bio-basespace-sdk 0.1.2

data/lib/basespace/api/basespace_error.rb

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+# Copyright 2012-2013 Joachim Baran
+#
+#     Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+# http://www.apache.org/licenses/LICENSE-2.0
+# 
+#     Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+module Bio
+module BaseSpace
+
+# Raised when a parameter in a call was not defined.
+class UndefinedParameterError < StandardError
+  # Create a new instance of the error.
+  #
+  # +parameter+:: Name of the parameter that is not defined.
+  def initialize(parameter)
+    super("The following parameter must be defined: #{parameter}")
+  end
+end
+
+# Raised when a parameter was provided that is unknown to the implementation.
+class UnknownParameterError < StandardError
+  # Create a new instance of the error.
+  #
+  # +parameter+:: Name of the parameter that is not recognized.
+  def initialize(parameter)
+    super("#{parameter} is not regcognized as a parameter for this call")
+  end
+end
+
+# Raised when a parameter was set to an invalid value.
+class IllegalParameterError < StandardError
+  # Create a new instance of the error.
+  #
+  # +value+:: Value that was passed and which is of an invalid value.
+  # +legal+:: Listing of valid values.
+  def initialize(value, legal)
+    super("#{value} is not well-defined, legal options are #{legal}")
+  end
+end
+
+# Raised when an unsupported or unsuitable file type is encountered.
+class WrongFiletypeError < StandardError
+  # Create a new instance of the error.
+  #
+  # +filetype+:: Filetype that was intended to be used.
+  def initialize(filetype)
+    super("This data request is not available for file #{filetype}")
+  end
+end
+
+# Raised when no response has been received from the API server (in a certain amount of time).
+class NoResponseError < StandardError
+  # Create a new instance of the error.
+  #
+  # +value+:: Value that was provided with the request.
+  def initialize(value)
+    super("No response was returned from the server for this request - #{value}")
+  end
+end
+
+# Raised when the model for holding data has not been initialized yet.
+class ModelNotInitializedError < StandardError
+  # Create a new instance of the error.
+  #
+  # +value+:: Value that was provided with the request.
+  def initialize(value)
+    super("The request cannot be completed as model has not been initialized - #{value}")
+  end
+end
+
+end # module BaseSpace
+end # module Bio
+

data/lib/basespace/api/billing_api.rb

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+# Copyright 2013 Toshiaki Katayama, Joachim Baran
+#
+#     Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+# http://www.apache.org/licenses/LICENSE-2.0
+# 
+#     Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+require 'basespace/api/base_api'
+require 'basespace/api/basespace_error'
+require 'basespace/model/query_parameters_purchased_product'
+
+module Bio
+module BaseSpace
+
+# The API class used for all communication with the BaseSpace Billng server.
+class BillingAPI < BaseAPI
+  # Create a new BillingAPI object.
+  #
+  # +api_server+:: URI of the BaseSpace API server.
+  # +version+:: Version of the API to use.
+  # +app_session_id+:: AppSession ID.
+  # +access_token+:: Access token that is provided by App triggering. 
+  def initialize(api_server, version, app_session_id = nil, access_token = nil)
+    end_with_slash = %r(/$)
+    unless api_server[end_with_slash]
+      api_server += '/'
+    end
+    
+    @app_session_id  = app_session_id
+    @api_server      = api_server + version
+    @version         = version
+
+    super(access_token)
+  end
+
+  # Creates a purchase with the specified products.
+  # 
+  # +products+:: List of dicts to purchase, each of which has a product 'id' and 'quantity' to purchase.
+  # +app_session_id+:: AppSession ID.
+  def create_purchase(products, app_session_id = nil)
+    my_model       = 'PurchaseResponse'
+    resource_path  = '/purchases/'
+    resource_path  = resource_path.sub('{format}', 'json')
+    method         = 'POST'
+    query_params   = {}
+    header_params  = {}
+    post_data      = {}
+    # 'Products' is list of dicts with 'id', 'quantity', and optnl 'tags[]'
+    post_data['Products']  = products
+    if app_session_id
+      post_data['AppSessionId'] = app_session_id
+    end
+    verbose        = false
+    return single_request(my_model, resource_path, method, query_params, header_params, post_data, verbose)
+  end
+          
+  # Request a purchase object by ID.
+  # 
+  # +id+:: The ID of the purchase.
+  def get_purchase_by_id(id)
+    my_model       = 'PurchaseResponse'
+    resource_path  = '/purchases/{Id}'
+    resource_path  = resource_path.sub('{format}', 'json')
+    resource_path  = resource_path.sub('{Id}', id)
+    method         = 'GET'
+    query_params   = {}
+    header_params  = {}
+    return single_request(my_model, resource_path, method, query_params, header_params)
+  end
+
+  # Returns the Products for the current user.
+  #
+  # +id+:: The ID of the user.
+  # +qps+:: Query parameters, a dictionary for filtering by 'Tags' and/or 'ProductIds'.
+  def get_user_products(id = 'current', qps = {})
+    query_pars     = QueryParametersPurchasedProduct.new(qps)
+    my_model       = 'PurchasedProduct'
+    resource_path  = '/users/{Id}/products'
+    resource_path  = resource_path.sub('{Id}', id.to_s)
+    method         = 'GET'
+    query_params   = query_pars.get_parameter_dict
+    header_params  = {}
+    return self.__listRequest__(my_model, resource_path, method, query_params, header_params)
+  end
+
+  # Creates a purchase with the specified products.
+  # 
+  # +purchase_id+:: The ID of the purchase.
+  # +refund_secret+:: The RefundSecret that was provided in the Response from createPurchase.
+  # +comment+:: An optional comment about the refund.
+  def refund_purchase(purchase_id, refund_secret, comment = nil)
+    my_model       = 'RefundPurchaseResponse'
+    resource_path  = '/purchases/{id}/refund'
+    resource_path  = resource_path.sub('{id}', purchase_id)
+    method         = 'POST'
+    query_params   = {}
+    header_params  = {}
+    post_data      = {}
+    post_data['RefundSecret']  = refund_secret
+    if comment
+      post_data['Comment']     = comment
+    end
+    verbose        = 0
+    return single_request(my_model, resource_path, method, query_params, header_params, post_data, verbose)
+  end
+end
+
+end # module BaseSpace
+end # module Bio

