bio-basespace-sdk 0.1.6 → 0.1.7

checksums.yaml

@@ -1,7 +1,7 @@
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data/README.md

@@ -72,10 +72,10 @@ Creating a `BaseSpaceAPI` object using `new`:
     include Bio::BaseSpace
     
     # Authentication and connection details:
-    client_id       = 'my client key'
-    client_secret   = 'my client secret'
-    app_session_id  = 'my app session id'
-    access_token    = 'my access token'
+    client_id       = '<my client key>'
+    client_secret   = '<my client secret>'
+    app_session_id  = '<my app session id>'
+    access_token    = '<my access token>'
     basespace_url   = 'https://api.basespace.illumina.com/'
     api_version     = 'v1pre3'
     
@@ -94,10 +94,10 @@ Creating a `BaseSpaceAPI` object using `credentials.json`:
 The file `credentials.json` contains the authentication/connection details in [JSON](http://json.org) format:
 
     {
-        "client_id":      "my client id",
-        "client_secret":  "my client secret",
-        "app_session_id": "my app session id",
-        "access_token":   "my access token",
+        "client_id":      "<my client id>",
+        "client_secret":  "<my client secret>",
+        "app_session_id": "<my app session id>",
+        "access_token":   "<my access token>",
         "basespace_url":  "https://api.basespace.illumina.com",
         "api_version":    "v1pre3"
     }
@@ -120,13 +120,13 @@ The initial HTTP request to our App from BaseSpace is identified by an `AppSessi
     # An app session contains a referral to one or more AppSessionLaunchObject instances, which reference the
     # data module the user launched the App on. This can be a list of projects, samples, or a mixture of objects
     puts "Type of data the app was triggered on can be seen in 'references':"
-    puts my_app_session.references.inspect  # `inspect` shows the object contents
+    puts my_app_session.references
 
 The output will be similar to:
 
     App session by 600602: Eri Kibukawa - Id: <my app session id> - status: Complete
     Type of data the app was triggered on can be seen in 'references':
-    [#<Bio::BaseSpace::AppSessionLaunchObject:0x007fc21a1ae0f8 @swagger_types={"Content"=>"dict", "Href"=>"str", "HrefContent"=>"str", "Rel"=>"str", "Type"=>"str"}, @attributes={"Content"=>#<Bio::BaseSpace::Project:0x007fc21a1ae378 @swagger_types={"Name"=>"str", "HrefSamples"=>"str", "HrefAppResults"=>"str", "HrefBaseSpaceUI"=>"str", "DateCreated"=>"datetime", "Id"=>"str", "Href"=>"str", "UserOwnedBy"=>"UserCompact"}, @attributes={"Name"=>"IGN_WGS_CEPH_Services_2.0", "HrefSamples"=>nil, "HrefAppResults"=>nil, "HrefBaseSpaceUI"=>nil, "DateCreated"=>#<DateTime: 2013-04-19T18:21:50+00:00 ((2456402j,66110s,0n),+0s,2299161j)>, "Id"=>"267267", "Href"=>"v1pre3/projects/267267", "UserOwnedBy"=>#<Bio::BaseSpace::UserCompact:0x007fc21a1ac758 @swagger_types={"Name"=>"str", "Id"=>"str", "Href"=>"str"}, @attributes={"Name"=>"Illumina Inc", "Id"=>"3004", "Href"=>"v1pre3/users/3004"}>}>, "Href"=>"v1pre3/projects/267267", "HrefContent"=>"v1pre3/projects/267267", "Rel"=>"Input", "Type"=>"Project"}>]
+    Project
 
 We can get a handle to the user who started the `AppSession` and further information on the `AppSessionLaunchObject`:
 
@@ -173,20 +173,9 @@ The output will be similar to:
     Scope string for requesting write access to the reference object:
     write project 848850
 
-We can request write access to the reference object now, so that our App can start contributing to an analysis. There is a distinction between requesting access for Web-Apps and other Apps (Desktop, Mobile, Native) though.
-
-The following call requests write permissions for a Web App:
-
-    verification_with_code_uri = bs_api.get_access(my_reference_content, 'write')
-    puts "Visit the URI within 15 seconds and grant access:"
-    puts verification_with_code_uri
-
-The output will be similar to:
+We can request write access to the reference object now, so that our App can start contributing to an analysis.
 
