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Auto import, figure, wheel, etc. #21

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joshmoore
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@joshmoore joshmoore commented Jan 30, 2019 •
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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 joshmoore changed the title Auto import, etc. Auto import, figure, wheel, etc. Jan 30, 2019
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joshmoore commented Jan 30, 2019 •
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Downloaded Figure PDF of auto-imported fake:

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

cc: @pwalczysko

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

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sbesson commented Mar 15, 2019

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.

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Conflicting PR. Removed from build DOCKER-merge#711. See the console output for more details.
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Conflicting PR. Removed from build DOCKER-merge#712. See the console output for more details.
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Conflicting PR. Removed from build DOCKER-merge#713. See the console output for more details.
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manics commented Mar 18, 2019

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

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Conflicting PR. Removed from build DOCKER-merge#714. See the console output for more details.
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Conflicting PR. Removed from build DOCKER-merge#773. See the console output for more details.
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@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?

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snoopycrimecop commented May 22, 2019 •
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Conflicting PR. Removed from build DOCKER-merge#777. See the console output for more details.
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--conflicts Conflict resolved in build DOCKER-merge#778. See the console output for more details.

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joshmoore commented May 22, 2019 •
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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

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minimal concept pushed

jburel
jburel reviewed May 23, 2019
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docker-compose.yml
#
services:
database:
image: "postgres:9.6"
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shouldn't it be moved to 10?

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

extended/95-background.sh
@@ -0,0 +1,10 @@
#!/bin/bash
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What does 95 mean in the name?

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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.

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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

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

  • Upstream changes
    • playbook.yml

--conflicts

manics added a commit to manics/omero-server-docker that referenced this pull request Dec 12, 2019
@manics
Add infrastructure for an server extras image
2d19154 
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)
@manics manics mentioned this pull request Dec 12, 2019
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manics added a commit to manics/omero-server-docker that referenced this pull request Jun 4, 2020
@manics
Add infrastructure for an server extras image
e0959e2 
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)
manics added a commit to manics/omero-server-docker that referenced this pull request Sep 17, 2020
@manics
Add infrastructure for an server extras image
3dc040e 
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)
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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

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

  • Upstream changes
    • playbook.yml

--conflicts

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@joshmoore @snoopycrimecop @sbesson @manics @imagesc-bot @jburel