Merge pull request #23 from unipept/feature/pept2filtered-cutoff

Add cutoff parameter to pept2filtered

app/controllers/mpa_controller.rb

@@ -44,6 +44,7 @@ def pept2data
 
   def pept2filtered
     peptides = params[:peptides] || []
+    cutoff = params[:cutoff] || 1000
     # missed = params[:missed] || false
     taxa_filter_ids = (params[:taxa] || []).map(&:to_i)
 
@@ -52,11 +53,18 @@ def pept2filtered
     @seq_entries = {}
     uniprot_ids = []
 
+    peptides_under_cutoff = Sequence
+                            .joins(:peptides)
+                            .where(sequence: peptides)
+                            .group('sequences.id')
+                            .having('count(peptides.id) < ?', cutoff)
+                            .pluck(:sequence)
+
     taxa_filter_ids.each_slice(5000) do |taxa_slice|
       sequence_subset = Sequence
                         .joins(peptides: [:uniprot_entry])
                         .includes(peptides: [:uniprot_entry])
-                        .where(sequence: peptides)
+                        .where(sequence: peptides_under_cutoff)
                         .where(uniprot_entry: { taxon_id: taxa_slice })
                         .uniq
 

config/application.rb

@@ -13,16 +13,16 @@ class Application < Rails::Application
     config.load_defaults 7.0
 
     config.versions = {
-      unipept: '4.6.4',
-      gem: '2.2.1',
-      uniprot: '2021.03',
-      desktop: '1.2.4'
+      unipept: '5.0.9',
+      gem: '3.0.2',
+      uniprot: '2023.03',
+      desktop: '2.0.0'
     }
-    
+
     config.api_only = true
 
     config.api_host = 'api.unipept.ugent.be'
-    
+
     MultiJson.use :Oj
   end
 end

config/database.yml

@@ -1,11 +1,12 @@
 default: &default
   adapter: mysql2
-  username: unipept
+  username: root
   password: unipept
   pool: <%= ENV.fetch("RAILS_MAX_THREADS") { 5 } %>
 
 development:
   <<: *default
+  username: unipept
   database: unipept
   # setup local port forwarding for this to work
   host: 127.0.0.1

config/deploy/feat.rb

@@ -2,12 +2,16 @@
 
 set :deploy_to, '/home/unipept/rails'
 
+set :server, ENV['server'] || 'rick.ugent.be'
+
+#set :rvm_custom_path, '/usr/share/rvm'
+
 # don't specify db as it's not needed for unipept
-server 'sherlock.ugent.be', user: 'unipept', roles: %i[web app], ssh_options: {
+server "#{fetch(:server)}", user: 'unipept', roles: %i[web app], ssh_options: {
   port: 4840
 }
 
-set :branch, 'feature/pept2filtered'
+set :branch, 'feature/pept2filtered-cutoff'
 set :rails_env, :development
 
 namespace :deploy do
@@ -22,4 +26,6 @@
       upload! StringIO.new(content), "#{release_path}/public/robots.txt"
     end
   end
+
 end
+

config/deploy/prod.rb

@@ -2,8 +2,12 @@
 
 set :deploy_to, '/home/unipept/rails'
 
+set :server, ENV['server'] || 'patty.ugent.be'
+
+#set :rvm_custom_path, '/usr/share/rvm'
+
 # don't specify db as it's not needed for unipept
-server 'rick.ugent.be', user: 'unipept', roles: %i[web app], ssh_options: {
+server "#{fetch(:server)}", user: 'unipept', roles: %i[web app], ssh_options: {
   port: 4840
 }
 

config/environments/development.rb

@@ -53,8 +53,9 @@
   config.active_record.migration_error = :page_load
 
   # Highlight code that triggered database queries in logs.
-  config.active_record.verbose_query_logs = true
+  # config.active_record.verbose_query_logs = true
 
+  # config.log_level = :info
 
   # Raises error for missing translations.
   # config.i18n.raise_on_missing_translations = true

config/environments/production.rb

@@ -71,6 +71,9 @@
   # Use default logging formatter so that PID and timestamp are not suppressed.
   config.log_formatter = ::Logger::Formatter.new
 
+  # Do not log SQL queries in production mode (this can cause the server to go out of disk space).
+  config.log_level = :info
+
   # Use a different logger for distributed setups.
   # require "syslog/logger"
   # config.logger = ActiveSupport::TaggedLogging.new(Syslog::Logger.new "app-name")