transcriptic 0.2.2 → 0.2.3

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
-  metadata.gz: df7520b6492d5e8e386b736c581a85139675ca58
-  data.tar.gz: 2fa1a96e201c8e7bfcb439709c4c8696027d622c
+  metadata.gz: 01ee5e633ccf6090da9f9c302ed28d5ebcb51a91
+  data.tar.gz: 082a53ce0fea38126c1ab6e3d2c1a8e88d568c94
 SHA512:
-  metadata.gz: c6e0a7a3a6d862678dceb771223d267c824b8a909d4a20e9baa95a0907eb13c8df136cbba72a443ae4378e6d7a4bba0f4c9c42274888f4ebeb33928f2af81295
-  data.tar.gz: 396a542b17b24a4dbd17c5e84b6c6afbb917e950a7e3c74d8ba6e6611eb55b36119465e220955170558efe20559c65e71a62550beb66f4d422d517802e3d6fea
+  metadata.gz: d547dcbf5cd749034f0a053dd5ce9e54db318bb2b084777e91c044c3db8343a3f64813ba7946cb004e61c40c964a84b63b1b516f934d6e76923ad5813962764c
+  data.tar.gz: 2a601e5d2f5dc0f3b78a9906b14d78978ac76904b4eb5a6853755596b67db115de69233f6ab02ad3d9c2acd3cb1bf321cb49e78b8a850e683558ee238d01037b

data/lib/transcriptic/cli.rb

@@ -96,12 +96,32 @@ module Transcriptic
         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"
@@ -112,14 +132,15 @@ module Transcriptic
       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}"

data/lib/transcriptic/client.rb

@@ -5,7 +5,8 @@
 #
 #   require 'transcriptic'
 #   transcriptic = Transcriptic::Client.new('me@example.com', 'mypass')
-#   transcriptic.create('myapp')
+#   transcriptic.list_resources
+#   transcriptic.run_info("run-625f827a")
 #
 class Transcriptic::Client
   include Transcriptic::UI
@@ -15,7 +16,7 @@ class Transcriptic::Client
   end
 
   def self.gem_version_string
-    "transcriptic-gem/#{version}"
+    "transcriptic/#{version}"
   end
 
   attr_accessor :host, :user, :api_key
@@ -31,49 +32,82 @@ class Transcriptic::Client
     @host = host
   end
 
-  def list_projects
-    json_decode get("/api/projects.json").to_s
+  def search_resources(term, limit = 10)
+    json_decode get("/api/resources/search.json?query=#{escape(term)}&limit=#{limit}").to_s
   end
 
-  def project_info(name)
-    json_decode get("/api/projects/#{name}.json").to_s
+  def list_resources
+    json_decode get("/api/resources.json").to_s
   end
 
-  class ProtocolException < RuntimeError; end
+  def resource_info(id)
+    json_decode get("/api/resources/#{id}.json").to_s
+  end
 
-  # Show a list of projects which you are a collaborator on.
-  def list
-    json_decode get('/api/runs.json').to_s
+  def list_runs
+    json_decode get("/api/runs.json").to_s
   end
 
-  def list_datasets(run_id = nil, project_id = nil)
-    json_decode get("/api/datasets.json?run_id=#{run_id}&project_id=#{project_id}").to_s
+  def run_info(id)
+    json_decode get("/api/runs/#{id}.json").to_s
   end
 
-  def get_dataset_info(dataset_id)
-    json_decode get("/api/datasets/#{dataset_id}").to_s
+  def create_run(fd, project_id)
+    payload = {
+      'zipdata' => Base64.encode64(File.open(fd).read),
+      'project_id' => project_id
+    }
+    json_decode post("/api/runs", payload, { 'Content-Type' => 'application/zip; charset=UTF-8' }).to_s
   end
 
-  def delete_dataset(dataset_id)
-    json_decode delete("/api/datasets/#{dataset_id}").to_s
+  def protocol(run_id)
+    Protocol.new(self, run_id)
   end
 
-  # Show info such as mode, custom domain, and collaborators on an app.
-  def info(name_or_domain)
-    name_or_domain = name_or_domain.gsub(/^(http:\/\/)?(www\.)?/, '')
+  def read_logs(run_id, options=[])
+    query = "&" + options.join("&") unless options.empty?
+    url = get("/api/runs/#{run_id}/logs.json?#{query}").to_s
+    if 'not_found' == url
+      error "Run #{run_id} not found!"
+    end
+
+    uri  = URI.parse(url);
+    http = Net::HTTP.new(uri.host, uri.port)
+
+    if uri.scheme == 'https'
+      http.use_ssl = true
+      http.verify_mode = OpenSSL::SSL::VERIFY_NONE
+    end
+
+    http.read_timeout = 60 * 60 * 24
+
+    begin
+      http.start do
+        http.request_get(uri.path + (uri.query ? "?" + uri.query : "")) do |request|
+          request.read_body do |chunk|
+            yield chunk
+          end
+        end
+      end
+    rescue Errno::ECONNREFUSED, Errno::ETIMEDOUT, SocketError
+      abort(" !    Could not connect to logging service")
+    rescue Timeout::Error, EOFError
+      abort("\n !    Request timed out")
+    end
   end
 
+  class ProtocolException < RuntimeError; end
+
   class Protocol
-    attr_accessor :attached, :upid
+    attr_accessor :attached
 
-    def initialize(client, protocol, upid=nil)
+    def initialize(client, protocol)
       @client = client
       @protocol = protocol
-      @upid = upid
     end
 
     # launch the protocol
-    def launch(command, attached=false)
+    def launch(command, attached = false)
       @attached = attached
       @response = @client.post(
         "/api/runs/#{@app}/confirm",
@@ -129,58 +163,6 @@ class Transcriptic::Client
     end
   end
 
-  def status(run_id)
-    json_decode get("/api/runs/#{run_id}").to_s
-  end
-
-  def create_run(fd, project_id)
-    payload = {
-      'zipdata' => Base64.encode64(File.open(fd).read),
-      'project_id' => project_id
-    }
-    json_decode post("/api/runs", payload, { 'Content-Type' => 'application/zip; charset=UTF-8' }).to_s
-  end
-
-  def launch_run(run_id)
-    json_decode post("/api/runs/#{run_id}/confirm").to_s
-  end
-
-  def protocol(run_id, upid)
-    Protocol.new(self, run_id, upid)
-  end
-
-  def read_logs(run_id, options=[])
-    query = "&" + options.join("&") unless options.empty?
-    url = get("/api/runs/#{run_id}/logs.json?#{query}").to_s
-    if 'not_found' == url
-      error "Run #{run_id} not found!"
-    end
-
-    uri  = URI.parse(url);
-    http = Net::HTTP.new(uri.host, uri.port)
-
-    if uri.scheme == 'https'
-      http.use_ssl = true
-      http.verify_mode = OpenSSL::SSL::VERIFY_NONE
-    end
-
-    http.read_timeout = 60 * 60 * 24
-
-    begin
-      http.start do
-        http.request_get(uri.path + (uri.query ? "?" + uri.query : "")) do |request|
-          request.read_body do |chunk|
-            yield chunk
-          end
-        end
-      end
-    rescue Errno::ECONNREFUSED, Errno::ETIMEDOUT, SocketError
-      abort(" !    Could not connect to logging service")
-    rescue Timeout::Error, EOFError
-      abort("\n !    Request timed out")
-    end
-  end
-
   def on_warning(&blk)
     @warning_callback = blk
   end

data/lib/transcriptic/sbt.rb

@@ -13,6 +13,11 @@ module Transcriptic
         sbt("stage")
       end
 
+      def update
+        ensure_installed
+        sbt("update")
+      end
+
       private
       def ensure_installed
         stat = `which sbt`

data/lib/transcriptic/templates/project/Build.erb

@@ -49,7 +49,7 @@ object AutoprotocolBuild extends Build {
     "<%= name %>",
     file("."),
     settings =
-      buildSettings ++ Seq (libraryDependencies ++= (Seq("org.autoprotocol" %% "autoprotocol" % "0.1.0-SNAPSHOT") ++
+      buildSettings ++ Seq (libraryDependencies ++= (Seq("org.autoprotocol" %% "autoprotocol-library" % "0.1.1-SNAPSHOT") ++
         dependencies), resolvers ++= Seq(transcriptic, autoprotocol, typesafe)) ++ Defaults.defaultSettings ++ 
         StartScriptPlugin.startScriptForClassesSettings
   ) settings (

data/lib/transcriptic/version.rb

@@ -1,4 +1,4 @@
 module Transcriptic
-  VERSION = "0.2.2"
+  VERSION = "0.2.3"
   AUTOPROTOCOL_VERSION = "0.1.0"
 end

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: transcriptic
 version: !ruby/object:Gem::Version
-  version: 0.2.2
+  version: 0.2.3
 platform: ruby
 authors:
 - Transcriptic
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2013-06-21 00:00:00.000000000 Z
+date: 2013-06-26 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: netrc