Refactor startup scripts, envvars for all omero parameter by manics · Pull Request #1 · ome/omero-server-docker

manics · 2017-06-05T14:56:06Z

Refactor the startup-scripts for OMERO.server:

All omero config properties can be set with environment variables
Database setup is separate from starting OMERO.server
Removed OMERO.grid support- this will be added back in a separate dependent repo
Use dumb-init
- @dpwrussell In theory this means you could start a backgrounded script which polls localhost to check whether the server is ready before creating a public user, before the final 99-run.sh script is run, avoiding the requirement to restart the server.

This is based on ome/omero-server-docker#1

dpwrussell

What's the rationale for not just calling the run-exec.sh file run.sh? That seems to be the norm.

dpwrussell · 2017-06-06T10:03:58Z

50-config.py

+
+
+for (k, v) in os.environ.iteritems():
+    omero = '/opt/omero/server/OMERO.server/bin/omero'


Need not be in loop

and probably should be caps

manics · 2017-06-06T13:55:06Z

I've renamed run-exec.sh to entrypoint.sh

dpwrussell · 2017-06-06T16:38:07Z

Works as expected.

joshmoore · 2017-06-07T14:15:54Z

README.md

+        -e CONFIG_omero_db_name=postgres \
+        -e ROOTPASS=omero-root-password \
+        -p 4063:4063 -p 4064:4064 \
+        -e ROOTPASS=omero openmicroscopy/omero-server


ROOTPASS twice?

joshmoore · 2017-06-07T14:21:32Z

Dockerfile

@@ -12,13 +12,15 @@ RUN yum -y install epel-release \
 ARG OMERO_VERSION=latest


If we're using the main release version (i.e. 5.3.2) for tags of this repo, then I'm assuming:

latest images are considered worst-practice

on each OMERO release, we'll branch from master and bump this string to include the version (5.3.3)

for bug fixes before an OMERO release, we'll suffix 5.3.3-1

Note: this doesn't yet give us a strategy for breaking changes in the image itself

I'm assuming this has everyone's implicit 👍 but now with 5.4 replacing 5.3

joshmoore · 2017-06-07T14:22:35Z

60-database.sh

+    DBHOST="$CONFIG_omero_db_host"
+else
+    DBHOST=db
+    $omero config set omero.db.host "$DBHOST"


Does this need to be outside the if block?

No, CONFIG_omero_db_host will already be converted into omero.db.host by 50-config.py- I'll update the comment at the top of the file. The only reason for special handling here is that the default of omero.db.host=localhost will never work, instead it defaults to db which should be set by docker run --link ....

joshmoore · 2017-06-07T14:23:06Z

50-config.py

@@ -0,0 +1,20 @@
+#!/usr/bin/env python
+# Set omero config properties from CONFIG_ envvars
+# Variable names should replace "." with "_" and "_" with "__"


Not particularly worried but there's obviously some danger of a __ conflict here.

I know. Do you have another suggestion?

Not sure how evil this is but:

$ env "a.b=1" python -c "import os; print os.environ['a.b']" 1 $ docker run -ti --rm -e a.b=1 centos python -c "import os; print os.environ['a.b']" 1

Unfortuntately it's also used in the bash script60-database.sh

Continuing discussion under #3

joshmoore · 2017-06-07T14:50:48Z

README.md

+    docker run -d --name postgres -e POSTGRES_PASSWORD=postgres \
+        -v omero-db:/var/lib/postgresql/data postgres
+    docker run -d --name omero-server --link postgres:db
+        -e CONFIG_omero_db_pass=dbpassword  -v omero-data:/OMERO \


This example isn't working for me:

FATAL: password authentication failed for user "omero" DETAIL: Connection matched pg_hba.conf line 95: "host all all 0.0.0.0/0 md5"

I didn't want to repeat all the -e CONFIG_omero_db_* params from the previous example, I'll try and make that clearer

manics · 2017-06-07T15:48:42Z

BTW, I've just realised https://github.com/openmicroscopy/omero-server-docker/blob/master/requirements.yml#L21 means this can't be tagged as production until ome/ansible-role-omero-server#12 is tagged

manics · 2017-06-08T10:31:49Z

oops...not sure what happened...

manics · 2017-06-08T10:36:10Z

I had a typo, accidently did git push ... -d.

joshmoore · 2017-06-08T10:37:27Z

I had a typo, accidently did git push ... -d.

That's kinda scary. Good to know.

manics · 2017-06-08T10:41:40Z

Updated in response to @joshmoore's comments.

