transcriptic 0.1.2 → 0.1.3

data/lib/transcriptic/api.rb

@@ -1,8 +1,12 @@
+require "base64"
+require "excon"
+require "securerandom"
+require "uri"
+require "zlib"
+
 require "transcriptic/api/errors"
 require "transcriptic/api/version"
 
-require "transcriptic/api/sequences"
-
 srand
 
 module Transcriptic
@@ -14,17 +18,18 @@ module Transcriptic
       options = {
         :headers  => {},
         :host     => 'transcriptic.com',
+        :nonblock => false,
         :scheme   => 'https'
       }.merge(options)
       options[:headers] = {
-        'Accept'                => 'application/json',
-        'Accept-Encoding'       => 'gzip',
-        'Accept-Language'       => 'en-US, en;q=0.8',
-        'Authorization'         => "Token token=\"#{@api_key}\"",
-        'User-Agent'            => "transcriptic-cli/#{Transcriptic::API::VERSION}",
-        'X-Transcriptic-API-Version'  => '3',
-        'X-Ruby-Version'        => RUBY_VERSION,
-        'X-Ruby-Platform'       => RUBY_PLATFORM
+        'Accept'                      => 'application/json',
+        'Accept-Encoding'             => 'gzip',
+        'Accept-Language'             => 'en-US, en;q=0.8',
+        'Authorization'               => "Token token=\"#{@api_key}\"",
+        'User-Agent'                  => "transcriptic-cli/#{Transcriptic::API::VERSION}",
+        'X-Transcriptic-API-Version'  => '1',
+        'X-Ruby-Version'              => RUBY_VERSION,
+        'X-Ruby-Platform'             => RUBY_PLATFORM
       }.merge(options[:headers])
       @connection = Excon.new("#{options[:scheme]}://#{options[:host]}", options)
     end
@@ -69,5 +74,9 @@ module Transcriptic
       response
     end
 
+    def escape(string)
+      CGI.escape(string).gsub('.', '%2E')
+    end
+
   end
 end

data/lib/transcriptic/client.rb

@@ -41,25 +41,6 @@ class Transcriptic::Client
     @host = host
   end
 
-  def get_keys
-    json_decode get("/api/keys").to_s
-  end
-
-  # Add an ssh public key to the current user.
-  def add_key(key)
-    json_decode post("/api/keys", key, { 'Content-Type' => 'text/ssh-authkey' }).to_s
-  end
-
-  # Remove an existing ssh public key from the current user.
-  def remove_key(key)
-    json_decode delete("/api/keys/#{escape(key)}").to_s
-  end
-
-  # Clear all keys on the current user.
-  def remove_all_keys
-    json_decode delete("/api/keys").to_s
-  end
-
   # Get a list of stacks available to the app, with the current one marked.
   def list_stacks(app_name, options={})
     include_deprecated = options.delete(:include_deprecated) || false
@@ -86,16 +67,6 @@ class Transcriptic::Client
     json_decode resource("/organizations").get(:accept => 'application/json').to_s
   end
 
-  # Add an ssh public key to the current user.
-  def add_sequence(organization, sequence)
-    post("/#{organization}/sequences", sequence, { 'Content-Type' => 'text/ssh-authkey' }).to_s
-  end
-
-  # Remove an existing ssh public key from the current user.
-  def remove_sequence(organization, sequence)
-    delete("/#{organization}/sequences/#{escape(key)}").to_s
-  end
-
   class Protocol
     attr_accessor :attached, :upid
 
@@ -163,7 +134,7 @@ class Transcriptic::Client
   end
 
   def status(run_id)
-    json_decode resource("/runs/#{run_id}/status").get(:accept => 'application/json').to_s
+    json_decode get("/api/runs/#{run_id}").to_s
   end
 
   def create_run(fd)
@@ -177,7 +148,7 @@ class Transcriptic::Client
 
   def read_logs(run_id, options=[])
     query = "&" + options.join("&") unless options.empty?
-    url = get("/runs/#{run_id}/logs?#{query}").to_s
+    url = get("/api/runs/#{run_id}/logs?#{query}").to_s
     uri  = URI.parse(url);
     http = Net::HTTP.new(uri.host, uri.port)
 
