bio-polymarker_db_batch 0.2.1 → 0.3.0

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
-  metadata.gz: f9b3076efa36fc6b89b3d296a559156e380d7f35
-  data.tar.gz: 283bc9eca6cecc30ac54526f89484fad503dd247
+  metadata.gz: 36b22aa90692cd1619c083ae7d5e39ba0a0aca1b
+  data.tar.gz: cf32c6616329af6bd5001bac8cf7e199ab496181
 SHA512:
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+  data.tar.gz: 9c84edf81a7116aeeb55732cadbf08e143ee700bd335765ec251dbbd7cff3355b707b384b257db2c14a333f161f0710b9e68862ec8c00cdd3b79e55b377c24c1

data/VERSION

@@ -1 +1 @@
-0.2.1
+0.3.0

data/bin/run_pending_polymarker.rb

@@ -2,6 +2,7 @@
 require 'bioruby-polyploid-tools'
 require 'optparse'
 require 'mysql'
+
 $: << File.expand_path(File.dirname(__FILE__) + '/../lib')
 $: << File.expand_path('.')
 path=File.expand_path(File.dirname(__FILE__) + '/../lib/bio-polymarker_db_batch.rb')

data/lib/bio-polymarker_db_batch.rb

@@ -7,6 +7,6 @@
 #   require 'bio/bio-plugin/plugin'
 #
 # In this file only require other files. Avoid other source code.
-
+require 'net/smtp'
 require 'bio-polymarker_db_batch/polymarker_db_batch.rb'
 

data/lib/bio-polymarker_db_batch/polymarker_db_batch.rb

@@ -28,7 +28,7 @@ class Bio::DB::Polymarker
   end
 
   def each_running
-    query="SELECT snp_file_id, filename FROM snp_file WHERE status NOT IN ('NEW', 'DONE', 'LOADED');"
+    query="SELECT snp_file_id, filename FROM snp_file WHERE status = 'RUNNING');"
     ret = 0
     if block_given?
       ret = execute_query(query){|row| yield row }
@@ -39,7 +39,7 @@ class Bio::DB::Polymarker
   end
 
   def each_snp_in_file(file_id)
-    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}';"
+    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;"
     ret = 0
     puts query
     if block_given?
@@ -77,7 +77,8 @@ class Bio::DB::Polymarker
     pst.execute new_status, snp_file_id
     con.commit
     begin
-      send_email(snp_file['email'],id, status)
+      hashed_id = "#{snp_file_id}:#{snp_file['hash']}"
+      send_email(snp_file['email'],hashed_id, new_status)
     rescue
       puts "Error sending email."
     end
@@ -95,7 +96,6 @@ 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
     smtp = Net::SMTP.new options["email_server"], 587
     smtp.enable_starttls

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: bio-polymarker_db_batch
 version: !ruby/object:Gem::Version
-  version: 0.2.1
+  version: 0.3.0
 platform: ruby
 authors:
 - Ricardo H.  Ramirez-Gonzalez
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2014-07-21 00:00:00.000000000 Z
+date: 2014-09-25 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: bio-polyploid-tools