czi dependency rake task

Author: andrew

.gitignore

@@ -33,5 +33,6 @@
 
 .env
 
-# Ignore generated csv files
-*.csv
+# Ignore generated files
+*.csv
+data/*

lib/tasks/czi.rake

@@ -0,0 +1,71 @@
+require 'csv'
+
+namespace :czi do
+  task :bioconductor => :environment do
+    # load csv file
+    csv = CSV.read('data/bioconductor_raw_df.csv', headers: true)
+
+    registry = Registry.find_by_ecosystem('bioconductor')
+
+    file = File.open("data/bioconductor.ndjson", "a")
+
+    processed_names = Set.new
+    missing_names = Set.new
+    dependencies = Set.new
+
+    csv.each do |row|
+      package = registry.packages.where('lower(name) = ?', row['Bioconductor Package'].downcase).first
+
+      if package
+        puts "#{package.name} - #{package.latest_release_number}"
+
+        obj = package.as_json(include: [latest_version: { include: :dependencies }])
+        
+        file.puts JSON.generate(obj)
+
+        processed_names << package.name.downcase
+        package.latest_version.dependencies.map(&:package_name).each do |name|
+          dependencies << name.downcase
+        end
+      else
+        puts "Package not found: #{row['Bioconductor Package']}"
+        missing_names << row['Bioconductor Package'].downcase
+      end
+    end
+
+    while dependencies.count > 0
+
+      first_level_dependencies = dependencies.flatten.uniq
+
+      dependencies = Set.new
+
+      first_level_dependencies.each do |name|
+        next if processed_names.include?(name)
+        next if missing_names.include?(name)
+        package = registry.packages.where('lower(name) = ?', name.downcase).first
+        if package
+          puts "#{package.name} - #{package.latest_release_number}"
+
+          obj = package.as_json(include: [latest_version: { include: :dependencies }])
+          
+          file.puts JSON.generate(obj)
+
+          processed_names << package.name.downcase
+          package.latest_version.dependencies.map(&:package_name).each do |name|
+            dependencies << name.downcase
+          end
+        else
+          puts "Package not found: #{name}"
+          missing_names << name.downcase
+        end
+      end
+
+      puts "Processed #{processed_names.uniq.count} packages"
+      puts "Found #{missing_names.uniq.count} missing packages"
+      puts "Found #{dependencies.uniq.count} dependencies"
+      puts '--------------------------'
+    end
+
+  end
+end
+