msf 0.1.0

data/lib/msf/sql/processing_node_parameter.rb

@@ -0,0 +1,46 @@
+module ThermoMSF
+  module Model
+    class ProcessingNodeParameter < Sequel::Model(:ProcessingNodeParameters)
+        set_primary_key [:ProcessingNodeNumber, :ParameterName]
+      # ruby style accessors
+      def processing_node_number
+        self.ProcessingNodeNumber
+      end
+      def parameter_name
+        self.ParameterName
+      end
+      def friendly_name
+        self.FriendlyName
+      end
+      def processing_node_id
+        self.ProcessingNodeID
+      end
+      def intended_purpose
+        self.IntendedPurpose
+      end
+      def purpose_details
+        self.PurposeDetails
+      end
+      def hidden
+        self.Hidden
+      end
+      def advanced
+        self.Advanced
+      end
+      def category
+        self.Category
+      end
+      def position
+        self.Position
+      end
+      def parameter_value
+        self.ParameterValue
+      end
+      def value_display_string
+        self.ValueDisplayString
+      end
+      # associations
+      many_to_one processing_node, :key => :ProcessingNodeID
+    end
+  end
+end

data/lib/msf/sql/processing_node_spectrum.rb

@@ -0,0 +1,16 @@
+module ThermoMSF
+  module Model
+    class ProcessingNodeSpectrum < Sequel::Model(:ProcessingNodesSpectra)
+        set_primary_key [:SendingProcessingNodeNumber, :SpectrumID]
+      # ruby style accessors
+      def sending_processing_node_number
+        self.SendingProcessingNodeNumber
+      end
+      def spectrum_id
+        self.SpectrumID
+      end
+      # associations
+      many_to_one spectrum, :key => :SpectrumID
+    end
+  end
+end

data/lib/msf/sql/quan_result.rb

@@ -0,0 +1,40 @@
+module ThermoMSF
+  module Model
+    class QuanResult < Sequel::Model(:QuanResults)
+        set_primary_key [:QuanResultID, :SpectrumID]
+      # ruby style accessors
+      def quan_result_id
+        self.QuanResultID
+      end
+      def spectrum_id
+        self.SpectrumID
+      end
+      def height
+        self.Height
+      end
+      def area
+        self.Area
+      end
+      def start_time
+        self.StartTime
+      end
+      def end_time
+        self.EndTime
+      end
+      def start_peak_time
+        self.StartPeakTime
+      end
+      def start_peak_intensity
+        self.StartPeakIntensity
+      end
+      def end_peak_time
+        self.EndPeakTime
+      end
+      def end_peak_intensity
+        self.EndPeakIntensity
+      end
+      # associations
+      many_to_one spectrum, :key => :SpectrumID
+    end
+  end
+end

data/lib/msf/sql/result_filter_set.rb

@@ -0,0 +1,12 @@
+module ThermoMSF
+  module Model
+    class ResultFilterSet < Sequel::Model(:ResultFilterSet)
+        set_primary_key :
+      # ruby style accessors
+      def result_filter_set
+        self.ResultFilterSet
+      end
+      # associations
+    end
+  end
+end

data/lib/msf/sql/taxonomy_node.rb

@@ -0,0 +1,26 @@
+module ThermoMSF
+  module Model
+    class TaxonomyNode < Sequel::Model(:TaxonomyNodes)
+        set_primary_key :TaxonomyID
+      # ruby style accessors
+      def taxonomy_id
+        self.TaxonomyID
+      end
+      def parent_taxonomy_id
+        self.ParentTaxonomyID
+      end
+      def taxonomy_rank
+        self.TaxonomyRank
+      end
+      def left_node_index
+        self.LeftNodeIndex
+      end
+      def right_node_index
+        self.RightNodeIndex
+      end
+      # associations
+      many_to_one taxonomy, :key => :TaxonomyID
+      many_to_one parent_taxonomy, :key => :ParentTaxonomyID
+    end
+  end
+end

