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Published 20 hours ago • verified publisher icon biocommons

Unable to use the uta_20210129 locally or in docker

Open LydiePrevost opened this issue 3 years ago • 4 comments

Hello, I have been trying to install through docker or locally uta_20210129

  1. The latest Docker biocommons/uta does not seem to have any tables
  2. when dumping uta_20210129.pgd.gz I followed the :installation notes.
  • My first run fails :`GRANT

GRANT USAGE ON SCHEMA uta_20210129 TO anonymous; ERROR: role "anonymous" does not exist ********* QUERY ********** COMMIT **************************` So I created the user.

  • My second run does not seem to terminate: REFRESH MATERIALIZED VIEW REFRESH MATERIALIZED VIEW uta_20210129.tx_def_summary_mv; REFRESH MATERIALIZED VIEW REFRESH MATERIALIZED VIEW uta_20210129.tx_similarity_mv; I have been waiting for 3 H, thi sis is the last line of the script, but it seems to hang and I see no tables created.

Could you please help me give the direction the install uta_20210129, my first choice being in Docker. Thank you

LydiePrevost avatar Jan 14 '22 01:01 LydiePrevost

Hi @LydiePrevost , I used this solution in order to locally download the 20210129 version.

korikuzma avatar Jan 14 '22 01:01 korikuzma

Hi @korikuzma , Thank you for the help, but the solution you mentioned does not refresh the materialized view and I am getting errors when trying to use the hgvs shell as mentioned in https://github.com/biocommons/uta/issues/228.

LydiePrevost avatar Jan 25 '22 18:01 LydiePrevost

@LydiePrevost , I know it's been a while, but the VIEW REFRESH MATERIALIZED VIEW uta_20210129.tx_similarity_mv; command takes ~5 hours. If you let the process run for this long, does the local installation work for you?

korikuzma avatar Apr 28 '22 00:04 korikuzma

you can also use my docker image i made for latest uta 20210129: https://hub.docker.com/r/koopmann/uta/tags

koopmann avatar May 18 '22 08:05 koopmann

koopmann

Hi @koopmann , I try to use your docker image for uta_20210129, when I checkthe docker log file, it gets stuck on the refresh of the last materialized view . Is this normal? And I wonder how long it may takes? Thanks!

GuoFengWang avatar Feb 23 '23 09:02 GuoFengWang

This step needs regularily a lot of time, i waited some hours on my local machine.

koopmann avatar Feb 23 '23 10:02 koopmann

finally you should see something like: 2023-02-13 09:43:45.379 UTC [1] LOG: database system is ready to accept connections

koopmann avatar Feb 23 '23 10:02 koopmann

The underlying issue was solved in #228. I'm closing this issue. Please comment in #228 if the issue persists.

reece avatar Sep 11 '23 04:09 reece