bio-basespace-sdk 0.1.3 → 0.1.5

data/examples/4_app_result_upload.rb

@@ -13,8 +13,8 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 
-# Creating an AppResult and uploading files
-#   https://developer.basespace.illumina.com/docs/content/documentation/sdk-samples/python-sdk-overview#Creating_an_AppResult_and_uploading_files
+# Creating an AppResult and Uploading Files
+# https://github.com/joejimbo/basespace-ruby-sdk#creating-an-appresult-and-uploading-files
 
 require 'bio-basespace-sdk'
 
@@ -39,64 +39,107 @@ unless opts.select{|k,v| v[/^<.*>$/]}.empty?
   exit 1 unless opts
 end
 
-# First, create a client for making calls for this user session.
+# Initialize a BaseSpace API object:
 bs_api = BaseSpaceAPI.new(opts['client_id'], opts['client_secret'], opts['basespace_url'], opts['api_version'], opts['app_session_id'], opts['access_token'])
 
-# Now we'll do some work of our own. First get a project to work on.
-# We need write permission for the project we are working on,
-# meaning we will need get a new token and instantiate a new BaseSpaceAPI.
-prj = bs_api.get_project_by_id('89')  # [TODO] Original ID '89' was not accessible. Writable project is needed.
+### Creating an AppResult ###
+
+#
+# Request privileges
+#
+
+device_info = bs_api.get_verification_code('browse global')
+link = device_info['verification_with_code_uri']
+puts "Visit the URI within 15 seconds and grant access:"
+puts link
+host = RbConfig::CONFIG['host_os']
+case host
+when /mswin|mingw|cygwin/
+  system("start #{link}")
+when /darwin/
+  system("open #{link}")
+when /linux/
+  system("xdg-open #{link}")
+end
+sleep(15)
+
+code = device_info['device_code']
+bs_api.update_privileges(code)
+
+#
+# Get a project
+#
+
+# NOTE THAT YOUR PROJECT ID WILL MOST LIKELY BE DIFFERENT!
+# YOU CAN GET IT VIA THE SDK OR FROM THE BASESPACE WEB INTERFACE!
+# FOR EXAMPLE: my_projects.first.id
+puts 'NOTE THAT YOU NEED TO UPDATE THE PROJECT ID IN THE EXAMPLE CODE TO MATCH A PROJECT OF YOURS!'
+prj = bs_api.get_project_by_id('469469')
+
+#
+# List the current analyses for the project
+#
 
-# Assuming we have write access to the project
-# we list the current App Results for the project.
 statuses = ['Running']
-app_res = prj.get_app_results(bs_api, {}, statuses)  # [TODO] should introduce hash options / keyword arguments (in Ruby 2.0)
-puts "The current running AppResults are #{app_res}"
-puts
+app_res = prj.get_app_results(bs_api, {}, statuses)
+puts "AppResult instances: #{app_res.map { |r| r.to_s }.join(', ')}"
 
 #
-# Retrieving results and setting status
+# Request project creation privileges
+#
+
+device_info = bs_api.get_verification_code("create project #{prj.id}")
+link = device_info['verification_with_code_uri']
+puts "Visit the URI within 15 seconds and grant access:"
+puts link
+host = RbConfig::CONFIG['host_os']
+case host
+when /mswin|mingw|cygwin/
+  system("start #{link}")
+when /darwin/
+  system("open #{link}")
+when /linux/
+  system("xdg-open #{link}")
+end
+sleep(15)
+
+code = device_info['device_code']
+bs_api.update_privileges(code)
+
+# NOTE THAT THE APP SESSION ID OF A RUNNING APP MUST BE PROVIDED!
+app_result = prj.create_app_result(bs_api, "testing", "this is my results", bs_api.app_session_id)
+puts "AppResult ID: #{app_result.id}"
+puts "AppResult's AppSession: #{app_result.app_session}"
+
+#
+# Change the status of our `AppSession` and add a status-summary as follows:
+#
+
+app_result.app_session.set_status(bs_api, 'needsattention', "We worked hard, but encountered some trouble.")
+
+# Updated status:
+puts "AppResult's AppSession: #{app_result.app_session}"
+
+# Set back to running:
+app_result.app_session.set_status(bs_api, 'running', "Back on track")
+
+### Uploading Files ###
+
+#
+# Attach a file to the `AppResult` object and upload it:
+#
+
+puts 'NOTE: THIS ASSUMES A FILE /tmp/testFile.txt IN YOUR FILESYSTEM!'
+app_result.upload_file(bs_api, '/tmp/testFile.txt', 'BaseSpaceTestFile.txt', '/mydir/', 'text/plain')
+
+# Let's see if our new file made it into the cloud:
+app_result_files = app_result.get_files(bs_api)
+puts "Files: #{app_result_files.map { |f| f.to_s }.join(', ')}"
+
 #
+# Download our newly uploaded file (will be saved as BaseSpaceTestFile.txt):
 
