msf 0.1.0

data/lib/msf.rb

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+require 'msf/msf'
+require 'msf/models'

data/lib/msf/models.rb

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+# Load all of the MSF models
+MSF_ROOT = File.expand_path(File.dirname(__FILE__))
+Dir.glob("#{MSF_ROOT}/models/*.rb").each do |r| require r end
+Dir.glob("#{MSF_ROOT}/models/*/*.rb").each do |r| require r end  

data/lib/msf/models/amino_acid.rb

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+# ActiveRecord model of MSF AminoAcid
+#
+#		Example:
+#
+#   AminoAcid.find(1)
+#		AminoAcid.first.monoisotopic_mass
+#   AminoAcid.first.amino_acid_modifications.first.modification_name
+class AminoAcid < ActiveRecord::Base
+  def self.masses
+    if @masses.nil?
+      @masses = {}
+      AminoAcid.select("OneLetterCode,MonoisotopicMass").where("OneLetterCode != ' '").map {|aa| @masses[aa.one_letter_code] =  aa.monoisotopic_mass}
+    end
+    @masses
+  end
+  def self.mass_for_one_letter_code(aa)
+    self.masses[aa]
+  end
+  def self.table_name
+    :AminoAcids
+  end
+  def self.primary_key
+    :AminoAcidID
+  end
+  def amino_acid_id
+    self.AminoAcidID
+  end
+  def amino_acid_name
+    self.AminoAcidName
+  end
+  def one_letter_code
+    self.OneLetterCode
+  end
+  def three_letter_code
+    self.ThreeLetterCode
+  end
+  def monoisotopic_mass
+    self.MonoisotopicMass
+  end
+  def average_mass
+    self.AverageMass
+  end
+  def sum_formula
+    self.SumFormula
+  end
+  # associations
+  has_many :amino_acid_modifications,
+    :class_name => 'AminoAcidModificationsAminoAcids',
+    :foreign_key => "AminoAcidID"
+end

data/lib/msf/models/amino_acid_modification.rb

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+# ActiveRecord model of MSF AminoAcidModification
+#
+#		Example:
+#
+#   AminoAcidModification.find(1)
+#		AminoAcidModification.first.modification_name
+#   AminoAcidModification.first.amino_acids.first.amino_acid_name
+class AminoAcidModification  < ActiveRecord::Base
+  def self.table_name
+    :AminoAcidModifications
+  end
+  def self.primary_key
+    :AminoAcidModificationID
+  end
+  def amino_acid_modification_id
+    self.AminoAcidModificationID
+  end
+  def modification_name
+    self.ModificationName
+  end
+  def delta_mass
+    self.DeltaMass
+  end
+  def substitution
+    self.Substitution
+  end
+  def leaving_group
+    self.LeavingGroup
+  end
+  def abbreviation
+    self.Abbreviation
+  end
+  def position_type
+    self.PositionType
+  end
+  def is_active
+    self.IsActive
+  end
+  def delta_average_mass
+    self.DeltaAverageMass
+  end
+  def unimod_accession
+    self.UnimodAccession
+  end
+  def is_substitution
+    self.IsSubstitution
+  end
+  # associations
+  # join table for amino_acid
+  has_one :amino_acid_modification_amino_acid,
+    :class_name => 'AminoAcidModificationsAminoAcids',
+    :foreign_key => "AminoAcidModificationID"
+  has_one :amino_acid, :through => :amino_acid_modification_amino_acid
+  
+end

data/lib/msf/models/amino_acid_modification_neutral_loss.rb

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+# ActiveRecord model of MSF AminoAcidModificationsNeutralLoss
+#
+#		Example:
+#
+#   AminoAcidModificationNeutralLoss.find(1)
+#		AminoAcidModificationNeutralLoss.first
+#   AminoAcidModificationNeutralLoss.first.amino_acids.first.monoisotopic_mass
+class AminoAcidModificationNeutralLoss  < ActiveRecord::Base
+  def self.table_name
+    :AminoAcidModificationsNeutralLosses
+  end
+  def self.primary_key
+    :NeutralLossID
+  end
+  def neutral_loss_id
+    self.NeutralLossID
+  end
+  def name
+    self.Name
+  end
+  def monoisotopic_mass
+    self.MonoisotopicMass
+  end
+  def average_mass
+    self.AverageMass
+  end
+  has_and_belongs_to_many :amino_acids,
+    :join_table => "AminoAcidModificationsAminoAcidsNL",
+    :foreign_key => "NeutralLossID",
+    :association_foreign_key => "AminoAcidID"
+end

