[manualpipe] Elan 20220216

[SamStudio8]

Brief description

All Ocarina commands exiting non-zero

Pipeline exit code: NA -- killed by @SamStudio8

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

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

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• [ ] 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]

183 has appeared due to an uncaught error in adding the dummy hoot files

[SamStudio8]

>>> for mag in models.DigitalResourceGroup.objects.filter(current_name="20220216", 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})
(22, {'majora2.MajoraArtifact_groups': 2, 'majora2.MajoraMetaRecord': 8, 'tatl.TatlVerb': 2, 'majora2.DigitalResourceArtifact': 2, 'majora2.TemporaryMajoraArtifactMetric_Sequence': 2, 'majora2.TemporaryMajoraArtifactMetric': 2, 'majora2.MajoraArtifactProcessRecord': 2, 'majora2.MajoraArtifact': 2})
(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})

>>> for mag in models.DigitalResourceGroup.objects.filter(current_name="20220216", parent_group__digitalresourcegroup__current_name="fasta"):                                                                                                                                                                                                                                                                                                                                                              
...   mag.delete()
... 
(2, {'majora2.MajoraArtifact_groups': 0, 'majora2.MajoraArtifactGroup_groups': 0, 'majora2.MajoraArtifactGroup_processes': 0, 'majora2.MajoraMetaRecord': 0, 'tatl.TatlVerb': 0, 'majora2.DigitalResourceGroup': 1, 'majora2.MajoraArtifactGroup': 1})
(2, {'majora2.MajoraArtifact_groups': 0, 'majora2.MajoraArtifactGroup_groups': 0, 'majora2.MajoraArtifactGroup_processes': 0, 'majora2.MajoraMetaRecord': 0, 'tatl.TatlVerb': 0, 'majora2.DigitalResourceGroup': 1, 'majora2.MajoraArtifactGroup': 1})
(2, {'majora2.MajoraArtifact_groups': 0, 'majora2.MajoraArtifactGroup_groups': 0, 'majora2.MajoraArtifactGroup_processes': 0, 'majora2.MajoraMetaRecord': 0, 'tatl.TatlVerb': 0, 'majora2.DigitalResourceGroup': 1, 'majora2.MajoraArtifactGroup': 1})
(2, {'majora2.MajoraArtifact_groups': 0, 'majora2.MajoraArtifactGroup_groups': 0, 'majora2.MajoraArtifactGroup_processes': 0, 'majora2.MajoraMetaRecord': 0, 'tatl.TatlVerb': 0, 'majora2.DigitalResourceGroup': 1, 'majora2.MajoraArtifactGroup': 1})

[SamStudio8]

we're cooking again

[SamStudio8]

ocarina step ok, post-publish conda env is toast for no discernible reason, @BioWilko taking a look

[BioWilko]

Glassed the conda env entirely and regenerated it with PYTHONNOUSERSITE=True and Python=3.8 to hopefully avoid the strange environment dependency issues we've been having

[BioWilko]

Elan finished, all fine now!