Invalid Analysis c1760c15-def7-4d06-9bdf-739f37b982a2

brady 2016-09-14 13:50:09 UTC #1

On our mirror site, if we click on demo link on "Data Analysis" page, we got the following message:

Analysis c1760c15-def7-4d06-9bdf-739f37b982a2 cannot be found on the server. It may no longer be valid with respect to current portal data.

It appears that the code is using wrong id for query. We still has issue with authentication with CUD, I am not sure if it is related.

btiernay 2016-09-14 17:20:05 UTC #2

Are you using Postgres? If not, then the database is recreated each reboot of the API

brady 2016-09-14 18:15:31 UTC #3

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.

andricDu 2016-09-14 19:23:10 UTC #4

Hi Brady,

You are right, I just took a peak at the Ansible roles, and it looks like the portal is configured to use the in-memory H2 database.

The section in the config should look more something like this:

# Datasource
spring.datasource:
  driver-class-name: org.postgresql.Driver
  url: jdbc:postgresql://<postgres_host>/dcc_portal

brady 2016-09-14 19:59:30 UTC #5

Hi Dusan,

Besides add hostname and username/password, do I need to create database manually on postgres server before portal server can use it?

andricDu 2016-09-14 20:00:59 UTC #6

You will need to create the database with the following schema:

github.com

icgc-dcc/dcc-portal/blob/develop/dcc-portal-server/src/main/sql/schema.sql

/*
 * Copyright (c) 2012-2014 The Ontario Institute for Cancer Research. All rights reserved.
 */

/* Script for setting up the dcc-portal schema using PostgreSQL 9.2.4 */

-- 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;

CREATE TABLE IF NOT EXISTS user_gene_set(
   id   UUID NOT NULL,
   data TEXT NOT NULL,
   
   PRIMARY KEY(id) 
);
GRANT SELECT, INSERT, UPDATE, DELETE ON user_gene_set TO dcc;

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felix 2016-11-07 07:50:25 UTC #7

Hi, i took over the job from Brady.

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).

Our mirror site is https://icgcportal.genomics.cn

Could you please help us?

andricDu 2016-11-10 15:22:43 UTC #8

Hi Felix,

Looks like there was a missing column in our schema.sql file.

We have pushed a fix.

github.com

icgc-dcc/dcc-portal/blob/develop/dcc-portal-server/src/main/sql/schema.sql

/*
 * Copyright (c) 2012-2014 The Ontario Institute for Cancer Research. All rights reserved.
 */

/* Script for setting up the dcc-portal schema using PostgreSQL 9.2.4 */

-- 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;

CREATE TABLE IF NOT EXISTS user_gene_set(
   id   UUID NOT NULL,
   data TEXT NOT NULL,
   
   PRIMARY KEY(id) 
);
GRANT SELECT, INSERT, UPDATE, DELETE ON user_gene_set TO dcc;

This file has been truncated. show original

felix 2016-11-14 14:03:51 UTC #9

Hi andricDu,

Thanks for you reply.

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).

btiernay 2017-01-11 13:00:51 UTC #10

Still looks like a permissions issue. Did you apply the same grants to all tables?

felix 2017-01-16 08:10:41 UTC #11

Yes, it is permission issue.

I rebuilt postgresql database, and got no such errors

Thanks