data/lib/basespace/model.rb

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+# Copyright 2013 Toshiaki Katayama, Joachim Baran
+#
+#     Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+# http://www.apache.org/licenses/LICENSE-2.0
+# 
+#     Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+module Bio
+module BaseSpace
+
+# Base class for all BaseSpace Ruby SDK model classes. Implements a
+# basic key/value store and provides convenience methods for accessing
+# the key/value store using `method_missing` magic.
+#
+# Keys in this model are referred to as "attribute names", whereas
+# values are called "attributes".
+class Model
+  attr_reader :swagger_types, :attributes
+
+  # Create a new (empty) model.
+  def initialize
+    @swagger_types = {}
+    @attributes = {}
+  end
+
+  # If a method was called on the object for which no implementations is
+  # provided, then execute this method and try to return the attribute
+  # value whose attribute key matches the method call's name.
+  #
+  # +method+:: Method call for which no implementation could be found.
+  # +args+:: Arguments that were provided to the method call.
+  # +block+:: If not nil, code block that follows the method call.
+  def method_missing(method, *args, &block)
+    attr_name = method.to_s.downcase.gsub('_', '')
+    attr_value = false
+    self.attributes.each do |key, value|
+      if key.downcase == attr_name
+        attr_value = value  # can be an object or nil
+      end
+    end
+    if attr_value == false
+      super
+    else
+      return attr_value
+    end
+  end
+
+  # Sets the value of a named attribute. Overrides the value of
+  # a previous assignment.
+  #
+  # +key+:: Attribute name whose value should be set.
+  # +value+:: Value that should be assigned.
+  def set_attr(key, value)
+    @attributes[key] = value
+    return @attributes
+  end
+
+  # Returns the value, if any, of the given attribute name.
+  #
+  # +key+:: Attribute name whose value should be returned.
+  def get_attr(key)
+    return @attributes[key]
+  end
+
+  # Returns a string representation of the model.
+  def to_str
+    return self.inspect
+  end
+end
+
+end # module BaseSpace
+end # module Bio

