quorum 0.1.0

data/spec/dummy/script/rails

@@ -0,0 +1,6 @@
+#!/usr/bin/env ruby
+# This command will automatically be run when you run "rails" with Rails 3 gems installed from the root of your application.
+
+APP_PATH = File.expand_path('../../config/application',  __FILE__)
+require File.expand_path('../../config/boot',  __FILE__)
+require 'rails/commands'

data/spec/models/blastn_job_report_spec.rb

@@ -0,0 +1,13 @@
+require 'spec_helper'
+
+describe Quorum::BlastnJobReport do
+  
+  it "should respond to default_order" do
+    Quorum::BlastnJobReport.methods.should include(:default_order) 
+  end
+
+  it "should respond to by_query" do
+    Quorum::BlastnJobReport.methods.should include(:by_query) 
+  end
+
+end

data/spec/models/blastn_job_spec.rb

@@ -0,0 +1,103 @@
+require 'spec_helper'
+
+describe Quorum::BlastnJob do
+
+  before(:each) do
+    @blastn_job = Quorum::BlastnJob.new()
+  end
+
+  it "fails validation with poorly formatted expectation (using error_on)" do
+    @blastn_job.expectation = "this is bad"
+    @blastn_job.should have(1).error_on(:expectation)
+  end
+
+  it "passes validation with valid expectation values (using error_on)" do
+    @blastn_job.expectation = 12
+    @blastn_job.should have(0).errors_on(:expectation)
+    @blastn_job.expectation = 12.1201
+    @blastn_job.should have(0).errors_on(:expectation)
+    @blastn_job.expectation = "12e-10"
+    @blastn_job.should have(0).errors_on(:expectation)
+    @blastn_job.expectation = "2e+10"
+    @blastn_job.should have(0).errors_on(:expectation)
+  end
+
+  it "fails validation with poorly formatted max_score (using error_on)" do
+    @blastn_job.max_score = 12.34
+    @blastn_job.should have(1).error_on(:max_score)
+    @blastn_job.max_score = "not a number"
+    @blastn_job.should have(1).error_on(:max_score)
+  end
+
+  it "passed validation with valid max_score (using error_on)" do
+    @blastn_job.max_score = 1235
+    @blastn_job.should have(0).errors_on(:max_score)
+  end
+
+  it "fails validation with poorly formatted gap_opening_penalty (using error_on)" do
+    @blastn_job.gap_opening_penalty = "not a number"
+    @blastn_job.should have(1).error_on(:gap_opening_penalty)
+    @blastn_job.gap_opening_penalty = 100.10
+    @blastn_job.should have(1).error_on(:gap_opening_penalty)
+  end
+
+  it "passed validation with valid gap_opening_penalty (using error_on)" do
+    @blastn_job.max_score = 13
+    @blastn_job.should have(0).errors_on(:gap_opening_penalty)
+  end
+
+  it "fails validation with poorly formatted gap_extension_penalty (using error_on)" do
+    @blastn_job.gap_extension_penalty = "who are you?"
+    @blastn_job.should have(1).error_on(:gap_extension_penalty)
+    @blastn_job.gap_extension_penalty = 0.3
+    @blastn_job.should have(1).error_on(:gap_extension_penalty)
+  end
+
+  it "passed validation with valid gap_extension_penalty (using error_on)" do
+    @blastn_job.max_score = 456
+    @blastn_job.should have(0).errors_on(:gap_extension_penalty)
+  end
+
+  it "fails validation without selecting gap_opening_extension with gapped_alignment (using error_on)" do
+    @blastn_job.gapped_alignments = true
+    @blastn_job.gap_opening_extension = ""
+    @blastn_job.should have(1).error_on(:gap_opening_extension)
+  end
+
+  it "fails validation without selecting gap_opening_extension with gapped_alignment (using error_on)" do
+    @blastn_job.gapped_alignments = true
+    @blastn_job.gap_opening_extension = "11, 2"
+    @blastn_job.should have(0).errors_on(:gap_opening_extension)
+  end
+
+  it "gapped_alignment? returns true if gapped_alignments is set" do
+    @blastn_job.gapped_alignments = true
+    @blastn_job.gapped_alignment?.should be_true
+  end
+
+  it "gapped_alignment? returns false if gapped_alignments is not set" do
+    @blastn_job.gapped_alignments = false
+    @blastn_job.gapped_alignment?.should be_false
+  end
+
+  it "gap_opening_extension values should return an Array of Arrays" do
+    @blastn_job.gap_opening_extension_values.should eq(
+      [
+        ['--Select--', ''],
+        ['32767, 32767', '32767,32767'],
+        ['11, 2', '11,2'],
+        ['10, 2', '10,2'],
+        ['9, 2', '9,2'],
+        ['8, 2', '8,2'],
+        ['7, 2', '7,2'],
+        ['6, 2', '6,2'],
+        ['13, 1', '13,1'],
+        ['12, 1', '12,1'],
+        ['11, 1', '11,1'],
+        ['10, 1', '10,1'],
+        ['9, 1', '9,1']
+      ]
+    )
+  end
+
+end

