quorum 0.7.1 → 0.8.0
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- data/.rspec +1 -0
- data/.travis.yml +5 -1
- data/Gemfile +4 -2
- data/Gemfile.lock +68 -47
- data/HISTORY.md +9 -0
- data/README.rdoc +1 -1
- data/app/assets/javascripts/quorum/quorum.js +4 -4
- data/app/controllers/quorum/application_controller.rb +1 -0
- data/app/controllers/quorum/jobs_controller.rb +65 -80
- data/app/models/quorum/blastn_job.rb +1 -1
- data/app/models/quorum/blastn_job_report.rb +4 -1
- data/app/models/quorum/blastp_job.rb +1 -1
- data/app/models/quorum/blastp_job_report.rb +4 -1
- data/app/models/quorum/blastx_job.rb +1 -1
- data/app/models/quorum/blastx_job_report.rb +4 -1
- data/app/models/quorum/job.rb +64 -56
- data/app/models/quorum/job_data.rb +22 -0
- data/app/models/quorum/job_fetch_data.rb +11 -0
- data/app/models/quorum/job_queue_observer.rb +11 -0
- data/app/models/quorum/job_queue_service.rb +66 -0
- data/app/models/quorum/job_report_searcher.rb +36 -0
- data/app/models/quorum/job_serializer.rb +96 -0
- data/app/models/quorum/tblastn_job.rb +1 -1
- data/app/models/quorum/tblastn_job_report.rb +4 -1
- data/app/views/quorum/jobs/show.html.erb +3 -0
- data/app/views/quorum/jobs/templates/_blast_detailed_report_template.html.erb +1 -1
- data/app/views/quorum/jobs/templates/_blast_template.html.erb +3 -1
- data/config/initializers/mime_types.rb +2 -0
- data/config/routes.rb +3 -3
- data/db/migrate/20120809155712_add_percent_identity_to_blast_reports.rb +8 -0
- data/db/migrate/20120921182416_add_mismatch_to_blast_reports.rb +8 -0
- data/lib/generators/templates/blast.rb +8 -1
- data/lib/quorum/engine.rb +2 -0
- data/lib/quorum/sequence.rb +35 -0
- data/lib/quorum/version.rb +1 -1
- data/lib/quorum.rb +3 -10
- data/lib/tasks/quorum_blastdb_build.rake +3 -1
- data/lib/workers/system.rb +3 -1
- data/quorum.gemspec +1 -0
- data/spec/dummy/config/environment.rb +18 -5
- data/spec/javascripts/helpers/jasmine-jquery.js +2 -2
- data/spec/javascripts/{jobs_spec.js → suites/jobs_spec.js} +0 -0
- data/spec/javascripts/{quorum_spec.js → suites/quorum_spec.js} +0 -0
- data/spec/javascripts/{string_spec.js → suites/string_spec.js} +0 -0
- data/spec/lib/tasks/travis.rake +9 -4
- data/spec/models/blastn_job_report_spec.rb +7 -3
- data/spec/models/blastp_job_report_spec.rb +8 -3
- data/spec/models/blastx_job_report_spec.rb +8 -3
- data/spec/models/job_data_spec.rb +21 -0
- data/spec/models/job_fetch_data_spec.rb +25 -0
- data/spec/models/job_queue_observer_spec.rb +18 -0
- data/spec/models/job_queue_service_spec.rb +49 -0
- data/spec/models/job_report_searcher_spec.rb +47 -0
- data/spec/models/job_serializer_spec.rb +60 -0
- data/spec/models/job_spec.rb +1 -16
- data/spec/models/tblastn_job_report_spec.rb +8 -3
- data/spec/quorum/quorum_sequence_spec.rb +2 -0
- data/spec/requests/jobs_spec.rb +16 -7
- data/spec/spec_helper.rb +2 -0
- metadata +38 -8
- data/spec/dummy/app/models/blast.rb +0 -2
data/.rspec
CHANGED
data/.travis.yml
CHANGED
@@ -5,6 +5,9 @@ rvm:
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gemfile:
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- gemfiles/Gemfile.rails-3.1.x
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- gemfiles/Gemfile.rails-3.2.x
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env:
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- DB=mysql
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- DB=postgresql
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before_install:
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- sudo apt-get update
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- sudo apt-get install ncbi-blast+ emboss
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- "export DISPLAY=:99.0"
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- "sh -e /etc/init.d/xvfb start"
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- bundle install
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- mysql -e
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- sh -c "if [ '$DB' = 'mysql' ]; then mysql -e 'create database quorum_test;'; fi"
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- sh -c "if [ '$DB' = 'postgresql' ]; then psql -c 'create database quorum_test;' -U postgres; fi"
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script: "rake travis:spec"
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notifications:
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email:
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data/Gemfile
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data/Gemfile.lock
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remote: .
