Auto import, figure, wheel, etc. by joshmoore · Pull Request #21 · ome/omero-server-docker

joshmoore · 2019-01-30T14:39:17Z

This branch started as a way to have files imported automatically on start as a proof-of-concept, but along with the work on ome/omero-web-docker#26 has become something of a grab bag of omero-server updates. Opening for discussion of the method and then we can split out the separate functionality if preferred.

Features include:

Add an import-all script (might should be unified with dropbox) (intended to be used -v data:/import)
Migrate wait-on-login from omero-test-infra (might should be migrated to core)
Enable figure by default
Use ice_python_wheel
public user

--exclude

joshmoore · 2019-01-30T15:06:15Z

Downloaded Figure PDF of auto-imported fake:

Figure_2019-1-30_15-5-3.pdf

cc: @pwalczysko

snoopycrimecop · 2019-01-31T01:09:12Z

Conflicting PR. Removed from build DOCKER-merge#667. See the console output for more details.
Possible conflicts:

PR Enable public user #2 dpwrussell 'Enable public user'
- Dockerfile
PR SQL backup/restore (WIP) #19 joshmoore 'SQL backup/restore (WIP)'
- Dockerfile

--conflicts

sbesson · 2019-03-15T15:08:10Z

Indirectly tested some of these changes via https://doi.org/10.5281/zenodo.2593260. From my side, the auto-import feature was extremely useful and should be included in the Docker image. Given the deployment architecture, my only local addition was to use --transfer=ln_s to prevent data copy as the files are imported from the server directly.

Happy to see this functionality extracted to a dedicated PR and sign off on it.

snoopycrimecop · 2019-03-16T01:09:14Z

Conflicting PR. Removed from build DOCKER-merge#711. See the console output for more details.
Possible conflicts:

PR Enable public user #2 dpwrussell 'Enable public user'
- Dockerfile
PR SQL backup/restore (WIP) #19 joshmoore 'SQL backup/restore (WIP)'
- Dockerfile

--conflicts

snoopycrimecop · 2019-03-17T01:09:11Z

Conflicting PR. Removed from build DOCKER-merge#712. See the console output for more details.
Possible conflicts:

PR Enable public user #2 dpwrussell 'Enable public user'
- Dockerfile
PR SQL backup/restore (WIP) #19 joshmoore 'SQL backup/restore (WIP)'
- Dockerfile

--conflicts

snoopycrimecop · 2019-03-18T01:09:12Z

Conflicting PR. Removed from build DOCKER-merge#713. See the console output for more details.
Possible conflicts:

PR Enable public user #2 dpwrussell 'Enable public user'
- Dockerfile
PR SQL backup/restore (WIP) #19 joshmoore 'SQL backup/restore (WIP)'
- Dockerfile

--conflicts

manics · 2019-03-18T10:47:04Z

We could follow the pattern of the omero-web-docker image where the base image is fairly empty and is designed to be extended, for instance as in the standalone image.

This would also be a chance to add either a default public user account, or more generic functionality for creating default users, as started in #2

snoopycrimecop · 2019-03-19T01:09:18Z

Conflicting PR. Removed from build DOCKER-merge#714. See the console output for more details.
Possible conflicts:

PR Enable public user #2 dpwrussell 'Enable public user'
- Dockerfile
PR SQL backup/restore (WIP) #19 joshmoore 'SQL backup/restore (WIP)'
- Dockerfile

--conflicts

see: ome/omero-web-docker#29

snoopycrimecop · 2019-05-18T00:09:18Z

Conflicting PR. Removed from build DOCKER-merge#773. See the console output for more details.
Possible conflicts:

PR Enable public user #2 dpwrussell 'Enable public user'
- Dockerfile
PR SQL backup/restore (WIP) #19 joshmoore 'SQL backup/restore (WIP)'
- Dockerfile
Upstream changes
- Dockerfile

--conflicts

joshmoore · 2019-05-21T10:13:13Z

@sbesson : thoughts on the kitchensink approach, and if so, any suggestions for a name? (since "standalone" doesn't quite work)

server-advanced
server-extended
server-public + server-import (but what if you want both??)

or have server-base and server?

snoopycrimecop · 2019-05-22T00:09:22Z

Conflicting PR. Removed from build DOCKER-merge#777. See the console output for more details.
Possible conflicts:

PR Enable public user #2 dpwrussell 'Enable public user'
- Dockerfile
PR SQL backup/restore (WIP) #19 joshmoore 'SQL backup/restore (WIP)'
- Dockerfile
Upstream changes
- Dockerfile

~~--conflicts~~ Conflict resolved in build DOCKER-merge#778. See the console output for more details.

joshmoore · 2019-05-22T21:15:22Z

Discussed with @sbesson:

server-minimal & server suggested as the first step
Makefile could move to build-infra (eventually to scc)
add public user in extended verison

joshmoore · 2019-05-22T21:54:42Z

minimal concept pushed

jburel · 2019-05-23T07:51:21Z

docker-compose.yml

+#
+services:
+  database:
+    image: "postgres:9.6"


shouldn't it be moved to 10?

Eventually, definitely. I'd suggest handling that across all repositories once the upgrade docs are in place.

jburel · 2019-05-23T07:52:24Z

extended/95-background.sh

@@ -0,0 +1,10 @@
+#!/bin/bash


What does 95 mean in the name?

All the startup scripts are numbered to be run in order. "95" means "pretty close to the end but give the user a few slots (96-98) before the final script (99) runs.

Thanks
since I noticed the pg version, for a minute I thought it was a pg matching version but the file was nothing to do with pg

snoopycrimecop · 2019-10-29T01:09:44Z

Conflicting PR. Removed from build DOCKER-merge#941. See the console output for more details.
Possible conflicts:

Upstream changes
- playbook.yml

--conflicts

This is based on the standalone image from https://github.com/ome/omero-web-docker/tree/5.6.0-m4 This just provides the infrastructure for building the extras image, it doesn't install or change anything (see ome#21 instead)

imagesc-bot · 2021-01-12T11:15:28Z

This pull request has been mentioned on Image.sc Forum. There might be relevant details there:

https://forum.image.sc/t/how-to-install-omero-web-add-on-apps-with-docker/47434/3

snoopycrimecop · 2021-01-25T09:13:21Z

Conflicting PR. Removed from build DOCKER-merge#1354. See the console output for more details.
Possible conflicts:

Upstream changes
- playbook.yml

--conflicts

joshmoore added 4 commits January 29, 2019 17:04

Add wait-on-login from omero-test-infra

c5767b5

Use ice_python_wheel for faster builds

c6ad6bc

Activate figure script

2267456

Import on startup all files in /import

e061111

joshmoore changed the title ~~Auto import, etc.~~ Auto import, figure, wheel, etc. Jan 30, 2019

Use merge build in docker-compose

b0274b6

see: ome/omero-web-docker#29

joshmoore force-pushed the auto-import branch from a5f36d0 to b0274b6 Compare May 17, 2019 10:21

Split server image into minimal & extended

eb93998

Merge branch 'master' into auto-import

2846ca9

jburel reviewed May 23, 2019

View reviewed changes

manics mentioned this pull request Dec 12, 2019

Add infrastructure for a server extras image #39

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