data/spec/models/blastp_job_report_spec.rb

@@ -0,0 +1,13 @@
+require 'spec_helper'
+
+describe Quorum::BlastpJobReport do
+  
+  it "should respond to default_order" do
+    Quorum::BlastpJobReport.methods.should include(:default_order) 
+  end
+
+  it "should respond to by_query" do
+    Quorum::BlastpJobReport.methods.should include(:by_query) 
+  end
+
+end

data/spec/models/blastp_job_spec.rb

@@ -0,0 +1,103 @@
+require 'spec_helper'
+
+describe Quorum::BlastpJob do
+
+  before(:each) do
+    @blastp_job = Quorum::BlastpJob.new()
+  end
+
+  it "fails validation with poorly formatted expectation (using error_on)" do
+    @blastp_job.expectation = "this is bad"
+    @blastp_job.should have(1).error_on(:expectation)
+  end
+
+  it "passes validation with valid expectation values (using error_on)" do
+    @blastp_job.expectation = 12
+    @blastp_job.should have(0).errors_on(:expectation)
+    @blastp_job.expectation = 12.1201
+    @blastp_job.should have(0).errors_on(:expectation)
+    @blastp_job.expectation = "12e-10"
+    @blastp_job.should have(0).errors_on(:expectation)
+    @blastp_job.expectation = "2e+10"
+    @blastp_job.should have(0).errors_on(:expectation)
+  end
+
+  it "fails validation with poorly formatted max_score (using error_on)" do
+    @blastp_job.max_score = 12.34
+    @blastp_job.should have(1).error_on(:max_score)
+    @blastp_job.max_score = "not a number"
+    @blastp_job.should have(1).error_on(:max_score)
+  end
+
+  it "passed validation with valid max_score (using error_on)" do
+    @blastp_job.max_score = 1235
+    @blastp_job.should have(0).errors_on(:max_score)
+  end
+
+  it "fails validation with poorly formatted gap_opening_penalty (using error_on)" do
+    @blastp_job.gap_opening_penalty = "not a number"
+    @blastp_job.should have(1).error_on(:gap_opening_penalty)
+    @blastp_job.gap_opening_penalty = 100.10
+    @blastp_job.should have(1).error_on(:gap_opening_penalty)
+  end
+
+  it "passed validation with valid gap_opening_penalty (using error_on)" do
+    @blastp_job.max_score = 13
+    @blastp_job.should have(0).errors_on(:gap_opening_penalty)
+  end
+
+  it "fails validation with poorly formatted gap_extension_penalty (using error_on)" do
+    @blastp_job.gap_extension_penalty = "who are you?"
+    @blastp_job.should have(1).error_on(:gap_extension_penalty)
+    @blastp_job.gap_extension_penalty = 0.3
+    @blastp_job.should have(1).error_on(:gap_extension_penalty)
+  end
+
+  it "passed validation with valid gap_extension_penalty (using error_on)" do
+    @blastp_job.max_score = 456
+    @blastp_job.should have(0).errors_on(:gap_extension_penalty)
+  end
+
+  it "fails validation without selecting gap_opening_extension with gapped_alignment (using error_on)" do
+    @blastp_job.gapped_alignments = true
+    @blastp_job.gap_opening_extension = ""
+    @blastp_job.should have(1).error_on(:gap_opening_extension)
+  end
+
+  it "fails validation without selecting gap_opening_extension with gapped_alignment (using error_on)" do
+    @blastp_job.gapped_alignments = true
+    @blastp_job.gap_opening_extension = "11, 2"
+    @blastp_job.should have(0).errors_on(:gap_opening_extension)
+  end
+
+  it "gapped_alignment? returns true if gapped_alignments is set" do
+    @blastp_job.gapped_alignments = true
+    @blastp_job.gapped_alignment?.should be_true
+  end
+
+  it "gapped_alignment? returns false if gapped_alignments is not set" do
+    @blastp_job.gapped_alignments = false
+    @blastp_job.gapped_alignment?.should be_false
+  end
+
+  it "gap_opening_extension values should return an Array of Arrays" do
+    @blastp_job.gap_opening_extension_values.should eq(
+      [
+        ['--Select--', ''],
+        ['32767, 32767', '32767,32767'],
+        ['11, 2', '11,2'],
+        ['10, 2', '10,2'],
+        ['9, 2', '9,2'],
+        ['8, 2', '8,2'],
+        ['7, 2', '7,2'],
+        ['6, 2', '6,2'],
+        ['13, 1', '13,1'],
+        ['12, 1', '12,1'],
+        ['11, 1', '11,1'],
+        ['10, 1', '10,1'],
+        ['9, 1', '9,1']
+      ]
+    )
+  end
+
+end

