Service - Merge develop into master

[harrietc52]

Changes proposed in this pull request:

• DPL-744 - As developers we need to modify the message that we send to the warehouse to ensure it contains the correct information for a Revio run #992
• DPL-764 - As a user I need to ensure that the Revio sequencing kit barcode is unique it can only have a maximum number of samples associated with it AND only be used twice #1011

Coupled with:
sanger/traction-ui#1263
sanger/unified_warehouse#525

[StephenHulme]

LGTM (looks good to me) 🙂

[codecov]

Codecov Report

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[harrietc52]

Production Deployment

Including:

• Service - Merge develop into master #1063
• UI - Merge develop into master traction-ui#1263
• Merge develop into master unified_warehouse#525

Steps

• Merge develop into master, for UI, Service and UWH
• Check all Pacbio plates have plate_number
• Deploy Traction Service (Current prod: v6.0.0)

ansible-playbook -vv deploy_traction_service.yml -i environments/<env> -e "github_branch=v6.1.0" -e "full_deploy=true reload_nginx=true skip_migrations=true"

• Rebroadcast to back populate MLWH plate_number

Pacbio::Run.all.each { |run| Messages.publish(run, Pipelines.pacbio.message) }

• Deploy Unified Warehouse, run the migrations (Current prod: v1.15.0)

ansible-playbook -vD deploy_unified_warehouse.yml -i environments/<env> -e "github_branch=v1.16.0" -e "full_deploy=true skip_migrations=false"

• Deploy Traction UI (Current prod: v7.0.0)

ansible-playbook -vD deploy_traction_ui.yml -i environments/<env> -e "github_branch=v7.1.0"

[harrietc52]

Deployment issues

Issues ran in to whilst rebroadcasting the Pacbio::Runs from Production

• There were 6 Pacbio::Requests with no samples, therefore the message to include a request.sample.name failed

Pacbio::Request.all.count
# 4521

# Pacbio::Request's ids with no sample
# 3016, 3017, 3018, 3019, 3020, 3023

Pacbio::Run.all.count
=> 686

• There were 5 Pacbio::Runs that therefore needed to be excluded from the rebroadcast

Pacbio::Request.find(3023).libraries.map(&:pool).map(&:wells).flatten.map(&:plate).map(&:run).map(&:id)

# Request id -> run id

# 3016, 530
# 3017, 509
# 3018, 522
# 3019, 530
# 3020, no run
# 3023, 531

Pacbio::Run.where.not(id: [530, 509, 522, 530, 531]).count
=> 682

• The Runs were excluded when rebroadcasting

Pacbio::Run.where.not(id: [530, 509, 522, 530, 531]).each { |run| Messages.publish(run, Pipelines.pacbio.message) }

runs_updated = _
[#<Pacbio::Run:0x00007f3be1ad2ce8
...
runs_updated.count
=> 682

• 3398 records in the pac_bio_run MLWH table were updated to have plate_number: 1. The 17526 records that were not updated are not Traction Pacbio runs.