-    Visit the URI within 15 seconds and grant access:
-    https://cloud-hoth.illumina.com//oauth/authorize?<authorization paramers>
-
-The following call requests write permissions for other Apps (Desktop, Mobile, Native):
+The following call requests write permissions:
 
     access_map = bs_api.get_access(my_reference_content, 'write')
     puts "Access map:"
@@ -197,7 +186,7 @@ The output will be similar to:
     Access map:
     {"device_code"=>"<my device code>", "user_code"=>"<my user code>", "verification_uri"=>"https://basespace.illumina.com/oauth/device", "verification_with_code_uri"=>"https://basespace.illumina.com/oauth/device?code=<my user code>", "expires_in"=>1800, "interval"=>1}
 
-Visit the verification URI and grant access within 15 seconds:
+Have the user visit the verification URI to grant us access:
 
     puts "Visit the URI within 15 seconds and grant access:"
     verification_with_code_uri = access_map['verification_with_code_uri']
@@ -208,9 +197,8 @@ The output will be:
     Visit the URI within 15 seconds and grant access:
     https://basespace.illumina.com/oauth/device?code=<my user code>
 
-In both cases, the URI can be opened in a web browser using this portable Ruby code:
+The URI can be opened in a web browser using this portable Ruby code:
 
-    link = access_map['verification_with_code_uri']
     host = RbConfig::CONFIG['host_os']
     case host
     when /mswin|mingw|cygwin/
@@ -227,7 +215,7 @@ Once the user has granted us access to objects we requested we can get the BaseS
     code = access_map['device_code']
     bs_api.update_privileges(code)
 
-For more details on access-requests and authentication and an example of the web-based case see example 1\_authentication.rb
+For more details on access-requests and authentication and an example of the web-based case see example [1\_authentication.rb](https://github.com/basespace/basespace-ruby-sdk/blob/master/examples/1_authentication.rb)
 
 ## BaseSpace Authentication
 
@@ -247,14 +235,13 @@ It will be useful if you are logged in to the BaseSpace web-site before launchin
 
 First, get the verification code and URI for scope 'browse global':
 
-    device_info = bs_api.get_verification_code('browse global')
-    puts
+    access_map = bs_api.get_verification_code('browse global')
     puts "URI for user to visit and grant access:"
-    puts device_info['verification_with_code_uri']
+    puts access_map['verification_with_code_uri']
 
 At this point the user must visit the verification URI to grant the requested privilege. From Ruby, it is possible to launch a browser pointing to the verification URI using:
 
-    link = device_info['verification_with_code_uri']
+    link = access_map['verification_with_code_uri']
     host = RbConfig::CONFIG['host_os']
     case host
     when /mswin|mingw|cygwin/
@@ -273,7 +260,7 @@ The output will be:
     
 Once access has been granted, we can get the BaseSpace `access_token` and start browsing simply by calling `update_privileges` on the baseSpaceApi instance.
 
-    code = device_info['device_code']
+    code = access_map['device_code']
     bs_api.update_privileges(code)
 
 As a reference the provided access-token can be obtained from the `BaseSpaceAPI` object:
@@ -410,8 +397,8 @@ Now, we have a look at some of the methods calls specific to BAM and VCF files.
 
     # Request privileges:
     # NOTE THAT YOUR PROJECT ID (469469 here) WILL MOST LIKELY BE DIFFERENT!
-    device_info = bs_api.get_verification_code('read project 469469')
-    link = device_info['verification_with_code_uri']
+    access_map = bs_api.get_verification_code('read project 469469')
+    link = access_map['verification_with_code_uri']
     puts "Visit the URI within 15 seconds and grant access:"
     puts link
     host = RbConfig::CONFIG['host_os']
@@ -425,7 +412,7 @@ Now, we have a look at some of the methods calls specific to BAM and VCF files.
     end
     sleep(15)
     
-    code = device_info['device_code']
+    code = access_map['device_code']
     bs_api.update_privileges(code)
     
     # Get the coverage for an interval + accompanying meta-data:
@@ -470,8 +457,8 @@ and upload result files to it as well as retrieve files from it.
 
 First we get a project to work on. We will need write permissions for the project we are working on -- meaning that we will need to update our privileges accordingly:
     
-    device_info = bs_api.get_verification_code('browse global')
-    link = device_info['verification_with_code_uri']
+    access_map = bs_api.get_verification_code('browse global')
+    link = access_map['verification_with_code_uri']
     puts "Visit the URI within 15 seconds and grant access:"
     puts link
     host = RbConfig::CONFIG['host_os']
@@ -485,7 +472,7 @@ First we get a project to work on. We will need write permissions for the projec
     end
     sleep(15)
     
-    code = device_info['device_code']
+    code = access_map['device_code']
     bs_api.update_privileges(code)
     
     # NOTE THAT YOUR PROJECT ID WILL MOST LIKELY BE DIFFERENT!
@@ -505,8 +492,8 @@ The output will be similar to:
 
 To create an `AppResult` for a project, request 'create' privileges, then simply give the name and description:
 
