == 'https',
   }
-  response = Net::HTTP.start(uri.hostname, uri.port, req_options) do |http|
+  Net::HTTP.start(uri.hostname, uri.port, req_options) do |http|
     http.request(request)
   end
-  response
 end
 
 # Get the list of workflows
@@ -33,34 +31,32 @@ def fetch_workflows(server)
   end
 end
 
-def fetch_workflowhub()
-  projects = JSON.parse(request("https://workflowhub.eu/projects").body)
-  project_mapping = projects['data'].map{|p| [p['id'], p['attributes']['title']]}.to_h
+def fetch_workflowhub
+  projects = JSON.parse(request('https://workflowhub.eu/projects').body)
+  project_mapping = projects['data'].to_h { |p| [p['id'], p['attributes']['title']] }
 
-  response = request("https://workflowhub.eu/workflows?filter[workflow_type]=galaxy")
+  response = request('https://workflowhub.eu/workflows?filter[workflow_type]=galaxy')
   data = JSON.parse(response.body)
   if !data['links']['next'].nil?
-    puts "ERROR: Cannot yet handle multiple pages"
+    puts 'ERROR: Cannot yet handle multiple pages'
     exit 42
   end
   puts "INFO: Fetching #{data['data'].length} workflows from WorkflowHub"
-  data['data'].map.with_index { |w, i|
+  data['data'].map.with_index do |w, _i|
     # {"id"=>"14", "type"=>"workflows", "attributes"=>{"title"=>"Cheminformatics - Docking"}, "links"=>{"self"=>"/workflows/14"}}
     wf_info = JSON.parse(request("https://workflowhub.eu#{w['links']['self']}").body)
     creator_list = []
 
     creator0 = wf_info['data']['attributes']['creators'][0]
-    owner = ""
-    if !creator0.nil?
-      # Primary
-      creator_list.push(creator0['given_name'] + " " + creator0['family_name'])
-    else
+    if creator0.nil?
       # Other creators
       other = wf_info['data']['attributes']['other_creators']
       if !other.nil? && other.length.positive?
-        creator_list.push(wf_info['data']['attributes']['other_creators'].split(',').map{|x| x.strip})
-      else
+        creator_list.push(wf_info['data']['attributes']['other_creators'].split(',').map(&:strip))
       end
+    else
+      # Primary
+      creator_list.push("#{creator0['given_name']} #{creator0['family_name']}")
     end
     # Projects
     wf_info['data']['relationships']['projects']['data'].each do |p|
@@ -76,31 +72,30 @@ def fetch_workflowhub()
         'number_of_steps' => wf_info['data']['attributes']['internals']['steps'].length,
         'server' => 'https://workflowhub.eu',
         'id' => wf_info['data']['id'],
-        'tags' => wf_info['data']['attributes']['tags'].map{|t| t.gsub(/^name:/, '')},
+        'tags' => wf_info['data']['attributes']['tags'].map { |t| t.gsub(/^name:/, '') },
         'update_time' => wf_info['data']['attributes']['updated_at'],
       }
-    rescue
+    rescue StandardError
       r = nil
     end
     r
-  }.reject{|x| x.nil? }
+  end.compact
 end
 
-
 # Parse the response
-workflows = Gtn::Usegalaxy.servers.map {|server|
+workflows = Gtn::Usegalaxy.servers.map do |server|
   workflows = fetch_workflows(server[:url])
   puts "INFO: Fetched #{workflows.length} workflows from #{server[:name]}"
   workflows
-}.flatten
+end.flatten
 
 # Cleanup the list
 workflows.filter! do |w|
   w['published'] == true && w['importable'] == true && w['deleted'] == false && w['hidden'] == false
 end
 
 # Add in WFHub workflows
-workflows += fetch_workflowhub()
+workflows += fetch_workflowhub
 
 # Group by name + owner
 cleaned = workflows.group_by { |w| "#{w['name']}<WFID>#{w['owner']}" }