bio-polymarker_db_batch 0.4.0 → 0.5.0
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- checksums.yaml +4 -4
- data/VERSION +1 -1
- data/bin/monitor_running_polymarker.rb +1 -4
- data/lib/bio-polymarker_db_batch/polymarker_db_batch.rb +27 -12
- metadata +2 -2
checksums.yaml
CHANGED
@@ -1,7 +1,7 @@
|
|
1
1
|
---
|
2
2
|
SHA1:
|
3
|
-
metadata.gz:
|
4
|
-
data.tar.gz:
|
3
|
+
metadata.gz: 660fa22d63f669c926d128aece6bd65f4f55e36f
|
4
|
+
data.tar.gz: 4b907713e95acc39e85825b49a01f97ebf477805
|
5
5
|
SHA512:
|
6
|
-
metadata.gz:
|
7
|
-
data.tar.gz:
|
6
|
+
metadata.gz: 3a055fa7de5e42d50a9d6d61b8b75afd8e5f94c2b50b41bb22efc9fb184dc60b87e44c349653e20fcf7ce6528e4a207b572df6ad82b3177afa41acc5eaddfd12
|
7
|
+
data.tar.gz: 683cf0eae0d13e9c7005387811f8c58e4f1f7d13f3d0774cec74f55cd67dc65b799b8c06370e3df68e5c1d367e4179a24f4ad550da28f4d0484339d83c2f8aa9
|
data/VERSION
CHANGED
@@ -1 +1 @@
|
|
1
|
-
0.
|
1
|
+
0.5.0
|
@@ -12,7 +12,7 @@ options = {}
|
|
12
12
|
|
13
13
|
|
14
14
|
OptionParser.new do |opts|
|
15
|
-
opts.banner = "Usage:
|
15
|
+
opts.banner = "Usage: monitor_running_polymarker.rb [options]"
|
16
16
|
|
17
17
|
opts.on("-p", "--preferences FILE" "File with the preferences") do |o|
|
18
18
|
options[:preferences] = o
|
@@ -25,13 +25,10 @@ pol=Bio::DB::Polymarker.new(options[:preferences])
|
|
25
25
|
|
26
26
|
#pol.mysql_version
|
27
27
|
pol.each_running do |row|
|
28
|
-
#puts row.join(",")
|
29
|
-
#puts row.inspect
|
30
28
|
pol.review_running_status(row[0], row[1])
|
31
29
|
end
|
32
30
|
|
33
31
|
pol.each_timeout do |row|
|
34
|
-
#puts "Timeouts: #{row[0]}"
|
35
32
|
pol.update_error_status(row[0], "Timeout")
|
36
33
|
end
|
37
34
|
|
@@ -4,7 +4,7 @@ class Bio::DB::Polymarker
|
|
4
4
|
|
5
5
|
def initialize( props)
|
6
6
|
@properties =Hash[*File.read(props).split(/[=\n]+/)]
|
7
|
-
|
7
|
+
puts @properties.inspect
|
8
8
|
end
|
9
9
|
|
10
10
|
def mysql_version
|
@@ -54,7 +54,7 @@ class Bio::DB::Polymarker
|
|
54
54
|
def each_snp_in_file(file_id)
|
55
55
|
query="SELECT name, chromosome, sequence FROM snp, snp_file_snp WHERE snp_file_snp.snpList_snpId = snp.snpId AND snp_file_snp.snp_file_snp_file_id = '#{file_id}' AND snp.process = 1;"
|
56
56
|
ret = 0
|
57
|
-
puts query
|
57
|
+
#puts query
|
58
58
|
if block_given?