@@ -305,7 +276,7 @@ class Transcriptic::Client
   def default_resource_options_for_uri(uri)
     if ENV["TRANSCRIPTIC_SSL_VERIFY"] == "disable"
       {}
-    elsif realize_full_uri(uri) =~ %r|^https://transcriptic.com|
+    elsif realize_full_uri(uri) =~ %r|^https://www.transcriptic.com|
       # OpenSSL::SSL::VERIFY_PEER
       { }
       #{ :verify_ssl => OpenSSL::SSL::VERIFY_NONE, :ssl_ca_file => local_ca_file }

data/lib/transcriptic/command/data.rb

@@ -3,6 +3,27 @@ module Transcriptic::Command
   # manage experimental data sets
   #
   class Data < Base
-    def index; end
+
+    # data RUNID
+    #
+    # list available datasets for RUNID
+    #
+    def index
+    end
+
+    # transcriptic data:download DATASETID
+    #
+    # download the dataset identified by DATASETID
+    #
+    def download
+    end
+
+    # transcriptic data:delete DATASETID
+    #
+    # delete the dataset identified by DATASETID
+    #
+    def delete
+    end
+
   end
 end

data/lib/transcriptic/command/help.rb

@@ -3,7 +3,7 @@ module Transcriptic::Command
   # list commands and display help
   #
   class Help < Base
-    PRIMARY_NAMESPACES = %w( analyze data history run status sequences)
+    PRIMARY_NAMESPACES = %w(run data)
     
       # help [COMMAND]
       #

data/lib/transcriptic/command/run.rb

@@ -7,24 +7,78 @@ module Transcriptic::Command
   #
   class Run < Base
 
-    # transcriptic run [FILENAME|DIRECTORY]
+    # run [FILENAME|DIRECTORY]
     #
     # upload FILENAME or DIRECTORY and launch it
     #
     def index
       path = args.shift
       fd = create_protocol_fd_for_path(path)
+      if 1 == fd
+        error "Couldn't create run!"
+      end
       display "Uploading `#{path}` to Transcriptic..."
       run_id = transcriptic.create_run(fd)["run_id"]
       display "Run launched (#{run_id})"
     end
 
+    # transcriptic run:analyze [FILENAME|DIRECTORY]
+    #
+    # upload FILENAME or DIRECTORY and analyze it
+    #
+    def analyze
+      path = args.shift
+    end
+
+    # transcriptic run:status [RUNID]
+    #
+    # show details of RUNID
+    #
+    def status
+      run_id = args.shift
+      if run_id.nil?
+        error("Usage: transcriptic status RUNID\nMust specify RUNID to get run status.")
+      end
+      ret = transcriptic.status(run_id)
+      if ret.nil?
+        error("#{run_id} not found for #{transcriptic.user}")
+        return
+      end
+      display(ret.inspect)
+    end
+
+    # transcriptic run:list
+    #
+    # list active runs
+    #
+    def list
+      ret = transcriptic.list
+      if ret.empty?
+        error("No runs for #{transcriptic.user}")
+        return
+      end
+      display("Runs:")
+      ret.each do |run|
+        display "  #{run.name}"
+      end
+    end
+
+    # transcriptic run:logs RUNID
+    #
+    # get log data for RUNID
+    #
+    def logs
+      run_id = args.shift
+      transcriptic.read_logs(run_id)
+    end
+
+    private
     def create_protocol_fd_for_path(path)
       begin
         stat = File.stat(path)
       rescue
         display "No such path: #{path}"
-        return
+        return 1
       end
       upfile = Tempfile.new('protocol')
       if stat.directory?

