We have postgres server set up. However, I don’t see postgres server is referred anywhere in application.yml. So I don’t think we are using postgres server.
We are using two portal servers. If we don’t use Postgres, do they sync there database contents? If not, the two servers will be out of sync. Could that result in this issue?
I shut down one portal server, and restart varnish server. It appears that the erichment analysis is stuck (an icon just keeping spinning). From portal log, it seems that portal server has completed analysis. Somehow it is not displayed.
Our mirror site is now up at https://116.6.21.111. You can see the problem at the site.
After manually create database using codes below, i still get this problem
-- CREATE DATABASE dcc_portal;
-- CREATE USER dcc WITH PASSWORD 'dcc';
-- GRANT ALL PRIVILEGES ON DATABASE dcc_portal to dcc;
--
-- GRANT SELECT, INSERT ON user_gene_set TO dcc;
Error information:
Internal Server Error. There was an error processing your request, with the message of ‘org.postgresql.util.PSQLException: ERROR: column “version” of relation “oncogrid_analysis” does not exist Position: 42 [statement:“INSERT INTO oncogrid_analysis (id, data, version) VALUES (:id, :data, :version)”, located:“INSERT INTO oncogrid_analysis (id, data, version) VALUES (:id, :data, :version)”, rewritten:“INSERT INTO oncogrid_analysis (id, data, version) VALUES (?, ?, ?)”, arguments:{ positional:{}, named:{data:’{“id”:“4565ed82-69f4-4f58-9da9-aed794e30bbd”,“geneSet”:“3b5183c6-1220-4f2f-8b73-8f31882de599”,“geneCount”:75,“geneSetName”:“Top 75 CGC Genes for Liver”,“donorSet”:“9b9e1f4b-4539-4ecd-ae73-620894028817”,“donorCount”:75,“donorSetName”:“Top 75 PCAWG Liver Donors”,“version”:1,“state”:“FINISHED”,“timestamp”:1478504901567}‘,id:4565ed82-69f4-4f58-9da9-aed794e30bbd,version:2}, finder:}]’. It has been logged (ID 3c12011a62fe574e).
After rebuilt table union_analysis, i still got some errors.
dcc-portal=# \d union_analysis;
Table "public.union_analysis"
Column | Type | Modifiers
---------+---------+-----------
id | uuid | not null
version | integer |
data | text | not null
Indexes:
"union_analysis_pkey" PRIMARY KEY, btree (id)
Error information:
Internal Server Error. There was an error processing your request, with the
message of 'org.postgresql.util.PSQLException: FATAL: terminating
connection due to administrator command [statement:"INSERT INTO
entity_set (id, data, version) VALUES (:id, :data, :version)",
located:"INSERT INTO entity_set (id, data, version) VALUES (:id, :data,
:version)", rewritten:"INSERT INTO entity_set (id, data, version) VALUES
(?, ?, ?)", arguments:{ positional:{},
named:{data:'{"id":"dda65eb7-f004-4834-a91d-b9601c7598f2","state":"PENDING","name":"Top
75 CGC Genes for
Liver","description":"","type":"GENE","version":2,"timestamp":1479131585638,"subtype":"TRANSIENT"}',id:dda65eb7-f004-4834-a91d-b9601c7598f2,version:2},
finder:[]}]'. It has been logged (ID 652e7e7083536abe).