staging: Deploy new Bioconductor stack

• swh-apps: Build image (if required)
• swh-charts: Reference new image (if required)
• swh/infra/ci-cd/swh-charts!174 (merged): Adapt values to reference the new lister and loader
• Deploy (push branch and let argocd do its job)
• Register a new listing task with type bioconductor
• Checks
  • Lister triggers and list the bioconductor forge [2]
  • Loaders are triggered and ingest the bioconductor origins [3]
• Tag grafana with "deployment service=loader-bioconductor service=lister-bioconductor environment=staging" [1]

Dashboard to follow [1]

[1] https://grafana.softwareheritage.org/goto/e-c3EAWIz?orgId=1

[2]

2023-10-10 10:55:12 swh-scheduler@db1:5432 λ select now(), instance_name, visit_type, count(*) from listed_origins lo inner join listers l on l.id=lo.lister_id where lister_id in (select id from listers where name='bioconductor') group by instance_name, visit_type order by count asc;
+-------------------------------+---------------+--------------+-------+
|              now              | instance_name |  visit_type  | count |
+-------------------------------+---------------+--------------+-------+
| 2023-10-10 08:55:22.276424+00 | bioconductor  | git          |  3022 |
| 2023-10-10 08:55:22.276424+00 | bioconductor  | bioconductor |  5788 |
+-------------------------------+---------------+--------------+-------+
(2 rows)

Time: 57.640 ms

[3]

period=1h; deployment=loader-bioconductor; kail --context archive-staging-rke2 -d $deployment --since $period | grep "succeeded"  | cut -d':' -f2- | jq -r .message
Task swh.loader.package.bioconductor.tasks.LoadBioconductor[b9db1f7e-fcef-4f78-a59d-c350194591ff] succeeded in 105.20165430298948s: {'status': 'eventful', 'snapshot_id': '48765481d79e3aacc048ae874ea23beb8ab390f2'}
Task swh.loader.package.bioconductor.tasks.LoadBioconductor[cd66dfb8-6df2-44a8-80a9-393fea176a15] succeeded in 10.934311490011169s: {'status': 'eventful', 'snapshot_id': '354646d21e216ef0a063ec3b18c07afa6db8a342'}
Task swh.loader.package.bioconductor.tasks.LoadBioconductor[0612004d-3404-4934-9e46-d79d1983d560] succeeded in 27.722351410004194s: {'status': 'eventful', 'snapshot_id': '87aac02f0fe8921b74071b14c07c7cee010ae91e'}
Task swh.loader.package.bioconductor.tasks.LoadBioconductor[21ab8705-6c36-4bae-ac20-d4989ccadd61] succeeded in 142.75712158399983s: {'status': 'eventful', 'snapshot_id': 'e58645f746780901240eeea68890e165c2ae6fc3'}
Task swh.loader.package.bioconductor.tasks.LoadBioconductor[a1c04640-ff8c-4e9b-85cd-554969638e55] succeeded in 17.988616397997248s: {'status': 'eventful', 'snapshot_id': '2e544daef719a1fd193f1a1d9839756b3595e448'}

Refs. swh/meta#5051