ncs_mdes 0.6.1 → 0.7.0
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- data/CHANGELOG.md +6 -0
- data/bin/mdes-console +3 -4
- data/documents/3.0/NCS_Transmission_Schema_3.0.00.00.xsd +37996 -0
- data/documents/3.0/disposition_codes.yml +2361 -0
- data/documents/3.0/extract_disposition_codes.rb +59 -0
- data/documents/3.0/heuristic_overrides.yml +526 -0
- data/lib/ncs_navigator/mdes/source_documents.rb +2 -0
- data/lib/ncs_navigator/mdes/version.rb +1 -1
- data/spec/ncs_navigator/mdes/source_documents_spec.rb +14 -0
- data/spec/ncs_navigator/mdes/specification_spec.rb +22 -0
- metadata +6 -8
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#!/usr/bin/env ruby
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##
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# A script to generate disposition_codes.yml from the MDES 2.2
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# spreadsheet's Dispositions tab.
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#
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# This script requires the 'roo' gem, which is not included in
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# ncs_mdes's gemspec because it has a huge number of dependencies and
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# is not needed at runtime.
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require 'rubygems'
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require 'roo'
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require 'yaml'
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MDES_XLSX = ARGV.first or fail 'Please provide the path to the MDES spreadsheet'
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TARGET = File.expand_path('../disposition_codes.yml', __FILE__)
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SHEET_NAME = 'Dispositions'
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MAPPED_COLUMNS = {
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'A' => 'final_category',
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'B' => 'sub_category',
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'C' => 'disposition'
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}
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def normalize_whitespace(s)
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s.strip.gsub(/\s+/, " ")
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end
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book = Excelx.new(MDES_XLSX)
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# This is the array of hashes that will eventually be serialized to
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# disposition_codes.yml.
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dispositions = []
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current_event = nil
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current_category_code = nil
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1.upto(book.last_row(SHEET_NAME)) do |row_number|
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a, b = %w(A B).collect { |col| book.cell(row_number, col, SHEET_NAME) }
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if a =~ /Category\s+(\d)\s+\((.*?)\)\s+Disposition\s+Codes/
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current_event = normalize_whitespace $2
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current_category_code = $1.to_i
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puts "Collecting for category #{current_event} (#{current_category_code})"
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elsif b =~ /\S/ && a !~ /FINAL/
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disposition_hash = MAPPED_COLUMNS.inject({}) do |h, (col, key)|
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h[key] = normalize_whitespace(book.cell(row_number, col, SHEET_NAME)); h
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end
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disposition_hash['event'] = current_event
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disposition_hash['category_code'] = current_category_code
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disposition_hash['interim_code'], disposition_hash['final_code'] =
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normalize_whitespace(book.cell(row_number, 'D', SHEET_NAME)).split('/')
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puts disposition_hash.inspect if disposition_hash['interim_code'] =~ /^02/
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dispositions << disposition_hash
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end
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end
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File.open(TARGET, 'w') do |f|
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f.write dispositions.sort_by { |h| [h['category_code'], h['final_code']] }.to_yaml
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end
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foreign_keys:
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birth_visit:
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new_address_id: address
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mail_address_id: address
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new_address_b_id: address
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birth_visit_2:
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new_address_id: address
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mail_address_id: address
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new_address_b_id: address
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birth_visit_3:
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cwork_address_id: address
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work_address_id: address
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birth_visit_baby_name:
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bv_id: birth_visit
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birth_visit_baby_name_2:
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bv_id: birth_visit_2
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birth_visit_decorate_room:
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bv_id: birth_visit
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birth_visit_decorate_room_2:
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bv_id: birth_visit_2
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birth_visit_li:
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new_address_id: address
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mail_address_id: address
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new_address_b_id: address
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birth_visit_renovate_room:
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bv_id: birth_visit
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birth_visit_renovate_room_2:
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bv_id: birth_visit_2
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drf_therm_verification:
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equip_id: env_equipment
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eighteen_mth_mother:
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c_addr1_id: address
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c_addr2_id: address
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r_p_id: participant
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eighteen_mth_mother_2:
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c_addr1_id: address
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c_addr2_id: address
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r_p_id: participant
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eighteen_mth_mother_cond:
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eighteen_mth_habits_id: eighteen_mth_mother_habits
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eighteen_mth_mother_saq:
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asq18_address_id: address
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r_p_id: participant
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env_equipment_prob_log:
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equip_id: env_equipment
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staff_id_reviewer: staff
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event:
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participant_id: participant
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household_enumeration_hidden_du:
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hdu_address_id: address
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incident:
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inc_staff_reporter_id: staff
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inc_staff_supervisor_id: staff
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inc_recip_is_participant: participant
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inc_recip_is_du: dwelling_unit
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inc_recip_is_staff: staff
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inc_recip_is_family: person
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inc_recip_is_acquaintance: person
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inc_contact_person: person
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multi_mode:
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r_p_id: participant
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nine_mth_mother:
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r_p_id: participant
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non_interview_respondent:
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r_p_id: participant
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participant_consent:
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person_who_consented_id: person
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person_wthdrw_consent_id: person
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participant_consent_reconsideration:
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r_p_id: participant
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participant_verif:
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r_p_id: participant
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c_address_id: address
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pa_phone_id: telephone
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s_address_id: address
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sa_phone_id: telephone
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participant_vis_consent:
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vis_person_who_consented_id: person
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participant_rvis:
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rvis_person: person
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pb_recruitment:
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address_pb_id: address
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pb_recruitment_2:
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address_pb_id: address
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pb_recruitment_info_source:
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pb_recruitment_id: pb_recruitment
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pb_recruitment_info_source_2:
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pb_recruitment_id: pb_recruitment_2
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pb_recruitment_prov_source:
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pb_recruitment_id: pb_recruitment