-# To create an appResults for a project, simply give the name and description.
-app_results = prj.create_app_result(bs_api, "testing", "this is my results")
-puts "Some info about our new app results"
-puts app_results
-puts app_results.id
-puts
-puts "The app results also comes with a reference to our AppSession"
-my_app_session = app_results.app_session
-puts my_app_session
-puts
-
-# We can change the status of our AppSession and add a status-summary as follows.
-my_app_session.set_status(bs_api, 'needsattention', "We worked hard, but encountered some trouble.")
-puts "After a change of status of the app sessions we get #{my_app_session}"
-puts
-# We set our appSession back to running so we can do some more work.
-my_app_session.set_status(bs_api, 'running', "Back on track")
-
-
-# Let's list all AppResults again and see if our new object shows up.
-app_res = prj.get_app_results(bs_api, {}, ['Running'])
-puts "The updated app results are #{app_res}"
-app_result2 = bs_api.get_app_result_by_id(app_results.id)
-puts app_result2
-puts
-
-# Now we will make another AppResult and try to upload a file to it
-app_results2 = prj.create_app_result(bs_api, "My second AppResult", "This one I will upload to")
-app_results2.upload_file(bs_api, '/home/mkallberg/Desktop/testFile2.txt', 'BaseSpaceTestFile.txt', '/mydir/', 'text/plain')
-puts "My AppResult number 2 #{app_results2}"
-puts
-
-# Let's see if our new file made it.
-app_result_files = app_results2.get_files(bs_api)
-puts "These are the files in the appResult"
-puts app_result_files
-f = app_result_files.last
-
-# We can even download our newly uploaded file.
-f = bs_api.get_file_by_id(f.id)
-f.download_file(bs_api, '/home/mkallberg/Desktop/')
+f = bs_api.get_file_by_id(app_result_files.last.id)
+f.download_file(bs_api, '/tmp/')
+puts 'NOTE: downloaded \'BaseSpaceTestFile.txt\' into the /tmp directory.'
 

data/examples/5_purchasing.rb

@@ -13,19 +13,13 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 
+# Purchasing
+# --- Sorry, we have not documented this yet. ---
+
 require 'bio-basespace-sdk'
 
 include Bio::BaseSpace
 
-# This example demonstrates the billing methods of BaseSpace.
-# 
-# Below a purchase is created, requiring the user to click 'Purchase' in a web
-# browser. The purchase is then refunded, and the purchase is again retrieved
-# via the API using the purchase id and tags, which are used by developers
-# to help clarify exactly what was purchased.
-# 
-# NOTE You will need to fill client values for your app below!
-
 opts = {
   # FILL IN WITH YOUR APP VALUES HERE!
   'client_id'            => '<your client key>',     # from dev portal app Credentials tab
@@ -48,7 +42,7 @@ unless opts['client_id'] or opts['product_id']
   raise "Please fill in client values (in the script) before running the script"
 end
 
-# First, create a client for making calls for this user session.
+# Initialize a BaseSpace API object:
 bill_api = BillingAPI.new(opts['basespace_store_url'], opts['api_version'], opts['app_session_id'], opts['access_token'])
 
 # Create a non-consumable purchase.

data/lib/basespace/api/api_client.rb

@@ -153,7 +153,7 @@ class APIClient
       # [TODO] confirm this works or not
       #request = urllib2.Request(url, headers)
       uri = URI.parse(url)
-      request = Net::HTTP::Get.new(uri.path, headers)
+      request = Net::HTTP::Get.new(uri, headers)
     when 'POST', 'PUT', 'DELETE'
       if cgi_params
         force_post_url = url 
@@ -161,16 +161,22 @@ class APIClient
       end
       if post_data
         # [TODO] Do we need to skip String, Integer, Float and bool in Ruby?
-        data = post_data.to_json # if not [str, int, float, bool].include?(type(post_data))
+        data = post_data # if not [str, int, float, bool].include?(type(post_data))
       end
       if force_post
         response = force_post_call(force_post_url, sent_query_params, headers)
       else
-        data = '\n' if data and data.empty? # temp fix, in case is no data in the file, to prevent post request from failing
+        data = {} if not data or (data and data.empty?) # temp fix, in case is no data in the file, to prevent post request from failing
         # [TODO] confirm this works or not
         #request = urllib2.Request(url, headers, data)#, @timeout)
         uri = URI.parse(url)
-        request = Net::HTTP::Post.new(uri.path, headers)
+        request = Net::HTTP::Post.new(uri, headers)
+        if data.kind_of?(Hash) then
+          request.set_form_data(data)
+        else
+          request.content_type = 'multipart/form-data'
+          request.body = data
+        end
       end
       if ['PUT', 'DELETE'].include?(method) # urllib doesnt do put and delete, default to pycurl here
         response = put_call(url, query_params, headers, data)
@@ -237,7 +243,7 @@ class APIClient
       instance = File.new 
     else
       # models in BaseSpace
-      klass = Object.const_get(obj_class)
+      klass = ::Bio::BaseSpace.const_get(obj_class)
       instance = klass.new
     end
 

