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hadim / docker-omero

Set of Dockerfile to build a ready-to-use OMERO server
MIT License
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Login failed #8

Open maxgittelman opened 6 years ago

maxgittelman commented 6 years ago

I'm having trouble ensuring docker is the correct version. Is Docker-CE v17.09 (Community Edition) considered greater than v1.13 by your standards?

Perhaps it would be helpful to include docker installation instructions because the version that apt-get installs is v1.12 which unfortunately makes it unsure whether the rest of the README instructions will be valid.

Currently this is what I have taken directly from Docker's website:

maxgitt@mgpc:~/devspace$ docker version
Client:
 Version:      17.09.0-ce
 API version:  1.32
 Go version:   go1.8.3
 Git commit:   afdb6d4
 Built:        Tue Sep 26 22:42:18 2017
 OS/Arch:      linux/amd64

Server:
 Version:      17.09.0-ce
 API version:  1.32 (minimum version 1.12)
 Go version:   go1.8.3
 Git commit:   afdb6d4
 Built:        Tue Sep 26 22:40:56 2017
 OS/Arch:      linux/amd64
 Experimental: false
maxgittelman commented 6 years ago

This newest version is valid. Simply follow the instructions for docker and docker-compose

bjuergens commented 6 years ago

can you tell me what exactly you did differently?

I followed the regular instructions and ended up with docker 17.09.0-ce, too. And I'm not sure if this is the reason why omero fails for me

maxgittelman commented 6 years ago

Are you also having trouble signing in?

bjuergens commented 6 years ago

yes

maxgittelman commented 6 years ago

any luck, @wotanii , @hadim I've been working on getting OMERO set up for 3 weeks. Your solution seems the most promising, any guidance as to why root and password would fail at sign in would be greatly appreciated

maxgittelman commented 6 years ago

I tried logging into omero via the Docker container

mgitt@mgpc:~$ docker exec -it omero-server bash

omero@0a17cb6afb20:/omero$ cd OMERO.server
omero@0a17cb6afb20:/omero/OMERO.server$ bin/omero login
Server: [localhost:4064]
Username: [omero]
Password:
internal server error

Even now, using password password isn't valid, I must be doing something trivially wrong.

hadim commented 6 years ago

Sorry but I am not using this project for months now and I don't have time to test it at the moment.

In the meantime maybe you could have a look at this https://hub.docker.com/u/openmicroscopy/ ?

bjuergens commented 6 years ago

thanks for this. At least now I know there is nothing wrong with my setup.

fyi: I managed to login once via the web-interface. But I wasn't able to reproduce this success. So the error is probably not trivial, but maybe timing related.

hadim commented 6 years ago

Are the log showing something special during setup or logging?

maxgittelman commented 6 years ago

@wotanii What username and password did you use?

bjuergens commented 6 years ago 
bjoern@b8book ~> bash
bjoern@b8book:~$ cd dev/project/
bjoern@b8book:~/dev/project$ mkdir omero/ && cd omero/
bjoern@b8book:~/dev/project/omero$ mkdir omero-data/
bjoern@b8book:~/dev/project/omero$ mkdir docker-omero/ && cd docker-omero/
bjoern@b8book:~/dev/project/omero/docker-omero$ wget https://raw.githubusercontent.com/hadim/docker-omero/master/docker-compose.yml
--2017-10-15 17:54:13--  https://raw.githubusercontent.com/hadim/docker-omero/master/docker-compose.yml
Auflösen des Hostnamens »raw.githubusercontent.com (raw.githubusercontent.com)« … 151.101.112.133
Verbindungsaufbau zu raw.githubusercontent.com (raw.githubusercontent.com)|151.101.112.133|:443 … verbunden.
HTTP-Anforderung gesendet, auf Antwort wird gewartet … 200 OK
Länge: 997 [text/plain]
Wird in »»docker-compose.yml«« gespeichert.

