bio-basespace-sdk 0.1.2

data/lib/basespace/model/app_session.rb

@@ -0,0 +1,99 @@
+# 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
+
+# App sessions records when an App is being launched.
+class AppSession < Model
+
+  # Create a new AppSession instance.
+  def initialize
+    @swagger_types = {
+      'Id'             => 'str',
+      'Href'           => 'str',
+      'Type'           => 'str',
+      'UserCreatedBy'  => 'User',
+      'DateCreated'    => 'datetime',
+      'Status'         => 'str',
+      'StatusSummary'  => 'str',
+      'Application'    => 'Application',
+      'References'     => 'list<AppSessionLaunchObject>',
+    }
+    @attributes = {
+      'Id'             => nil,
+      'Href'           => nil, # The URI of BaseSpace
+      'Type'           => nil,
+      # TODO UserUserCreatedBy in Python code would be typo of UserCreatedBy (bug in Python SDK)
+      'UserCreatedBy'  => nil, # The user that triggered your application
+      'DateCreated'    => nil, # The datetime the user acted in BaseSpace
+      'Status'         => nil,
+      'StatusSummary'  => nil,
+      'Application'    => nil,
+      'References'     => nil,
+    }
+  end
+
+  # Return a string representation of the object, showing user information, ID and status.
+  def to_s
+    return "App session by #{get_attr('UserCreatedBy')} - Id: #{get_attr('Id')} - status: #{get_attr('Status')}"
+  end
+
+  # Serialize references.
+  #
+  # +api+:: BaseSpaceAPI instance.
+  def serialize_references(api)
+    ref = []
+    # [TODO] should this attribute initialized with []?
+    get_attr('References').each do |r|
+      res = r.serialize_object(api)  # AppSessionLaunchObject
+      ref << res
+    end
+    set_attr('References', ref)
+    return self
+  end
+
+  # Returns whether the App is running.
+  def can_work_on
+    return ['running'].include?(get_attr('Status').downcase)
+  end
+    
+  # Sets the status of the AppSession.
+  #
+  # Note: once set to 'completed' or 'aborted', no more work can be done to the instance
+  # 
+  # +api+:: BaseSpaceAPI instance.
+  # +status+:: Status value, either: completed, aborted, working, or suspended.
+  # +summary+:: Status summary.
+  def set_status(api, status, summary)
+    current_status = get_attr('Status')
+    if current_status.downcase == 'complete' or current_status.downcase == 'aborted'
+      raise "The status of AppSession = #{self.to_s} is #{current_status}, no further status changes are allowed."
+    end
+
+    # To prevent the AppResult object from being in an inconsistent state
+    # and having two identical objects floating around, we update the current object
+    # and discard the returned object
+    new_session = api.set_app_session_state(get_attr('Id'), status, summary)
+    set_attr('Status', new_session.status)
+    set_attr('StatusSummary', new_session.status_summary)
+    return self
+  end
+ 
+end
+ 
+end # module BaseSpace
+end # module Bio
+

data/lib/basespace/model/app_session_compact.rb

@@ -0,0 +1,43 @@
+# 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
+
+# Returned from GET purchases.
+class AppSessionCompact < Model
+
+  # Create a new object.
+  def initialize
+    @swagger_types = {
+      'Id'    => 'str',
+      'Name'  => 'str',
+    }
+    @attributes = {
+      'Id'    => nil,
+      'Name'  => nil,
+    }
+  end
+
+  # Return the name of the object.
+  def to_s
+    return get_attr('Name').to_s
+  end
+
+end
+
+end # module BaseSpace
+end # module Bio
+

data/lib/basespace/model/app_session_launch_object.rb

@@ -0,0 +1,58 @@
+# 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
+
+# Records the launch as part of an AppSession.
+class AppSessionLaunchObject < Model
+
+  # Create a new instance.
+  def initialize
+    @swagger_types = {
+      'Content'      => 'dict',
+      'Href'         => 'str',
+      'HrefContent'  => 'str',
+      'Rel'          => 'str',
+      'Type'         => 'str',
+    }
+    @attributes = {
+      'Content'      => nil,
+      'Href'         => nil,
+      'HrefContent'  => nil,
+      'Rel'          => nil,
+      'Type'         => nil,
+    }
+  end
+
+  # Returns the type of the object.
+  def to_s
+    return get_attr('Type').to_s
+  end
+
+  # Serializes the object.
+  #
+  # +api+:: BaseSpaceAPI instance.
+  def serialize_object(api)
+    res = api.serialize_object(get_attr('Content'), get_attr('Type'))
+    set_attr('Content', res)
+    return self
+  end
+
+end
+
+end # module BaseSpace
+end # module Bio
+