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DEPENDENCIES
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quorum!
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data/HISTORY.md
CHANGED
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## 0.8.0 (2012-11-30)
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* Major refactoring and bug fixes.
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* Merged feature branch data_export. Search results are available as .txt (tab
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delimited), .gff (GFF3) and JSONi (default).
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* Shortened search url to /quorum/jobs/:id/search?algo=[ie: blastn]
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* Search returns [{ enqueued: false }] if algorithm was not enqueued.
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* Upgrading? Install migrations and run generators.
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## 0.7.1 (2012-11-07)
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* Added quorum:delete_jobs rake task.
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data/README.rdoc
CHANGED
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= Quorum {<img src="https://secure.travis-ci.org/ncgr/quorum.png?branch=master"alt="Build Status" />}[http://travis-ci.org/ncgr/quorum]
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= Quorum {<img src="https://secure.travis-ci.org/ncgr/quorum.png?branch=master" alt="Build Status" />}[http://travis-ci.org/ncgr/quorum]
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A flexible bioinformatics search tool.
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@@ -18,7 +18,7 @@ QUORUM.algorithms = ["blastn", "blastx", "tblastn", "blastp"];
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QUORUM.pollResults = function(callback, callback_obj, interval, algos) {
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var self = this,
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url = document.URL + '/
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url = document.URL + '/search',
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interval = interval || 5000,
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algos = algos || self.algorithms,
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error = false,
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QUORUM.viewDetailedReport = function(focus_id, query, algo) {
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url = document.URL + '/
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url = document.URL + '/search';
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// Create the modal box.
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QUORUM.downloadSequence = function(algo_id, algo, el) {
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var self = this,
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url = document.URL + '/
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url = document.URL + '/get_blast_hit_sequence';
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$(el).html('Fetching sequence...');
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@@ -357,7 +357,7 @@ QUORUM.downloadSequence = function(algo_id, algo, el) {
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QUORUM.getSequenceFile = function(meta_id, el) {
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var self = this,
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url = document.URL + '/
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+
url = document.URL + '/send_blast_hit_sequence?meta_id=' + meta_id,
|
361
361
|
timeoutId = 0;
|
362
362
|
|
363
363
|
function downloadFile(data) {
|
@@ -1,7 +1,7 @@
|
|
1
1
|
module Quorum
|
2
2
|
class JobsController < ApplicationController
|
3
3
|
|
4
|
-
respond_to :html, :json
|
4
|
+
respond_to :html, :json, :gff, :txt
|
5
5
|
before_filter :set_blast_dbs, :only => [:new, :create]
|
6
6
|
|
7
7
|
def index
|
@@ -9,31 +9,16 @@ module Quorum
|
|
9
9
|
end
|
10
10
|
|
11
11
|
def new
|
12
|
-
|
13
|
-
@job.build_blastn_job
|
14
|
-
@job.build_blastx_job
|
15
|
-
@job.build_tblastn_job
|
16
|
-
@job.build_blastp_job
|
12
|
+
build_blast_jobs
|
17
13
|
end
|
18
14
|
|
19
15
|
def create
|
20
|
-
|
21
|
-
file = params[:job][:sequence_file].read
|
22
|
-
params[:job].delete(:sequence_file)
|
23
|
-
end
|
24
|
-
|
16
|
+
read_sequence_file
|
25
17
|
@job = Job.new(params[:job])
|
26
|
-
|
27
|
-
if file
|
28
|
-
@job.sequence = ""
|
29
|
-
@job.sequence << file
|
30
|
-
end
|
18
|
+
set_sequence
|
31
19
|
|
32
20
|
unless @job.save
|
33
|
-
|
34
|
-
@job.build_blastx_job if @job.blastx_job.nil?
|
35
|
-
@job.build_tblastn_job if @job.tblastn_job.nil?
