workflow_manager 0.2.5 → 0.2.6
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- data/.rspec +2 -0
- data/bin/wfm_monitoring +3 -2
- data/lib/workflow_manager/cluster.rb +17 -1
- data/lib/workflow_manager/server.rb +113 -7
- data/lib/workflow_manager/version.rb +1 -1
- data/spec/cluster_spec.rb +97 -0
- data/spec/server_spec.rb +210 -0
- data/spec/spec_helper.rb +96 -0
- metadata +10 -4
data/.rspec
ADDED
data/bin/wfm_monitoring
CHANGED
@@ -1,7 +1,7 @@
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|
1
1
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#!/usr/bin/env ruby
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2
2
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# encoding: utf-8
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3
3
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# 20121112 masa workflow manager client
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4
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-
Version = '
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4
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+
Version = '20160317-153614'
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5
5
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6
6
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require 'drb/drb'
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7
7
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require 'workflow_manager/optparse_ex'
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@@ -52,4 +52,5 @@ sge_options << "-n #{opt.nodes}" if opt.nodes
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52
52
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53
53
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script_content = File.read(script_file)
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54
54
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workflow_manager = DRbObject.new_with_uri(uri)
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55
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-
puts workflow_manager.start_monitoring(script_file, user, 0, script_content, project_number, sge_options.join(' '), opt.log)
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55
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+
#puts workflow_manager.start_monitoring(script_file, user, 0, script_content, project_number, sge_options.join(' '), opt.log)
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56
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+
puts workflow_manager.start_monitoring2(script_file, script_content, user, project_number, sge_options.join(' '), opt.log)
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@@ -26,6 +26,8 @@ module WorkflowManager
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26
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end
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27
27
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def job_ends?(log_file)
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28
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end
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29
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+
def job_pending?(job_id)
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30
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+
end
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29
31
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def copy_commands(org_dir, dest_parent_dir, now=nil)
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30
32
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end
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31
33
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def kill_command(job_id)
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@@ -105,7 +107,8 @@ module WorkflowManager
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105
107
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qstat_flag = false
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108
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IO.popen('qstat -u "*"') do |io|
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107
109
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while line=io.gets
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108
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-
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110
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+
jobid, prior, name, user, state, *others = line.chomp.split
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111
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+
if jobid.strip == job_id and state == 'r'
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109
112
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qstat_flag = true
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110
113
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break
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111
114
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end
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@@ -125,6 +128,19 @@ module WorkflowManager
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125
128
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end
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126
129
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log_flag
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127
130
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end
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131
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+
def job_pending?(job_id)
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132
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qstat_flag = false
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133
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IO.popen('qstat -u "*"') do |io|
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134
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+
while line=io.gets
|
135
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+
jobid, prior, name, user, state, *others = line.chomp.split
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136
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+
if jobid.strip == job_id and state == 'qw'
|
137
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+
qstat_flag = true
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138
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+
break
|
139
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+
end
|
140
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+
end
|
141
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+
end
|
