bsi-pipeline 0.0.6 → 0.0.7

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
-  metadata.gz: 50e0b28ec4df04a63b0d9c6a530b36c30e7072b7
-  data.tar.gz: 58b68121e0ea1345f0321d00d46ef63f2f3b1a9c
+  metadata.gz: 11b6084509041d9383bbd7da9c598f8dd33b878c
+  data.tar.gz: 49ec957ecd98ab166fb42babf1a80117d24110a5
 SHA512:
-  metadata.gz: 67ba71b202d5062375f2585f580f2dd589d520217ffe039b01de598e2877092b70078b56e7e1fbfea3d35872c41501b5570e2cf13c3d894f3e629f9c2d0353aa
-  data.tar.gz: aeb9871c95343cc74790eee7bb9661dc280715d412d790be1dcab265504c6eb115b36ec15c3d326ababb59f363858ee530f41103a615855abf5fee5e32ee8c96
+  metadata.gz: 02b307658911575f375192be08971d1217e5175867ae01cf4cecd806be594f7c78dcca95a70430eaaf5a8e4b2ed352081dfd74b6ddba13515488212d2d5980c7
+  data.tar.gz: 541706c49e3fdb3ea41abbe11b4bcd972d46bcd3e43f79ea42189ad15928668f92fff31b289c1fe791bd27a2db5655a23aea5773bbe4180685fbf412be36fb4a

data/lib/bsi-pipeline/importer.rb

@@ -33,7 +33,11 @@ module Pipeline
 
         def format
           # Find out how many seminal parents there are
-          num_seminal_parents = @specimens.select{|s| ['N/A', ''].include?( s.parent_id.to_s )}.length
+
+          # Old way of estimating number of seminal parents, different now that we import in groups.
+          # num_seminal_parents = @specimens.select{|s| ['N/A', ''].include?( s.parent_id.to_s )}.length
+
+          num_seminal_parents = @specimens.map{|s| [s.date_drawn, s.specimen_type]}.uniq.length
 
           fails = 0
           begin
@@ -56,7 +60,11 @@ module Pipeline
               specimen_family.each_with_index do |spec, i|
                 # Assign sample and sequence numbers
                 spec.sample_id  = family_sample_id
-                spec.sequence   = i+1
+                unless specimen_family.length == 1
+                  spec.sequence   = i+1
+                else
+                  spec.sequence   = 0
+                end
               end
             end
           end
@@ -74,7 +82,7 @@ module Pipeline
         attr_accessor :specimens, :batches, :batch_delimiter
 
         def initialize(key, options={})
-          @bsi              = RBC.new(key)
+          @bsi              = RBC.new(key, options)
           @specimens        = specimens
           @batches          = Array.new
         end

data/lib/bsi-pipeline/version.rb

@@ -1,5 +1,5 @@
 module Bsi
   module Pipeline
-    VERSION = "0.0.6"
+    VERSION = "0.0.7"
   end
 end

data/spec/add_batch_spec.rb

@@ -3,7 +3,7 @@ require'spec_helper'
 describe AddBatch do
   before :all do
     @bsi = RBC.new(
-      { :user     => 'ecog_bot',
+      { :user     => 'biorepository_bot',
         :pass     => ENV['ECOG_BOT_PASS'],
         :server   => 'PCF',
         :url      => 'https://websvc-mirror.bsisystems.com:2271/bsi/xmlrpc'
@@ -74,8 +74,4 @@ describe AddBatch do
   describe '#commit' do
     it 'commits specimens in the batch to the BSI database if all edit checks pass'
   end
-
-  after :all do
-    @bsi.common.logoff
-  end
 end

data/spec/importer_spec.rb

@@ -3,12 +3,12 @@ require 'spec_helper'
 describe SpecimenImporter do
   before :each do
       key = {
-        :user     => 'ecog_bot',
+        :user     => 'biorepository_bot',
         :pass     => ENV['ECOG_BOT_PASS'],
         :server   => 'PCF',
         :url      => 'https://websvc-mirror.bsisystems.com:2271/bsi/xmlrpc'
       }
-    @importer = SpecimenImporter.new(key)
+    @importer = SpecimenImporter.new(key, {:instance => 'mirror', :debug => 'false'})
 
   end
 

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: bsi-pipeline
 version: !ruby/object:Gem::Version
-  version: 0.0.6
+  version: 0.0.7
 platform: ruby
 authors:
 - Elijah Christensen
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2014-07-31 00:00:00.000000000 Z
+date: 2014-09-10 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: bundler