data/lib/msf/models/amino_acid_modifications_amino_acid_nls.rb

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+# ActiveRecord model of MSF AminoAcidModificationsAminoAcidNLs
+# Join table for AminoAcid and AminoAcidModificationsNeutralLosses HABTM
+#
+#		Example:
+#
+#		AminoAcidModificationsAminoAcidNLs.first
+class AminoAcidModificationsAminoAcidNLs < ActiveRecord::Base
+  def self.table_name
+    :AminoAcidModificationsAminoAcidsNL
+  end
+  def self.primary_key
+    [:AminoAcidModificationID, :AminoAcidID, :NeutralLossID]
+  end
+  def amino_acid_modification_id
+    self.AminoAcidModificationID
+  end
+  def amino_acid_id
+    self.AminoAcidID
+  end
+  def neutral_loss_id
+    self.NeutralLossID
+  end
+end

data/lib/msf/models/amino_acid_modifications_amino_acids.rb

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+# ActiveRecord model of MSF AminoAcidModificationsAminoAcids
+# Join table for AminoAcid and AminoAcidModification HABTM
+#
+#		Example:
+#
+#		AminoAcidModificationsAminoAcids.first.classification
+class AminoAcidModificationsAminoAcids < ActiveRecord::Base
+  def self.table_name
+    :AminoAcidModificationsAminoAcids
+  end
+  def self.primary_key
+    [:AminoAcidModificationID, :AminoAcidID]
+  end
+  def amino_acid_modification_id
+    self.AminoAcidModificationID
+  end
+  def amino_acid_id
+    self.AminoAcidID
+  end
+  def classification
+    self.Classification
+  end
+  belongs_to :amino_acid,
+    :foreign_key => "AminoAcidID"
+  belongs_to :amino_acid_modification,
+    :foreign_key => "AminoAcidModificationID"
+end

data/lib/msf/models/annotation_data_version.rb

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+# ActiveRecord model of MSF AnnotationDataVersion
+#
+#		Example:
+#
+#   AnnotationDataVersion.find(1)
+#		AnnotationDataVersion.first.name
+class AnnotationDataVersion < ActiveRecord::Base
+  def self.table_name
+    :AnnotationDataVersion
+  end
+  def self.primary_key
+    :PcDataVersion
+  end
+  def pc_data_version
+    self.PcDataVersion
+  end
+  def pc_data_release
+    self.PcDataRelease
+  end
+end

data/lib/msf/models/annotation_dataset.rb

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+# ActiveRecord model of MSF AnnotationDataset
+#
+#		Example:
+#
+#   AnnotationDataset.find(1)
+#		AnnotationDataset.first.name
+class AnnotationDataset < ActiveRecord::Base
+  def self.table_name
+    :AnnotationDataset
+  end
+  def self.primary_key
+    :DatasetId
+  end
+  def dataset_id
+    self.DatasetId
+  end
+  def name
+    self.Name
+  end
+  def display_name
+    self.DisplayName
+  end
+  def guid
+    self.Guid
+  end
+  def description
+    self.Description
+  end
+end

data/lib/msf/models/annotation_group.rb

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+# ActiveRecord model of MSF AnnotationGroup
+#
+#		Example:
+#
+#   AnnotationGroup.find(1)
+#		AnnotationGroup.first.name
+class AnnotationGroup < ActiveRecord::Base
+  def self.table_name
+    :AnnotationGroups
+  end
+  def self.primary_key
+    [:AnnotationGroupId, :DatasetId]
+  end
+  def annotation_group_id
+    self.AnnotationGroupId
+  end
+  def dataset_id
+    self.DatasetId
+  end
+  def description
+    self.Description
+  end
+  def position
+    self.Position
+  end
+  def color_r
+    self.ColorR
+  end
+  def color_g
+    self.ColorG
+  end
+  def color_b
+    self.ColorB
+  end
+  def group_definition
+    self.GroupDefinition
+  end
+end