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pb_recruitment_prov_source_2:
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pb_recruitment_id: pb_recruitment_2
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pb_recruitment_prov_svc:
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pb_recruitment_id: pb_recruitment
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pb_recruitment_prov_svc_2:
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pb_recruitment_id: pb_recruitment_2
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pb_samp_frame:
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practice_address_id: address
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contact_address_id: address
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contact_email_id: email
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contact_phone_num_id: telephone
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contact_address_larger_id: address
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contact_email_larger_id: email
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contact_phone_num_larger_id: telephone
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pbs_elig_screener:
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r_phone_1_id: telephone
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r_phone_2_id: telephone
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r_email_id: email
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pbs_elig_screener_pr_office:
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pr_address_id: address
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person:
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new_address_id: address
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prec_therm_cert:
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equip_id: env_equipment
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pre_preg:
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c_addr1_id: address
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c_addr2_id: address
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preg_screen_eh:
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mail_address_id: address
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new_address_id: address
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preg_screen_eh_2:
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mail_address_id: address
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new_address_id: address
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preg_screen_eh_know_ncs:
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ps_eh_id: preg_screen_eh
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preg_screen_eh_know_ncs_2:
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ps_eh_id: preg_screen_eh_2
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preg_screen_eh_race:
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ps_eh_id: preg_screen_eh
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preg_screen_eh_race_2:
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ps_eh_id: preg_screen_eh_2
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preg_screen_hi:
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mail_address_id: address
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new_address_id: address
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preg_screen_hi_2:
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mail_address_id: address
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new_address_id: address
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preg_screen_hi_know_ncs:
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ps_hi_id: preg_screen_hi
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preg_screen_hi_know_ncs_2:
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ps_hi_id: preg_screen_hi_2
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preg_screen_hi_race:
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ps_hi_id: preg_screen_hi
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preg_screen_hi_race_2:
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ps_hi_id: preg_screen_hi_2
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preg_screen_pb:
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mail_address_id: address
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new_address_id: address
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preg_screen_pb_2:
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mail_address_id: address
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new_address_id: address
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preg_screen_pb_know_ncs:
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ps_pb_id: preg_screen_pb
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preg_screen_pb_know_ncs_2:
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ps_pb_id: preg_screen_pb_2
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preg_screen_pb_race:
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ps_pb_id: preg_screen_pb
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preg_screen_pb_race_2:
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ps_pb_id: preg_screen_pb_2
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preg_visit_1:
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b_address_id: address
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c_addr1_id: address
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c_addr2_id: address
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preg_visit_1_2:
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b_address_id: address
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c_addr1_id: address
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c_addr2_id: address
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preg_visit_1_3:
