bsi-pipeline 0.0.4 → 0.0.5

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
-  metadata.gz: da8770522f67c26feadc1b7c0dda5c3fd0102ee8
-  data.tar.gz: 7b7015a241731259f6e2f1c464d340560165bcd7
+  metadata.gz: e760c06f87edb57bc12c989c853a24d011ea87a1
+  data.tar.gz: 65d77160c4c42829be1db9842146916c8e667ba2
 SHA512:
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-  data.tar.gz: 061831ad86709de8cb98ca27c62ec9366fbc03c65e22ae00dde8c9a08c2acb56145c7338148fa206830715972fa195d4b1cbb1e25102b88f0a97a8637a07823d
+  metadata.gz: c957a5e5f1a99aa80f1faaf21d8c76cb0d7b47415b9d45d9b9bf71e9a532cce0019c745a14456ebfe126775bb101ffaf002bfaadd88bdce9a1e4f12cb41b051e
+  data.tar.gz: 4d359b7fd19877a0cd20c1bbb14a6ed016d78bb7e9ca6ec8bc3330773455fc54e1244e4da248fe2dc7f8cdeb3a695eee71b28ffdfd416f508b9c78da0c16a930

data/lib/bsi-pipeline/importer.rb

@@ -27,7 +27,7 @@ module Pipeline
         def add_specimens(specimens)
           @specimens = specimens
           format
-          @bsi.batch.addVials( @id, specimens.map{ |s| s.to_bfh } )
+          @bsi.batch.addVials( @id, @specimens.map{ |s| s.to_bfh } )
           nil
         end
 
@@ -40,12 +40,26 @@ module Pipeline
           # Reserve Sample ID's for all the seminal parent's
           # Returns and array of strings with both the sampleID and the sequence number in the format: AAA000000 0000
             # Only keep first 6 characters which represent the sample id's (remove the sequence suffix)
-            @seminal_parents = @bsi.batch.reserveAvailableBsiIds( @id, 'LAA000000', num_seminal_parents ).map{|i| i[0..-6]} if num_seminal_parents > 0
+            @sample_id_pool = @bsi.batch.reserveAvailableBsiIds( @id, 'LAA000000', num_seminal_parents ).map{|i| i[0..-6]} if num_seminal_parents > 0
           # Not sure why I've been getting this error periodically, but it happens
           rescue NoMethodError
             fails += 1
             retry if fails < 3
           end
+
+          collection_dates = @specimens.map{|s| s.date_drawn}.uniq
+          specimen_types   = @specimens.map{|s| s.specimen_type}.uniq
+          collection_dates.each do |date|
+            specimen_types.each do |type|
+              specimen_family = @specimens.select{|s| s.date_drawn == date && s.specimen_type == type}
+              family_sample_id = @sample_id_pool.pop
+              specimen_family.each_with_index do |spec, i|
+                # Assign sample and sequence numbers
+                spec.sample_id  = family_sample_id
+                spec.sequence    = i+1
+              end
+            end
+          end
         end
 
         def perform_edit_checks

data/lib/bsi-pipeline/models.rb

@@ -9,41 +9,32 @@ module Pipeline
 
         REQUIRED_FIELDS = %w(study_id subject_id specimen_type date_drawn date_received label_status billing_method thaws).map{|v| v.to_sym}
         BSI_CORE_FIELDS = {
+          # Sample level fields
+          :subject_id             => 'sample.subject_id',
+          :sample_id              => 'sample.sample_id',
+          :date_drawn             => 'sample.date_drawn',
+          :kit_id                 => 'sample.kit_id',
+          :pickup_location        => 'sample.pickup_location',
+          :sample_modifiers       => 'sample.sample_modifiers',
+          # Vial fields
           :study_id               => 'vial.study_id',
-          :specimen_type          => 'vial.mat_type',
+          :repos_id               => 'vial.repos_id',
+          :sequence               => 'vial.seq_num',
           :current_label          => 'vial.current_label',
+          :specimen_type          => 'vial.mat_type',
           :parent_id              => 'vial.parent_id',
           :measurement            => 'vial.volume',
-          :measurement_est        => 'vial.volume_est',
-          :measurement_unit       => 'vial.volume_unit',
-          :stain_type             => 'vial.field_268',
-          :block_status           => 'vial.field_266',
-          :biobank                => 'vial.field_269',
-          :grade                  => 'vial.field_271',
+          :vial_status            => 'vial.vial_status',
+          # Location Fields
           :room                   => 'location.room',
           :building               => 'location.building',
           :freezer                => 'location.freezer',
           :shelf                  => 'location.shelf',
           :rack                   => 'location.rack',
           :box                    => 'location.box',
+          # Vial-Location fields
           :row                    => 'vial_location.row',
-          :col                    => 'vial_location.col',
-          :sample_id              => 'sample.sample_id',
-          :appointment_time       => 'sample.appointment_time',
-          :center                 => 'sample.center',
-          :data_manager           => 'sample.data_manager',
-          :date_drawn             => 'sample.date_drawn',
-          :cra                    => 'sample.cra',
-          :kit_id                 => 'sample.kit_id',
-          :pickup_location        => 'sample.pickup_location',
-          :subject_id             => 'sample.subject_id',
-          :surgeon                => 'sample.surgeon',
-          :referring_physician    => 'sample.field_273',
-          :surgical_case_number   => 'sample.surgical_case_number',
-          :surgical_case_part     => 'sample.field_267',
-          :telephone              => 'sample.telephone',
-          :timepoint              => 'sample.time_point',
-          :sample_modifiers       => 'sample.sample_modifiers'
+          :col                    => 'vial_location.col'
         }
 
         # Define Defaults

data/lib/bsi-pipeline/version.rb

@@ -1,5 +1,5 @@
 module Bsi
   module Pipeline
-    VERSION = "0.0.4"
+    VERSION = "0.0.5"
   end
 end

data/spec/factories/specimen.rb

@@ -24,7 +24,6 @@ FactoryGirl.define do
     # Generic Slide Specimen
     trait :slide do
       specimen_type "SLDTS"
-      stain_type    "H&E"
     end
 
     factory :slide_specimen, traits: [:slide]

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: bsi-pipeline
 version: !ruby/object:Gem::Version
-  version: 0.0.4
+  version: 0.0.5
 platform: ruby
 authors:
 - Elijah Christensen
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2014-07-23 00:00:00.000000000 Z
+date: 2014-07-29 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: bundler