data/msf.gemspec

@@ -0,0 +1,143 @@
+# Generated by jeweler
+# DO NOT EDIT THIS FILE DIRECTLY
+# Instead, edit Jeweler::Tasks in Rakefile, and run 'rake gemspec'
+# -*- encoding: utf-8 -*-
+
+Gem::Specification.new do |s|
+  s.name = "msf"
+  s.version = "0.1.0"
+
+  s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
+  s.authors = ["William Van Etten"]
+  s.date = "2012-11-07"
+  s.description = "An MSF file is sqlite3 dtabase. ActiveRecord is a great ORM for accessing the data. Much taken from Angel Pizarro's thermo_msf."
+  s.email = "bill@bioteam.net"
+  s.executables = ["ibspectra"]
+  s.extra_rdoc_files = [
+    "LICENSE.txt",
+    "README.md"
+  ]
+  s.files = [
+    ".document",
+    ".rspec",
+    "Gemfile",
+    "Gemfile.lock",
+    "LICENSE.txt",
+    "README.md",
+    "Rakefile",
+    "VERSION",
+    "bin/ibspectra",
+    "erd/config.png",
+    "erd/empty.png",
+    "erd/erd.png",
+    "erd/msf.xcdatamodeld/.xccurrentversion",
+    "erd/msf.xcdatamodeld/msf.xcdatamodel/contents",
+    "erd/schema.txt",
+    "lib/msf.rb",
+    "lib/msf/models.rb",
+    "lib/msf/models/amino_acid.rb",
+    "lib/msf/models/amino_acid_modification.rb",
+    "lib/msf/models/amino_acid_modification_neutral_loss.rb",
+    "lib/msf/models/amino_acid_modifications_amino_acid_nls.rb",
+    "lib/msf/models/amino_acid_modifications_amino_acids.rb",
+    "lib/msf/models/annotation_data_version.rb",
+    "lib/msf/models/annotation_dataset.rb",
+    "lib/msf/models/annotation_group.rb",
+    "lib/msf/models/annotation_type.rb",
+    "lib/msf/models/chromatogram.rb",
+    "lib/msf/models/custom_data_field.rb",
+    "lib/msf/models/custom_data_peptide.rb",
+    "lib/msf/models/custom_data_processing_node.rb",
+    "lib/msf/models/custom_data_protein.rb",
+    "lib/msf/models/custom_data_spectrum.rb",
+    "lib/msf/models/enzyme.rb",
+    "lib/msf/models/fasta_file.rb",
+    "lib/msf/models/file_info.rb",
+    "lib/msf/models/mass_peak.rb",
+    "lib/msf/models/peptide.rb",
+    "lib/msf/models/peptide_score.rb",
+    "lib/msf/models/peptide_score_decoy.rb",
+    "lib/msf/models/peptide_terminal_modification.rb",
+    "lib/msf/models/peptides_amino_acid_modifications.rb",
+    "lib/msf/models/peptides_proteins.rb",
+    "lib/msf/models/processing_node.rb",
+    "lib/msf/models/processing_node_score.rb",
+    "lib/msf/models/protein.rb",
+    "lib/msf/models/protein_annotation.rb",
+    "lib/msf/models/protein_identification_group.rb",
+    "lib/msf/models/protein_score.rb",
+    "lib/msf/models/reporter_ion_quan_result.rb",
+    "lib/msf/models/reporter_ion_quan_result_search_spectrum.rb",
+    "lib/msf/models/scan_event.rb",
+    "lib/msf/models/schema_info.rb",
+    "lib/msf/models/spectrum.rb",
+    "lib/msf/models/spectrum_header.rb",
+    "lib/msf/models/spectrum_score.rb",
+    "lib/msf/models/taxonomy_name.rb",
