bio-basespace-sdk 0.1.2

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

data/lib/basespace/model/coverage_metadata.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
+
+# Models coverage metadata.
+class CoverageMetadata < Model
+
+  # Create a new CoeverageMetadata instance.
+  def initialize
+    @swagger_types = {
+      'MaxCoverage'          => 'int',
+      'CoverageGranularity'  => 'int',
+    }
+    @attributes = {
+      'MaxCoverage'          => nil, # int Maximum coverage value of any base, on a per-base level, for the entire chromosome. Useful for scaling
+      'CoverageGranularity'  => nil, # int Supported granularity of queries
+    }
+  end
+
+  # Return a string denoting the maximum coverage and coverage granularity.
+  def to_s
+    return "CoverageMeta: max=#{get_attr('MaxCoverage')} gran=#{get_attr('CoverageGranularity')}"
+  end
+
+end
+
+end # module BaseSpace
+end # module Bio
+

data/lib/basespace/model/coverage_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
+
+# Response of a coverage object.
+class CoverageResponse < Model
+
+  # Create a new CoverageResponse.
+  def initialize
+    @swagger_types = {
+      'ResponseStatus'  => 'ResponseStatus',
+      'Response'        => 'Coverage',
+      '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/file.rb

@@ -0,0 +1,172 @@
+# 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
+
+# Represents a BaseSpace file object.
+class File < Model
+
+  # Create a new File instance.
+  def initialize
+    @swagger_types = {
+      'Name'          => 'str',
+      'HrefCoverage'  => 'str',
+      'HrefParts'     => 'str',
+      'DateCreated'   => 'datetime',
+      'UploadStatus'  => 'str',
+      'Id'            => 'str',
+      'Href'          => 'str',
+      'HrefContent'   => 'str',
+      'HrefVariants'  => 'str',
+      'ContentType'   => 'str',
+      'Path'          => 'str',
+      'Size'          => 'int',
+    }
+    @attributes = {
+      'Name'          => nil, # str
+      # If set, provides the relative Uri to fetch the mean coverage statistics for data stored in the file
+      'HrefCoverage'  => nil, # str
+      # If set, provides the relative Uri to fetch a list of completed file parts for multi-part file uploads in progress
+      'HrefParts'     => nil, # str
+      'DateCreated'   => nil, # datetime
+      'UploadStatus'  => nil, # str
+      'Id'            => nil, # str
+      'Href'          => nil, # str
+      'HrefContent'   => nil, # str
+      # If set, provides the relative Uri to fetch the variants stored in the file
+      'HrefVariants'  => nil, # str
+      'ContentType'   => nil, # str
+      'Path'          => nil, # str
+      'Size'          => nil, # int
+    }
+  end
+
+  # Returns the name of the file, its ID, size and upload status.
+  def to_s
+    str = get_attr('Name')
+    begin
+      str += " - id: '#{get_attr('Id')}', size: '#{get_attr('Size')}'"
+      str += ", status: '#{get_attr('UploadStatus')}'" if get_attr('UploadStatus')
+    rescue => err
+      # [TODO] What to do with this 'err'?
+      $stderr.puts "    # ----- File#to_s ----- "
+      $stderr.puts "    # Error: #{err}"
+      $stderr.puts "    # "
+    end
+    return str
+  end
+
+  # Tests if the File instance has been initialized.
+  # 
+  # Throws ModelNotInitializedError, if the instance has not been populated yet.
+  def is_init
+    raise ModelNotInitializedError.new('The File model has not been initialized yet') unless get_attr('Id')
+  end
+        
+  # Tests if the File instance matches the filetype parameter.
+  #       
+  # +filetype+:: The filetype for coverage or variant requests (bam|vcf).
+  def is_valid_file_option(filetype)
+    if filetype == 'bam'
+      raise WrongFiletypeError.new(get_attr('Name')) unless get_attr('HrefCoverage')
+    end
+    if filetype == 'vcf'
+      raise WrongFiletypeError.new(get_attr('Name')) unless get_attr('HrefVariants')
+    end
+  end                
+
+  # Download the file object to the specified local directory or a byte range of the file,
+  # by specifying the start and stop byte in the range.
+  # 
+  # +api+:: A BaseSpaceAPI instance with read access to the file object.
+  # +local_dir+:: The local directory to place the file in.
+  # :range+:: Two-item array with start and stop byte of the file chunk that needs retrieved.
+  def download_file(api, local_dir, range = [])
+    if range.empty?
+      return api.file_download(get_attr('Id'),local_dir, get_attr('Name'))
+    else
+      return api.file_download(get_attr('Id'),local_dir, get_attr('Name'), range)
+    end
+  end
+
+  # Return the S3 URL of the file.
+  # 
+  # +api+:: A BaseSpaceAPI instance with read access to the file object.
+  def get_file_url(api)
+    return api.file_url(get_attr('Id'))
+  end
+
+  # Delete the file; not implemented yet.
+  # 
+  # +api+:: A BaseSpaceAPI instance with delete permissions on the file object.
+  def delete_file(api)
+    raise 'Not yet implemented'
+  end
+
+  # Return a coverage object for the specified region and chromosome.
+  # 
+  # +api+:: BaseSpaceAPI instance.
+  # +chrom+:: Chromosome as a string - for example 'chr2'.
+  # +start_pos+:: The start position of region of interest as a string.
+  # +end_pos+:: The end position of region of interest as a string.
+  def get_interval_coverage(api, chrom, start_pos, end_pos)
+    is_init
+    is_valid_file_option('bam')
+    set_attr('Id', get_attr('HrefCoverage').split('/').last)
+    return api.get_interval_coverage(get_attr('Id'), chrom, start_pos, end_pos)
+  end
+    
+  # Returns a list of Variant objects available in the specified region.
+  # 
+  # +api+:: BaseSpaceAPI instance.
+  # +chrom+:: Chromosome as a string - for example 'chr2'.
+  # +start_pos+:: The start position of region of interest as a string.
+  # +end_pos+:: The end position of region of interest as a string.
+  # +qp+: TODO queryParameters object for custom filtering.
+  def filter_variant(api, chrom, start_pos, end_pos, qp = nil)
+    is_init
+    is_valid_file_option('vcf')
+    set_attr('Id', get_attr('HrefVariants').split('/').last)
+    return api.filter_variant_set(get_attr('Id'), chrom, start_pos, end_pos, 'txt')
+  end
+
+  # Return an object of CoverageMetadata for the selected region.
+  # 
+  # +api+:: BaseSpaceAPI instance.
+  # +chrom+:: Chromosome as a string - for example 'chr2'.
+  def get_coverage_meta(api, chrom)
+    is_init
+    is_valid_file_option('bam')
+    set_attr('Id', get_attr('HrefCoverage').split('/').last)
+    return api.get_coverage_meta_info(get_attr('Id'), chrom)
+  end
+
+  # Return the the meta info for a VCF file as a VariantInfo object.
+  # 
+  # +api+:: BaseSpaceAPI instance.
+  def get_variant_meta(api)
+    is_init
+    is_valid_file_option('vcf')
+    set_attr('Id', get_attr('HrefVariants').split('/').last)
+    return api.get_variant_metadata(get_attr('Id'), 'txt')
+  end
+
+end
+
+end # module BaseSpace
+end # module Bio
+