142
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+
qstat_flag
|
143
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+
end
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128
144
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def copy_commands(org_dir, dest_parent_dir, now=nil)
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129
145
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commands = if now
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130
146
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["g-req copynow #{org_dir} #{dest_parent_dir}"]
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@@ -3,6 +3,7 @@
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3
3
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|
4
4
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require 'drb/drb'
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5
5
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require 'fileutils'
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6
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+
require 'csv'
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6
7
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begin
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7
8
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require 'kyotocabinet'
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8
9
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NO_KYOTO = false
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@@ -105,7 +106,7 @@ module WorkflowManager
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105
106
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log_puts("Server starts")
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106
107
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end
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107
108
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def hello
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108
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-
'hello, '+ @cluster.name
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109
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+
'hello test hoge, '+ @cluster.name
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109
110
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end
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110
111
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def copy_commands(org_dir, dest_parent_dir, now=nil)
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111
112
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@cluster.copy_commands(org_dir, dest_parent_dir, now)
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@@ -131,6 +132,111 @@ module WorkflowManager
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131
132
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end
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132
133
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end
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133
134
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end
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135
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+
def input_dataset_tsv_path(script_content)
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136
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+
gstore_dir = nil
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137
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path = nil
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138
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script_content.split(/\n/).each do |line|
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139
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if line =~ /GSTORE_DIR=(.+)/
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140
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gstore_dir = $1.chomp
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141
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+
elsif line =~ /INPUT_DATASET=(.+)/
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142
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path = $1.chomp
|
143
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break
|
144
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+
end
|
145
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+
end
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146
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+
[gstore_dir, path]
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147
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+
end
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148
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+
def input_dataset_file_list(dataset_tsv_path)
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149
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+
file_list = []
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150
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+
CSV.foreach(dataset_tsv_path, :headers=>true, :col_sep=>"\t") do |row|
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151
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row.each do |header, value|
|
152
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if header =~ /\[File\]/
|
153
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file_list << value
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154
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+
end
|
155
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end
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156
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+
end
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157
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+
file_list
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158
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+
end
|
159
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+
def input_dataset_exist?(file_list)
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160
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+
flag = true
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161
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file_list.each do |file|
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162
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+
unless File.exist?(file)
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163
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flag = false
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164
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+
break
|
165
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+
