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microbiomedata / nmdc_automation

Prototype automation
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162 workflow results are not incrementing correctly #165

Closed mbthornton-lbl closed 4 months ago

mbthornton-lbl commented 4 months ago

Duplicate records data file provided by Michal. Dependent on #164

Results from running delete-old-records locally:

./re_id_tool.py --target NAPA delete-old-records data/duplicate_delete_records.json
INFO:root:Using NAPA config: ../../../configs/.local_napa_user_config.toml
INFO:root:Deleting old objects found in : data/duplicate_delete_records.json
INFO:pymongo.serverSelection:{"message": "Waiting for suitable server to become available", "selector": "Primary()", "operation": "listDatabases", "topologyDescription": "<TopologyDescription id: 664503c4c42ce62b504345e9, topology_type: Single, servers: [<ServerDescription ('localhost', 27017) server_type: Unknown, rtt: None>]>", "clientId": {"$oid": "664503c4c42ce62b504345e9"}, "remainingTimeMS": 4}
INFO:root:Deleting 28 records from metagenome_annotation_activity_set
INFO:root:Deleted 28 records from metagenome_annotation_activity_set
INFO:root:Deleting 91 records from mags_activity_set
INFO:root:Deleted 91 records from mags_activity_set
INFO:root:Deleting 28 functional annotation records
INFO:root:Deleted 0 functional annotation records
INFO:root:Writing 119 deleted record identifiers to /Users/MBThornton/Documents/code/nmdc_automation/nmdc_automation/re_iding/scripts/data/duplicate_deleted_record_identifiers.tsv
INFO:root:Elapsed time: 0.04718208312988281
(nmdc-automation-py3.9) (base) MBThornton@MBThornton-M92 scripts %

Has not yet been run on Napa instance