bio-polymarker_db_batch 0.1.0 → 0.2.0

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 CHANGED
@@ -1,7 +1,7 @@
1
1
  ---
2
2
  SHA1:
3
- metadata.gz: ee5ff333221f066ab5de033a6344672cf152b587
4
- data.tar.gz: 9a940c4c6f79cff4877cc43b70572ce405ad02fe
3
+ metadata.gz: da45b3e074939e929a4f033239ea1266513885e6
4
+ data.tar.gz: 4d5a1811ae63656af0180ca532b6618048c371e1
5
5
  SHA512:
6
- metadata.gz: feb868e237d4ec8759a563df9d89abb4a8b123c419edd43833a8c3115b3a37b7a3ecd5b329d88980f3c91afa1ae0112005b048760263a9a58da22e8756378e08
7
- data.tar.gz: 163c4fc4b2943988a1003cbd3b4855900abe09b06c2d7a65d2b45e6b762c2ae17b1f09fd97ca1ad08b6c0be68ec3de2802d2019d206ee63152f99826f13f0155
6
+ metadata.gz: 8a0df21c2eaf9d19fdcf5df49248415b88931f2197139f1a3cef62c776cda476008518f56b42f9e5b7ea1601a87d0fb67117ed7122ead257589dcf97457620cd
7
+ data.tar.gz: 379bc02e20d8599eb2a88deb2e037a51d8043a125217d8ff3fa07376bd11a42b034a65aff544771d4e143c0bd8b0f6acecb79b73c59e4cde3db3144ee46ecb77
data/VERSION CHANGED
@@ -1 +1 @@
1
- 0.1.0
1
+ 0.2.0
@@ -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
- puts @properties.inspect
7
+ #puts @properties.inspect
8
8
  end
9
9
 
10
10
  def mysql_version
@@ -69,24 +69,31 @@ class Bio::DB::Polymarker
69
69
  pst = con.prepare "UPDATE snp_file SET status = ? WHERE snp_file_id = ?"
70
70
  pst.execute new_status, snp_file_id
71
71
  con.commit
72
+ begin
73
+ send_email(to,id, status)
74
+ rescue
75
+ puts "Error sending email."
76
+ end
72
77
  end
73
78
 
74
- def send_email(to,opts={})
75
- opts[:server] ||= 'localhost'
76
- opts[:from] ||= 'polymarker@tgac.ac.uk'
77
- opts[:from_alias] ||= 'Example Emailer'
78
- opts[:subject] ||= "You need to see this"
79
- opts[:body] ||= "Important stuff!"
79
+ def send_email(to,id, status)
80
+ options = @properties
80
81
 
81
82
  msg = <<END_OF_MESSAGE
82
- From: #{opts[:from_alias]} <#{opts[:from]}>
83
+ From: #{options['email_from_alias']} <#{options['email_from']}>
83
84
  To: <#{to}>
84
- Subject: #{opts[:subject]}
85
+ Subject: Polymarker #{id} #{status}
86
+
87
+ The current status of your request (#{id}) is #{status}
88
+ The latest status and results (when done) are available in: #{options['web_domain']}/status?id=#{id}
89
+
85
90
 
86
91
  #{opts[:body]}
87
92
  END_OF_MESSAGE
88
- Net::SMTP.start(opts[:server]) do |smtp|
89
- smtp.send_message msg, opts[:from], to
93
+ smtp = Net::SMTP.new options["email_server"], 587
94
+ smtp.enable_starttls
95
+ smtp.start( options["email_domain"], options["email_user"], options["email_pwd"], :login) do
96
+ smtp.send_message(msg, options["email_from"], to)
90
97
  end
91
98
  end
92
99
 
@@ -0,0 +1,43 @@
1
+ #!/usr/bin/env ruby
2
+ #require 'bioruby-polyploid-tools'
3
+ require 'optparse'
4
+ require 'mysql'
5
+ require 'net/smtp'
6
+
7
+ #$: << File.expand_path(File.dirname(__FILE__) + '/../lib')
8
+ #$: << File.expand_path('.')
9
+ #path=File.expand_path(File.dirname(__FILE__) + '/../lib/bio-polymarker_db_batch.rb')
10
+ #$stderr.puts "Loading: #{path}"
11
+ #require path
12
+
13
+ #options = {}
14
+ props = ""
15
+
16
+ OptionParser.new do |opts|
17
+ opts.banner = "Usage: run_pending_polymarker.rb [options]"
18
+
19
+ opts.on("-p", "--preferences FILE" "File with the preferences") do |o|
20
+ props = o
21
+ end
22
+
23
+ end.parse!
24
+ options =Hash[*File.read(props).split(/[=\n]+/)]
25
+ to = "ricardo.ramirez-gonzalez@tgac.ac.uk"
26
+ msg = <<END_OF_MESSAGE
27
+ From: #{options['email_from_alias']} <#{options['email_from']}>
28
+ To: <#{to}>
29
+ Subject: Test from ruby
30
+
31
+ The text we are sending!
32
+ END_OF_MESSAGE
33
+
34
+ puts options.inspect
35
+ smtp = Net::SMTP.new options["email_server"], 587
36
+ smtp.enable_starttls
37
+ smtp.start( options["email_domain"], options["email_user"], options["email_pwd"], :login) do
38
+ smtp.send_message(msg, options["email_from"], to)
39
+ end
40
+
41
+ #Net::SMTP.start(options["email_server"], 25, options["email_domain"], options["email_user"], options["email_pwd"], :cram_md5) do |smtp|
42
+ # smtp.send_message msg, opts[:from], to
43
+ #end
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: 0.1.0
4
+ version: 0.2.0
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: 2014-07-18 00:00:00.000000000 Z
11
+ date: 2014-07-21 00:00:00.000000000 Z
12
12
  dependencies:
13
13
  - !ruby/object:Gem::Dependency
14
14
  name: bio-polyploid-tools
@@ -147,6 +147,7 @@ files:
147
147
  - lib/bio-polymarker_db_batch/polymarker_db_batch.rb
148
148
  - test/helper.rb
149
149
  - test/test_bio-polymarker_db_batch.rb
150
+ - test/test_email.rb
150
151
  homepage: http://github.com/homonecloco/bioruby-polymarker_db_batch
151
152
  licenses:
152
153
  - MIT