How to reproduce:

Check out this repository
Start molgenis using docker-compose up
The snapshot war will be downloaded from sonatype
Bring down molgenis using docker-compose down and remove the volumes using docker volume rm
Update the version mentioned in the Dockerfile to the latest snapshot version of molgenis
Bring molgenis back up

Expected behavior

A new version of the snapshot war will be downloaded from sonatype
If you surf to localhost:8081, you'll see the timestamp in the footer corresponds to the latest snapshot build

Actual

The old version is still cached somewhere and has started up.
Timestamp in the footer corresponds to the old build
There are no instructions explaining how to update to a newer version

Start a molgenis, visit http://localhost/molgenis.R
You get a wall of text.
Check the molgenis api url

Expected: http://localhost/api/

Actual: http://localhost:8080/api/

How to reproduce:

Check out this repository
Start molgenis using docker-compose up
access and login from an (external) address other than http:/llocalhost (can be easily mimicked by browsing to http://127.0.0.1)

Expected behaviour:

after login the user is redirected to the url used to access the instance.

Actual:

After a (succesful) login in the user is always redirected to http://localhost.
This breaks the user experience if the molgenis instance is used on any other ip/domain than localhost because the user ends up on http://localhost.

Additional info:

• The login is succesful and the incorrect redirect seems to be specific for the login, because the application can be accessed and navigated when visiting the instance again on the correct address after login.
• Probably related to issues #72 and #77
• Removing the "proxy_set_header X-Forwarded-Port $server_port; and proxy_set_header X-Forwarded-Host $server_name;" lines in backend.conf fixes the issue, but may have other consequences I cannot oversee.

How to reproduce

It is now not possible to import "medium" large datasets.

• Login as admin
• Goto the Advanced Importer
• Import the full BBMRI dataset (available on cluster)

Expected behavoir

Import is successfull

Observed behavior

Import fails on SQL errors

Steps to be taken to solve the issue

• Use MOLGENIS image in docker-compose from Dockerhub
• Use MOLGENIS opencpu image from Dockerhub in docker-compose
• Add MOLGENIS specific postgres configuration (check Ansible configuration)
  • Extend the default image and add your own configuration
  • Create docker build on Jenkins save the image on Dockerhub
  • Use image in docker-compose
• Add MOLGENIS specific elasticsearch configuration (check Ansible configuration)
  • Extend the default image and add your own configuration
  • Create docker build on Jenkins save the image on Dockerhub
  • Use image in docker-compose

Not sure which versions but at the very least booting 7.2 and 7.4 results in a molgenis that cannot access the postgres instance.

Booting latest works correctly.

app_1            | 2019-03-07_11:49:02.538 [C3P0PooledConnectionPoolManager[identityToken->1bqx2bpa1oeu9qirgxssq|623e0f55]-HelperThread-#1] WARN  c.m.v.resourcepool.BasicResourcePool - com.mchange.v2.resourcepool.BasicResourcePool$ScatteredAcquireTask@13bc66c0 -- Acquisition Attempt Failed!!! Clearing pending acquires. While trying to acquire a needed new resource, we failed to succeed more than the maximum number of allowed acquisition attempts (30). Last acquisition attempt exception:
app_1            | org.postgresql.util.PSQLException: Connection to 127.0.0.1:5432 refused. Check that the hostname and port are correct and that the postmaster is accepting TCP/IP connections.

When running Docker on Windows 7 it is executed in a MINGW64 environment. The following part of the manual cannot be executed because sysctl does not exist in MINGW64:

sysctl -w vm.max_map_count=262144
To set this value permanently, update the vm.max_map_count setting in /etc/sysctl.conf.

Without this setting Elasticsearch terminated on startup:

When enabling authentication settings and allowing users to signup (moderated by the admins), we get the following browser error:

GET http://localhost:8081/captcha?_=1518774171299 500 (Internal Server Error)

Same for 127.0.0.1. Is this a captcha issue specific to a local setup?

The config for dev and versions 8.7 and up uses profiles which are only supported in docker compose 1.28.0 (2021-01-20) and up.

when running docker compose up,
the version 8.1 does not start correctly :
molgenis_1 | Exception in thread "schedulerFactoryBean_Worker-1" java.lang.NoClassDefFoundError: ch/qos/logback/core/status/WarnStatus
molgenis_1 | at ch.qos.logback.classic.LoggerContext.noAppenderDefinedWarning(LoggerContext.java:186)

no problem with version 8

Version 8.4

in docker-compose.yml changed ports: - "81:80"
to map internal molgenis port 80 to 81 on my machine since 80 is taken by another process.
Docker comes up and allows login window. But as soon as given credentials it maps to localhost/login instead localhost:81/login. Deadend.

Is there a base_url configuration to provide in docker-compose-yml?

How to Reproduce

• Install Ubuntu 16.04 (LTS version)
• Install Docker community version according to the instruction from Docker https://docs.docker.com/engine/installation/linux/docker-ce/ubuntu/
• clone the MOLGENIS docker git repository
• follow the instruction in the readme to run MOLGENIS

Expected behavior

• The 4 containers for MOLGENIS are all running and MOLGENIS is accessible on http:/localhost:8081/

Observed behavior

• MOLGENIS is not accessible
• ElasticSearch container is not running, it aborts after approximately 50 seconds

Sytem details

Ubuntu 16.04: Docker version 17.06.0-ce, build 02c1d87
Ubuntu 17.04: Docker version 17.04.0-ce, build 4845c56

I'm trying to run the NGS_RNA pipeline.

I have installed and composed the molgenis docker, and access the localhost:8081 in Firefox via X11, CentOS 7.

The http://localhost:8081/menu/main/home page is empty aside from the Sign In button. What is the expected behaviour for this page?
dockerBuild.out.txt

We're trying to test the new Molgenis version from the provided docker-compose file in this repository but can't get it to work.

All containers seem to start up nominally, but then the molgenis container keeps throwing the following error:

molgenis_1          | 2023-02-08_10:48:54.686 [main] ERROR o.m.d.e.client.ClientFactory - Failed to connect to Elasticsearch cluster on http://host.docker.internal:9200. Retry count = 2
molgenis_1          | 2023-02-08_10:48:58.689 [main] ERROR o.m.d.e.client.ClientFactory - Failed to connect to Elasticsearch cluster on http://host.docker.internal:9200. Retry count = 3
molgenis_1          | 2023-02-08_10:49:06.695 [main] ERROR o.m.d.e.client.ClientFactory - Failed to connect to Elasticsearch cluster on http://host.docker.internal:9200. Retry count = 4
molgenis_1          | 2023-02-08_10:49:22.701 [main] ERROR o.m.d.e.client.ClientFactory - Failed to connect to Elasticsearch cluster on http://host.docker.internal:9200. Retry count = 5

At this point, further initialisation of molgenis stalls, and the frontend is not reachable in the browser.

We starting the containers with docker-compose up and tried this on different machines using the latest docker-compose version 2.15. We could not find any hints or documentation what configuration needs to be adjusted to let molgenis connect with elastic search. Do you have any advice?