bio-polymarker_db_batch 0.1.0 → 0.2.0

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
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-  data.tar.gz: 9a940c4c6f79cff4877cc43b70572ce405ad02fe
+  metadata.gz: da45b3e074939e929a4f033239ea1266513885e6
+  data.tar.gz: 4d5a1811ae63656af0180ca532b6618048c371e1
 SHA512:
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+  data.tar.gz: 379bc02e20d8599eb2a88deb2e037a51d8043a125217d8ff3fa07376bd11a42b034a65aff544771d4e143c0bd8b0f6acecb79b73c59e4cde3db3144ee46ecb77

data/VERSION

@@ -1 +1 @@
-0.1.0
+0.2.0

data/lib/bio-polymarker_db_batch/polymarker_db_batch.rb

@@ -4,7 +4,7 @@ class Bio::DB::Polymarker
 
   def initialize( props)
     @properties =Hash[*File.read(props).split(/[=\n]+/)]
-    puts @properties.inspect
+    #puts @properties.inspect
   end
 
   def mysql_version
@@ -69,24 +69,31 @@ class Bio::DB::Polymarker
     pst = con.prepare "UPDATE snp_file SET status = ? WHERE snp_file_id = ?"
     pst.execute new_status, snp_file_id
     con.commit
+    begin
+      send_email(to,id, status)
+    rescue
+      puts "Error sending email."
+    end
   end
 
-  def send_email(to,opts={})
-    opts[:server]      ||= 'localhost'
-    opts[:from]        ||= 'polymarker@tgac.ac.uk'
-    opts[:from_alias]  ||= 'Example Emailer'
-    opts[:subject]     ||= "You need to see this"
-    opts[:body]        ||= "Important stuff!"
+  def send_email(to,id, status)
+    options = @properties
 
     msg = <<END_OF_MESSAGE
-From: #{opts[:from_alias]} <#{opts[:from]}>
+From: #{options['email_from_alias']} <#{options['email_from']}>
 To: <#{to}>
-Subject: #{opts[:subject]}
+Subject: Polymarker #{id} #{status}
+
+The current status of your request (#{id}) is #{status}
+The latest status and results (when done) are available in: #{options['web_domain']}/status?id=#{id}
+
 
 #{opts[:body]}
 END_OF_MESSAGE
-    Net::SMTP.start(opts[:server]) do |smtp|
-      smtp.send_message msg, opts[:from], to
+    smtp = Net::SMTP.new options["email_server"], 587
+    smtp.enable_starttls
+    smtp.start( options["email_domain"], options["email_user"], options["email_pwd"], :login) do
+      smtp.send_message(msg, options["email_from"], to)
     end
   end
   

data/test/test_email.rb

@@ -0,0 +1,43 @@
+#!/usr/bin/env ruby
+#require 'bioruby-polyploid-tools'
+require 'optparse'
+require 'mysql'
+require 'net/smtp'
+
+#$: << File.expand_path(File.dirname(__FILE__) + '/../lib')
+#$: << File.expand_path('.')
+#path=File.expand_path(File.dirname(__FILE__) + '/../lib/bio-polymarker_db_batch.rb')
+#$stderr.puts "Loading: #{path}"
+#require path
+
+#options = {}
+props = ""
+
+OptionParser.new do |opts|
+  opts.banner = "Usage: run_pending_polymarker.rb [options]"
+  
+  opts.on("-p", "--preferences FILE" "File with the preferences") do |o|
+     props = o
+   end
+      
+end.parse!
+options =Hash[*File.read(props).split(/[=\n]+/)]
+to = "ricardo.ramirez-gonzalez@tgac.ac.uk"
+msg = <<END_OF_MESSAGE
+From: #{options['email_from_alias']} <#{options['email_from']}>
+To: <#{to}>
+Subject: Test from ruby
+
+The text we are sending!
+END_OF_MESSAGE
+
+puts options.inspect
+smtp = Net::SMTP.new options["email_server"], 587
+smtp.enable_starttls
+smtp.start( options["email_domain"], options["email_user"], options["email_pwd"], :login) do
+   smtp.send_message(msg, options["email_from"], to)
+end
+
+#Net::SMTP.start(options["email_server"], 25, options["email_domain"], options["email_user"], options["email_pwd"], :cram_md5) do |smtp|
+#      smtp.send_message msg, opts[:from], to
+#end

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: bio-polymarker_db_batch
 version: !ruby/object:Gem::Version
-  version: 0.1.0
+  version: 0.2.0
 platform: ruby
 authors:
 - Ricardo H.  Ramirez-Gonzalez
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2014-07-18 00:00:00.000000000 Z
+date: 2014-07-21 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: bio-polyploid-tools
@@ -147,6 +147,7 @@ files:
 - lib/bio-polymarker_db_batch/polymarker_db_batch.rb
 - test/helper.rb
 - test/test_bio-polymarker_db_batch.rb
+- test/test_email.rb
 homepage: http://github.com/homonecloco/bioruby-polymarker_db_batch
 licenses:
 - MIT