+    "lib/msf/models/workflow_info.rb",
+    "lib/msf/models/workflow_message.rb",
+    "lib/msf/msf.rb",
+    "lib/msf/sql/enzyme_cleavage_specificity.rb",
+    "lib/msf/sql/false_discovery_rate.rb",
+    "lib/msf/sql/fasta_file_protein_annotation.rb",
+    "lib/msf/sql/mass_peak_relation.rb",
+    "lib/msf/sql/peptide_amino_acid_modification_decoy.rb",
+    "lib/msf/sql/peptide_decoy.rb",
+    "lib/msf/sql/peptide_terminal_modification_decoy.rb",
+    "lib/msf/sql/precursor_ion_quan_result.rb",
+    "lib/msf/sql/precursor_ion_quan_result_event_spectrum.rb",
+    "lib/msf/sql/precursor_ion_quan_result_search_spectrum.rb",
+    "lib/msf/sql/processing_node_filter_parameter.rb",
+    "lib/msf/sql/processing_node_interface.rb",
+    "lib/msf/sql/processing_node_parameter.rb",
+    "lib/msf/sql/processing_node_spectrum.rb",
+    "lib/msf/sql/quan_result.rb",
+    "lib/msf/sql/result_filter_set.rb",
+    "lib/msf/sql/taxonomy_node.rb",
+    "msf.gemspec",
+    "spec/msf_spec.rb",
+    "spec/spec_helper.rb"
+  ]
+  s.homepage = "http://github.com/vanetten/msf"
+  s.licenses = ["MIT"]
+  s.require_paths = ["lib"]
+  s.rubygems_version = "1.8.24"
+  s.summary = "ActiveRecord access to MSF file (sqlite3 database)."
+
+  if s.respond_to? :specification_version then
+    s.specification_version = 3
+
+    if Gem::Version.new(Gem::VERSION) >= Gem::Version.new('1.2.0') then
+      s.add_runtime_dependency(%q<bundler>, ["~> 1.2.1"])
+      s.add_runtime_dependency(%q<activerecord>, ["~> 3.2.0"])
+      s.add_runtime_dependency(%q<sqlite3>, ["~> 1.3.0"])
+      s.add_development_dependency(%q<rspec>, ["~> 2.8.0"])
+      s.add_development_dependency(%q<simplecov>, ["~> 0.7.1"])
+      s.add_development_dependency(%q<jeweler>, ["~> 1.8.4"])
+      s.add_development_dependency(%q<debugger>, [">= 1.2.0"])
+      s.add_development_dependency(%q<yard>, ["~> 0.7"])
+      s.add_development_dependency(%q<redcarpet>, ["~> 2.2.2"])
+    else
+      s.add_dependency(%q<bundler>, ["~> 1.2.1"])
+      s.add_dependency(%q<activerecord>, ["~> 3.2.0"])
+      s.add_dependency(%q<sqlite3>, ["~> 1.3.0"])
+      s.add_dependency(%q<rspec>, ["~> 2.8.0"])
+      s.add_dependency(%q<simplecov>, ["~> 0.7.1"])
+      s.add_dependency(%q<jeweler>, ["~> 1.8.4"])
+      s.add_dependency(%q<debugger>, [">= 1.2.0"])
+      s.add_dependency(%q<yard>, ["~> 0.7"])
+      s.add_dependency(%q<redcarpet>, ["~> 2.2.2"])
+    end
+  else
+    s.add_dependency(%q<bundler>, ["~> 1.2.1"])
+    s.add_dependency(%q<activerecord>, ["~> 3.2.0"])
+    s.add_dependency(%q<sqlite3>, ["~> 1.3.0"])
+    s.add_dependency(%q<rspec>, ["~> 2.8.0"])
+    s.add_dependency(%q<simplecov>, ["~> 0.7.1"])
+    s.add_dependency(%q<jeweler>, ["~> 1.8.4"])
+    s.add_dependency(%q<debugger>, [">= 1.2.0"])
+    s.add_dependency(%q<yard>, ["~> 0.7"])
+    s.add_dependency(%q<redcarpet>, ["~> 2.2.2"])
+  end
+end
+

