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  1. NIF
  2. NIF-11570

nlx_151671 (ClinVar) data import stuck in compare

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    • NIF

    Description

      Resource nlx_151671 data import is stuck in compare. Has completed data ingest, but has not proceeded past compare stage. Most of the tables appear to have been updated on the server, but a few tables are missing. Ingest seemed to stall when the server was going through a copying stage.

      Can you investigate to determine why this is crashing in compare? The ingest takes a long time, close to 24 hours, so a crash can cause a significant delay.

      Server readout when the ingest stalled included the following errors:
      Loading driver
      Connecting to jdbc:postgresql://nif-db.crbs.ucsd.edu:5432/disco_crawler
      Copying text data rows from stdin
      org.postgresql.util.PSQLException: ERROR: tuple concurrently updated

      and

      org.postgresql.util.PSQLException: ERROR: relation "l2_nlx_151671_xml_ref_assert_replacement" does not exist

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            rwang Rixin Wang
            larawayb Bryan Laraway
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              Updated:
              Resolved: