psycopg2.OperationalError: could not connect to server: Connection refused

[wentgithub]

I google this error in #277
but it seems that my error it is because of "Sorry... the password is also "anonymous" (no quotes)"

I set the env

export UTA_DB_URL=postgresql://anonymous@localhost:15032/uta/uta_20170117
export HGVS_SEQREPO_DIR=/data/ngs/softs/b_hgvs/seqrepo/seqrepo/2019-06-20

and do as following

import hgvs.dataproviders.uta
hdp = hgvs.dataproviders.uta.connect()

I also tried the method in https://github.com/biocommons/uta/

psql -h localhost -p 50827 -U anonymous -d uta -c 'select * from uta_20150827.meta'
psql: could not connect to server: Connection refused
Is the server running on host "localhost" (::1) and accepting
TCP/IP connections on port 50827?
could not connect to server: Connection refused
Is the server running on host "localhost" (127.0.0.1) and accepting

is there anything I am wrong, I do not know how to solve.

[reece]

Where did you get 50827? If you did what's shown above, it should be 15032.

[wentgithub]

Where did you get 50827? If you did what's shown above, it should be 15032.

I do not know, I just do as the guide told me , first docker pull, then export the port the default setting.

the 50827 comes from I test the code you supplied in this link https://github.com/biocommons/uta/

here is a new try today

[wentgithub]

here is another again new try, still showing connect unreachable, but not the same

some simple code are ok

[wentgithub]

with the test on, I found a very strange result. here is the process.

1
export UTA_DB_URL=postgresql://anonymous@localhost:15032/uta/uta_20170117
export HGVS_SEQREPO_DIR=/data/ngs/softs/b_hgvs/seqrepo/seqrepo/2019-06-20

2 hgvs-shell

3 after step2, it entered the interactive python interface

4 result

### "NO T in the test result"
whch is different from the result you supplied in https://hgvs.readthedocs.io/en/stable/examples/using-hgvs.html#normalizing-variants

and the validation is True, a little suprised

[worker000000]

any updates on this?

[reece]

There are two distinct questions on this issue.

1. Regarding the port issues, the short advice is to ensure that the port used when executing docker matches the port in the UTA_DB_URL. You should be able to connect to the UTA database the UTA_DB_URL, with the schema removed. For example, with:
   $ export UTA_DB_URL=postgresql://anonymous:anonymous@localhost:5432/uta/uta_20180821
   connect with
   $ psql postgresql://anonymous:anonymous@localhost:5432/uta

2. Regarding the dupT, that's minor. The spec permits either. In the 1.0.0 release, we added the ability to control the max length of the reference sequence to display.

By default, as you noted:

>>> v = hp.parse("NM_001166478.1:c.30_31insT")                                                                                                                                                                                   
>>> str(hn.normalize(v))                                                                                                                                                                                                         
'NM_001166478.1:c.35dup'

Set the maximum ref seq length to 5:

>>> import hgvs                                                                                                                                                                                                                  
>>> hgvs.global_config.formatting.max_ref_length = 5                                                                                                                                                                             
>>> str(hn.normalize(v))                                                                                                                                                                                                         
'NM_001166478.1:c.35dupT'

[reece]

This appears to have been resolved. Closing.