end
|
166
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+
end
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167
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+
flag
|
168
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+
end
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169
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+
def update_time_status(job_id, current_status, script_name, user, project_number)
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170
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+
# if the current status changed from last time, then save, otherwise do nothing
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171
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+
# once status changes into success or fail, then the thread is expected to be killed in later process
|
172
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@statuses.transaction do |statuses|
|
173
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+
start_time = nil
|
174
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+
if stat = statuses[job_id]
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175
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+
last_status, script_name, start_time, user, project_number = stat.split(/,/)
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176
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end
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177
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time = if start_time
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178
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if current_status == 'success' or current_status == 'fail'
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179
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start_time + '/' + Time.now.strftime("%Y-%m-%d %H:%M:%S")
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180
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+
elsif current_status != last_status
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181
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Time.now.strftime("%Y-%m-%d %H:%M:%S")
|
182
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+
end
|
183
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+
else
|
184
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Time.now.strftime("%Y-%m-%d %H:%M:%S")
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185
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+
end
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186
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if time
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187
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statuses[job_id] = [current_status, script_name, time, user, project_number].join(',')
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188
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+
end
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189
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+
end
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190
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+
end
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191
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def finalize_monitoring(current_status, log_file, log_dir)
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192
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if current_status == 'success' or current_status == 'fail'
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193
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unless log_dir.empty?
|
194
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copy_commands(log_file, log_dir).each do |command|
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195
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log_puts(command)
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196
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system command
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197
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+
end
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198
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err_file = log_file.gsub('_o.log','_e.log')
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199
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copy_commands(err_file, log_dir).each do |command|
|
200
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+
log_puts(command)
|
201
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+
system command
|
202
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+
end
|
203
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+
end
|
204
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+
Thread.current.kill
|
205
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+
end
|
206
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+
end
|
207
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def start_monitoring2(script_path, script_content, user='sushi_lover', project_number=0, sge_options='', log_dir='')
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208
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+
# script_path is only used to generate a log file name
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209
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# It is not used to read the script contents
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210
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+
gstore_dir, input_dataset = input_dataset_tsv_path(script_content)
|
211
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+
if gstore_dir and input_dataset
|
212
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+
path = File.join(gstore_dir, input_dataset)
|
213
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+
file_list = input_dataset_file_list(path)
|
214
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+
if input_dataset_exist?(file_list)
|
215
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+
# wait until the files come
|
216
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+
end
|
217
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+
end
|
218
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+
|
219
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+
job_id, log_file, command = @cluster.submit_job(script_path, script_content, sge_options)
|
220
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+
|
221
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+
if job_id and log_file
|
222
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+
worker = Thread.new(job_id, log_file, log_dir, script_path) do |job_id, log_file, log_dir, script_path|