data/lib/basespace/model/app_session_response.rb

@@ -0,0 +1,41 @@
+# 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
+
+# Response of an AppSession.
+class AppSessionResponse < Model
+
+  # Create a new instance.
+  def initialize
+    @swagger_types = {
+      'ResponseStatus'  => 'ResponseStatus',
+      'Response'        => 'AppSession',
+      'Notifications'   => 'list<Str>',
+    }
+    @attributes = {
+      'ResponseStatus'  => nil, # ResponseStatus
+      'Response'        => nil, # Coverage
+      'Notifications'   => nil, # list<Str>'
+    }
+  end
+
+end
+
+end # module BaseSpace
+end # module Bio
+
+

data/lib/basespace/model/application.rb

@@ -0,0 +1,47 @@
+# 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 App representation, which contains data such as name, homepage URI, a short
+# description and the data the App was created.
+class Application < Model
+
+  # Create a new instance.
+  def initialize
+    @swagger_types = {
+      'Id'                => 'str',
+      'Href'              => 'str',
+      'Name'              => 'str',
+      'HomepageUri'       => 'str',
+      'ShortDescription'  => 'str',
+      'DateCreated'       => 'datetime',
+    }
+    @attributes = {
+      'Id'                => nil,
+      'Href'              => nil,
+      'Name'              => nil,
+      'HomepageUri'       => nil,
+      'ShortDescription'  => nil,
+      'DateCreated'       => nil,
+    }
+  end
+
+end
+
+end # module BaseSpace
+end # module Bio
+

data/lib/basespace/model/application_compact.rb

@@ -0,0 +1,44 @@
+# 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
+
+# Application data returned by GET purchase.
+class ApplicationCompact < Model
+
+  # Create a new instance.
+  def initialize
+    @swagger_types = {
+      'Id'           => 'str',
+      'Name'         => 'str',
+      'CompanyName'  => 'str',
+    }
+    @attributes = {
+      'Id'           => nil,
+      'Name'         => nil,
+      'CompanyName'  => nil,
+    }
+  end
+
+  # Return the name of the App data returned by a GET purchase.
+  def to_s
+    return get_attr('Name').to_s
+  end
+
+end
+
+end # module BaseSpace
+end # module Bio

data/lib/basespace/model/basespace_model.rb

@@ -0,0 +1,60 @@
+# 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
+
+# Basic representation of a BaseSpace model.
+class BaseSpaceModel < Model
+  attr_accessor :api
+
+  # Create a new BaseSpaceModel instance.
+  def initialize
+    # [TODO] This class is not similar to other modles. Need to check if this port is OK.
+    @swagger_types = {
+      'Id'  => 'str',
+    }
+    @attributes = {
+      'Id'  => nil,
+    }
+  end
+
+  # Returns the ID of the model.
+  def id
+    get_attr('Id')
+  end
+
+  # Returns the ID of the model.
+  def to_s
+    is_init
+    return get_attr('Id')
+  end
+  
+  # Returns whether this object has been initialized, which is always the case (i.e., true).
+  def is_init
+    return true
+  end
+  
+  # Set a BaseSpaceAPI object for this BaseSpaceModel.
+  #
+  # +api+:: BaseSpaceAPI instance.
+  def set_api(api)
+    @api = api
+  end
+end
+
+end # module BaseSpace
+end # module Bio
+

data/lib/basespace/model/coverage.rb

@@ -0,0 +1,48 @@
+# 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
+
+# Representation of coverage.
+class Coverage < Model
+
+  # Create a new Coverage instance.
+  def initialize
+    @swagger_types = {
+      'Chrom'         => 'str',
+      'BucketSize'    => 'int',
+      'MeanCoverage'  => 'list<int>',
+      'EndPos'        => 'int',
+      'StartPos'      => 'int',
+    }
+    @attributes = {
+      'Chrom'         => nil, # str
+      'BucketSize'    => nil, # int Each returned number will represent coverage of this many bases.
+      'MeanCoverage'  => nil, # list<Str>
+      'EndPos'        => nil, # int End position, possibly adjusted to match zoom boundaries
+      'StartPos'      => nil, # int Start position, possibly adjusted to match zoom boundaries
+    }
+  end
+
+  # Return the genomic position and bucket size of the object.
+  def to_s
+    return "Chrom #{get_attr('Chrom')}: #{get_attr('StartPos')}-#{get_attr('EndPos')}, BucketSize=#{get_attr('BucketSize')}"
+  end
+end
+
+end # module BaseSpace
+end # module Bio
+