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6 changes: 3 additions & 3 deletions
6
...efault_records/submission_templates/010_rvi_bait_capture_library_submission_templates.yml
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,10 +1,10 @@ | ||
| # This submission template is associated with the Limber Bait Capture Library preparation pipeline. | ||
| # To create this run WIP=010_bait_capture_library_submission_templates rake record_loader:all | ||
| --- | ||
| Limber-Htp - RVI - Bait Capture Library: | ||
| Limber-Htp - RVI Bait Capture Library - NovaSeq 6000 Paired end sequencing: | ||
| submission_class_name: "LinearSubmission" | ||
| related_records: | ||
| request_type_keys: ["limber_bait_capture_library_prep", "limber_multiplexing"] | ||
| request_type_keys: | ||
| ["limber_bait_capture_library_prep", "limber_multiplexing", "illumina_htp_novaseq_6000_paired_end_sequencing"] | ||
| project_name: Respiratory Virus and Microbiome Initiative | ||
| product_line_name: Illumina-HTP | ||
| product_catalogue_name: Bait Capture Library |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,83 @@ | ||
| # frozen_string_literal: true | ||
|
|
||
| # Rails task to add missing asset audit records from a CSV file | ||
| namespace :asset_audit do | ||
| # This rake task is used to add missing asset audit records from a CSV file. | ||
| # If there are any errors in the CSV file, no records will be inserted. | ||
| # Usage: rails asset_audit:add_missing_records['/path/to/file.csv'] | ||
| # The CSV file should have the following headers: | ||
| # barcode, message, created_by, created_at | ||
| # The message column should have one of the following values: | ||
| # 'Destroying location', 'Destroying labware' | ||
|
|
||
| desc 'Add missing asset audit records' | ||
| task :add_missing_records, [:file_path] => :environment do |_, args| | ||
| required_csv_headers = %w[barcode message created_by created_at] | ||
|
|
||
| # Check if the file path is provided and valid | ||
| file_path = args[:file_path] == 'nil' ? nil : args[:file_path] | ||
| raise 'Please provide a valid file path' if file_path.nil? || !File.exist?(file_path) | ||
|
|
||
| # Read the CSV file and validate the headers | ||
| begin | ||
| csv_data = CSV.read(file_path, headers: true) | ||
| rescue StandardError => e | ||
| raise "Failed to read CSV file: #{e.message}" | ||
| end | ||
|
|
||
| unless csv_data.headers.length == required_csv_headers.length | ||
| raise 'Failed to read CSV file: Invalid number of header columns.' | ||
| end | ||
|
|
||
| # Process the CSV data and create asset audit records data array to insert | ||
| asset_audit_data = [] | ||
| csv_data.each do |row| | ||
| missing_columns = required_csv_headers.select { |header| row[header].nil? } | ||
|
|
||
| # Check if any of the required columns are missing | ||
| raise 'Failed to read CSV file: Missing columns.' unless missing_columns.empty? | ||
|
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| # Find the asset by barcode | ||
| asset = Labware.find_by_barcode(row['barcode'].strip) | ||
| raise "Asset with barcode #{row['barcode']} not found." if asset.nil? | ||
|
|
||
| # Check if the message is valid | ||
| key = | ||
| case row['message'] | ||
| when 'Destroying location' | ||
| 'destroy_location' | ||
| when 'Destroying labware' | ||
| 'destroy_labware' | ||
| end | ||
|
|
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| raise "Invalid message for asset with barcode #{row['barcode']}." if key.nil? | ||
|
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| # Create the asset audit record data | ||
| data = { | ||
| asset_id: asset.id, | ||
| created_by: row['created_by'], | ||
| created_at: row['created_at'], | ||
| message: "Process '#{row['message']}' performed on instrument Destroying instrument", | ||
| key: key | ||
| } | ||
| asset_audit_data << data | ||
| end | ||
|
|
||
| # Insert the asset audit records | ||
| ActiveRecord::Base.transaction do | ||
| asset_audit_data.each do |data| | ||
| AssetAudit.create!( | ||
| message: data[:message], | ||
| created_by: data[:created_by], | ||
| created_at: data[:created_at], | ||
| asset_id: data[:asset_id], | ||
| key: data[:key] | ||
| ) | ||
| end | ||
| puts 'All records successfully inserted.' | ||
| rescue ActiveRecord::ActiveRecordError => e | ||
| puts "Failed to insert records: #{e.message}" | ||
| raise ActiveRecord::Rollback | ||
| end | ||
| end | ||
| end |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,2 @@ | ||
| barcode,message,created_by,created_at | ||
| SQPD-9002;"Destroying location;User1,2021-01-01 12:00:00 |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,2 @@ | ||
| barcode,message,created_by,created_at | ||
| SQPD-1,Destroying test,User1,2021-01-01 12:00:00 |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,2 @@ | ||
| barcode,message,created_by,created_at | ||
| SQPD-1,Destroying location,2021-01-01 12:00:00 |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,2 @@ | ||
| barcode,created_by,created_at | ||
| SQPD-1,Destroying location,2021-01-01 12:00:00 |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,3 @@ | ||
| barcode,message,created_by,created_at | ||
| SQPD-1,Destroying location,User1,2021-01-01 12:00:00 | ||
| SQPD-2,Destroying labware,User2,2021-01-02 12:00:00 |
4 changes: 4 additions & 0 deletions
4
spec/data/record_loader/application_record_loader/example.wip.yml
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| # Test record loader records | ||
| --- | ||
| Test Record: | ||
| test_attribute: "A Value" |
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