Files upload impossible

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Maria Sorokina

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Dec 10, 2018, 9:42:51 AM12/10/18
to SEEK Developers
Dear all,

I have a local SEEK instance (upgraded to version 1.7). I am not the one who set it up a couple of years ago, but I now have to manage and administrate it totally.
I'm running it with docker-compose.
Almost everything works fine, except the file upload, when I try to create a new data file (of any format, any size) I just have this message: "We're sorry but something went wrong with your request"
And I don't find any additional information in the logs, apart from the docker-compose logs. The mysql container part is the following:

seek-mysql_cbs  | 2018-12-10T14:26:00.463611Z 0 [Note] Server hostname (bind-address): '*'; port: 3306

seek-mysql_cbs  | 2018-12-10T14:26:00.463647Z 0 [Note] IPv6 is available.

seek-mysql_cbs  | 2018-12-10T14:26:00.463656Z 0 [Note]   - '::' resolves to '::';

seek-mysql_cbs  | 2018-12-10T14:26:00.463671Z 0 [Note] Server socket created on IP: '::'.

seek-mysql_cbs  | 2018-12-10T14:26:00.464426Z 0 [Warning] Insecure configuration for --pid-file: Location '/var/run/mysqld' in the path is accessible to all OS users. Consider choosing a different directory.

seek-mysql_cbs  | 2018-12-10T14:26:00.465258Z 0 [Warning] 'user' entry 'root@localhost' ignored in --skip-name-resolve mode.

seek-mysql_cbs  | 2018-12-10T14:26:00.465286Z 0 [Warning] 'user' entry 'mysql.session@localhost' ignored in --skip-name-resolve mode.

seek-mysql_cbs  | 2018-12-10T14:26:00.465294Z 0 [Warning] 'user' entry 'mysql.sys@localhost' ignored in --skip-name-resolve mode.

seek-mysql_cbs  | 2018-12-10T14:26:00.465311Z 0 [Warning] 'user' entry '@localhost' ignored in --skip-name-resolve mode.

seek-mysql_cbs  | 2018-12-10T14:26:00.465322Z 0 [Warning] 'user' entry 'www-dat@localhost' ignored in --skip-name-resolve mode.

seek-mysql_cbs  | 2018-12-10T14:26:00.465351Z 0 [Warning] 'db' entry 'performance_schema mysql.session@localhost' ignored in --skip-name-resolve mode.

seek-mysql_cbs  | 2018-12-10T14:26:00.465362Z 0 [Warning] 'db' entry 'sys mysql.sys@localhost' ignored in --skip-name-resolve mode.

seek-mysql_cbs  | 2018-12-10T14:26:00.465367Z 0 [Warning] 'db' entry 'my_database @localhost' ignored in --skip-name-resolve mode.

seek-mysql_cbs  | 2018-12-10T14:26:00.465380Z 0 [Warning] 'proxies_priv' entry '@ root@localhost' ignored in --skip-name-resolve mode.

seek-mysql_cbs  | 2018-12-10T14:26:00.467414Z 0 [Warning] 'tables_priv' entry 'user mysql.session@localhost' ignored in --skip-name-resolve mode.

seek-mysql_cbs  | 2018-12-10T14:26:00.467429Z 0 [Warning] 'tables_priv' entry 'sys_config mysql.sys@localhost' ignored in --skip-name-resolve mode.

seek-mysql_cbs  | 2018-12-10T14:26:00.472474Z 0 [Note] Event Scheduler: Loaded 0 events

seek-mysql_cbs  | 2018-12-10T14:26:00.472744Z 0 [Note] mysqld: ready for connections.

seek-mysql_cbs  | Version: '5.7.23'  socket: '/var/run/mysqld/mysqld.sock'  port: 3306  MySQL Community Server (GPL)

seek-mysql_cbs  | 2018-12-10T14:26:02.534028Z 2 [Note] Access denied for user 'www-data'@'172.19.0.7' (using password: NO)

seek-mysql_cbs  | 2018-12-10T14:26:03.679494Z 4 [Note] Access denied for user 'www-data'@'172.19.0.8' (using password: NO)


I don't know where the 'www-data' user is coming from, but I present that the files uploading problem is coming from its access denied.
I can access the MySQL database in its container as a root and normal user without problems.

Can you help me to solve this problem, please,
Maria

Stuart Owen

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Dec 11, 2018, 6:14:21 AM12/11/18
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If most things work fine, then I doubt it would be a problem with the database connection. If this was the case, then nothing would work.

When you did the update, did you also run the upgrade script? Details of how to run this script can be found at the end of https://docs.seek4science.org/tech/docker/docker-compose.html

This script makes necessary database modifications, and various other updates. Also, did you upgrade from a 1.6 version? (it is necessary to upgrade between minor versions in steps, i.e 1.5.x -> 1.6.x -> 1.7.x   - x is the patch version and you don't need to upgrade individually between these).

regards,

Stuart.

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Maria Sorokina

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Dec 11, 2018, 6:44:29 AM12/11/18
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Thank you for your reply, it was a bug coming from Safari actually.
And re-upgrading from the version 1.7.0 to 1.7.1 solved the problem even in Safari!

Maria Sorokina, PhD
Steinbeck Research Group
Analytical Chemistry - Cheminformatics and Chemometrics
Friedrich-Schiller-University Jena, Germany
http://cheminf.uni-jena.de
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