|
223
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+
loop do
|
224
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+
# check status
|
225
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+
current_status = check_status(job_id, log_file)
|
226
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+
|
227
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+
# save time and status
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228
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+
update_time_status(job_id, current_status, script_path, user, project_number)
|
229
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+
|
230
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+
# finalize (kill current thred) in case of success or fail
|
231
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+
finalize_monitoring(current_status, log_file, log_dir)
|
232
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+
|
233
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+
# wait
|
234
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+
sleep @interval
|
235
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+
end # loop
|
236
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+
end # thread
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237
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+
job_id
|
238
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+
end
|
239
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+
end
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134
240
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def start_monitoring(submit_command, user = 'sushi lover', resubmit = 0, script = '', project_number = 0, sge_options='', log_dir = '')
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135
241
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log_puts("monitoring: script=" + submit_command + " user=" + user + " resubmit=" + resubmit.to_s + " project=" + project_number.to_s + " sge option=" + sge_options + " log dir=" + log_dir.to_s)
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136
242
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@@ -227,7 +333,7 @@ module WorkflowManager
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227
333
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#@statuses.open(@db_stat)
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228
334
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@statuses.transaction do |statuses|
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229
335
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if new_status and stat = statuses[job_id.to_s]
|
230
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-
status_list = ['success', 'running', 'fail']
|
336
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+
status_list = ['success', 'running', 'pending', 'fail']
|
231
337
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if status_list.include?(new_status)
|
232
338
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items = stat.split(/,/)
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233
339
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items.shift
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@@ -294,17 +400,17 @@ module WorkflowManager
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294
400
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script
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295
401
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end
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296
402
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def success_or_fail(job_id, log_file)
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297
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-
|
298
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-
job_ends = @cluster.job_ends?(log_file)
|
299
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-
msg = if job_running
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403
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+
msg = if @cluster.job_running?(job_id)
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300
404
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'running'
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301
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-
elsif job_ends
|
405
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+
elsif @cluster.job_ends?(log_file)
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302
406
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'success'
|
407
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+
elsif @cluster.job_pending?(job_id)
|
408
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+
'pending'
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303
409
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else
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304
410
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'fail'
|
305
411
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end
|
306
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-
msg
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307
412
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end
|
413
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+
alias_method :check_status, :success_or_fail
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308
414
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end
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309
415
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end
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310
416
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@@ -0,0 +1,97 @@
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1
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+
#!/usr/bin/env ruby
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2
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+
# encoding: utf-8
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3
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+
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4
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+
require './lib/workflow_manager/cluster'
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5
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+
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6
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+
include WorkflowManager
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7
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+
describe Cluster do
|
8
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+
subject(:cluster) {Cluster.new}
|
9