|
59
59
|
ret = execute_query(query){|row| yield row }
|
60
60
|
else
|
@@ -64,21 +64,38 @@ class Bio::DB::Polymarker
|
|
64
64
|
end
|
65
65
|
|
66
66
|
def write_output_file_and_execute(file_id, filename)
|
67
|
-
puts "Writting: #{file_id}_#{filename}"
|
67
|
+
#puts "Writting: #{file_id}_#{filename}"
|
68
68
|
path =@properties["execution_path"]+"/#{file_id}_#{filename}"
|
69
69
|
puts "Writting: #{path}"
|
70
70
|
f=File.open(path, "w")
|
71
|
-
|
72
71
|
each_snp_in_file(file_id) do |row|
|
73
72
|
f.puts(row.join(","))
|
74
73
|
end
|
75
|
-
execute_polymarker(path)
|
76
|
-
update_status(file_id, "SUBMITTED")
|
77
74
|
f.close
|
75
|
+
execute_polymarker(file_id, path)
|
76
|
+
update_status(file_id, "SUBMITTED")
|
77
|
+
|
78
|
+
end
|
79
|
+
|
80
|
+
def get_preferences(file_id)
|
81
|
+
query="SELECT name, value FROM preferences \
|
82
|
+
join snp_file_preferences on preferenceID = preferences_preferenceID \
|
83
|
+
where snp_file_snp_file_id = #{file_id};"
|
84
|
+
preferences = Hash.new
|
85
|
+
execute_query(query) do |row|
|
86
|
+
preferences[row[0].to_sym] = row[1]
|
87
|
+
end
|
88
|
+
return preferences
|
78
89
|
end
|
79
90
|
|
80
|
-
def execute_polymarker(snp_file)
|
81
|
-
|
91
|
+
def execute_polymarker(file_id, snp_file)
|
92
|
+
|
93
|
+
preferences = get_preferences(file_id)
|
94
|
+
|
95
|
+
cmd=@properties['wrapper_prefix']
|
96
|
+
cmd << "polymarker.rb -m #{snp_file} -o #{snp_file}_out "
|
97
|
+
cmd << "-c #{@properties['path_to_chromosomes']}/#{preferences[:reference]} "
|
98
|
+
cmd << @properties['wrapper_suffix']
|
82
99
|
#polymarker.rb -m 1_GWAS_SNPs.csv -o 1_test -c /Users/ramirezr/Documents/TGAC/references/Triticum_aestivum.IWGSP1.21.dna_rm.genome.fa
|
83
100
|
execute_command(cmd)
|
84
101
|
end
|
@@ -101,8 +118,6 @@ class Bio::DB::Polymarker
|
|
101
118
|
def update_error_status(snp_file_id, error_message)
|
102
119
|
snp_file = get_snp_file(snp_file_id)
|
103
120
|
return if snp_file['status'] == "ERROR"
|
104
|
-
|
105
|
-
|
106
121
|
pst = con.prepare "UPDATE snp_file SET status = 'ERROR', error=? WHERE snp_file_id = ?"
|
107
122
|
puts "update_error_status: #{pst}"
|
108
123
|
pst.execute error_message, snp_file_id
|
@@ -161,7 +176,7 @@ END_OF_MESSAGE
|
|
161
176
|
|
162
177
|
lines.each do |l|
|
163
178
|
error = l.include?("ERROR") unless error
|
164
|
-
error_message <<
|
179
|
+
error_message << lines if error
|
165
180
|
end
|
166
181
|
end
|
167
182
|
|
@@ -222,7 +237,7 @@ END_OF_MESSAGE
|
|
222
237
|
return n_rows unless block_given?
|
223
238
|
return ret
|
224
239
|
end
|
225
|
-
raise "Unsuported query #{query}"
|
240
|
+
raise "Unsuported query '#{query}'"
|
226
241
|
|
227
242
|
end
|
228
243
|
|
metadata
CHANGED
@@ -1,14 +1,14 @@
|
|
1
1
|
--- !ruby/object:Gem::Specification
|
2
2
|
name: bio-polymarker_db_batch
|
3
3
|
version: !ruby/object:Gem::Version
|
4
|
-
version: 0.
|
4
|
+
version: 0.5.0
|
5
5
|
platform: ruby
|
6
6
|
authors:
|
7
7
|
- Ricardo H. Ramirez-Gonzalez
|
8
8
|
autorequire:
|
9
9
|
bindir: bin
|
10
10
|
cert_chain: []
|
11
|
-
date:
|
11
|
+
date: 2015-03-05 00:00:00.000000000 Z
|
12
12
|
dependencies:
|
13
13
|
- !ruby/object:Gem::Dependency
|
14
14
|
name: bio-polyploid-tools
|