lib/transcriptic/cli.rb in transcriptic-0.2.2 vs lib/transcriptic/cli.rb in transcriptic-0.2.3

@@ -94,33 +94,54 @@
         ret.each do |run|
           say "  #{run.name}"
         end
       end
 
+      desc "lookup QUERY", "Search for resources"
+      long_desc <<-LONGDESC
+        Search your organization's resource library as well as all public resources (i.e., commercial reagents).  Useful
+        \x5 for looking up resource IDs of the format VENDOR/SKU as required for use in protocols.  Example:
+
+        transcriptic lookup phusion
+        \x5===> NEB/M0530   Phusion High-Fidelity DNA Polymerase
+        \x5===> NEB/M0535   Phusion Hot Start Flex DNA Polymerase
+        \x5===> NEB/B0519   Phusion GC Buffer
+        \x5===> NEB/B0518   Phusion HF Buffer
+      LONGDESC
+      method_option :limit, type: :numeric, desc: "Maximum number of results to return"
+      def lookup(term)
+        ret = transcriptic.search_resources(term)
+        ret["results"].each do |result|
+          output_with_arrow "#{result[:resource_id]}: #{result[:name]}"
+        end
+      end
+
       desc "update", "Update the project's dependencies"
       def update
         require_labfile!
         output_with_arrow "Updating dependencies..."
         labfile = Transcriptic::Labfile.from_file(Transcriptic.find_labfile)
         Transcriptic::DependenciesGenerator.new([Dir.pwd, labfile.dependencies], options).invoke_all
+        Transcriptic::SBT.update
       end
 
       desc "compile", "Compile the project"
       def compile
         require_labfile!
         update
         Transcriptic::SBT.compile
       end
 
       desc "analyze OBJECTPATH", "Analyze a protocol.  Object path is of the form edu.foo.bar where bar is the name of your Protocol object."
-      method_options :raw => :boolean, :iterations => :integer
+      method_options :raw => :boolean, :iterations => :numeric, :linearize => :boolean
       def analyze(object_path)
         raw = options.raw ? "--raw" : ""
+        linearize = options.linearize ? "--linearize" : ""
         iterations = options.iterations ? options.iterations : 5
         require_labfile!
         update
         Transcriptic::SBT.stage
-        data = `target/start #{object_path} --verify #{raw} --iterations #{iterations}`
+        data = `target/start #{object_path} --verify #{raw} #{linearize} --iterations #{iterations}`
         if not options.raw
           json = json_decode(data)
           output_with_arrow "Verification successful for #{object_path}"
           output_with_indent "Expected cost: $#{json["price_avg"]}, maximum observed cost: $#{json["price_max"]}"
         else