data/lib/transcriptic/helpers.rb

@@ -32,6 +32,16 @@ module Transcriptic
       display
     end
 
+    def format_with_bang(message)
+      return '' if message.to_s.strip == ""
+      " !    " + message.split("\n").join("\n !    ")
+    end
+
+    def output_with_bang(message="", new_line=true)
+      return if message.to_s.strip == ""
+      display(format_with_bang(message), new_line)
+    end
+
     def error(msg)
       STDERR.puts(msg)
       exit 1
@@ -275,6 +285,61 @@ module Transcriptic
         end
       end
     end
+
+    def string_distance(first, last)
+      distances = [] # 0x0s
+      0.upto(first.length) do |index|
+        distances << [index] + [0] * last.length
+      end
+      distances[0] = 0.upto(last.length).to_a
+      1.upto(last.length) do |last_index|
+        1.upto(first.length) do |first_index|
+          first_char = first[first_index - 1, 1]
+          last_char = last[last_index - 1, 1]
+          if first_char == last_char
+            distances[first_index][last_index] = distances[first_index - 1][last_index - 1] # noop
+          else
+            distances[first_index][last_index] = [
+              distances[first_index - 1][last_index],     # deletion
+              distances[first_index][last_index - 1],     # insertion
+              distances[first_index - 1][last_index - 1]  # substitution
+            ].min + 1 # cost
+            if first_index > 1 && last_index > 1
+              first_previous_char = first[first_index - 2, 1]
+              last_previous_char = last[last_index - 2, 1]
+              if first_char == last_previous_char && first_previous_char == last_char
+                distances[first_index][last_index] = [
+                  distances[first_index][last_index],
+                  distances[first_index - 2][last_index - 2] + 1 # transposition
+                ].min
+              end
+            end
+          end
+        end
+      end
+      distances[first.length][last.length]
+    end
+
+    def suggestion(actual, possibilities)
+      distances = Hash.new {|hash,key| hash[key] = []}
+
+      possibilities.each do |suggestion|
+        distances[string_distance(actual, suggestion)] << suggestion
+      end
+
+      minimum_distance = distances.keys.min
+      if minimum_distance < 4
+        suggestions = distances[minimum_distance].sort
+        if suggestions.length == 1
+          "Perhaps you meant `#{suggestions.first}`."
+        else
+          "Perhaps you meant #{suggestions[0...-1].map {|suggestion| "`#{suggestion}`"}.join(', ')} or `#{suggestions.last}`."
+        end
+      else
+        nil
+      end
+    end
+
   end
 end
 

data/lib/transcriptic/version.rb

@@ -1,3 +1,3 @@
 module Transcriptic
-  VERSION = "0.1.2"
+  VERSION = "0.1.3"
 end

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: transcriptic
 version: !ruby/object:Gem::Version
-  version: 0.1.2
+  version: 0.1.3
   prerelease: 
 platform: ruby
 authors:
@@ -9,11 +9,11 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2012-10-24 00:00:00.000000000Z
+date: 2012-10-29 00:00:00.000000000Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: thrift
-  requirement: &70219859440740 !ruby/object:Gem::Requirement
+  requirement: &70351850156680 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
@@ -21,10 +21,10 @@ dependencies:
         version: '0.8'
   type: :runtime
   prerelease: false
-  version_requirements: *70219859440740
+  version_requirements: *70351850156680
 - !ruby/object:Gem::Dependency
   name: netrc
-  requirement: &70219859440240 !ruby/object:Gem::Requirement
+  requirement: &70351850156180 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
@@ -32,10 +32,10 @@ dependencies:
         version: 0.7.7
   type: :runtime
   prerelease: false
-  version_requirements: *70219859440240
+  version_requirements: *70351850156180
 - !ruby/object:Gem::Dependency
   name: rest-client
-  requirement: &70219859439780 !ruby/object:Gem::Requirement
+  requirement: &70351850155720 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
@@ -43,10 +43,10 @@ dependencies:
         version: 1.6.1
   type: :runtime
   prerelease: false
-  version_requirements: *70219859439780
+  version_requirements: *70351850155720
 - !ruby/object:Gem::Dependency
   name: launchy
-  requirement: &70219859439320 !ruby/object:Gem::Requirement
+  requirement: &70351850155260 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -54,10 +54,10 @@ dependencies:
         version: 0.3.2
   type: :runtime
   prerelease: false
-  version_requirements: *70219859439320
+  version_requirements: *70351850155260
 - !ruby/object:Gem::Dependency
   name: zipruby
-  requirement: &70219859438940 !ruby/object:Gem::Requirement
+  requirement: &70351850154880 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -65,10 +65,10 @@ dependencies:
         version: '0'
   type: :runtime
   prerelease: false
-  version_requirements: *70219859438940
+  version_requirements: *70351850154880
 - !ruby/object:Gem::Dependency
   name: multipart-post
-  requirement: &70219859438480 !ruby/object:Gem::Requirement
+  requirement: &70351850154420 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -76,7 +76,7 @@ dependencies:
         version: '0'
   type: :runtime
   prerelease: false
-  version_requirements: *70219859438480
+  version_requirements: *70351850154420
 description: Client library and command-line tool to work with Transcriptic Platform.
 email: support@transcriptic.com
 executables:
@@ -87,23 +87,17 @@ files:
 - lib/transcriptic.rb
 - lib/transcriptic/api.rb
 - lib/transcriptic/api/errors.rb
-- lib/transcriptic/api/sequences.rb
 - lib/transcriptic/api/version.rb
 - lib/transcriptic/auth.rb
 - lib/transcriptic/cli.rb
 - lib/transcriptic/client.rb
 - lib/transcriptic/command.rb
-- lib/transcriptic/command/analyze.rb
 - lib/transcriptic/command/base.rb
 - lib/transcriptic/command/console.rb
 - lib/transcriptic/command/data.rb
 - lib/transcriptic/command/help.rb
-- lib/transcriptic/command/history.rb
-- lib/transcriptic/command/keys.rb
 - lib/transcriptic/command/login.rb
 - lib/transcriptic/command/run.rb
-- lib/transcriptic/command/sequences.rb
-- lib/transcriptic/command/status.rb
 - lib/transcriptic/helpers.rb
 - lib/transcriptic/version.rb
 - lib/vendor/transcriptic/okjson.rb

