[manualpipe] Elan 20220128

[SamStudio8]

Brief description

183

Pipeline exit code: [Exit code]

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Executed by: [Name or initials] [Site code]

• [x] I am sure this pipeline is not already running (Only relevant for non-flocked pipelines)

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• [x] Engage pipeline via mqtt from a clean dedicated mqtt environment
• [ ] Disable NXF cache destruction (only applicable for ENA BAM pipe)
• [ ] Check output if necessary
• [ ] Check mqtt message is sent confirming completion, or send one if required (check in #tael-steam)
• [ ] Re-enable NXF cache destruction (if disabled)

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• [ ] Set appropriate issue flags and assignee

• [ ] Manual intervention complete

• "Normal" service disrupted? YES/NO

• If yes, describe impact:

[SamStudio8]

not ideal

>>> models.DigitalResourceGroup.objects.filter(current_name="20220128", parent_group__digitalresourcegroup__current_name="fasta")
<PolymorphicQuerySet [<DigitalResourceGroup: 20220128 (03a620db-8796-4cba-9c6d-c42dacb9a184)>, <DigitalResourceGroup: 20220128 (2e98031a-15ee-4623-9bcb-b7c72eccd00c)>, <DigitalResourceGroup: 20220128 (cdfb6ee9-b37a-49d0-b34d-e69c6fa33b74)>]>

[SamStudio8]

>>> for mag in models.DigitalResourceGroup.objects.filter(current_name="20220128", parent_group__digitalresourcegroup__current_name="fasta"):
...   models.DigitalResourceArtifact.objects.filter(primary_group=mag).delete()
... 
(11, {'majora2.MajoraArtifact_groups': 1, 'majora2.MajoraMetaRecord': 4, 'tatl.TatlVerb': 1, 'majora2.DigitalResourceArtifact': 1, 'majora2.TemporaryMajoraArtifactMetric_Sequence': 1, 'majora2.TemporaryMajoraArtifactMetric': 1, 'majora2.MajoraArtifactProcessRecord': 1, 'majora2.MajoraArtifact': 1})
(11, {'majora2.MajoraArtifact_groups': 1, 'majora2.MajoraMetaRecord': 4, 'tatl.TatlVerb': 1, 'majora2.DigitalResourceArtifact': 1, 'majora2.TemporaryMajoraArtifactMetric_Sequence': 1, 'majora2.TemporaryMajoraArtifactMetric': 1, 'majora2.MajoraArtifactProcessRecord': 1, 'majora2.MajoraArtifact': 1})
(11, {'majora2.MajoraArtifact_groups': 1, 'majora2.MajoraMetaRecord': 4, 'tatl.TatlVerb': 1, 'majora2.DigitalResourceArtifact': 1, 'majora2.TemporaryMajoraArtifactMetric_Sequence': 1, 'majora2.TemporaryMajoraArtifactMetric': 1, 'majora2.MajoraArtifactProcessRecord': 1, 'majora2.MajoraArtifact': 1})

Remove offending artifacts so we can remove two of the MAGs

[SamStudio8]

MAGs removed, Elan restarted and will pick up from Ocarina step :rocket:

[SamStudio8]

All good here. We've accidentally stopped publishing the dated published artifacts directory as a result of the publishing changes, but we were going to stop making those anyway. Datapipe is now aware of the change and we don't think any users rely on the non-latest directory.