bsi-pipeline 0.0.5 → 0.0.6

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
-  metadata.gz: e760c06f87edb57bc12c989c853a24d011ea87a1
-  data.tar.gz: 65d77160c4c42829be1db9842146916c8e667ba2
+  metadata.gz: 50e0b28ec4df04a63b0d9c6a530b36c30e7072b7
+  data.tar.gz: 58b68121e0ea1345f0321d00d46ef63f2f3b1a9c
 SHA512:
-  metadata.gz: c957a5e5f1a99aa80f1faaf21d8c76cb0d7b47415b9d45d9b9bf71e9a532cce0019c745a14456ebfe126775bb101ffaf002bfaadd88bdce9a1e4f12cb41b051e
-  data.tar.gz: 4d359b7fd19877a0cd20c1bbb14a6ed016d78bb7e9ca6ec8bc3330773455fc54e1244e4da248fe2dc7f8cdeb3a695eee71b28ffdfd416f508b9c78da0c16a930
+  metadata.gz: 67ba71b202d5062375f2585f580f2dd589d520217ffe039b01de598e2877092b70078b56e7e1fbfea3d35872c41501b5570e2cf13c3d894f3e629f9c2d0353aa
+  data.tar.gz: aeb9871c95343cc74790eee7bb9661dc280715d412d790be1dcab265504c6eb115b36ec15c3d326ababb59f363858ee530f41103a615855abf5fee5e32ee8c96

data/lib/bsi-pipeline/importer.rb

@@ -56,7 +56,7 @@ 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
+                spec.sequence   = i+1
               end
             end
           end
@@ -81,21 +81,25 @@ module Pipeline
 
         def import(all_specimens, options={})
           @specimens = all_specimens
+          study_ids   = @specimens.map{|e| e.study_id}.uniq
           subject_ids = @specimens.map{|e| e.subject_id}.uniq
 
-          subject_ids.each_with_index do |sid, i|
-            # Filter by subject_id
-            subset = @specimens.select{|e| e.subject_id == sid}
+          study_ids.each do |study|
+            subject_ids.each_with_index do |sid, i|
+              # Filter by subject_id and study_id
+              subset = @specimens.select{|e| e.study_id == study && e.subject_id == sid}
 
-            batch_properties = {
-              'batch.description' => "Subject: #{sid}"
-            }
+              batch_properties = {
+                'batch.description' => "Subject: #{sid}",
+                'batch.study_id'    => study.to_s
+              }
 
-            @batch = AddBatch.new(@bsi, batch_properties)
-            @batch.add_specimens(subset)
-            @batch.commit if options['commit']
+              @batch = AddBatch.new(@bsi, batch_properties)
+              @batch.add_specimens(subset)
+              @batch.commit if options['commit']
 
-            @batches << @batch
+              @batches << @batch
+            end
           end
 
           @bsi.common.logoff

data/lib/bsi-pipeline/version.rb

@@ -1,5 +1,5 @@
 module Bsi
   module Pipeline
-    VERSION = "0.0.5"
+    VERSION = "0.0.6"
   end
 end

data/spec/add_batch_spec.rb

@@ -51,6 +51,7 @@ describe AddBatch do
       end
 
       it 'returns array of Pipeline::BSI::Models::Specimen objects' do
+        expect(@batch.specimens).to be_instance_of Array
       end
     end
   end

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: bsi-pipeline
 version: !ruby/object:Gem::Version
-  version: 0.0.5
+  version: 0.0.6
 platform: ruby
 authors:
 - Elijah Christensen
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2014-07-29 00:00:00.000000000 Z
+date: 2014-07-31 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: bundler