search

biocommons / uta

Universal Transcript Archive: comprehensive genome-transcript alignments; multiple transcript sources, versions, and alignment methods; available as a docker image
Apache License 2.0
62 stars 26 forks source link

why I can not find table uta_20180821.meta ?(docker version) #227

Closed nordhuang closed 6 months ago

nordhuang commented 4 years ago

$ sudo docker run --name uta_20180821 -v uta_20180821:/var/lib/postgresql/data -p 50827:5432 biocommons/uta:uta_20180821

$ psql -h localhost -p 50827 -U anonymous -d uta -c "select from uta_20180821.meta" ERROR: relation "uta_20180821.meta" does not exist LINE 1: select from uta_20180821.meta

why I can not find table uta_20180821.meta ?

docker show the below sentences: 2020-05-29 03:43:17.433 UTC [1] LOG: listening on IPv4 address "0.0.0.0", port 5432 2020-05-29 03:43:17.433 UTC [1] LOG: listening on IPv6 address "::", port 5432 2020-05-29 03:43:17.435 UTC [1] LOG: listening on Unix socket "/var/run/postgresql/.s.PGSQL.5432" 2020-05-29 03:43:17.450 UTC [24] LOG: database system was shut down at 2020-05-29 03:42:29 UTC 2020-05-29 03:43:17.456 UTC [1] LOG: database system is ready to accept connections 2020-05-29 03:43:33.051 UTC [31] ERROR: relation "uta_20180821.meta" does not exist at character 15 2020-05-29 03:43:33.051 UTC [31] STATEMENT: select * from uta_20180821.meta

reece commented 4 years ago

If you're running a new container, the first operation is to download data and load into the postgresql instance. That takes about 3 minutes on my fast laptop with an SSD. While the data are loaded, postgresql is available but doesn't contain anything. I just ran the same commands and it worked fine.

Here's an abridged transcript:

$ docker volume rm uta_20180821
$ docker volume create uta_20180821
$ docker run --name uta_20180821 -v uta_20180821:/var/lib/postgresql/data -p 50827:5432 biocommons/uta:uta_20180821
The files belonging to this database system will be owned by user "postgres".
This user must also own the server process.
...
[a bunch of text, including CREATE TABLE, COPY, ALTER TABLE, GRANT, and REFRESH MATERIALIZED VIEW commands]
...
=======================================================================
=======================================================================
== 
== uta_20180821 installed from
== http://dl.biocommons.org/uta/uta_20180821.pgd.gz
== 
...
2020-06-12 00:58:12.399 UTC [1] LOG:  database system is ready to accept connections

I ran the psql command in another window.

The easiest explanation for what you see is that you didn't wait until data were loaded. If you don't see the uta_20180821 installed from line, it's not ready.

github-actions[bot] commented 9 months ago

This issue is stale because it has been open 30 days with no activity. Remove stale label or comment or this will be closed in 7 days.

github-actions[bot] commented 9 months ago

This issue was closed because it has been stalled for 7 days with no activity.

github-actions[bot] commented 6 months ago

This issue is stale because it has been open 90 days with no activity. Remove stale label or comment or this will be closed in 7 days.

github-actions[bot] commented 6 months ago

This issue was closed because it has been stalled for 7 days with no activity.