data/spec/models/blastx_job_report_spec.rb

@@ -0,0 +1,13 @@
+require 'spec_helper'
+
+describe Quorum::BlastxJobReport do
+  
+  it "should respond to default_order" do
+    Quorum::BlastxJobReport.methods.should include(:default_order) 
+  end
+
+  it "should respond to default_order" do
+    Quorum::BlastxJobReport.methods.should include(:by_query) 
+  end
+
+end

data/spec/models/blastx_job_spec.rb

@@ -0,0 +1,103 @@
+require 'spec_helper'
+
+describe Quorum::BlastxJob do
+
+  before(:each) do
+    @blastx_job = Quorum::BlastxJob.new()
+  end
+
+  it "fails validation with poorly formatted expectation (using error_on)" do
+    @blastx_job.expectation = "this is bad"
+    @blastx_job.should have(1).error_on(:expectation)
+  end
+
+  it "passes validation with valid expectation values (using error_on)" do
+    @blastx_job.expectation = 12
+    @blastx_job.should have(0).errors_on(:expectation)
+    @blastx_job.expectation = 12.1201
+    @blastx_job.should have(0).errors_on(:expectation)
+    @blastx_job.expectation = "12e-10"
+    @blastx_job.should have(0).errors_on(:expectation)
+    @blastx_job.expectation = "2e+10"
+    @blastx_job.should have(0).errors_on(:expectation)
+  end
+
+  it "fails validation with poorly formatted max_score (using error_on)" do
+    @blastx_job.max_score = 12.34
+    @blastx_job.should have(1).error_on(:max_score)
+    @blastx_job.max_score = "not a number"
+    @blastx_job.should have(1).error_on(:max_score)
+  end
+
+  it "passed validation with valid max_score (using error_on)" do
+    @blastx_job.max_score = 1235
+    @blastx_job.should have(0).errors_on(:max_score)
+  end
+
+  it "fails validation with poorly formatted gap_opening_penalty (using error_on)" do
+    @blastx_job.gap_opening_penalty = "not a number"
+    @blastx_job.should have(1).error_on(:gap_opening_penalty)
+    @blastx_job.gap_opening_penalty = 100.10
+    @blastx_job.should have(1).error_on(:gap_opening_penalty)
+  end
+
+  it "passed validation with valid gap_opening_penalty (using error_on)" do
+    @blastx_job.max_score = 13
+    @blastx_job.should have(0).errors_on(:gap_opening_penalty)
+  end
+
+  it "fails validation with poorly formatted gap_extension_penalty (using error_on)" do
+    @blastx_job.gap_extension_penalty = "who are you?"
+    @blastx_job.should have(1).error_on(:gap_extension_penalty)
+    @blastx_job.gap_extension_penalty = 0.3
+    @blastx_job.should have(1).error_on(:gap_extension_penalty)
+  end
+
+  it "passed validation with valid gap_extension_penalty (using error_on)" do
+    @blastx_job.max_score = 456
+    @blastx_job.should have(0).errors_on(:gap_extension_penalty)
+  end
+
+  it "fails validation without selecting gap_opening_extension with gapped_alignment (using error_on)" do
+    @blastx_job.gapped_alignments = true
+    @blastx_job.gap_opening_extension = ""
+    @blastx_job.should have(1).error_on(:gap_opening_extension)
+  end
+
+  it "fails validation without selecting gap_opening_extension with gapped_alignment (using error_on)" do
+    @blastx_job.gapped_alignments = true
+    @blastx_job.gap_opening_extension = "11, 2"
+    @blastx_job.should have(0).errors_on(:gap_opening_extension)
+  end
+
+  it "gapped_alignment? returns true if gapped_alignments is set" do
+    @blastx_job.gapped_alignments = true
+    @blastx_job.gapped_alignment?.should be_true
+  end
+
+  it "gapped_alignment? returns false if gapped_alignments is not set" do
+    @blastx_job.gapped_alignments = false
+    @blastx_job.gapped_alignment?.should be_false
+  end
+
+  it "gap_opening_extension values should return an Array of Arrays" do
+    @blastx_job.gap_opening_extension_values.should eq(
+      [
+        ['--Select--', ''],
+        ['32767, 32767', '32767,32767'],
+        ['11, 2', '11,2'],
+        ['10, 2', '10,2'],
+        ['9, 2', '9,2'],
+        ['8, 2', '8,2'],
+        ['7, 2', '7,2'],
+        ['6, 2', '6,2'],
+        ['13, 1', '13,1'],
+        ['12, 1', '12,1'],
+        ['11, 1', '11,1'],
+        ['10, 1', '10,1'],
+        ['9, 1', '9,1']
+      ]
+    )
+  end
+
+end