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b_address_id: address
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work_address_id: address
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preg_visit_1_commute:
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pv1_id: preg_visit_1
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preg_visit_1_commute_2:
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pv1_id: preg_visit_1_2
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preg_visit_1_cool:
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pv1_id: preg_visit_1
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preg_visit_1_cool_2:
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pv1_id: preg_visit_1_2
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preg_visit_1_diagnose_2:
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pv1_id: preg_visit_1
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preg_visit_1_diagnose_2_2:
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pv1_id: preg_visit_1_2
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preg_visit_1_heat2:
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pv1_id: preg_visit_1
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preg_visit_1_heat2_2:
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pv1_id: preg_visit_1_2
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preg_visit_1_local_trav:
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pv1_id: preg_visit_1
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preg_visit_1_local_trav_2:
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pv1_id: preg_visit_1_2
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preg_visit_1_nonenglish2_2:
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pv1_id: preg_visit_1_2
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preg_visit_1_pdecorate_room:
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pv1_id: preg_visit_1
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preg_visit_1_pdecorate_room_2:
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pv1_id: preg_visit_1_2
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preg_visit_1_pet_type:
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pv1_id: preg_visit_1
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preg_visit_1_pet_type_2:
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pv1_id: preg_visit_1_2
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preg_visit_1_prenovate2_room:
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pv1_id: preg_visit_1
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preg_visit_1_prenovate_room:
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pv1_id: preg_visit_1
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preg_visit_1_prenovate_room_2:
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pv1_id: preg_visit_1_2
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preg_visit_1_room_mold:
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pv1_id: preg_visit_1
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preg_visit_1_room_mold_2:
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pv1_id: preg_visit_1_2
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preg_visit_1_saq_2:
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f_addr_id: address
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preg_visit_1_saq_3:
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f_addr_id: address
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preg_visit_1_saq_4:
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f_addr_id: address
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f_phone_id: telephone
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+
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preg_visit_1_sp_race:
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pv1_id: preg_visit_1
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preg_visit_1_sp_race_2:
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pv1_id: preg_visit_1_2
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+
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preg_visit_2:
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b_address_id: address
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c_addr1_id: address
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c_addr2_id: address
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preg_visit_2_2:
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b_address_id: address
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c_addr1_id: address
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c_addr2_id: address
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preg_visit_2_3:
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b_address_id: address
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work_address_id: address
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322
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+
cwork_address_id: address
|
323
|
+
|
324
|
+
preg_visit_2_cool:
|
325
|
+
pv2_id: preg_visit_2
|
326
|
+
|
327
|
+
preg_visit_2_cool_2:
|
328
|
+
pv2_id: preg_visit_2_2
|
329
|
+
|
330
|
+
preg_visit_2_diagnose_2:
|
331
|
+
pv2_id: preg_visit_2
|
332
|
+
|
333
|
+
preg_visit_2_diagnose_2_2:
|
334
|
+
pv2_id: preg_visit_2_2
|
335
|
+
|
336
|
+
preg_visit_2_heat2:
|
337
|
+
pv2_id: preg_visit_2
|
338
|
+
|
339
|
+
preg_visit_2_heat2_2:
|
340
|
+
pv2_id: preg_visit_2_2
|
341
|
+
|
342
|
+
preg_visit_2_pdecorate2_room:
|
343
|
+
pv2_id: preg_visit_2
|
344
|
+
|
345
|
+
preg_visit_2_pdecorate2_room_2:
|
346
|
+
pv2_id: preg_visit_2_2
|
347
|
+
|
348
|
+
preg_visit_2_prenovate_room:
|
349
|
+
pv2_id: preg_visit_2
|
350
|
+
|
351
|
+
preg_visit_2_prenovate_room_2:
|
352
|
+
pv2_id: preg_visit_2_2
|
353
|
+
|
354
|
+
preg_visit_2_room_mold:
|
355
|
+
pv2_id: preg_visit_2
|
356
|
+
|
357
|
+
preg_visit_2_room_mold_2:
|
358
|
+
pv2_id: preg_visit_2_2
|
359
|
+
|