-    device_info = bs_api.get_verification_code("create project #{prj.id}")
-    link = device_info['verification_with_code_uri']
+    access_map = bs_api.get_verification_code("create project #{prj.id}")
+    link = access_map['verification_with_code_uri']
     puts "Visit the URI within 15 seconds and grant access:"
     puts link
     host = RbConfig::CONFIG['host_os']
@@ -520,7 +507,7 @@ To create an `AppResult` for a project, request 'create' privileges, then simply
     end
     sleep(15)
     
-    code = device_info['device_code']
+    code = access_map['device_code']
     bs_api.update_privileges(code)
 
     # NOTE THAT THE APP SESSION ID OF A RUNNING APP MUST BE PROVIDED!

data/VERSION

@@ -1 +1 @@
-0.1.6
+0.1.7

data/examples/0_app_triggering.rb

@@ -47,7 +47,7 @@ puts my_app_session
 # An app session contains a referral to one or more AppSessionLaunchObject instances, which reference the
 # data module the user launched the App on. This can be a list of projects, samples, or a mixture of objects
 puts "Type of data the app was triggered on can be seen in 'references':"
-puts my_app_session.references.inspect  # `inspect` shows the object contents
+puts my_app_session.references
 
 #
 # We can get a handle to the user who started the `AppSession` and further information on the `AppSessionLaunchObject`:
@@ -84,15 +84,7 @@ puts "Scope string for requesting write access to the reference object:"
 puts my_reference_content.get_access_str('write')
 
 #
-# The following call requests write permissions for a Web App:
-#
-
-verification_with_code_uri = bs_api.get_access(my_reference_content, 'write')
-puts "Visit the URI within 15 seconds and grant access:"
-puts verification_with_code_uri
-
-#
-# The following call requests write permissions for other Apps (Desktop, Mobile, Native):
+# The following call requests write permissions:
 #
 
 access_map = bs_api.get_access(my_reference_content, 'write')
@@ -107,7 +99,6 @@ puts "Visit the URI within 15 seconds and grant access:"
 verification_with_code_uri = access_map['verification_with_code_uri']
 puts verification_with_code_uri
 
-link = access_map['verification_with_code_uri']
 host = RbConfig::CONFIG['host_os']
 case host
 when /mswin|mingw|cygwin/

data/examples/1_authentication.rb

@@ -43,16 +43,15 @@ bs_api = BaseSpaceAPI.new(opts['client_id'], opts['client_secret'], opts['basesp
 # Get the verification code and uri for scope 'browse global':
 #
 
-device_info = bs_api.get_verification_code('browse global')
-puts
+access_map = bs_api.get_verification_code('browse global')
 puts "URI for user to visit and grant access:"
-puts device_info['verification_with_code_uri']
+puts access_map['verification_with_code_uri']
 
 #
 # Grant access privileges:
 #
 
-link = device_info['verification_with_code_uri']
+link = access_map['verification_with_code_uri']
 host = RbConfig::CONFIG['host_os']
 case host
 when /mswin|mingw|cygwin/
@@ -64,7 +63,7 @@ when /linux/
 end
 sleep(15)
 
-code = device_info['device_code']
+code = access_map['device_code']
 bs_api.update_privileges(code)
 
 puts "Access-token: #{bs_api.get_access_token}"

data/examples/3_accessing_files.rb

@@ -82,8 +82,8 @@ end
 
 # NOTE THAT YOUR PROJECT ID (469469 here) WILL MOST LIKELY BE DIFFERENT!
 puts 'NOTE: CHANGE THE PROJECT ID IN THE EXAMPLE TO MATCH A PROJECT OF YOURS!'
-device_info = bs_api.get_verification_code('read project 469469')
-link = device_info['verification_with_code_uri']
+access_map = bs_api.get_verification_code('read project 469469')
+link = access_map['verification_with_code_uri']
 puts "Visit the URI within 15 seconds and grant access:"
 puts link
 host = RbConfig::CONFIG['host_os']
@@ -97,7 +97,7 @@ when /linux/
 end
 sleep(15)
 
-code = device_info['device_code']
+code = access_map['device_code']
 bs_api.update_privileges(code)
 
 #

data/examples/4_app_result_upload.rb

@@ -48,8 +48,8 @@ bs_api = BaseSpaceAPI.new(opts['client_id'], opts['client_secret'], opts['basesp
 # Request privileges
 #
 
-device_info = bs_api.get_verification_code('browse global')
-link = device_info['verification_with_code_uri']
+access_map = bs_api.get_verification_code('browse global')
+link = access_map['verification_with_code_uri']
 puts "Visit the URI within 15 seconds and grant access:"
 puts link
 host = RbConfig::CONFIG['host_os']
@@ -63,7 +63,7 @@ when /linux/
 end
 sleep(15)
 