|
36
|
-
@job.build_blastp_job if @job.blastp_job.nil?
|
21
|
+
build_blast_jobs
|
37
22
|
render :action => "new"
|
38
23
|
return
|
39
24
|
end
|
@@ -50,56 +35,36 @@ module Quorum
|
|
50
35
|
end
|
51
36
|
|
52
37
|
#
|
53
|
-
# Returns
|
54
|
-
#
|
55
|
-
|
56
|
-
|
57
|
-
|
58
|
-
|
59
|
-
|
60
|
-
|
61
|
-
|
62
|
-
|
63
|
-
|
64
|
-
|
65
|
-
|
66
|
-
|
67
|
-
|
68
|
-
|
69
|
-
|
70
|
-
|
71
|
-
|
72
|
-
json = job.method(report).call.default_order
|
73
|
-
end
|
74
|
-
else
|
75
|
-
json = []
|
76
|
-
end
|
77
|
-
end
|
78
|
-
end
|
38
|
+
# Returns Quorum's search results.
|
39
|
+
#
|
40
|
+
# This method should be used to gather Resque worker results, or user
|
41
|
+
# supplied query params.
|
42
|
+
#
|
43
|
+
def search
|
44
|
+
data = Job.search(params)
|
45
|
+
|
46
|
+
# Respond with :json, :txt (tab delimited Blast results), or GFF3.
|
47
|
+
respond_with data.flatten!(1) do |format|
|
48
|
+
format.json {
|
49
|
+
render :json => Quorum::JobSerializer.as_json(data)
|
50
|
+
}
|
51
|
+
format.gff {
|
52
|
+
render :text => Quorum::JobSerializer.as_gff(data)
|
53
|
+
}
|
54
|
+
format.txt {
|
55
|
+
render :text => Quorum::JobSerializer.as_txt(data)
|
56
|
+
}
|
79
57
|
end
|
80
|
-
|
81
|
-
respond_with json
|
82
58
|
end
|
83
59
|
|
84
60
|
#
|
85
|
-
# Find hit sequence
|
86
|
-
#
|
87
|
-
#
|
88
|
-
def
|
89
|
-
|
90
|
-
|
91
|
-
|
92
|
-
rescue ActiveRecord::RecordNotFound => e
|
93
|
-
logger.error e.message
|
94
|
-
else
|
95
|
-
data = job.fetch_quorum_blast_sequence(
|
96
|
-
params[:algo], params[:algo_id]
|
97
|
-
)
|
98
|
-
json = [{ :meta_id => data.meta_id }]
|
99
|
-
end
|
100
|
-
end
|
101
|
-
|
102
|
-
respond_with json || []
|
61
|
+
# Find hit sequence and return worker meta_id for lookup. If the method
|
62
|
+
# returns [], try again.
|
63
|
+
#
|
64
|
+
def get_blast_hit_sequence
|
65
|
+
fetch_data = Job.set_blast_hit_sequence_lookup_values(params)
|
66
|
+
data = Quorum::JobQueueService.queue_fetch_worker(fetch_data)
|
67
|
+
respond_with data || []
|
103
68
|
end
|
104
69
|
|
105
70
|
#
|
@@ -108,25 +73,24 @@ module Quorum
|
|
108
73
|
#
|
109
74
|
# See lib/generators/templates/blast_db.rb for more info.
|
110
75
|
#
|
111
|
-
def
|
76
|
+
def send_blast_hit_sequence
|
112
77
|
data = Workers::System.get_meta(params[:meta_id])
|
113
|
-
|
114
|
-
if data.result.downcase.include?("error")
|
115
|
-
render :text => data.result
|
116
|
-
return
|
117
|
-
else
|
118
|
-
send_data data.result,
|
119
|
-
:filename => "#{params[:meta_id]}.fa",
|
120
|
-
:type => "text/plain",
|
121
|
-
:disposition => "attachment"
|
122
|
-
return
|
123
|
-
end
|
124
|
-
end
|
125
|
-
render :text => ""
|
78
|
+
sequence(data)
|
126
79
|
end
|
127
80
|
|
128
81
|
private
|
129
82
|
|
83
|
+
#
|
84
|
+
# Create new Job and build associations.
|
85
|
+
#
|
86
|
+
def build_blast_jobs
|
87
|
+
@job ||= Job.new
|
88
|
+
@job.build_blastn_job if @job.blastn_job.nil?