data/lib/transcriptic/api/sequences.rb

@@ -1,33 +0,0 @@
-module Transcriptic
-  class API
-
-    # DELETE /:organization/sequences/:sequence
-    def delete_sequence(organization, sequence)
-      request(
-        :expects  => 200,
-        :method   => :delete,
-        :path     => "/#{organization}/sequences/#{sequence}"
-      )
-    end
-
-    # GET /:organization/sequences
-    def get_sequences(organization)
-      request(
-        :expects  => 200,
-        :method   => :get,
-        :path     => "/#{organization}/sequences"
-      )
-    end
-
-    # POST /:organization/sequences
-    def post_domain(organization, sequence)
-      request(
-        :expects  => 201,
-        :method   => :post,
-        :path     => "/#{organization}/sequences",
-        :query    => {'sequence' => sequence}
-      )
-    end
-
-  end
-end

data/lib/transcriptic/command/analyze.rb

@@ -1,12 +0,0 @@
-require "transcriptic/command/base"
-
-module Transcriptic::Command
-
-  # analyze an autoprotocol script or project
-  #
-  class Analyze < Base
-  
-    def index; end
-  
-  end
-end

data/lib/transcriptic/command/history.rb

@@ -1,8 +0,0 @@
-module Transcriptic::Command
-
-  # show the history (audit trail) for a run
-  #
-  class History < Base
-    def index; end
-  end
-end