data/lib/basespace/api/base_api.rb

@@ -140,13 +140,13 @@ class BaseAPI
     # convert list response dict to object type
     # TODO check that Response is present -- errors sometime don't include
     # [TODO] check why the Python SDK only uses the first element in the response_objects
-    convertet = []
+    converted = []
     if response_object = response_objects.first
       response_object.convert_to_object_list.each do |c|
-        convertet << @api_client.deserialize(c, my_model)
+        converted << @api_client.deserialize(c, my_model)
       end
     end
-    return convertet
+    return converted
   end
 
   # URL encode a Hash of data values.

data/lib/basespace/api/basespace_api.rb

@@ -162,7 +162,7 @@ class BaseSpaceAPI < BaseAPI
   #
   # +obj+:: The data object we wish to get access to.
   # +access_type+:: The type of access (read|write), default is write.
-  # +web+:: True if the App is web-based, default is false meaning a device based App.
+  # +web+:: If the App is web-based, then set this parameter to 'true'. The default value is false, which means that the request is for a device based App.
   # +redirect_url+:: For the web-based case, a redirection URL.
   # +state+:: (unclear from Python port)
   def get_access(obj, access_type = 'write', web = nil, redirect_url = nil, state = nil)
@@ -188,7 +188,7 @@ class BaseSpaceAPI < BaseAPI
     #curlCall = 'curl -d "response_type=device_code" -d "client_id=' + @key + '" -d "scope=' + scope + '" ' + @api_server + DEVICE_URL
     #puts curlCall
     unless @key
-      raise "This BaseSpaceAPI instance has no client_secret (key) set and no alternative id was supplied for method get_verification_code"
+      raise "This BaseSpaceAPI instance has no client_secret (key) set and no alternative id was supplied for method get_verification_code."
     end
     data = {'client_id' => @key, 'scope' => scope, 'response_type' => 'device_code'}
     return make_curl_request(data, @api_server + DEVICE_URL)
@@ -201,7 +201,7 @@ class BaseSpaceAPI < BaseAPI
   # +state+:: An optional state parameter that will passed through to the redirect response.
   def get_web_verification_code(scope, redirect_url, state = nil)
     if (not @key)
-      raise "This BaseSpaceAPI instance has no client_id (key) set and no alternative id was supplied for method get_verification_code"
+      raise "This BaseSpaceAPI instance has no client_id (key) set and no alternative id was supplied for method get_verification_code."
     end
     data = {'client_id' => @key, 'redirect_uri' => redirect_url, 'scope' => scope, 'response_type' => 'code', "state" => state}
     return @weburl + WEB_AUTHORIZE + '?' + hash2urlencode(data)
@@ -212,7 +212,7 @@ class BaseSpaceAPI < BaseAPI
   # +device_code+:: The device code returned by the verification code method.
   def obtain_access_token(device_code)
     if (not @key) or (not @secret)
-      raise "This BaseSpaceAPI instance has either no client_secret or no client_id set and no alternative id was supplied for method get_verification_code"
+      raise "This BaseSpaceAPI instance has either no client_secret or no client_id set and no alternative id was supplied for method get_verification_code."
     end
     data = {'client_id' => @key, 'client_secret' => @secret, 'code' => device_code, 'grant_type' => 'device', 'redirect_uri' => 'google.com'}
     dict = make_curl_request(data, @api_server + TOKEN_URL)
@@ -584,7 +584,7 @@ class BaseSpaceAPI < BaseAPI
       sid = query_params['appsessionid']
       session = get_app_session(sid)
       unless session.can_work_on
-        raise 'AppSession status must be "running," to create and AppResults. Current status is ' + session.status
+        raise 'AppSession status must be "running," to create and AppResults. Current status is: ' + session.status
       end
     end
         
@@ -628,7 +628,7 @@ class BaseSpaceAPI < BaseAPI
       # Set force post as this need to use POST though no data is being streamed
       return single_request(my_model, resource_path, method, query_params, header_params, post_data, verbose, force_post)
     else
-      post_data = File.open(local_path).read
+      post_data = ::File.open(local_path).read
       return single_request(my_model, resource_path, method, query_params, header_params, post_data, verbose)
     end
   end
@@ -664,15 +664,15 @@ class BaseSpaceAPI < BaseAPI
     end
     