|
89
|
+
@job.build_blastx_job if @job.blastx_job.nil?
|
90
|
+
@job.build_tblastn_job if @job.tblastn_job.nil?
|
91
|
+
@job.build_blastp_job if @job.blastp_job.nil?
|
92
|
+
end
|
93
|
+
|
130
94
|
#
|
131
95
|
# Blast Database options for select.
|
132
96
|
#
|
@@ -139,5 +103,26 @@ module Quorum
|
|
139
103
|
}
|
140
104
|
end
|
141
105
|
|
106
|
+
#
|
107
|
+
# Read and remove uploaded sequence file from params.
|
108
|
+
#
|
109
|
+
def read_sequence_file
|
110
|
+
if params[:job][:sequence_file]
|
111
|
+
@file = params[:job][:sequence_file].read
|
112
|
+
params[:job].delete(:sequence_file)
|
113
|
+
end
|
114
|
+
end
|
115
|
+
|
116
|
+
#
|
117
|
+
# Set uploaded sequence file.
|
118
|
+
#
|
119
|
+
def set_sequence
|
120
|
+
if @file
|
121
|
+
@job.sequence = ""
|
122
|
+
@job.sequence << @file
|
123
|
+
end
|
124
|
+
@file = nil
|
125
|
+
end
|
126
|
+
|
142
127
|
end
|
143
128
|
end
|
@@ -17,7 +17,7 @@ module Quorum
|
|
17
17
|
:blast_dbs
|
18
18
|
|
19
19
|
validates_format_of :expectation,
|
20
|
-
:with =>
|
20
|
+
:with => /\A[+-]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)?\z/,
|
21
21
|
:message => " - Valid formats (12, 32.05, 43e-123)",
|
22
22
|
:allow_blank => true
|
23
23
|
validates_numericality_of :max_target_seqs,
|
@@ -1,7 +1,10 @@
|
|
1
1
|
module Quorum
|
2
2
|
class BlastnJobReport < ActiveRecord::Base
|
3
|
+
|
4
|
+
extend Quorum::JobReportSearcher
|
5
|
+
|
3
6
|
belongs_to :blastn_job
|
4
7
|
scope :default_order, order("query ASC, bit_score DESC")
|
5
|
-
|
8
|
+
|
6
9
|
end
|
7
10
|
end
|
@@ -17,7 +17,7 @@ module Quorum
|
|
17
17
|
:blast_dbs
|
18
18
|
|
19
19
|
validates_format_of :expectation,
|
20
|
-
:with =>
|
20
|
+
:with => /\A[+-]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)?\z/,
|
21
21
|
:message => " - Valid formats (12, 32.05, 43e-123)",
|
22
22
|
:allow_blank => true
|
23
23
|
validates_numericality_of :max_target_seqs,
|
@@ -1,7 +1,10 @@
|
|
1
1
|
module Quorum
|
2
2
|
class BlastpJobReport < ActiveRecord::Base
|
3
|
+
|
4
|
+
extend Quorum::JobReportSearcher
|
5
|
+
|
3
6
|
belongs_to :blastp_job
|
4
7
|
scope :default_order, order("query ASC, bit_score DESC")
|
5
|
-
|
8
|
+
|
6
9
|
end
|
7
10
|
end
|
@@ -17,7 +17,7 @@ module Quorum
|
|
17
17
|
:blast_dbs
|
18
18
|
|
19
19
|
validates_format_of :expectation,
|
20
|
-
:with =>
|
20
|
+
:with => /\A[+-]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)?\z/,
|
21
21
|
:message => " - Valid formats (12, 32.05, 43e-123)",
|
22
22
|
:allow_blank => true
|
23
23
|
validates_numericality_of :max_target_seqs,
|
@@ -1,7 +1,10 @@
|
|
1
1
|
module Quorum
|
2
2
|
class BlastxJobReport < ActiveRecord::Base
|
3
|
+
|
4
|
+
extend Quorum::JobReportSearcher
|
5
|
+
|
3
6
|
belongs_to :blastx_job
|
4
7
|
scope :default_order, order("query ASC, bit_score DESC")
|
5
|
-
|
8
|
+
|
6
9
|
end
|
7
10
|
end
|