data/spec/models/job_spec.rb

@@ -0,0 +1,40 @@
+require 'spec_helper'
+
+describe Quorum::Job do
+  
+  before(:each) do
+    @job = Quorum::Job.new()
+  end
+
+  it "fails validation without params (using error_on)" do
+    @job.should have(1).error_on(:sequence)
+    @job.should have(1).error_on(:algorithm)
+  end
+
+  it "passes validation with algorithm and valid sequence data" do
+    @job.sequence = File.open(
+      File.expand_path("../../data/nucl_prot_seqs.txt", __FILE__)
+    ).read
+    @job.build_blastn_job
+    @job.blastn_job.queue = true
+    @job.should have(0).errors_on(:sequence)
+    @job.should have(0).errors_on(:algorithm)
+  end
+
+  it "queues workers after save" do
+    resque = double("Resque")
+    resque.stub(:enqueue)
+  
+    @job.sequence = File.open(
+      File.expand_path("../../data/nucl_prot_seqs.txt", __FILE__)
+    ).read
+
+    @job.build_blastn_job
+    @job.blastn_job.queue     = true
+    @job.blastn_job.blast_dbs = ["tmp"]
+
+    @job.should_receive(:queue_workers)
+    @job.save!
+  end
+
+end

data/spec/models/tblastn_job_report_spec.rb

@@ -0,0 +1,13 @@
+require 'spec_helper'
+
+describe Quorum::TblastnJobReport do
+  
+  it "should respond to default_order" do
+    Quorum::TblastnJobReport.methods.should include(:default_order) 
+  end
+
+  it "should respond to default_order" do
+    Quorum::TblastnJobReport.methods.should include(:by_query) 
+  end
+
+end