data/lib/basespace/model/app_result.rb

@@ -0,0 +1,158 @@
+# Copyright 2013 Toshiaki Katayama, Joachim Baran
+#
+#     Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+# http://www.apache.org/licenses/LICENSE-2.0
+# 
+#     Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+require 'basespace/api/basespace_error'
+require 'basespace/model'
+require 'basespace/model/query_parameters'
+
+module Bio
+module BaseSpace
+
+# Contains the files that are output by an App.
+#
+# App results are usually BAM or VCF files, even though other file types
+# may also be provided.
+class AppResult < Model
+
+  # Create a new AppResult instance.
+  def initialize
+    @swagger_types = {
+      'Name'           => 'str',
+      #'Status'        => 'str',        # will be deprecated
+      'Description'    => 'str',
+      'StatusSummary'  => 'str',
+      'HrefFiles'      => 'str',
+      'DateCreated'    => 'datetime',
+      'Id'             => 'str',
+      'Href'           => 'str',
+      'UserOwnedBy'    => 'UserCompact',
+      'StatusDetail'   => 'str',
+      'HrefGenome'     => 'str',
+      'AppSession'     => 'AppSession',
+      'References'     => 'dict',
+    }
+    @attributes = {
+      'Name'           => nil,
+      'Description'    => nil,
+      'StatusSummary'  => nil,
+      'HrefFiles'      => nil,
+      'DateCreated'    => nil,
+      'Id'             => nil,
+      'Href'           => nil,
+      'UserOwnedBy'    => nil, # UserCompact
+      'StatusDetail'   => nil,
+      'HrefGenome'     => nil,
+      'AppSession'     => nil, # AppSession
+      'References'     => nil,
+    }
+  end
+
+  # Return the name of the AppResult.
+  def to_s
+    # NOTE Simplified in Ruby to align with the Sample class.
+    #      See example 3_accessing_files.rb (3_AccessingFiles.py)
+    #return "AppResult: #{get_attr('Name')}" #+ " - #{get_attr('Status')"
+    return get_attr('Name')
+  end
+
+  # Returns the scope-string to be used for requesting BaseSpace access to the object.
+  #
+  # +scope+:: The scope-type that is request (write|read).
+  def get_access_str(scope = 'write')
+    is_init
+    return "#{scope} appresult #{get_attr('Id')}"
+  end
+
+  # Tests if the Project instance has been initialized.
+  #
+  # Throws ModelNotInitializedError, if the instance has not been populated.
+  def is_init
+    raise ModelNotInitializedError.new('The AppResult model has not been initialized yet') unless get_attr('Id')
+  end
+
+  # Return a list of sample IDs for the samples referenced.
+  def get_referenced_samples_ids
+    res= []
+    get_attr('References').each do |s|
+      # [TODO] check this Hash contains the key :type (or should we use 'Type'?)
+      if s[:type] == 'Sample'
+        id = s[:href_content].split('/').last
+        res << id
+      end
+    end
+    return res
+  end
+
+  # Returns a list of sample objects references by the AppResult.
+  #
+  # NOTE This method makes one request to REST server per sample.
+  #
+  # +api+:: BaseSpaceAPI instance.
+  def get_referenced_samples(api)
+    res = []
+    ids = get_referenced_samples_ids
+    ids.each do |id|
+      begin
+        sample = api.get_sample_by_id(id)
+        res << sample
+      rescue => err
+        # [TODO] What to do with this 'err'?
+        $stderr.puts "    # ----- AppResult#get_referenced_samples ----- "
+        $stderr.puts "    # Error: #{err}"
+        $stderr.puts "    # "
+      end
+    end
+    return res
+  end
+
+  # Returns a list of file objects in the result set.
+  #
+  # +api+:: BaseSpaceAPI instance.
+  # +my_qp+:: QueryParameters for sorting and filtering the file list.
+  def get_files(api, my_qp = {})
+    is_init
+    query_pars = QueryParameters.new(my_qp)
+    return api.get_app_result_files(get_attr('Id'), query_pars)
+  end
+
+  # Uploads a local file to the BaseSpace AppResult.
+  #
+  # +api+:: BaseSpaceAPI instance.
+  # +local_path+: Local path of the file.
+  # +file_name+:: Filename.
+  # +directory+: The remote directory that the file is uploaded to.
+  # +param content_type+:: Content-type of the file.
+  def upload_file(api, local_path, file_name, directory, content_type)
+    is_init
+    return api.app_result_file_upload(get_attr('Id'), local_path, file_name, directory, content_type)
+  end
+
+  # Upload a file in multi-part mode. Returns an object of type MultipartUpload used for managing the upload.
+  # 
+  # +api+:: BaseSpaceAPI instance.
+  # +local_path+:: Local path of the file.
+  # +file_name+ Filename.
+  # +directory+:: The remote directory that the file is uploaded to.
+  # +content_type+:: Content-type of the file.
+  # +cpu_count+:: Number of CPUs to used for the upload.
+  # +part_size+:: Size of each upload chunk.
+  # def upload_multipart_file(api, local_path, file_name, directory, content_type,temp_dir = '', cpu_count = 1, part_size = 10, verbose = 0)
+  #   is_init
+  #   return api.multipart_file_upload(get_attr('Id'), local_path, file_name, directory, content_type, temp_dir, cpu_count, part_size, verbose)
+  # end
+
+end
+
+end # module BaseSpace
+end # module Bio
+

data/lib/basespace/model/app_result_response.rb

@@ -0,0 +1,40 @@
+# Copyright 2013 Toshiaki Katayama, Joachim Baran
+#
+#     Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+# http://www.apache.org/licenses/LICENSE-2.0
+# 
+#     Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+require 'basespace/model'
+
+module Bio
+module BaseSpace
+
+# An AppResultResponse is used to initiate the creation of an AppResults object.
+class AppResultResponse < Model
+
+  # Create a new result response instance.
+  def initialize
+    @swagger_types = {
+      'ResponseStatus'  => 'ResponseStatus',
+      'Response'        => 'AppResult',
+      'Notifications'   => 'list<Str>',
+    }
+    @attributes = {
+      'ResponseStatus'  => nil, # ResponseStatus
+      'Response'        => nil, # Analysis
+      'Notifications'   => nil,  # list<Str>
+    }
+  end
+
+end
+
+end # module BaseSpace
+end # module Bio
+