bsi-pipeline 0.0.4 → 0.0.5
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- checksums.yaml +4 -4
- data/lib/bsi-pipeline/importer.rb +16 -2
- data/lib/bsi-pipeline/models.rb +15 -24
- data/lib/bsi-pipeline/version.rb +1 -1
- data/spec/factories/specimen.rb +0 -1
- metadata +2 -2
checksums.yaml
CHANGED
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@@ -1,7 +1,7 @@
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---
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SHA1:
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metadata.gz:
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data.tar.gz:
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metadata.gz: e760c06f87edb57bc12c989c853a24d011ea87a1
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data.tar.gz: 65d77160c4c42829be1db9842146916c8e667ba2
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SHA512:
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metadata.gz:
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data.tar.gz:
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metadata.gz: c957a5e5f1a99aa80f1faaf21d8c76cb0d7b47415b9d45d9b9bf71e9a532cce0019c745a14456ebfe126775bb101ffaf002bfaadd88bdce9a1e4f12cb41b051e
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7
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data.tar.gz: 4d359b7fd19877a0cd20c1bbb14a6ed016d78bb7e9ca6ec8bc3330773455fc54e1244e4da248fe2dc7f8cdeb3a695eee71b28ffdfd416f508b9c78da0c16a930
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@@ -27,7 +27,7 @@ module Pipeline
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def add_specimens(specimens)
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@specimens = specimens
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format
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@bsi.batch.addVials( @id, specimens.map{ |s| s.to_bfh } )
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@bsi.batch.addVials( @id, @specimens.map{ |s| s.to_bfh } )
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nil
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end
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@@ -40,12 +40,26 @@ module Pipeline
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# Reserve Sample ID's for all the seminal parent's
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# Returns and array of strings with both the sampleID and the sequence number in the format: AAA000000 0000
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# Only keep first 6 characters which represent the sample id's (remove the sequence suffix)
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-
@
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@sample_id_pool = @bsi.batch.reserveAvailableBsiIds( @id, 'LAA000000', num_seminal_parents ).map{|i| i[0..-6]} if num_seminal_parents > 0
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# Not sure why I've been getting this error periodically, but it happens
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rescue NoMethodError
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fails += 1
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retry if fails < 3
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end
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+
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collection_dates = @specimens.map{|s| s.date_drawn}.uniq
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specimen_types = @specimens.map{|s| s.specimen_type}.uniq
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collection_dates.each do |date|
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specimen_types.each do |type|
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specimen_family = @specimens.select{|s| s.date_drawn == date && s.specimen_type == type}
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family_sample_id = @sample_id_pool.pop
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specimen_family.each_with_index do |spec, i|
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# Assign sample and sequence numbers
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spec.sample_id = family_sample_id
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spec.sequence = i+1
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end
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end
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end
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end
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def perform_edit_checks
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data/lib/bsi-pipeline/models.rb
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@@ -9,41 +9,32 @@ module Pipeline
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REQUIRED_FIELDS = %w(study_id subject_id specimen_type date_drawn date_received label_status billing_method thaws).map{|v| v.to_sym}
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BSI_CORE_FIELDS = {
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# Sample level fields
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:subject_id => 'sample.subject_id',
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:sample_id => 'sample.sample_id',
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:date_drawn => 'sample.date_drawn',
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:kit_id => 'sample.kit_id',
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:pickup_location => 'sample.pickup_location',
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:sample_modifiers => 'sample.sample_modifiers',
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# Vial fields
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:study_id => 'vial.study_id',
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:
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:repos_id => 'vial.repos_id',
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:sequence => 'vial.seq_num',
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:current_label => 'vial.current_label',
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:specimen_type => 'vial.mat_type',
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:parent_id => 'vial.parent_id',
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:measurement => 'vial.volume',
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:
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:stain_type => 'vial.field_268',
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:block_status => 'vial.field_266',
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:biobank => 'vial.field_269',
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:grade => 'vial.field_271',
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:vial_status => 'vial.vial_status',
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# Location Fields
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:room => 'location.room',
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:building => 'location.building',
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:freezer => 'location.freezer',
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:shelf => 'location.shelf',
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:rack => 'location.rack',
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:box => 'location.box',
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# Vial-Location fields
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:row => 'vial_location.row',
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:col => 'vial_location.col'
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:sample_id => 'sample.sample_id',
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:appointment_time => 'sample.appointment_time',
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:center => 'sample.center',
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:data_manager => 'sample.data_manager',
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:date_drawn => 'sample.date_drawn',
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:cra => 'sample.cra',
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:kit_id => 'sample.kit_id',
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:pickup_location => 'sample.pickup_location',
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:subject_id => 'sample.subject_id',
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:surgeon => 'sample.surgeon',
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:referring_physician => 'sample.field_273',
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:surgical_case_number => 'sample.surgical_case_number',
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:surgical_case_part => 'sample.field_267',
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:telephone => 'sample.telephone',
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:timepoint => 'sample.time_point',
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:sample_modifiers => 'sample.sample_modifiers'
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:col => 'vial_location.col'
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}
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# Define Defaults
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data/lib/bsi-pipeline/version.rb
CHANGED
data/spec/factories/specimen.rb
CHANGED
metadata
CHANGED
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@@ -1,14 +1,14 @@
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--- !ruby/object:Gem::Specification
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name: bsi-pipeline
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version: !ruby/object:Gem::Version
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version: 0.0.
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version: 0.0.5
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platform: ruby
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authors:
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- Elijah Christensen
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autorequire:
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bindir: bin
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cert_chain: []
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date: 2014-07-
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date: 2014-07-29 00:00:00.000000000 Z
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dependencies:
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- !ruby/object:Gem::Dependency
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name: bundler
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