The data definitely looks gone:
sql>select s.name, t.name from tables t, schemas s where t.schema_id = s.id and s.name='fullgenomestable';
+------+------+
| name | name |
+======+======+
+------+------+
0 tuples
sql>select s.name, t.name from tables t, schemas s where t.schema_id = s.id and s.name='ranges_from_gff';
+------+------+
| name | name |
+======+======+
+------+------+
0 tuples
sql>
I think the monetdb upgrade had issues. Our previous monetdb version was 2 updates behind (so not that old). There were no errors in the log file after the update, but since 1 database always crashed when trying to access it, and the second one seems to be missing tables, something is obviously wrong.
I “destroyed” then recreated the db that was crashing after the upgrade. It is now working fine. I will do the same to the large db.
Would be interesting to hear is anyone else has problems upgrading to the June2020 release.
Thanks for your time, Jennie.
From: users-list on behalf of Ying Zhang
Reply-To: Communication channel for MonetDB users
Date: Monday, June 29, 2020 at 11:46 AM
To: Communication channel for MonetDB users
Subject: Re: inadvertantly last schema
On 29 Jun 2020, at 16:49, Lynn Carol Johnson mailto:lcj34@cornell.edu> wrote:
Jennie - What command can I run in monetdb to verify the tables are there? It does look like nothing have been removed from the bat folders.
See the query below I used.
Also, for some very basic verification, you can just do
SELECT COUNT(*) FROM <myschema>.<mytable>;
From: users-list mailto:users-list-bounces+lcj34=cornell.edu@monetdb.org> on behalf of Ying Zhang mailto:Y.Zhang@cwi.nl>
Reply-To: Communication channel for MonetDB users mailto:users-list@monetdb.org>
Date: Monday, June 29, 2020 at 10:47 AM
To: Communication channel for MonetDB users mailto:users-list@monetdb.org>
Subject: Re: inadvertantly last schema
Hai Lynn,
This is very strange. Which MonetDB version are you using (i.e. mserver5 --version)?
I quickly tried your scenario in the Jun2020 version, but I don’t have this problem:
sql>schema test ;
syntax error, unexpected SCHEMA in: "schema"
sql>select s.name, t.name from tables t, schemas s where t.schema_id = s.idhttp://s.id/ and s.name = 'test';
+------+------+
| name | name |
+======+======+
| test | t |
+------+------+
1 tuple
sql>set schema test ;
operation successful
sql>\d
TABLE test.t
Are you sure you’ve lost all data? Because such error should never have affected your data. Can you check if your data tables are still there, even if the “\d” command doesn’t return anything?
- Jennie
On 28 Jun 2020, at 18:07, Lynn Carol Johnson mailto:lcj34@cornell.edu> wrote:
Hi all –
I have a monetdb instance with a lot of tables and a lot of data. This data is organized into schemas. While logging on today as the admistrator, I inadvertently typed:
sql>schema maizeFullGenome;
syntax error, unexpected SCHEMA in: "schema"
sql>
Instead of “set schema maizeFullGenome;”
This has apparently overwritten the data I had in my maizeFullGenome Schema. Is there anyway to get this back besides finding an old copy of the db? The following shows the schema as now gone:
sql>set schema maizeFullGenome;
operation successful
sql>\d
sql>
Yes, a very stupid mistake.
Lynn
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