data/spec/models/tblastn_job_spec.rb

@@ -0,0 +1,103 @@
+require 'spec_helper'
+
+describe Quorum::TblastnJob do
+
+  before(:each) do
+    @tblastn_job = Quorum::TblastnJob.new()
+  end
+
+  it "fails validation with poorly formatted expectation (using error_on)" do
+    @tblastn_job.expectation = "this is bad"
+    @tblastn_job.should have(1).error_on(:expectation)
+  end
+
+  it "passes validation with valid expectation values (using error_on)" do
+    @tblastn_job.expectation = 12
+    @tblastn_job.should have(0).errors_on(:expectation)
+    @tblastn_job.expectation = 12.1201
+    @tblastn_job.should have(0).errors_on(:expectation)
+    @tblastn_job.expectation = "12e-10"
+    @tblastn_job.should have(0).errors_on(:expectation)
+    @tblastn_job.expectation = "2e+10"
+    @tblastn_job.should have(0).errors_on(:expectation)
+  end
+
+  it "fails validation with poorly formatted max_score (using error_on)" do
+    @tblastn_job.max_score = 12.34
+    @tblastn_job.should have(1).error_on(:max_score)
+    @tblastn_job.max_score = "not a number"
+    @tblastn_job.should have(1).error_on(:max_score)
+  end
+
+  it "passed validation with valid max_score (using error_on)" do
+    @tblastn_job.max_score = 1235
+    @tblastn_job.should have(0).errors_on(:max_score)
+  end
+
+  it "fails validation with poorly formatted gap_opening_penalty (using error_on)" do
+    @tblastn_job.gap_opening_penalty = "not a number"
+    @tblastn_job.should have(1).error_on(:gap_opening_penalty)
+    @tblastn_job.gap_opening_penalty = 100.10
+    @tblastn_job.should have(1).error_on(:gap_opening_penalty)
+  end
+
+  it "passed validation with valid gap_opening_penalty (using error_on)" do
+    @tblastn_job.max_score = 13
+    @tblastn_job.should have(0).errors_on(:gap_opening_penalty)
+  end
+
+  it "fails validation with poorly formatted gap_extension_penalty (using error_on)" do
+    @tblastn_job.gap_extension_penalty = "who are you?"
+    @tblastn_job.should have(1).error_on(:gap_extension_penalty)
+    @tblastn_job.gap_extension_penalty = 0.3
+    @tblastn_job.should have(1).error_on(:gap_extension_penalty)
+  end
+
+  it "passed validation with valid gap_extension_penalty (using error_on)" do
+    @tblastn_job.max_score = 456
+    @tblastn_job.should have(0).errors_on(:gap_extension_penalty)
+  end
+
+  it "fails validation without selecting gap_opening_extension with gapped_alignment (using error_on)" do
+    @tblastn_job.gapped_alignments = true
+    @tblastn_job.gap_opening_extension = ""
+    @tblastn_job.should have(1).error_on(:gap_opening_extension)
+  end
+
+  it "fails validation without selecting gap_opening_extension with gapped_alignment (using error_on)" do
+    @tblastn_job.gapped_alignments = true
+    @tblastn_job.gap_opening_extension = "11, 2"
+    @tblastn_job.should have(0).errors_on(:gap_opening_extension)
+  end
+
+  it "gapped_alignment? returns true if gapped_alignments is set" do
+    @tblastn_job.gapped_alignments = true
+    @tblastn_job.gapped_alignment?.should be_true
+  end
+
+  it "gapped_alignment? returns false if gapped_alignments is not set" do
+    @tblastn_job.gapped_alignments = false
+    @tblastn_job.gapped_alignment?.should be_false
+  end
+
+  it "gap_opening_extension values should return an Array of Arrays" do
+    @tblastn_job.gap_opening_extension_values.should eq(
+      [
+        ['--Select--', ''],
+        ['32767, 32767', '32767,32767'],
+        ['11, 2', '11,2'],
+        ['10, 2', '10,2'],
+        ['9, 2', '9,2'],
+        ['8, 2', '8,2'],
+        ['7, 2', '7,2'],
+        ['6, 2', '6,2'],
+        ['13, 1', '13,1'],
+        ['12, 1', '12,1'],
+        ['11, 1', '11,1'],
+        ['10, 1', '10,1'],
+        ['9, 1', '9,1']
+      ]
+    )
+  end
+
+end