     # Do the download
-    File.open(File.join(local_dir, name), "wb") do |fp|
+    ::File.open(::File.join(local_dir, name), "wb") do |fp|
       http_opts = {}
+      uri = URI.parse(file_url)
       if uri.scheme == "https"
         http_opts[:use_ssl] = true
       end
-      uri = URI.parse(file_url)
       res = Net::HTTP.start(uri.host, uri.port, http_opts) { |http|
         # [TODO] Do we need user and pass here also?
-        http.get(uri.path, header)
+        http.get(uri, header)
       }
       fp.print res.body
     end

data/lib/basespace/model/project.rb

@@ -57,7 +57,7 @@ class Project < Model
     raise ModelNotInitializedError.new('The project model has not been initialized yet') unless get_attr('Id')
   end
   
-  # Returns the scope-string to used for requesting BaseSpace access to the object.
+  # Returns the scope-string to be used for requesting BaseSpace access to the object.
   # 
   # +scope+:: The scope-type that is requested (write|read).
   def get_access_str(scope = 'write')

data/lib/basespace/model/sample.rb

@@ -28,8 +28,8 @@ class Sample < Model
       'SampleNumber'    => 'int',
       'ExperimentName'  => 'str',
       'HrefFiles'       => 'str',
-      # AppSession
-      'IsPairedEnd'     => 'int',
+      'AppSession'      => 'dict',
+      'IsPairedEnd'     => 'bool',
       'Read1'           => 'int',
       'Read2'           => 'int',
       'NumReadsRaw'     => 'int',
@@ -42,12 +42,13 @@ class Sample < Model
       'Status'          => 'str',
       'StatusSummary'   => 'str',
       'DateCreated'     => 'datetime',
-      'References'      => 'dict',
+      'References'      => 'dict', # NOTE Is this correct? Because references is a list.
       'Run'             => 'RunCompact',
     }
     @attributes = {
       'Name'            => nil, # str
       'HrefFiles'       => nil, # str
+      'AppSession'      => nil, # dict
       'DateCreated'     => nil, # datetime
       'SampleNumber'    => nil, # int
       'Id'              => nil, # str
@@ -56,7 +57,7 @@ class Sample < Model
       'ExperimentName'  => nil, # str
       'Run'             => nil, # RunCompact
       'HrefGenome'      => nil, # str
-      'IsPairedEnd'     => nil, # int
+      'IsPairedEnd'     => nil, # bool
       'Read1'           => nil, # int
       'Read2'           => nil, # int
       'NumReadsRaw'     => nil, # int
@@ -95,7 +96,7 @@ class Sample < Model
   # Return the AppResults referenced by this sample.
   #
   # Note: the returned AppResult objects do not have their "References" field set,
-  # to get a fully populate AppResult object you must use getAppResultById in BaseSpaceAPI.
+  # to get a fully populate AppResult object you must use get_app_result_by_id in BaseSpaceAPI.
   #
   # +api+:: BaseSpaceAPI instance.
   def get_referenced_app_results(api)

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: bio-basespace-sdk
 version: !ruby/object:Gem::Version
-  version: 0.1.3
+  version: 0.1.5
 platform: ruby
 authors:
 - Joachim Baran
@@ -12,7 +12,7 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2013-07-20 00:00:00.000000000 Z
+date: 2013-07-29 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: getopt
@@ -113,11 +113,9 @@ dependencies:
       - !ruby/object:Gem::Version
         version: '3.12'
 description: |-
-  Bio::BaseSpace is a Ruby based SDK ported from the Python based BaseSpacePy SDK to be used in the development of Apps and scripts for working with Illumina's BaseSpace cloud-computing solution for next-gen sequencing data analysis.
+  BaseSpace Ruby SDK is a Ruby based Software Development Kit to be used in the development of Apps and scripts for working with Illumina's BaseSpace cloud-computing solution for next-gen sequencing data analysis.
 
     The primary purpose of the SDK is to provide an easy-to-use Ruby environment enabling developers to authenticate a user, retrieve data, and upload data/results from their own analysis to BaseSpace.
-
-    If you haven't already done so, you may wish to familiarize yourself with the general BaseSpace developers documentation (https://developer.basespace.illumina.com/) and create a new BaseSpace App to be used when working through the examples provided in 'examples' folder.
 email: joachim.baran@gmail.com
 executables: []
 extensions: []
@@ -211,7 +209,7 @@ rubyforge_project:
 rubygems_version: 2.0.5
 signing_key: 
 specification_version: 4
-summary: Bio::BaseSpace is a Ruby based SDK to be used in the development of Apps
-  and scripts for working with Illumina's BaseSpace cloud-computing solution for next-gen
-  sequencing data analysis.
+summary: BaseSpace Ruby SDK is a Ruby based Software Development Kit to be used in
+  the development of Apps and scripts for working with Illumina's BaseSpace cloud-computing
+  solution for next-gen sequencing data analysis.
 test_files: []