In addition I've switched from loading .omero files from /config/ to /opt/omero/server/config/ as used in https://github.com/openmicroscopy/ansible-role-omero-server/tree/2.0.0-m1

One issue you may want to consider before ansible-role-omero-server is officially tagged 2.0.0: the configuration script /opt/omero/server/config/omero-server-config-update.sh is in the same directory that's used for .omero files /opt/omero/server/config so you can mount .omero files but not the entire directory.

joshmoore · 2017-06-13T09:05:33Z

Discussion now points to:

merging in order:
and then considering omero-server the current candidate production image.

manics · 2017-07-03T13:50:37Z

--depends on ome/omego#108

This needed to allow installations without a DB to proceed
You can temporarily test this using manics@34b1b07

dpwrussell

If there could potentially be mounted filesystems that might want to be mounted as the same UID as the omero server, should this be made configurable? The host os is likely to have more restrictions on what uids they can use than the container one.

joshmoore · 2017-07-06T20:40:24Z

No objections from my side to having uid and gid be ARGs, but in general, then, you could also subclass the image and usermod. More critical from my POV is: what's the expectation when pulling the image from hub?

To your question in particular: I haven't run into a situation where I can't chown the directory with a particular UID before mounting but I could imagine not wanting to if that were to put something in particular at risk. (i.e. I don't trust the 1000 user on the host system in question)

manics · 2017-07-07T08:23:32Z

@dpwrussell I agree with you. The correct way to solve this is to treat the omero-server Docker filesystem as readonly with the exception of defined directories for logs and temp-files (which is our long-term goal) which will need to be mounted as volumes. Then you can simply use docker run --user UID ... to set the user OMERO runs as.

The purpose of the last commit is to make the default omero-server UID well-known as opposed to using whatever useradd picks as the UID.

manics · 2017-07-07T08:25:33Z

Though what would be even better is if all OMERO logs went to stdout/stderr, so just /tmp would need to be writeable (which it generally is by any user).

joshmoore · 2017-07-07T13:38:33Z

latest is now 5.4. Shall we go with the flow and this repo matches the milestones of the 5.4 series with the intent of releasing this as production with 5.4.0?

cc: @dpwrussell @manics @sbesson @jburel

mtbc · 2017-07-13T08:10:12Z

README.md

+        /config/extra.omero:/opt/omero/server/config/extra.omero:ro
+        openmicroscopy/omero-server
+
+Parameters required for initialising the server such as database configuration *must* be set using environment variables.


initializing

joshmoore · 2017-07-13T10:51:44Z

Re-ran travis to get this green. Merging, untagged. I'd suggest when 5.4.0-m1 is tagged, that someone create a commit changing latest to v5.4.0-m1 and tag that commit which should then be built on hub.

cc: @mtbc

manics added 8 commits May 30, 2017 12:16

Add /startup/ folder for executable startup scripts

e9bbbcc

Use dump-init

cd6d1c4

Add 50-config.py, ensure 99-run.sh runs last

f05009c

Remove support for grid. Separate out db config script.

dfb8eb2

Remove slave/grid from tests

0e9d08b

Set db params from CONFIG_omero_db_

d7bbf5a

Use db config from omero when runnign omego

cc58d70

Add README back again

1cf0093

manics added a commit to manics-archive/omero-grid-docker that referenced this pull request Jun 5, 2017

omero-grid now builds separate master and slave images only

e5ab8cc

This is based on ome/omero-server-docker#1

manics mentioned this pull request Jun 5, 2017

Remove web. Rewrite to use openmicroscopy/omero-server ome/docker-example-omero-grid#9

Closed

Fix errors in README

307ace2

dpwrussell reviewed Jun 6, 2017

View reviewed changes

manics added 2 commits June 6, 2017 14:50

Rename run-exec.sh entrypoint.sh

4c59444

Move constant out of loop in 50-config.py

a0a0edd

joshmoore requested changes Jun 7, 2017

View reviewed changes

manics added 2 commits June 8, 2017 11:10

Improve comments

6f3b08e

Use standard /opt/omero/server/config instead of /config

d7c74ef

manics closed this Jun 8, 2017

manics deleted the devel branch June 8, 2017 10:31

Remove processing of /config/*.omero

24a577e

manics reopened this Jun 8, 2017

manics mentioned this pull request Jun 13, 2017

Bump to 0.4.0 (no-read-only) IDR/omero-grid-docker#1

Closed

dpwrussell mentioned this pull request Jun 13, 2017

Enable public user #2

Open

manics mentioned this pull request Jun 16, 2017

Simplify install/upgrade commands and db flags ome/omego#107

Merged

Update requirements

7c3c12b

manics mentioned this pull request Jul 3, 2017

Don't check database if managedb not set ome/omego#108

Merged

Use a fixed UID (1000) for omero-server

15eb386

dpwrussell reviewed Jul 6, 2017

View reviewed changes

joshmoore approved these changes Jul 7, 2017

View reviewed changes

mtbc reviewed Jul 13, 2017

View reviewed changes

Use US spelling in README

73b3a9c

joshmoore merged commit 45635db into ome:master Jul 13, 2017

manics mentioned this pull request Jul 13, 2017

Issues to consider before releasing as production #3

Open

3 tasks

ghost mentioned this pull request Apr 8, 2019

... #23

Closed



		for (k, v) in os.environ.iteritems():
		omero = '/opt/omero/server/OMERO.server/bin/omero'

		@@ -12,13 +12,15 @@ RUN yum -y install epel-release \
		ARG OMERO_VERSION=latest

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