data/spec/quorum/quorum_sequence_spec.rb

@@ -0,0 +1,64 @@
+require 'spec_helper'
+require 'quorum/sequence'
+
+include Quorum::Sequence
+
+describe "Quorum::Sequence" do
+  describe "#create_hash" do
+    it "creates a MD5.hexdigest of a sequence" do
+      sequence = File.open(
+        File.expand_path("../../data/nucl_prot_seqs.txt", __FILE__)
+      ).read
+      create_hash(sequence).should_not be_nil 
+    end
+  end
+
+  describe "#write_input_sequence_to_file" do
+    it "writes valid FASTA input sequence to file" do
+      sequence = File.open(
+        File.expand_path("../../data/nucl_prot_seqs.txt", __FILE__)
+      ).read
+      dir  = File.join(::Rails.root.to_s, "log")
+      hash = create_hash(sequence)
+      write_input_sequence_to_file(dir, hash, sequence)
+
+      File.size(
+        File.join(dir, hash + ".seq")
+      ).should be > 0
+
+      File.size(
+        File.join(dir, hash + ".fa")
+      ).should be > 0
+
+      `rm #{File.join(dir, hash + "*")}`
+    end
+
+    it "raises an exception if seqret's exit status is > 0" do
+      sequence = File.open(
+        File.expand_path("../../data/seqs_not_fa.txt", __FILE__)
+      ).read
+      dir  = File.join(::Rails.root.to_s, "log")
+      hash = create_hash(sequence)
+      lambda {
+        write_input_sequence_to_file(dir, hash, sequence)
+      }.should raise_error
+      `rm #{File.join(dir, hash + "*")}`
+    end
+  end
+
+  describe "#discover_input_sequence_type" do
+    it "should return 'nucleic_acid' when fed nucleic acid sequences" do
+      sequence = File.open(
+        File.expand_path("../../data/nucl_seqs.txt", __FILE__)
+      ).read
+      discover_input_sequence_type(sequence).should eq("nucleic_acid")
+    end
+
+    it "should return 'amino_acid' when fed amino acid sequences" do
+      sequence = File.open(
+        File.expand_path("../../data/prot_seqs.txt", __FILE__)
+      ).read
+      discover_input_sequence_type(sequence).should eq("amino_acid")
+    end
+  end
+end

data/spec/quorum_installed_spec.rb

@@ -0,0 +1,64 @@
+require 'spec_helper'
+
+describe "Quorum" do
+  before(:all) do
+    @dummy_path = File.expand_path("../dummy/", __FILE__)
+  end
+
+  it "checks for generated config file" do
+    File.exists?(
+      File.join(@dummy_path, "config", "quorum_settings.yml")
+    ).should be_true
+  end
+
+  it "checks for generated initializer" do
+    File.exists?(
+      File.join(@dummy_path, "config", "initializers", "quorum_initializer.rb")
+    ).should be_true
+  end
+
+  it "checks for generated locale" do
+    File.exists?(
+      File.join(@dummy_path, "config", "locales", "quorum.en.yml")
+    ).should be_true
+  end
+
+  it "checks for quorum directory" do
+    File.directory?(File.join(@dummy_path, "quorum")).should be_true
+  end
+
+  it "checks for quorum/lib files" do
+    File.exists?(
+      File.join(@dummy_path, "quorum", "lib", "search_tools", "blast.rb")
+    ).should be_true
+
+    File.exists?(
+      File.join(@dummy_path, "quorum", "lib", "logger.rb")
+    ).should be_true
+
+    File.exists?(
+      File.join(@dummy_path, "quorum", "lib", "trollop.rb")
+    ).should be_true
+  end
+
+  it "checks for quorum/bin files and ensures they are executable" do
+    File.exists?(
+      File.join(@dummy_path, "quorum", "bin", "search")
+    ).should be_true
+
+    File.executable?(
+      File.join(@dummy_path, "quorum", "bin", "search")
+    ).should be_true
+  end
+
+  it "checks for generated directories" do
+    File.directory?(File.join(@dummy_path, "quorum", "log")).should be_true
+
+    File.directory?(File.join(@dummy_path, "quorum", "tmp")).should be_true
+  end
+
+  it "ensures Quorum::Engine is mounted in dummy/config/routes.rb" do
+    f = File.open(File.join(@dummy_path, "config", "routes.rb"), "r")
+    f.read.include?("mount Quorum::Engine => \"/quorum\"").should be_true
+  end
+end