data/lib/transcriptic/command/keys.rb

@@ -1,115 +0,0 @@
-require "transcriptic/command/base"
-
-module Transcriptic::Command
-
-  # manage authentication keys
-  #
-  class Keys < Base
-
-    # keys
-    #
-    # display keys for the current user
-    #
-    # -l, --long  # display extended information for each key
-    #
-    #Examples:
-    #
-    # $ transcriptic keys
-    # === email@example.com Keys
-    # ssh-rsa ABCDEFGHIJK...OPQRSTUV== email@example.com
-    #
-    # $ transcriptic keys --long
-    # === email@example.com Keys
-    # ssh-rsa AAAAB3NzaC1yc2EAAAABIwAAAQEAp9AJD5QABmOcrkHm6SINuQkDefaR0MUrfgZ1Pxir3a4fM1fwa00dsUwbUaRuR7FEFD8n1E9WwDf8SwQTHtyZsJg09G9myNqUzkYXCmydN7oGr5IdVhRyv5ixcdiE0hj7dRnOJg2poSQ3Qi+Ka8SVJzF7nIw1YhuicHPSbNIFKi5s0D5a+nZb/E6MNGvhxoFCQX2IcNxaJMqhzy1ESwlixz45aT72mXYq0LIxTTpoTqma1HuKdRY8HxoREiivjmMQulYP+CxXFcMyV9kxTKIUZ/FXqlC6G5vSm3J4YScSatPOj9ID5HowpdlIx8F6y4p1/28r2tTl4CY40FFyoke4MQ== email@example.com
-    #
-    def index
-      validate_arguments!
-      keys = transcriptic.get_keys
-      if keys.length > 0
-        display("#{Transcriptic::Auth.user} Keys")
-        keys = if options[:long]
-          keys.map {|key| key["contents"].strip}
-        else
-          keys.map {|key| format_key_for_display(key["contents"])}
-        end
-        styled_array(keys)
-      else
-        display("You have no keys.")
-      end
-    end
-
-    # keys:add [KEY]
-    #
-    # add a key for the current user
-    #
-    # if no KEY is specified, will try to find ~/.ssh/id_[rd]sa.pub
-    #
-    #Examples:
-    #
-    # $ transcriptic keys:add
-    # Could not find an existing public key.
-    # Would you like to generate one? [Yn] y
-    # Generating new SSH public key.
-    # Uploading SSH public key /.ssh/id_rsa.pub... done
-    #
-    # $ transcriptic keys:add /my/key.pub
-    # Uploading SSH public key /my/key.pub... done
-    #
-    def add
-      keyfile = shift_argument
-      validate_arguments!
-
-      if keyfile
-        Transcriptic::Auth.associate_key(keyfile)
-      else
-        # make sure we have credentials
-        Transcriptic::Auth.get_credentials
-        Transcriptic::Auth.associate_or_generate_ssh_key
-      end
-    end
-
-    # keys:remove KEY
-    #
-    # remove a key from the current user
-    #
-    #Examples:
-    #
-    # $ transcriptic keys:remove email@example.com
-    # Removing email@example.com SSH key... done
-    #
-    def remove
-      key = shift_argument
-      if key.nil? || key.empty?
-        error("Usage: transcriptic keys:remove KEY\nMust specify KEY to remove.")
-      end
-      validate_arguments!
-
-      action("Removing #{key} SSH key") do
-        api.delete_key(key)
-      end
-    end
-
-    # keys:clear
-    #
-    # remove all authentication keys from the current user
-    #
-    #Examples:
-    #
-    # $ transcriptic keys:cleare
-    # Removing all SSH keys... done
-    #
-    def clear
-      validate_arguments!
-
-      action("Removing all SSH keys") do
-        api.delete_keys
-      end
-    end
-
-    protected
-      def format_key_for_display(key)
-        type, hex, local = key.strip.split(/\s/)
-        [type, hex[0,10] + '...' + hex[-10,10], local].join(' ')
-      end
-  end
-end

data/lib/transcriptic/command/sequences.rb

@@ -1,45 +0,0 @@
-module Transcriptic::Command
-  
-  # manage sequence data
-  #
-  class Sequences < Base
-  
-    # sequences
-    #
-    # list all sequence entries
-    #
-    #Examples:
-    #
-    # $ transcriptic sequences
-    # ...
-    #
-    def index
-      validate_arguments!
-    end
-    
-    # sequences:add FILENAME.EXT
-    #
-    # upload new sequence data file. EXT must be .gb or .fasta
-    #
-    #Examples:
-    #
-    # $ transcriptic sequences:add myvector.fasta
-    # ...
-    #
-    def add
-    end
-  
-    # sequences:delete NAME
-    #
-    # delete sequence by name NAME
-    #
-    #Examples:
-    #
-    # $ transcriptic sequences:delete myvector20110204
-    # ...
-    #
-    def remove
-    end
-
-  end
-end

data/lib/transcriptic/command/status.rb

@@ -1,20 +0,0 @@
-module Transcriptic::Command
-
-  # view the status of your runs
-  #
-  class Status < Base
-  
-    # transcriptic status [RUNID]
-    #
-    # list active runs, or if RUNID supplied, show details of that run
-    #
-    def index
-      run_id = args.shift
-      if run_id.nil?
-        error("Usage: transcriptic status RUNID\nMust specify RUNID to get run status.")
-      end
-      puts run_id
-    end
-    
-  end
-end