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+
context 'when new' do
|
10
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+
it {is_expected.to be_an_instance_of Cluster} # RSpec3
|
11
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+
# it {should be_an_instance_of Cluster} # RSpec2
|
12
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+
# example {expect(cluster).to be_an_instance_of Cluster} # RSpec3
|
13
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+
# its(:options) {should be_empty} # RSpec2, does not work anymore
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14
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+
# example {expect(cluster.options).to be_empty}
|
15
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+
end
|
16
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+
describe '#job_running?' do
|
17
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+
subject {cluster.job_running?('job_id')}
|
18
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+
it {is_expected.to be_nil}
|
19
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+
end
|
20
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+
describe '#job_ends?' do
|
21
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+
subject {cluster.job_ends?('log_file')}
|
22
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+
it {is_expected.to be_nil}
|
23
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+
end
|
24
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+
describe '#job_pending?' do
|
25
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+
subject {cluster.job_pending?('job_id')}
|
26
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+
it {is_expected.to be_nil}
|
27
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+
end
|
28
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+
end
|
29
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+
|
30
|
+
describe FGCZCluster do
|
31
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+
subject(:cluster) {FGCZCluster.new}
|
32
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+
context 'when new' do
|
33
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+
it {is_expected.to be_an_instance_of FGCZCluster}
|
34
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+
end
|
35
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+
describe '#job_running?' do
|
36
|
+
let(:line) {' 72757 0.50661 Gcal017211 pacbio r 03/11/2016'}
|
37
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+
let(:job_id) {'72757'}
|
38
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+
subject {cluster.job_running?(job_id)}
|
39
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+
let(:io) {double('io')}
|
40
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+
before do
|
41
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+
allow(IO).to receive(:popen).and_yield(io)
|
42
|
+
end
|
43
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+
context 'when running' do
|
44
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+
before do
|
45
|
+
allow(io).to receive(:gets).and_return(line)
|
46
|
+
end
|
47
|
+
it {is_expected.to eq true}
|
48
|
+
end
|
49
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+
context 'when not running?' do
|
50
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+
before do
|
51
|
+
allow(io).to receive(:gets).and_return(nil)
|
52
|
+
end
|
53
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+
it {is_expected.to eq false}
|
54
|
+
end
|
55
|
+
end
|
56
|
+
describe '#job_ends?' do
|
57
|
+
let(:log_file) {'log_file'}
|
58
|
+
subject {cluster.job_ends?(log_file)}
|
59
|
+
let(:io) {double('io')}
|
60
|
+
before do
|
61
|
+
allow(IO).to receive(:popen).and_yield(io)
|
62
|
+
end
|
63
|
+
context 'when job ends' do
|
64
|
+
before do
|
65
|
+
allow(io).to receive(:gets).and_return('__SCRIPT END__')
|
66
|
+
end
|
67
|
+
it {is_expected.to eq true}
|
68
|
+
end
|
69
|
+
context 'when job not ends' do
|
70
|
+
before do
|
71
|
+
allow(io).to receive(:gets).and_return(nil)
|
72
|
+
end
|
73
|
+
it {is_expected.to eq false}
|
74
|
+
end
|
75
|
+
end
|
76
|
+
describe '#job_pending?' do
|
77
|
+
let(:job_id) {'1234'}
|
78
|
+
let(:line) {' 1234 0.50661 Gcal017211 pacbio qw 03/11/2016'}
|
79
|
+
subject {cluster.job_pending?(job_id)}
|
80
|
+
let(:io) {double('io')}
|
81
|
+
before do
|
82
|
+
allow(IO).to receive(:popen).and_yield(io)
|
83
|
+
end
|
84
|
+
context 'when pending' do
|
85
|
+
before do
|
86
|
+
allow(io).to receive(:gets).and_return(line)
|
87
|
+
end
|
88
|
+
it {is_expected.to eq true}
|
89
|
+
end
|
90
|
+
context 'when not pending' do
|
91
|
+
before do
|
92
|
+
allow(io).to receive(:gets).and_return(nil)
|
93
|
+
end
|
94
|
+
it {is_expected.to eq false}
|
95
|
+
end
|
96
|
+
end
|
97
|
+
end
|
data/spec/server_spec.rb
ADDED
@@ -0,0 +1,210 @@
|
|
1
|
+
#!/usr/bin/env ruby
|
2
|
+
# encoding: utf-8
|
3
|
+
|
4
|
+
require './lib/workflow_manager/server'
|
5
|
+
|
6
|
+
include WorkflowManager
|
7
|
+
describe Server do
|
8
|
+
subject(:server) {Server.new}
|
9
|
+
let(:cluster){double('local_computer')}
|
10
|
+
before do
|
11
|
+
WorkflowManager::Server.configure do |config|
|
12
|
+
config.log_dir = '/srv/GT/analysis/masaomi/workflow_manager/run_workflow_manager/logs'
|
13
|
+
config.db_dir = '/srv/GT/analysis/masaomi/workflow_manager/run_workflow_manager/dbs'
|
14
|
+
config.interval = 30
|
15
|
+
config.resubmit = 0
|
16
|
+
#config.cluster = WorkflowManager::LocalComputer.new('local_computer')
|
17
|
+
config.cluster = cluster
|
18
|
+
allow(config.cluster).to receive_messages(:log_dir= => nil, :name => 'local_computer')
|
19
|
+
end
|
20
|
+
# suppress puts
|
21
|
+
allow($stdout).to receive(:write)
|
22
|
+
end
|
23
|
+
context 'when new' do
|
24
|
+
it {is_expected.to be_an_instance_of Server} # RSpec3
|
25
|
+
end
|
26
|
+
describe '#input_dataset_exist?' do
|
27
|
+
let(:file_list) {['file1', 'file2']}
|
28
|
+
subject{server.input_dataset_exist?(file_list)}
|
29
|
+
context 'when file exist' do
|
30
|
+
before do
|
31
|
+
allow(File).to receive(:exist?).and_return(true)
|
32
|
+
end
|
33
|
+
it {is_expected.to eq true}
|
34
|
+
end
|
35
|
+
context 'when file not exist' do
|
36
|
+
before do
|
37
|
+
allow(File).to receive(:exist?).and_return(false)
|
38
|
+
end
|
39
|
+
it {is_expected.to eq false}
|
40
|
+
end
|
41
|
+
end
|
42
|
+
describe '#input_dataset_file_list' do
|
43
|
+
subject{server.input_dataset_file_list('input_dataset_tsv_path')}
|
44
|
+
let(:rows) {{'Read1 [File]'=>'file1', 'Read2 [File]'=>'file2'} }
|
45
|
+
before do
|
46
|
+
allow(CSV).to receive(:foreach).and_yield(rows)
|
47
|
+
end
|
48
|
+
let(:sample_file_list) { ['file1', 'file2'] }
|
49
|
+
it {is_expected.to eq sample_file_list}
|
50
|
+
end
|
