bio-basespace-sdk 0.1.2

data/lib/basespace/model/run_compact.rb

@@ -0,0 +1,55 @@
+# 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
+
+# Run compact model.
+class RunCompact < Model
+
+  # Create a new RunCompact instance.
+  def initialize
+    @swagger_types = {
+      'DateCreated'     => 'datetime',
+      'Id'              => 'str',
+      'Href'            => 'str',
+      'ExperimentName'  => 'str',
+    }
+    @attributes = {
+      'DateCreated'     => nil, # datetime
+      'Id'              => nil, # str
+      'Href'            => nil, # str
+      'ExperimentName'  => nil, # str
+    }
+  end
+
+  # Return the experiment name.
+  def to_s
+    return get_attr('ExperimentName')
+  end
+
+  # Returns the scope-string to used for requesting BaseSpace access to the object.
+  #
+  # +scope+:: The type that is requested (write|read).
+  def get_access_str(scope = 'write')
+    is_init
+    return scope + ' run ' + get_attr('Id').to_s
+  end
+
+end
+
+end # module BaseSpace
+end # module Bio
+

data/lib/basespace/model/sample.rb

@@ -0,0 +1,127 @@
+# 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
+
+# Representation of a BaseSpace Sample object.
+class Sample < Model
+
+  # Return a new Sample instance.
+  def initialize
+    @swagger_types = {
+      'HrefGenome'      => 'str',
+      'SampleNumber'    => 'int',
+      'ExperimentName'  => 'str',
+      'HrefFiles'       => 'str',
+      # AppSession
+      'IsPairedEnd'     => 'int',
+      'Read1'           => 'int',
+      'Read2'           => 'int',
+      'NumReadsRaw'     => 'int',
+      'NumReadsPF'      => 'int',
+      'Id'              => 'str',
+      'Href'            => 'str',
+      'UserOwnedBy'     => 'UserCompact',
+      'Name'            => 'str',
+      'SampleId'        => 'str',
+      'Status'          => 'str',
+      'StatusSummary'   => 'str',
+      'DateCreated'     => 'datetime',
+      'References'      => 'dict',
+      'Run'             => 'RunCompact',
+    }
+    @attributes = {
+      'Name'            => nil, # str
+      'HrefFiles'       => nil, # str
+      'DateCreated'     => nil, # datetime
+      'SampleNumber'    => nil, # int
+      'Id'              => nil, # str
+      'Href'            => nil, # str
+      'UserOwnedBy'     => nil, # UserCompact
+      'ExperimentName'  => nil, # str
+      'Run'             => nil, # RunCompact
+      'HrefGenome'      => nil, # str
+      'IsPairedEnd'     => nil, # int
+      'Read1'           => nil, # int
+      'Read2'           => nil, # int
+      'NumReadsRaw'     => nil, # int
+      'NumReadsPF'      => nil, # int
+      'References'      => nil, # dict
+      'SampleId'        => nil, # dict
+      'Status'          => nil, # dict
+      'StatusSummary'   => nil, # dict
+    }
+  end
+
+  # Return the name of the sample.
+  def to_s
+    return get_attr('Name')
+  end
+
+  # Test if the sample instance has been initialized.
+  # 
+  # Throws ModelNotInitializedError, if the Id variable is not set.
+  def is_init
+    raise ModelNotInitializedError.new('The sample model has not been initialized yet') unless get_attr('Id')
+  end
+
+  #def get_genome
+  #  pass
+  #end
+
+  # Returns the scope-string to be used for requesting BaseSpace access to the sample.
+  # 
+  # +scope+:: The scope type that is requested (write|read).
+  def get_access_str(scope = 'write')
+    is_init
+    return scope + ' sample ' + get_attr('Id').to_s
+  end
+
+  # 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.
+  #
+  # +api+:: BaseSpaceAPI instance.
+  def get_referenced_app_results(api)
+    res = []
+    get_attr('References').each do |s|
+      if s[:type] == 'AppResult'
+        json_app_result = s[:content]
+        my_ar = api.serialize_object(json_app_result, 'AppResult')
+        res << my_ar
+      end
+    end
+    return res
+  end
+    
+  # Returns a list of File objects.
+  # 
+  # +api+:: BaseSpaceAPI instance.
+  # +my_qp+:: Query parameters to sort and filter the file list by.
+  def get_files(api, my_qp = {})
+    is_init
+    query_pars = QueryParameters.new(my_qp)
+    return api.get_files_by_sample(get_attr('Id'), query_pars)
+  end
+
+end
+
+end # module BaseSpace
+end # module Bio
+