data/spec/msf_spec.rb

@@ -0,0 +1,7 @@
+require File.expand_path(File.dirname(__FILE__) + '/spec_helper')
+
+describe MSF do
+  it "fails" do
+    fail "hey buddy, you should probably rename this file and start specing for real"
+  end
+end

data/spec/spec_helper.rb

@@ -0,0 +1,14 @@
+$LOAD_PATH.unshift(File.join(File.dirname(__FILE__), '..', 'lib'))
+$LOAD_PATH.unshift(File.dirname(__FILE__))
+require 'simplecov'
+SimpleCov.start
+require 'rspec'
+require 'msf'
+
+# Requires supporting files with custom matchers and macros, etc,
+# in ./support/ and its subdirectories.
+Dir["#{File.dirname(__FILE__)}/support/**/*.rb"].each {|f| require f}
+
+RSpec.configure do |config|
+  
+end

metadata

@@ -0,0 +1,275 @@
+--- !ruby/object:Gem::Specification
+name: msf
+version: !ruby/object:Gem::Version
+  version: 0.1.0
+  prerelease: 
+platform: ruby
+authors:
+- William Van Etten
+autorequire: 
+bindir: bin
+cert_chain: []
+date: 2012-11-07 00:00:00.000000000 Z
+dependencies:
+- !ruby/object:Gem::Dependency
+  name: bundler
+  requirement: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 1.2.1
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 1.2.1
+- !ruby/object:Gem::Dependency
+  name: activerecord
+  requirement: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 3.2.0
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 3.2.0
+- !ruby/object:Gem::Dependency
+  name: sqlite3
+  requirement: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 1.3.0
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 1.3.0
+- !ruby/object:Gem::Dependency
+  name: rspec
+  requirement: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 2.8.0
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 2.8.0
+- !ruby/object:Gem::Dependency
+  name: simplecov
+  requirement: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 0.7.1
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 0.7.1
+- !ruby/object:Gem::Dependency
+  name: jeweler
+  requirement: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 1.8.4
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 1.8.4
+- !ruby/object:Gem::Dependency
+  name: debugger
+  requirement: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: 1.2.0
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: 1.2.0
+- !ruby/object:Gem::Dependency
+  name: yard
+  requirement: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: '0.7'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: '0.7'
+- !ruby/object:Gem::Dependency
+  name: redcarpet
+  requirement: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 2.2.2
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 2.2.2
+description: An MSF file is sqlite3 dtabase. ActiveRecord is a great ORM for accessing
+  the data. Much taken from Angel Pizarro's thermo_msf.
+email: bill@bioteam.net
+executables:
+- ibspectra
+extensions: []
+extra_rdoc_files:
+- LICENSE.txt
+- README.md
+files:
+- .document
+- .rspec
+- Gemfile
+- Gemfile.lock
+- LICENSE.txt
+- README.md
+- Rakefile
+- VERSION
+- bin/ibspectra
+- erd/config.png
+- erd/empty.png
+- erd/erd.png
+- erd/msf.xcdatamodeld/.xccurrentversion
+- erd/msf.xcdatamodeld/msf.xcdatamodel/contents
+- erd/schema.txt
+- lib/msf.rb
+- lib/msf/models.rb
+- lib/msf/models/amino_acid.rb
+- lib/msf/models/amino_acid_modification.rb
+- lib/msf/models/amino_acid_modification_neutral_loss.rb
+- lib/msf/models/amino_acid_modifications_amino_acid_nls.rb
+- lib/msf/models/amino_acid_modifications_amino_acids.rb
+- lib/msf/models/annotation_data_version.rb
+- lib/msf/models/annotation_dataset.rb
+- lib/msf/models/annotation_group.rb
+- lib/msf/models/annotation_type.rb
+- lib/msf/models/chromatogram.rb
+- lib/msf/models/custom_data_field.rb
+- lib/msf/models/custom_data_peptide.rb
+- lib/msf/models/custom_data_processing_node.rb
+- lib/msf/models/custom_data_protein.rb
+- lib/msf/models/custom_data_spectrum.rb
+- lib/msf/models/enzyme.rb
+- lib/msf/models/fasta_file.rb
+- lib/msf/models/file_info.rb
+- lib/msf/models/mass_peak.rb
+- lib/msf/models/peptide.rb
+- lib/msf/models/peptide_score.rb
+- lib/msf/models/peptide_score_decoy.rb
+- lib/msf/models/peptide_terminal_modification.rb
+- lib/msf/models/peptides_amino_acid_modifications.rb
+- lib/msf/models/peptides_proteins.rb
+- lib/msf/models/processing_node.rb
+- lib/msf/models/processing_node_score.rb
+- lib/msf/models/protein.rb
+- lib/msf/models/protein_annotation.rb
+- lib/msf/models/protein_identification_group.rb
+- lib/msf/models/protein_score.rb
+- lib/msf/models/reporter_ion_quan_result.rb
+- lib/msf/models/reporter_ion_quan_result_search_spectrum.rb
+- lib/msf/models/scan_event.rb
+- lib/msf/models/schema_info.rb
+- lib/msf/models/spectrum.rb
+- lib/msf/models/spectrum_header.rb
+- lib/msf/models/spectrum_score.rb
+- lib/msf/models/taxonomy_name.rb
+- lib/msf/models/workflow_info.rb
+- lib/msf/models/workflow_message.rb
+- lib/msf/msf.rb
+- lib/msf/sql/enzyme_cleavage_specificity.rb
+- lib/msf/sql/false_discovery_rate.rb
+- lib/msf/sql/fasta_file_protein_annotation.rb
+- lib/msf/sql/mass_peak_relation.rb
+- lib/msf/sql/peptide_amino_acid_modification_decoy.rb
+- lib/msf/sql/peptide_decoy.rb
+- lib/msf/sql/peptide_terminal_modification_decoy.rb
+- lib/msf/sql/precursor_ion_quan_result.rb
+- lib/msf/sql/precursor_ion_quan_result_event_spectrum.rb
+- lib/msf/sql/precursor_ion_quan_result_search_spectrum.rb
+- lib/msf/sql/processing_node_filter_parameter.rb
+- lib/msf/sql/processing_node_interface.rb
+- lib/msf/sql/processing_node_parameter.rb
+- lib/msf/sql/processing_node_spectrum.rb
+- lib/msf/sql/quan_result.rb
+- lib/msf/sql/result_filter_set.rb
+- lib/msf/sql/taxonomy_node.rb
+- msf.gemspec
+- spec/msf_spec.rb
+- spec/spec_helper.rb
+homepage: http://github.com/vanetten/msf
+licenses:
+- MIT
+post_install_message: 
+rdoc_options: []
+require_paths:
+- lib
+required_ruby_version: !ruby/object:Gem::Requirement
+  none: false
+  requirements:
+  - - ! '>='
+    - !ruby/object:Gem::Version
+      version: '0'
+      segments:
+      - 0
+      hash: -3318715706776057630
+required_rubygems_version: !ruby/object:Gem::Requirement
+  none: false
+  requirements:
+  - - ! '>='
+    - !ruby/object:Gem::Version
+      version: '0'
+requirements: []
+rubyforge_project: 
+rubygems_version: 1.8.24
+signing_key: 
+specification_version: 3
+summary: ActiveRecord access to MSF file (sqlite3 database).
+test_files: []