51
|
+
describe '#input_dataset_tsv_path' do
|
52
|
+
let(:sample_script) {
|
53
|
+
"SCRATCH_DIR=/scratch/test_masa_2016-03-03--16-36-42_temp$$
|
54
|
+
GSTORE_DIR=/srv/gstore/projects
|
55
|
+
INPUT_DATASET=/srv/gstore/projects/p1535/test_masa/input_dataset.tsv"
|
56
|
+
}
|
57
|
+
let(:path){
|
58
|
+
[
|
59
|
+
'/srv/gstore/projects',
|
60
|
+
'/srv/gstore/projects/p1535/test_masa/input_dataset.tsv'
|
61
|
+
]
|
62
|
+
}
|
63
|
+
subject{server.input_dataset_tsv_path(sample_script)}
|
64
|
+
it {is_expected.to eq path}
|
65
|
+
end
|
66
|
+
describe '#start_monitoring2' do
|
67
|
+
let(:script_path){'script_file'}
|
68
|
+
let(:script_content){'script_content'}
|
69
|
+
let(:cluster){double('cluster')}
|
70
|
+
before do
|
71
|
+
allow(server).to receive(:input_dataset_tsv_path)
|
72
|
+
allow(server).to receive(:input_dataset_file_list)
|
73
|
+
allow(server).to receive(:input_dataset_exist?)
|
74
|
+
end
|
75
|
+
context 'when submit_job failed' do
|
76
|
+
before do
|
77
|
+
allow(cluster).to receive(:submit_job)
|
78
|
+
end
|
79
|
+
subject {server.start_monitoring2(script_path, script_content)}
|
80
|
+
it {is_expected.to be_nil}
|
81
|
+
end
|
82
|
+
context 'when submit_job successed' do
|
83
|
+
before do
|
84
|
+
allow(cluster).to receive(:submit_job).and_return(['job_id', 'log_file', 'command'])
|
85
|
+
allow(Thread).to receive(:new)
|
86
|
+
end
|
87
|
+
subject {server.start_monitoring2(script_path, script_content)}
|
88
|
+
it {is_expected.to eq 'job_id'}
|
89
|
+
end
|
90
|
+
end
|
91
|
+
describe '#success_or_fail' do
|
92
|
+
let(:job_id){'job_id'}
|
93
|
+
let(:log_file){'log_file'}
|
94
|
+
let(:cluster){double('cluster')}
|
95
|
+
before do
|
96
|
+
server.instance_variable_set(:@cluster, cluster)
|
97
|
+
end
|
98
|
+
context 'when job running' do
|
99
|
+
before do
|
100
|
+
allow(cluster).to receive(:job_running?).and_return(true)
|
101
|
+
allow(cluster).to receive(:job_ends?).and_return(nil)
|
102
|
+
allow(cluster).to receive(:job_pending?).and_return(nil)
|
103
|
+
end
|
104
|
+
subject {server.success_or_fail(job_id, log_file)}
|
105
|
+
it {is_expected.to eq 'running'}
|
106
|
+
end
|
107
|
+
context 'when job ends' do
|
108
|
+
before do
|
109
|
+
allow(cluster).to receive(:job_running?).and_return(nil)
|
110
|
+
allow(cluster).to receive(:job_ends?).and_return(true)
|
111
|
+
allow(cluster).to receive(:job_pending?).and_return(nil)
|
112
|
+
end
|
113
|
+
subject {server.success_or_fail(job_id, log_file)}
|
114
|
+
it {is_expected.to eq 'success'}
|
115
|
+
end
|
116
|
+
context 'when job pending' do
|
117
|
+
before do
|
118
|
+
allow(cluster).to receive(:job_running?).and_return(nil)
|
119
|
+
allow(cluster).to receive(:job_ends?).and_return(nil)
|
120
|
+
allow(cluster).to receive(:job_pending?).and_return(true)
|
121
|
+
end
|
122
|
+
subject {server.success_or_fail(job_id, log_file)}
|
123
|
+
it {is_expected.to eq 'pending'}
|
124
|
+
end
|
125
|
+
end
|
126
|
+
describe '#status' do
|
127
|
+
let(:statuses) {double('statuses')}
|
128
|
+
before do
|
129
|
+
server.instance_variable_set(:@statuses, statuses)
|
130
|
+
end
|
131
|
+
context 'when read status' do
|
132
|
+
before do
|
133
|
+
allow(statuses).to receive(:transaction).and_yield({'job_id'=>'stat'})
|
134
|
+
end
|
135
|
+
subject {server.status('job_id')}
|
136
|
+
it {is_expected.to eq 'stat'}
|
137
|
+
end
|
138
|
+
context 'when assign status' do
|
139
|
+
before do
|
140
|
+
allow(statuses).to receive(:transaction).and_yield({'job_id'=>'running'})
|
141
|
+
end
|
142
|
+
subject {server.status('job_id', 'success')}
|
143
|
+
it {is_expected.to eq 'success'}
|
144
|
+
end
|
145
|
+
end
|
146
|
+
describe '#update_time_status' do
|
147
|
+
let(:statuses) {double('statuses')}
|
148
|
+
before do
|
149
|
+
server.instance_variable_set(:@statuses, statuses)
|
150
|
+
end
|
151
|
+
context 'when initial call' do
|
152
|
+
before do
|
153
|
+
allow(statuses).to receive(:transaction).and_yield({'job_id' => nil})
|
154
|
+
allow(Time).to receive_message_chain(:now, :strftime).and_return('time')
|
155
|
+
end
|
156
|
+
let(:expected) {'current_status,script_name,time,user,project_number'}
|
157
|
+
subject {server.update_time_status('job_id', 'current_status', 'script_name', 'user', 'project_number')}
|
158
|
+
it {is_expected.to eq expected}
|
159
|
+
end
|
160
|
+
context 'when changing status from running to success' do
|
161
|
+
let(:last_status) {'running,script_name,start_time,user,project_number'}
|
162
|
+
before do
|
163
|
+
allow(statuses).to receive(:transaction).and_yield({'job_id' => last_status})
|
164
|
+
allow(Time).to receive_message_chain(:now, :strftime).and_return('end_time')
|
165
|
+
end
|
166
|
+
subject {server.update_time_status('job_id', 'success', 'script_name', 'user', 'project_number')}
|
167
|
+
let(:expected) {'success,script_name,start_time/end_time,user,project_number'}
|
168
|
+
it {is_expected.to eq expected}
|
169
|
+
end
|
170
|
+
context 'when current_status and new_sutatus are same' do
|
171
|
+
let(:last_status) {'running,script_name,start_time,user,project_number'}
|
172
|
+
before do
|
173
|
+
allow(statuses).to receive(:transaction).and_yield({'job_id' => last_status})
|
174
|
+
allow(Time).to receive_message_chain(:now, :strftime).and_return('end_time')
|
175
|
+
end
|
176
|
+
subject {server.update_time_status('job_id', 'running', 'script_name', 'user', 'project_number')}
|
177
|
+
it {is_expected.to be_nil}
|
178
|
+
end
|
179
|
+
context 'when current_status==running and last_status==pending' do
|
180
|
+
let(:last_status) {'pending,script_name,start_time,user,project_number'}
|
181
|
+
before do
|
182
|
+
allow(statuses).to receive(:transaction).and_yield({'job_id' => last_status})
|
183
|
+
allow(Time).to receive_message_chain(:now, :strftime).and_return('end_time')
|
184
|
+
end
|
185
|
+
subject {server.update_time_status('job_id', 'running', 'script_name', 'user', 'project_number')}
|
186
|
+
let(:expected) {"running,script_name,end_time,user,project_number"}
|
187
|
+
it {is_expected.to eq expected}
|
188
|
+
end
|
189
|
+
end
|
190
|
+
describe '#finalize_monitoring' do
|
191
|
+
context 'when status == running' do
|
192
|
+
before do
|
193
|
+
allow(server).to receive(:log_puts)
|
194
|
+
allow(Thread).to receive_message_chain(:current, :kill)
|
195
|
+
end
|
196
|
+
subject {server.finalize_monitoring('running', 'log_file', 'log_dir')}
|
197
|
+
it {is_expected.to be_nil}
|
198
|
+
end
|
199
|
+
context 'when status == success' do
|
200
|
+
before do
|
201
|
+
allow(server).to receive(:log_puts)
|
202
|
+
allow(Thread).to receive_message_chain(:current, :kill)
|
203
|
+
#expect(server).to receive(:system).twice
|
204
|
+
expect(server).to receive(:copy_commands).twice.and_return([])