-code = device_info['device_code']
+code = access_map['device_code']
 bs_api.update_privileges(code)
 
 #
@@ -88,8 +88,8 @@ puts "AppResult instances: #{app_res.map { |r| r.to_s }.join(', ')}"
 # Request project creation privileges
 #
 
-device_info = bs_api.get_verification_code("create project #{prj.id}")
-link = device_info['verification_with_code_uri']
+access_map = bs_api.get_verification_code("create project #{prj.id}")
+link = access_map['verification_with_code_uri']
 puts "Visit the URI within 15 seconds and grant access:"
 puts link
 host = RbConfig::CONFIG['host_os']
@@ -103,7 +103,7 @@ when /linux/
 end
 sleep(15)
 
-code = device_info['device_code']
+code = access_map['device_code']
 bs_api.update_privileges(code)
 
 # NOTE THAT THE APP SESSION ID OF A RUNNING APP MUST BE PROVIDED!

data/lib/basespace/api/api_client.rb

@@ -150,27 +150,44 @@ class APIClient
       if cgi_params
         url += "?#{cgi_params}"
       end
-      # [TODO] confirm this works or not
-      #request = urllib2.Request(url, headers)
       uri = URI.parse(url)
-      request = Net::HTTP::Get.new(uri, headers)
+      # https://www.ruby-forum.com/topic/4411398
+      # In Ruby 1.9: Use Net::HTTP::Get.new(uri.path) or Net::HTTP::Get.new(uri.path + '?' + uri.query)
+      # In Ruby 2.0: Use Net::HTTP::Get.new(uri)
+      case RUBY_VERSION
+      when /^1.9/
+        if uri.query and not uri.query.empty?
+          request = Net::HTTP::Get.new(uri.path + '?' + uri.query, headers)
+        else
+          request = Net::HTTP::Get.new(uri.path, headers)
+        end
+      else
+        request = Net::HTTP::Get.new(uri, headers)
+      end
     when 'POST', 'PUT', 'DELETE'
       if cgi_params
         force_post_url = url 
         url += "?#{cgi_params}"
       end
       if post_data
-        # [TODO] Do we need to skip String, Integer, Float and bool in Ruby?
+        # [TODO] Do we need to skip String, Integer, Float and bool also in Ruby?
         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 = {} 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, headers)
+        case RUBY_VERSION
+        when /^1.9/
+          if uri.query and not uri.query.empty?
+            request = Net::HTTP::Post.new(uri.path + '?' + uri.query, headers)
+          else
+            request = Net::HTTP::Post.new(uri.path, headers)
+          end
+        else
+          request = Net::HTTP::Post.new(uri, headers)
+        end
         if data.kind_of?(Hash) then
           request.set_form_data(data)
         else

data/lib/basespace/api/basespace_api.rb

@@ -149,7 +149,16 @@ class BaseSpaceAPI < BaseAPI
       http_opts[:use_ssl] = true
     end
     response = Net::HTTP.start(uri.host, uri.port, http_opts) { |http|
-      request = Net::HTTP::Get.new(uri.path)
+      case RUBY_VERSION
+      when /^1.9/
+        if uri.query and not uri.query.empty?
+          request = Net::HTTP::Get.new(uri.path + '?' + uri.query)
+        else
+          request = Net::HTTP::Get.new(uri.path)
+        end
+      else
+        request = Net::HTTP::Get.new(uri)
+      end
       request.basic_auth uri.user, uri.password
       http.request(request)
     }
@@ -672,7 +681,16 @@ class BaseSpaceAPI < BaseAPI
       end
       res = Net::HTTP.start(uri.host, uri.port, http_opts) { |http|
         # [TODO] Do we need user and pass here also?
-        http.get(uri, header)
+        case RUBY_VERSION
+        when /^1.9/
+          if uri.query and not uri.query.empty?
+            http.get(uri.path + '?' + uri.query, header)
+          else
+            http.get(uri.path, header)
+          end
+        else
+          http.get(uri, header)
+        end
       }
       fp.print res.body
     end

data/lib/basespace/model.rb

@@ -69,7 +69,7 @@ class Model
   end
 
   # Returns a string representation of the model.
-  def to_str
+  def to_s
     return self.inspect
   end
 end

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: bio-basespace-sdk
 version: !ruby/object:Gem::Version
-  version: 0.1.6
+  version: 0.1.7
 platform: ruby
 authors:
 - Joachim Baran
@@ -12,7 +12,7 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2013-08-05 00:00:00.000000000 Z
+date: 2013-08-08 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: getopt