360
|
+
preg_visit_li:
|
361
|
+
b_address_id: address
|
362
|
+
|
363
|
+
preg_visit_li_2:
|
364
|
+
b_address_id: address
|
365
|
+
|
366
|
+
preg_visit_li_cool:
|
367
|
+
pv_li_id: preg_visit_li
|
368
|
+
|
369
|
+
preg_visit_li_cool_2:
|
370
|
+
pv_li_id: preg_visit_li_2
|
371
|
+
|
372
|
+
ref_freezer_verification:
|
373
|
+
equip_id: env_equipment
|
374
|
+
|
375
|
+
sample_receipt_store:
|
376
|
+
equip_id: env_equipment
|
377
|
+
|
378
|
+
sample_shipping:
|
379
|
+
staff_id_track: staff
|
380
|
+
|
381
|
+
six_mth_mother:
|
382
|
+
c_addr1_id: address
|
383
|
+
c_addr2_id: address
|
384
|
+
r_p_id: participant
|
385
|
+
|
386
|
+
six_mth_saq_formula_type:
|
387
|
+
six_mth_saq_id: six_mth_saq
|
388
|
+
|
389
|
+
six_mth_saq_2:
|
390
|
+
r_p_id: participant
|
391
|
+
|
392
|
+
six_mth_saq_3:
|
393
|
+
r_p_id: participant
|
394
|
+
|
395
|
+
six_mth_saq_formula_type_2:
|
396
|
+
six_mth_saq_id: six_mth_saq_2
|
397
|
+
|
398
|
+
six_mth_saq_supp:
|
399
|
+
six_mth_saq_id: six_mth_saq
|
400
|
+
|
401
|
+
six_mth_saq_supp_2:
|
402
|
+
six_mth_saq_id: six_mth_saq_2
|
403
|
+
|
404
|
+
six_mth_saq_water:
|
405
|
+
six_mth_saq_id: six_mth_saq
|
406
|
+
|
407
|
+
six_mth_saq_water_2:
|
408
|
+
six_mth_saq_id: six_mth_saq_2
|
409
|
+
|
410
|
+
spec_blood:
|
411
|
+
# According to the corresponding instrument, equip_id is manually entered
|
412
|
+
# and not a reference to another table.
|
413
|
+
equip_id: false
|
414
|
+
|
415
|
+
spec_blood_2:
|
416
|
+
# According to the corresponding instrument, equip_id is manually entered
|
417
|
+
# and not a reference to another table.
|
418
|
+
equip_id: false
|
419
|
+
|
420
|
+
spec_cord_blood_specimen:
|
421
|
+
spec_cord_blood_id: spec_cord_blood
|
422
|
+
|
423
|
+
spec_cord_blood_specimen_2:
|
424
|
+
spec_cord_blood_id: spec_cord_blood_2
|
425
|
+
|
426
|
+
spec_receipt:
|
427
|
+
# Insufficient info to determine what this is supposed to link to
|
428
|
+
storage_container_id: false
|
429
|
+
equip_id: spec_equipment
|
430
|
+
|
431
|
+
spec_shipping:
|
432
|
+
# Insufficient info to determine what this is supposed to link to
|
433
|
+
shipper_id: false
|
434
|
+
|
435
|
+
spec_storage:
|
436
|
+
equip_id: spec_equipment
|
437
|
+
|
438
|
+
staff_exp_mngmnt_tasks:
|
439
|
+
staff_weekly_expense_id: staff_weekly_expense
|
440
|
+
|
441
|
+
staff_exp_data_cllctn_tasks:
|
442
|
+
staff_weekly_expense_id: staff_weekly_expense
|
443
|
+
|
444
|
+
three_mth_mother:
|
445
|
+
r_p_id: participant
|
446
|
+
|
447
|
+
three_mth_mother_2:
|
448
|
+
r_p_id: participant
|
449
|
+
|
450
|
+
tracing_int:
|
451
|
+
r_p_id: participant
|
452
|
+
new_address_id: address
|
453
|
+
home_phone_id: telephone
|
454
|
+
cell_phone_id: telephone
|
455
|
+
c_addr1_id: address
|
456
|
+
contact_phone_id: telephone
|
457
|
+
contact_phone_2_1_id: telephone
|
458
|
+
c_addr2_id: address
|
459
|
+
contact_phone_2_id: telephone
|
460
|
+
contact_phone_2_2_id: telephone
|
461
|
+
c_addr3_id: address
|
462
|
+
contact_phone_3_id: telephone
|
463
|
+
contact_phone_2_3_id: telephone
|
464
|
+
|
465
|
+
trh_meter_calibration:
|
466
|
+
equip_id: spec_equipment
|
467
|
+
|
468
|
+
twelve_mth_mother:
|
469
|
+
c_addr1_id: address
|
470
|
+
c_addr2_id: address
|
471
|
+
r_p_id: participant
|
472
|
+
|
473
|
+
twelve_mth_mother_2:
|
474
|
+
r_p_id: participant
|
475
|
+
c_addr1_id: address
|
476
|
+
c_addr2_id: address
|
477
|
+
|
478
|
+
twelve_mth_saq_2:
|
479
|
+
r_p_id: participant
|
480
|
+
|
481
|
+
twelve_mth_saq_formula_brand:
|
482
|
+
twelve_mth_saq_id: twelve_mth_saq
|
483
|
+
|
484
|
+
twelve_mth_saq_formula_brand_2:
|
485
|
+
twelve_mth_saq_id: twelve_mth_saq_2
|
486
|
+
|
487
|
+
twelve_mth_saq_formula_type:
|
488
|
+
twelve_mth_saq_id: twelve_mth_saq
|
489
|
+
|
490
|
+
twelve_mth_saq_formula_type_2:
|
491
|
+
twelve_mth_saq_id: twelve_mth_saq_2
|
492
|
+
|
493
|
+
twelve_mth_saq_supplement:
|
494
|
+
twelve_mth_saq_id: twelve_mth_saq
|
495
|
+
|
496
|
+
twelve_mth_saq_supplement_2:
|
497
|
+
twelve_mth_saq_id: twelve_mth_saq_2
|
498
|
+
|
499
|
+
twelve_mth_saq_water:
|
500
|
+
twelve_mth_saq_id: twelve_mth_saq
|
501
|
+
|
502
|
+
twelve_mth_saq_water_2:
|
503
|
+
twelve_mth_saq_id: twelve_mth_saq_2
|
504
|
+
|
505
|
+
twenty_four_mth_mother:
|
506
|
+
c_addr1_id: address
|
507
|
+
c_addr2_id: address
|
508
|
+
r_p_id: participant
|
509
|
+
|
510
|
+
twenty_four_mth_mother_2:
|
511
|
+
c_addr1_id: address
|
512
|
+
c_addr2_id: address
|
513
|
+
r_p_id: participant
|
514
|
+
|
515
|
+
twenty_four_mth_mother_otc:
|
516
|
+
twenty_four_mth_mother_id: twenty_four_mth_mother
|
517
|
+
|
518
|
+
twenty_four_mth_mother_prescr:
|
519
|
+
twenty_four_mth_mother_id: twenty_four_mth_mother
|
520
|
+
|
521
|
+
twenty_four_mth_mother_suppl:
|
522
|
+
twenty_four_mth_mother_id: twenty_four_mth_mother
|
523
|
+
|
524
|
+
twenty_four_mth_saq:
|
525
|
+
asq24_address_id: address
|
526
|
+
r_p_id: participant
|
@@ -55,6 +55,8 @@ module NcsNavigator::Mdes
|
|
55
55
|
create('2.1', '2.1/NCS_Transmission_Schema_2.1.00.00.xsd', '2.1.00.00')
|
56
56
|
when '2.2'
|
57
57
|
create('2.2', '2.2/NCS_Transmission_Schema_2.2.01.00.xsd', '2.2.01.00')
|
58
|
+
when '3.0'
|
59
|
+
create('3.0', '3.0/NCS_Transmission_Schema_3.0.00.00.xsd', '3.0.00.00')
|
58
60
|
else
|
59
61
|
raise "MDES #{version} is not supported by this version of ncs_mdes"
|
60
62
|
end
|
@@ -144,6 +144,20 @@ module NcsNavigator::Mdes
|
|
144
144
|
end
|
145
145
|
end
|
146
146
|
|
147
|
+
describe '3.0' do
|
148
|
+
let(:version) { '3.0' }
|
149
|
+
|
150
|
+
include_context 'version docs'
|
151
|
+
|
152
|
+
it 'has the correct path for the schema' do
|
153
|
+
subject.schema.should =~ %r{3.0/NCS_Transmission_Schema_3.0.00.00.xsd$}
|
154
|
+
end
|
155
|
+
|
156
|
+
it 'has a different specification_version' do
|
157
|
+
subject.specification_version.should == '3.0.00.00'
|
158
|
+
end
|
159
|
+
end
|
160
|
+
|
147
161
|
it 'fails for an unsupported version' do
|
148
162
|
lambda { SourceDocuments.get('1.0') }.