|
205
|
+
end
|
206
|
+
subject {server.finalize_monitoring('success', 'log_file', 'log_dir')}
|
207
|
+
it {is_expected.to be_nil}
|
208
|
+
end
|
209
|
+
end
|
210
|
+
end
|
data/spec/spec_helper.rb
ADDED
@@ -0,0 +1,96 @@
|
|
1
|
+
# This file was generated by the `rspec --init` command. Conventionally, all
|
2
|
+
# specs live under a `spec` directory, which RSpec adds to the `$LOAD_PATH`.
|
3
|
+
# The generated `.rspec` file contains `--require spec_helper` which will cause
|
4
|
+
# this file to always be loaded, without a need to explicitly require it in any
|
5
|
+
# files.
|
6
|
+
#
|
7
|
+
# Given that it is always loaded, you are encouraged to keep this file as
|
8
|
+
# light-weight as possible. Requiring heavyweight dependencies from this file
|
9
|
+
# will add to the boot time of your test suite on EVERY test run, even for an
|
10
|
+
# individual file that may not need all of that loaded. Instead, consider making
|
11
|
+
# a separate helper file that requires the additional dependencies and performs
|
12
|
+
# the additional setup, and require it from the spec files that actually need
|
13
|
+
# it.
|
14
|
+
#
|
15
|
+
# The `.rspec` file also contains a few flags that are not defaults but that
|
16
|
+
# users commonly want.
|
17
|
+
#
|
18
|
+
# See http://rubydoc.info/gems/rspec-core/RSpec/Core/Configuration
|
19
|
+
RSpec.configure do |config|
|
20
|
+
# rspec-expectations config goes here. You can use an alternate
|
21
|
+
# assertion/expectation library such as wrong or the stdlib/minitest
|
22
|
+
# assertions if you prefer.
|
23
|
+
config.expect_with :rspec do |expectations|
|
24
|
+
# This option will default to `true` in RSpec 4. It makes the `description`
|
25
|
+
# and `failure_message` of custom matchers include text for helper methods
|
26
|
+
# defined using `chain`, e.g.:
|
27
|
+
# be_bigger_than(2).and_smaller_than(4).description
|
28
|
+
# # => "be bigger than 2 and smaller than 4"
|
29
|
+
# ...rather than:
|
30
|
+
# # => "be bigger than 2"
|
31
|
+
expectations.include_chain_clauses_in_custom_matcher_descriptions = true
|
32
|
+
end
|
33
|
+
|
34
|
+
# rspec-mocks config goes here. You can use an alternate test double
|
35
|
+
# library (such as bogus or mocha) by changing the `mock_with` option here.
|
36
|
+
config.mock_with :rspec do |mocks|
|
37
|
+
# Prevents you from mocking or stubbing a method that does not exist on
|
38
|
+
# a real object. This is generally recommended, and will default to
|
39
|
+
# `true` in RSpec 4.
|
40
|
+
mocks.verify_partial_doubles = true
|
41
|
+
end
|
42
|
+
|
43
|
+
# The settings below are suggested to provide a good initial experience
|
44
|
+
# with RSpec, but feel free to customize to your heart's content.
|
45
|
+
=begin
|
46
|
+
# These two settings work together to allow you to limit a spec run
|
47
|
+
# to individual examples or groups you care about by tagging them with
|
48
|
+
# `:focus` metadata. When nothing is tagged with `:focus`, all examples
|
49
|
+
# get run.
|
50
|
+
config.filter_run :focus
|
51
|
+
config.run_all_when_everything_filtered = true
|
52
|
+
|
53
|
+
# Allows RSpec to persist some state between runs in order to support
|
54
|
+
# the `--only-failures` and `--next-failure` CLI options. We recommend
|
55
|
+
# you configure your source control system to ignore this file.
|
56
|
+
config.example_status_persistence_file_path = "spec/examples.txt"
|
57
|
+
|
58
|
+
# Limits the available syntax to the non-monkey patched syntax that is
|
59
|
+
# recommended. For more details, see:
|
60
|
+
# - http://rspec.info/blog/2012/06/rspecs-new-expectation-syntax/
|
61
|
+
# - http://www.teaisaweso.me/blog/2013/05/27/rspecs-new-message-expectation-syntax/
|
62
|
+
# - http://rspec.info/blog/2014/05/notable-changes-in-rspec-3/#zero-monkey-patching-mode
|
63
|
+
config.disable_monkey_patching!