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

data/lib/basespace/model/genome_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
+
+# Genome response object.
+class GenomeResponse < Model
+
+  # Create a new GenomeResponse instance.
+  def initialize
+    @swagger_types = {
+      'ResponseStatus'  => 'ResponseStatus',
+      'Response'        => 'GenomeV1',
+      'Notifications'   => 'list<Str>',
+    }
+    @attributes = {
+      'ResponseStatus'  => nil, # ResponseStatus
+      'Response'        => nil, # GenomeV1
+      'Notifications'   => nil, # list<Str>
+    }
+  end
+
+end
+
+end # module BaseSpace
+end # module Bio
+

data/lib/basespace/model/genome_v1.rb

@@ -0,0 +1,56 @@
+# 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
+
+# Genome model.
+class GenomeV1 < Model
+
+  # Create a new GenomeV1 instance.
+  def initialize
+    @swagger_types = {
+      'Source'       => 'str',
+      'SpeciesName'  => 'str',
+      'Build'        => 'str',
+      'Id'           => 'str',
+      'Href'         => 'str',
+      'DisplayName'  => 'str',
+    }
+    @attributes = {
+      'Source'       => nil, # str
+      'SpeciesName'  => nil, # str
+      'Build'        => nil, # str
+      'Id'           => nil, # str
+      'Href'         => nil, # str
+      'DisplayName'  => nil, # str
+    }
+  end
+
+  # Return species name, or if absent, return display name, or if absent too, return the Href.
+  def to_s
+    if get_attr('SpeciesName')
+      return get_attr('SpeciesName')
+    elsif get_attr('DisplayName')
+      return get_attr('DisplayName')
+    else
+      return "Genome @ #{get_attr('Href')}"
+    end
+  end
+end
+
+end # module BaseSpace
+end # module Bio
+

data/lib/basespace/model/list_response.rb

@@ -0,0 +1,53 @@
+# 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 'json'
+require 'basespace/model'
+
+module Bio
+module BaseSpace
+
+# A list response object.
+class ListResponse < Model
+
+  # Create a new ListResponse instance.
+  def initialize
+    @swagger_types = {
+      'ResponseStatus'  => 'ResponseStatus',
+      'Response'        => 'ResourceList',
+      'Notifications'   => 'list<Str>',
+    }
+    @attributes = {
+      'ResponseStatus'  => nil, # ResponseStatus
+      'Response'        => nil, # ResourceList
+      'Notifications'   => nil, # list<Str>
+    }
+  end
+
+  # Converts the object to a Ruby Array.
+  def convert_to_object_list
+    l = []
+    get_attr('Response').items.each do |m|
+      io = eval(m)
+      s = io.to_json
+      mj = JSON.parse(s)
+      l << mj
+    end
+    return l
+  end
+
+end
+
+end # module BaseSpace
+end # module Bio
+