|
149
163
|
should raise_error('MDES 1.0 is not supported by this version of ncs_mdes')
|
@@ -82,6 +82,13 @@ module NcsNavigator::Mdes
|
|
82
82
|
|
83
83
|
include_examples 'tables fully resolved'
|
84
84
|
end
|
85
|
+
|
86
|
+
context 'in version 3.0' do
|
87
|
+
let(:version) { '3.0' }
|
88
|
+
let(:expected_table_count) { 397 }
|
89
|
+
|
90
|
+
include_examples 'tables fully resolved'
|
91
|
+
end
|
85
92
|
end
|
86
93
|
|
87
94
|
describe '#specification_version' do
|
@@ -141,6 +148,14 @@ module NcsNavigator::Mdes
|
|
141
148
|
disposition_codes.size.should == 251
|
142
149
|
end
|
143
150
|
end
|
151
|
+
|
152
|
+
context 'in version 3.0' do
|
153
|
+
let(:disposition_codes) { Specification.new('3.0', :log => logger).disposition_codes }
|
154
|
+
|
155
|
+
it 'has 332 codes' do
|
156
|
+
disposition_codes.size.should == 332
|
157
|
+
end
|
158
|
+
end
|
144
159
|
end
|
145
160
|
|
146
161
|
describe '#[]' do
|
@@ -208,6 +223,13 @@ module NcsNavigator::Mdes
|
|
208
223
|
|
209
224
|
include_examples 'types fully resolved'
|
210
225
|
end
|
226
|
+
|
227
|
+
context 'version 3.0' do
|
228
|
+
let(:version) { '3.0' }
|
229
|
+
let(:expected_type_count) { 514 }
|
230
|
+
|
231
|
+
include_examples 'types fully resolved'
|
232
|
+
end
|
211
233
|
end
|
212
234
|
end
|
213
235
|
end
|
metadata
CHANGED
@@ -1,7 +1,7 @@
|
|
1
1
|
--- !ruby/object:Gem::Specification
|
2
2
|
name: ncs_mdes
|
3
3
|
version: !ruby/object:Gem::Version
|
4
|
-
version: 0.
|
4
|
+
version: 0.7.0
|
5
5
|
prerelease:
|
6
6
|
platform: ruby
|
7
7
|
authors:
|
@@ -9,7 +9,7 @@ authors:
|
|
9
9
|
autorequire:
|
10
10
|
bindir: bin
|
11
11
|
cert_chain: []
|
12
|
-
date: 2012-06-
|
12
|
+
date: 2012-06-15 00:00:00.000000000 Z
|
13
13
|
dependencies:
|
14
14
|
- !ruby/object:Gem::Dependency
|
15
15
|
name: nokogiri
|
@@ -129,6 +129,10 @@ files:
|
|
129
129
|
- documents/2.2/disposition_codes.yml
|
130
130
|
- documents/2.2/extract_disposition_codes.rb
|
131
131
|
- documents/2.2/heuristic_overrides.yml
|
132
|
+
- documents/3.0/NCS_Transmission_Schema_3.0.00.00.xsd
|
133
|
+
- documents/3.0/disposition_codes.yml
|
134
|
+
- documents/3.0/extract_disposition_codes.rb
|
135
|
+
- documents/3.0/heuristic_overrides.yml
|
132
136
|
- lib/ncs_navigator/mdes.rb
|
133
137
|
- lib/ncs_navigator/mdes/disposition_code.rb
|
134
138
|
- lib/ncs_navigator/mdes/source_documents.rb
|
@@ -158,18 +162,12 @@ required_ruby_version: !ruby/object:Gem::Requirement
|
|
158
162
|
- - ! '>='
|
159
163
|
- !ruby/object:Gem::Version
|
160
164
|
version: '0'
|
161
|
-
segments:
|
162
|
-
- 0
|
163
|
-
hash: -4331102622694639655
|
164
165
|
required_rubygems_version: !ruby/object:Gem::Requirement
|
165
166
|
none: false
|
166
167
|
requirements:
|
167
168
|
- - ! '>='
|
168
169
|
- !ruby/object:Gem::Version
|
169
170
|
version: '0'
|
170
|
-
segments:
|
171
|
-
- 0
|
172
|
-
hash: -4331102622694639655
|
173
171
|
requirements: []
|
174
172
|
rubyforge_project:
|
175
173
|
rubygems_version: 1.8.21
|