data/lib/basespace/model/sample_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
+
+# Sample response model.
+class SampleResponse < Model
+
+  # Create a new SampleResponse instance.
+  def initialize
+    @swagger_types = {
+      'ResponseStatus'  => 'ResponseStatus',
+      'Response'        => 'Sample',
+      'Notifications'   => 'list<Str>',
+    }
+    @attributes = {
+      'ResponseStatus'  => nil, # ResponseStatus
+      'Response'        => nil, # Sample
+      'Notifications'   => nil, # list<Str>
+    }
+  end
+
+end
+
+end # module BaseSpace
+end # module Bio
+

data/lib/basespace/model/user.rb

@@ -0,0 +1,80 @@
+# 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'
+
+module Bio
+module BaseSpace
+
+# User model.
+class User < Model
+
+  # Create a new User instance.
+  def initialize
+    @swagger_types = {
+      'Name'            => 'str',
+      'Email'           => 'str',
+      'DateLastActive'  => 'datetime',
+      'GravatarUrl'     => 'str',
+      'HrefProjects'    => 'str',
+      'DateCreated'     => 'datetime',
+      'Id'              => 'str',
+      'Href'            => 'str',
+      'HrefRuns'        => 'str',
+    }
+    @attributes = {
+      'Name'            => nil, # str
+      'Email'           => nil, # str
+      'DateLastActive'  => nil, # datetime
+      'GravatarUrl'     => nil, # str
+      'HrefProjects'    => nil, # str
+      'DateCreated'     => nil, # datetime
+      'Id'              => nil, # str
+      'Href'            => nil, # str
+      'HrefRuns'        => nil, # str
+    }
+  end
+    
+  # Return the ID and name of the user as string.
+  def to_s
+    return "#{get_attr('Id')}: #{get_attr('Name')}"
+  end
+
+  # Test if the Project instance has been initialized.
+  #
+  # Throws ModelNotInitializedError, if the Id variable is not set.
+  def is_init
+    raise ModelNotInitializedError.new('The user model has not been initialized yet') unless get_attr('Id')
+  end
+  
+  # Get a list of projects for the user.
+  #
+  # +api+:: BaseSpaceAPI instance.
+  def get_projects(api)
+    is_init
+    return api.get_project_by_user(get_attr('Id'))
+  end
+
+  # Returns a list of accessible runs for the current user.
+  #
+  # +api+:: BaseSpaceAPI instance.
+  def get_runs(api)
+    is_init
+    return api.get_accessible_runs_by_user('current')
+  end
+end
+
+end # module BaseSpace
+end # module Bio
+

data/lib/basespace/model/user_compact.rb

@@ -0,0 +1,45 @@
+# 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
+
+# User compact model.
+class UserCompact < Model
+
+  # Return a new UserCompact instance.
+  def initialize
+    @swagger_types = {
+      'Name'  => 'str',
+      'Id'    => 'str',
+      'Href'  => 'str',
+    }
+    @attributes = {
+      'Name'  => nil, # str
+      'Id'    => nil, # str
+      'Href'  => nil, # str
+    }
+  end
+
+  # Return the user ID and name as string.
+  def to_s
+    return "#{get_attr('Id')}: #{get_attr('Name')}"
+  end
+
+end
+
+end # module BaseSpace
+end # module Bio
+

data/lib/basespace/model/user_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
+
+# User response model.
+class UserResponse < Model
+
+  # Create a new UserResponse instance.
+  def initialize
+    @swagger_types = {
+      'ResponseStatus'  => 'ResponseStatus',
+      'Response'        => 'User',
+      'Notifications'   => 'list<Str>',
+    }
+    @attributes = {
+      'ResponseStatus'  => nil, # ResponseStatus
+      'Response'        => nil, # User
+      'Notifications'   => nil, # list<Str>
+    }
+  end
+
+end
+
+end # module BaseSpace
+end # module Bio
+

data/lib/basespace/model/variant.rb

@@ -0,0 +1,57 @@
+# 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
+
+# Variant model.
+class Variant < Model
+
+  # Create a new Variant instance.
+  def initialize
+    @swagger_types = {
+      'CHROM'         => 'str',                 
+      'ALT'           => 'str',
+      'ID'            => 'list<Str>',
+      'SampleFormat'  => 'dict',
+      'FILTER'        => 'str',
+      'INFO'          => 'dict',
+      'POS'           => 'int',
+      'QUAL'          => 'int',
+      'REF'           => 'str',
+    }
+    @attributes = {
+      'CHROM'         => nil,
+      'ALT'           => nil,
+      'ID'            => nil,
+      'SampleFormat'  => nil,
+      'FILTER'        => nil,
+      'INFO'          => nil,
+      'POS'           => nil,
+      'QUAL'          => nil,
+      'REF'           => nil,
+    }
+  end
+
+  # Return the genomic coordinate and ID of the variant as string.
+  def to_s
+    return "Variant - #{get_attr('CHROM')}: #{get_attr('POS')} id=#{get_attr('Id')}"
+  end
+
+end
+
+end # module BaseSpace
+end # module Bio
+