docker-compose.yml  100%[===================>]     997  --.-KB/s    in 0s      

2017-10-15 17:54:13 (55,4 MB/s) - »docker-compose.yml« gespeichert [997/997]

bjoern@b8book:~/dev/project/omero/docker-omero$ docker-compose up  # You can use the -d option to run in the background.
Pulling omero-data (hadim/omero-data:1.0.4)...
1.0.4: Pulling from hadim/omero-data
4b0bc1c4050b: Pull complete
fdeda2f48bcf: Pull complete
4c9e4da48fe1: Pull complete
24db4f3aad04: Pull complete
60cee1420c06: Pull complete
bc876761a375: Pull complete
d349107d940d: Pull complete
Digest: sha256:9aac7a3bc84708c3d7e1b167332411a2d69131c5abf1e7211682e6e5cba0a268
Status: Downloaded newer image for hadim/omero-data:1.0.4
Pulling omero-db (hadim/omero-db:1.0.4)...
1.0.4: Pulling from hadim/omero-db
5040bd298390: Pull complete
f08454c3c700: Pull complete
4db038cdfe03: Pull complete
e1d9ba315f03: Pull complete
25e0ee93170e: Pull complete
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62f1da30a989: Pull complete
Digest: sha256:04455a888d18d7e2d6c13387be48afb71329291a60ace431528d4c7d252f2531
Status: Downloaded newer image for hadim/omero-db:1.0.4
Pulling omero-server (hadim/omero-server:1.0.4)...
1.0.4: Pulling from hadim/omero-server
8aec416115fd: Pull complete
695f074e24e3: Pull complete
946d6c48c2a7: Pull complete
bc7277e579f0: Pull complete
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0f59dfe8d2f5: Pull complete
Digest: sha256:39be70a94b155f6799e037b8a1818d5e36dca22aa2257c5a751e8537a016b782
Status: Downloaded newer image for hadim/omero-server:1.0.4
Pulling omero-web (hadim/omero-web:1.0.4)...
1.0.4: Pulling from hadim/omero-web
8aec416115fd: Already exists
695f074e24e3: Already exists
946d6c48c2a7: Already exists
bc7277e579f0: Already exists
2508cbcde94b: Already exists
c9eb9065e9f8: Already exists
ccaa2d24a59d: Already exists
b44b3cc94149: Already exists
f30347ab14dd: Already exists
61ee8864aee8: Already exists
4bc4be568ed4: Already exists
8f73a218d733: Already exists
cd8017a242b6: Already exists
904655119942: Already exists
48421d52c9b9: Already exists
310265976823: Pull complete
17073060e367: Pull complete
68f895e7d580: Pull complete
9477821049c1: Pull complete
ee5fdbf6a7d9: Pull complete
269f381a076e: Pull complete
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25a32f474e3f: Pull complete
88ac556c7e73: Pull complete
0471f6880516: Pull complete
d1894e8ab4eb: Pull complete
Digest: sha256:4933d276371788f059dc46383395eb27fb9fb741c0cc33f8b11aa438d2f10657
Status: Downloaded newer image for hadim/omero-web:1.0.4
Creating omero-data ... 
Creating omero-data ... done
Creating omero-db ... 
Creating omero-db ... done
Creating omero-server ... 
Creating omero-server ... done
Creating omero-web ... 
Creating omero-web ... done
Attaching to omero-data, omero-db, omero-server, omero-web
omero-db        | The files belonging to this database system will be owned by user "postgres".
omero-db        | This user must also own the server process.
omero-db        | 
omero-db        | The database cluster will be initialized with locale "en_US.utf8".
omero-db        | The default database encoding has accordingly been set to "UTF8".
omero-db        | The default text search configuration will be set to "english".
omero-db        | 
omero-db        | Data page checksums are disabled.
omero-db        | 
omero-server    | Waiting for database server to be up.
omero-db        | fixing permissions on existing directory /data/postgres ... ok
omero-db        | creating subdirectories ... ok
omero-db        | selecting default max_connections ... 100
omero-db        | selecting default shared_buffers ... 128MB
omero-db        | selecting dynamic shared memory implementation ... posix
omero-db        | creating configuration files ... ok
omero-db        | creating template1 database in /data/postgres/base/1 ... ok
omero-data exited with code 0
omero-db        | initializing pg_authid ... ok
omero-db        | initializing dependencies ... ok
omero-db        | creating system views ... ok
omero-web       | 2017-10-15 15:55:47,666 CRIT Supervisor running as root (no user in config file)
omero-web       | 2017-10-15 15:55:47,669 INFO supervisord started with pid 1
omero-db        | loading system objects' descriptions ... ok
omero-db        | creating collations ... ok
omero-db        | creating conversions ... ok
omero-db        | creating dictionaries ... ok
omero-db        | setting privileges on built-in objects ... ok
omero-db        | creating information schema ... ok
omero-db        | loading PL/pgSQL server-side language ... ok
omero-db        | vacuuming database template1 ... ok
omero-db        | copying template1 to template0 ... ok
omero-db        | copying template1 to postgres ... ok
omero-db        | syncing data to disk ... ok
omero-db        | 
omero-db        | Success. You can now start the database server using:
omero-db        | 
omero-db        |     /usr/lib/postgresql/9.4/bin/postgres -D /data/postgres
omero-db        | or
omero-db        |     /usr/lib/postgresql/9.4/bin/pg_ctl -D /data/postgres -l logfile start
omero-db        | 
omero-db        | 
omero-db        | WARNING: enabling "trust" authentication for local connections
omero-db        | You can change this by editing pg_hba.conf or using the option -A, or
omero-db        | --auth-local and --auth-host, the next time you run initdb.
omero-db        | LOG:  database system was shut down at 2017-10-15 15:55:48 UTC
omero-db        | LOG:  MultiXact member wraparound protections are now enabled
omero-db        | LOG:  database system is ready to accept connections
omero-db        | LOG:  autovacuum launcher started
omero-web       | 2017-10-15 15:55:48,674 INFO spawned: 'nginx' with pid 10
omero-web       | 2017-10-15 15:55:48,679 INFO spawned: 'omero_web' with pid 11
omero-web       | 2017-10-15 15:55:48,721 INFO exited: nginx (exit status 1; not expected)
omero-web       | 2017-10-15 15:55:48,792 INFO exited: omero_web (exit status 127; not expected)
omero-web       | 2017-10-15 15:55:49,796 INFO spawned: 'nginx' with pid 19
omero-web       | 2017-10-15 15:55:49,800 INFO spawned: 'omero_web' with pid 20
omero-web       | 2017-10-15 15:55:50,806 INFO success: nginx entered RUNNING state, process has stayed up for > than 1 seconds (startsecs)
omero-web       | 2017-10-15 15:55:50,806 INFO success: omero_web entered RUNNING state, process has stayed up for > than 1 seconds (startsecs)
omero-db        | FATAL:  role "omero" does not exist
omero-server    | WARNING: Positional arguments are deprecated
omero-server    | Using OMERO5.2 for version
omero-server    | Using 0 for patch
omero-server    | Using password from commandline
omero-web       | 2017-10-15 15:55:54,051 INFO exited: omero_web (exit status 0; expected)
omero-web       | 2017-10-15 15:55:54,116 INFO reaped unknown pid 48
omero-web       | 2017-10-15 15:55:54,117 INFO reaped unknown pid 49
omero-server    | BEGIN
omero-server    | CREATE FUNCTION