|
64
|
+
|
65
|
+
# This setting enables warnings. It's recommended, but in some cases may
|
66
|
+
# be too noisy due to issues in dependencies.
|
67
|
+
config.warnings = true
|
68
|
+
|
69
|
+
# Many RSpec users commonly either run the entire suite or an individual
|
70
|
+
# file, and it's useful to allow more verbose output when running an
|
71
|
+
# individual spec file.
|
72
|
+
if config.files_to_run.one?
|
73
|
+
# Use the documentation formatter for detailed output,
|
74
|
+
# unless a formatter has already been configured
|
75
|
+
# (e.g. via a command-line flag).
|
76
|
+
config.default_formatter = 'doc'
|
77
|
+
end
|
78
|
+
|
79
|
+
# Print the 10 slowest examples and example groups at the
|
80
|
+
# end of the spec run, to help surface which specs are running
|
81
|
+
# particularly slow.
|
82
|
+
config.profile_examples = 10
|
83
|
+
|
84
|
+
# Run specs in random order to surface order dependencies. If you find an
|
85
|
+
# order dependency and want to debug it, you can fix the order by providing
|
86
|
+
# the seed, which is printed after each run.
|
87
|
+
# --seed 1234
|
88
|
+
config.order = :random
|
89
|
+
|
90
|
+
# Seed global randomization in this process using the `--seed` CLI option.
|
91
|
+
# Setting this allows you to use `--seed` to deterministically reproduce
|
92
|
+
# test failures related to randomization by passing the same `--seed` value
|
93
|
+
# as the one that triggered the failure.
|
94
|
+
Kernel.srand config.seed
|
95
|
+
=end
|
96
|
+
end
|
metadata
CHANGED
@@ -2,7 +2,7 @@
|
|
2
2
|
name: workflow_manager
|
3
3
|
version: !ruby/object:Gem::Version
|
4
4
|
prerelease:
|
5
|
-
version: 0.2.
|
5
|
+
version: 0.2.6
|
6
6
|
platform: ruby
|
7
7
|
authors:
|
8
8
|
- Functional Genomics Center Zurich
|
@@ -10,7 +10,7 @@ autorequire:
|
|
10
10
|
bindir: bin
|
11
11
|
cert_chain: []
|
12
12
|
|
13
|
-
date:
|
13
|
+
date: 2016-03-21 00:00:00 Z
|
14
14
|
dependencies:
|
15
15
|
- !ruby/object:Gem::Dependency
|
16
16
|
name: bundler
|
@@ -53,6 +53,7 @@ extra_rdoc_files: []
|
|
53
53
|
|
54
54
|
files:
|
55
55
|
- .gitignore
|
56
|
+
- .rspec
|
56
57
|
- Gemfile
|
57
58
|
- LICENSE.txt
|
58
59
|
- README.md
|
@@ -73,6 +74,9 @@ files:
|
|
73
74
|
- lib/workflow_manager/optparse_ex.rb
|
74
75
|
- lib/workflow_manager/server.rb
|
75
76
|
- lib/workflow_manager/version.rb
|
77
|
+
- spec/cluster_spec.rb
|
78
|
+
- spec/server_spec.rb
|
79
|
+
- spec/spec_helper.rb
|
76
80
|
- workflow_manager.gemspec
|
77
81
|
homepage: ""
|
78
82
|
licenses:
|
@@ -101,5 +105,7 @@ rubygems_version: 1.8.23
|
|
101
105
|
signing_key:
|
102
106
|
specification_version: 3
|
103
107
|
summary: Workflow Manager manages job submissions using dRuby.
|
104
|
-
test_files:
|
105
|
-
|
108
|
+
test_files:
|
109
|
+
- spec/cluster_spec.rb
|
110
|
+
- spec/server_spec.rb
|
111
|
+
- spec/spec_helper.rb
|