data/lib/msf/models/annotation_type.rb

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+# ActiveRecord model of MSF AnnotationType
+#
+#		Example:
+#
+#   AnnotationType.find(1)
+#		AnnotationType.first.name
+class AnnotationType < ActiveRecord::Base
+  def self.table_name
+    :AnnotationTypes
+  end
+  def self.primary_key
+    :AnnotationTypeId
+  end
+  def annotation_type_id
+    self.AnnotationTypeId
+  end
+  def name
+    self.Name
+  end
+  def description
+    self.Description
+  end
+end

data/lib/msf/models/chromatogram.rb

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+# ActiveRecord model of MSF Chromatogram
+#
+#		Example:
+#
+#   Chromatogram.find(1)
+#		Chromatogram.all.first.trace_type
+#   Chromatogram.first.file_infos.file_name
+class Chromatogram < ActiveRecord::Base
+  def self.table_name
+    :Chromatograms
+  end
+  def self.primary_key
+    [:FileID, :TraceType]
+  end
+  def file_id
+    self.FileID
+  end
+  def trace_type
+    self.TraceType
+  end
+  def chromatogram
+    self.Chromatogram
+  end
+  belongs_to :file_info,
+    :foreign_key => "FileID"
+end

data/lib/msf/models/custom_data_field.rb

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+# ActiveRecord model of MSF CustomDataField
+#
+#		Example:
+#
+#   CustomDataField.find(1)
+#		CustomDataField.first.display_name
+class CustomDataField < ActiveRecord::Base
+  def self.table_name
+    :CustomDataFields
+  end
+  def self.primary_key
+    :FieldID
+  end
+  def field_id
+    self.FieldID
+  end
+  def guid
+    self.Guid
+  end
+  def display_name
+    self.DisplayName
+  end
+  def source_node_number
+    self.SourceNodeNumber
+  end
+  def target_node_number
+    self.TargetNodeNumber
+  end
+  def data_type
+    self.DataType
+  end
+  def data_target
+    self.DataTarget
+  end
+  def version
+    self.Version
+  end
+  def access_mode
+    self.AccessMode
+  end
+  def visibility
+    self.Visibility
+  end
+  def group_visibility
+    self.GroupVisibility
+  end
+  def format
+    self.Format
+  end
+  def plot_type
+    self.PlotType
+  end
+  def data_purpose
+    self.DataPurpose
+  end
+end

data/lib/msf/models/custom_data_peptide.rb

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+# ActiveRecord model of MSF CustomDataPeptide
+#
+#		Example:
+#
+#   CustomDataPeptide.find(1)
+#		CustomDataPeptide.first.field_value
+class CustomDataPeptide < ActiveRecord::Base
+  def self.table_name
+    :CustomDataPeptides
+  end
+  def self.primary_key
+    [:FieldID, :PeptideID]
+  end
+  def field_id
+    self.FieldID
+  end
+  def peptide_id
+    self.PeptideID
+  end
+  def field_value
+    self.FieldValue
+  end
+  belongs_to :custom_data_field,
+    :foreign_key => "FieldID"
+end

data/lib/msf/models/custom_data_processing_node.rb

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+# ActiveRecord model of MSF CustomDataProcessingNode
+#
+#		Example:
+#
+#   CustomDataProcessingNode.find(1)
+#		CustomDataProcessingNode.first.field_value
+class CustomDataProcessingNode < ActiveRecord::Base
+  def self.table_name
+    :CustomDataProcessingNodes
+  end
+  def self.primary_key
+    [:FieldID, :ProcessingNodeNumber]
+  end
+  def field_id
+    self.FieldID
+  end
+  def processing_node_number
+    self.ProcessingNodeNumber
+  end
+  def field_value
+    self.FieldValue
+  end
+  belongs_to :custom_data_field,
+    :foreign_key => "FieldID"
+end