### ... lots of sql

omero-server    | ALTER TABLE
omero-server    | ALTER TABLE
omero-server    | UPDATE 1
omero-server    | COMMIT
omero-server    | No descriptor given. Using etc/grid/default.xml
omero-db        | LOG:  unexpected EOF on client connection with an open transaction

the list line appeared with a little delay again

trying to login at https://localhost/ results in Error: Server is not responding, please contact administrator

after restarting the container the log looks like: 

omero-db        | LOG:  unexpected EOF on client connection with an open transaction
^CGracefully stopping... (press Ctrl+C again to force)
Stopping omero-web ... done
Stopping omero-server ... done
Stopping omero-db ... done
bjoern@b8book:~/dev/project/omero/docker-omero$ docker-compose up  # You can use the -d option to run in the background.
Starting omero-data ... 
Starting omero-data ... done
Starting omero-db ... 
Starting omero-db ... done
Starting omero-server ... 
Starting omero-server ... done
Starting omero-web ... 
Starting omero-web ... done
Attaching to omero-data, omero-db, omero-server, omero-web
omero-db        | LOG:  database system was interrupted; last known up at 2017-10-15 16:03:02 UTC
omero-db        | LOG:  database system was not properly shut down; automatic recovery in progress
omero-db        | LOG:  record with zero length at 0/2068A00
omero-db        | LOG:  redo is not required
omero-db        | LOG:  MultiXact member wraparound protections are now enabled
omero-db        | LOG:  autovacuum launcher started
omero-db        | LOG:  database system is ready to accept connections
omero-data exited with code 0
omero-web       | 2017-10-15 16:03:17,863 CRIT Supervisor running as root (no user in config file)
omero-web       | 2017-10-15 16:03:17,865 INFO supervisord started with pid 1
omero-web       | 2017-10-15 16:03:18,867 INFO spawned: 'nginx' with pid 9
omero-web       | 2017-10-15 16:03:18,868 INFO spawned: 'omero_web' with pid 10
omero-web       | 2017-10-15 16:03:19,921 INFO success: nginx entered RUNNING state, process has stayed up for > than 1 seconds (startsecs)
omero-web       | 2017-10-15 16:03:19,921 INFO success: omero_web entered RUNNING state, process has stayed up for > than 1 seconds (startsecs)
omero-web       | 2017-10-15 16:03:22,619 INFO exited: omero_web (exit status 96; not expected)
omero-server    | No descriptor given. Using etc/grid/default.xml
omero-web       | 2017-10-15 16:03:23,625 INFO spawned: 'omero_web' with pid 38
omero-web       | 2017-10-15 16:03:25,147 INFO success: omero_web entered RUNNING state, process has stayed up for > than 1 seconds (startsecs)
omero-web       | 2017-10-15 16:03:28,704 INFO exited: omero_web (exit status 0; expected)
omero-web       | 2017-10-15 16:03:28,802 INFO reaped unknown pid 60
omero-web       | 2017-10-15 16:03:28,803 INFO reaped unknown pid 61
omero-db        | LOG:  unexpected EOF on client connection with an open transaction

the list line appeared with a little delay again

trying to login at https://localhost/ results in the same as before

bjuergens commented 6 years ago

pass word always: root/password

I suspect the last line: omero-db | LOG: unexpected EOF on client connection with an open transaction is the reason for the failure

maxgittelman commented 6 years ago

@wotanii I have the exact same output, not entirely in the same order, but all of the same exit statuses, and LOGs, and INFO messages. Whatever is missing, is missing for both of us

bjuergens commented 6 years ago

@maxgittelman some more observations with the official images: 

docker run --name postgres -e POSTGRES_PASSWORD=postgres -d postgres

docker run --name omero-server -d --link postgres:db \
    -e CONFIG_omero_db_user=postgres \
    -e CONFIG_omero_db_pass=postgres \
    -e CONFIG_omero_db_name=postgres \
    -e ROOTPASS=pass \
    -p 4063:4063 -p 4064:4064 \
    openmicroscopy/omero-server

docker exec -it omero-server bash
cd /opt/omero/server/OMERO.server
bin/omero login
Server: [localhost:4064]
Username: [omero-server]root
Password:
Password check failed for 'root': [id=0]
Password:
Password check failed for 'root': [id=0]
Password:
Created session 9d352180-1158-42d6-a539-cddac4dc9af1 (root@localhost:4064). Idle timeout: 10 min. Current group: system

so this is probably what a successful login looks like. (after entering a wrong password twice).

but login in via OMERO.insight-5.4.0 still doesn't- work (at least on ubuntu). So then I entered bin/omero version and found out it was 5.3.3 and not 5.4, as I assumed. Then I tried OMERO.insight-5.3.3 and it works with the setup above.

manics commented 6 years ago

@wotanii Looks like we missed a step in our deployment process so our official Docker images didn't get updated to 5.4. In future if you have problems with running or using OMERO feel free to ask on our forums or mailing lists: http://www.openmicroscopy.org/support/

manics commented 6 years ago

Actually it looks like it's just the latest tag that wasn't updated, openmicroscopy/omero-server:5.4.0 exists

maxgittelman commented 6 years ago

@wotanii I actually tried to setup the Docker images for OMERO.server and OMERO.web but to with no luck I posted an issue in the repository. Were you able to get the official OMERO.server and OMERO.web up and running in conjunction?

@manics I tried posting my issue of not being able to get hadim's docker image up and running to the community, but was told to use the Ubuntu installation instead of Docker.

bjuergens commented 6 years ago

@maxgittelman yes. The above example uses the official 5.3 images

@manics thanks. I'm just getting started, so I didn't "dare" to contact the big guys :-)

joshmoore commented 6 years ago

@wotanii: that's what we're here for!

maxgittelman commented 6 years ago

@wotanii Thank you for the information. I see that I should use 5.3 instead of 5.4. The only question is I'm not sure what to do with that information. Should I be pulling openmicroscopy/omero-web:5.3.5 to fix my issue?

I'm quite novice at figuring out what all of these env variables mean. A quick couple of steps to run on the commandline would really help me get on my feet.

bjuergens commented 6 years ago

@maxgittelman What I wrote above was the commandline for creating a working server

maxgittelman commented 6 years ago

@wotanii I managed to get omero up and running through the official Omero-web and Omero-server repositories. See comments here.

Have you been able to launch the docker-compose in this repository?