New omero-scripts not automatically included

[JensWendt]

Hello,

I was setting up a new OMERO.server recently and to my surprise did not see Tom's new KV_from_csv.py scripts.
Upon reading this repos README.md, it says

All scripts (e.g. *.py) present in the directory will be automatically distributed with all binary builds.

I then tried for fun to install the omero-scripts package in the server and web venv and for both installations it did not automatically import/overwrite the older present scripts. I don't know if this is intended or not.

In the end, I just simply did upload the new scripts manually. But for new users this might be a bit of a hurdle already. An automatic distribution as indicated in the README.md is preferable.

[jburel]

Which version of OMERO did you install?

[sbesson]

I was setting up a new OMERO.server recently and to my surprise did not see Tom's new KV_from_csv.py scripts.

Echoing @jburel's answer:

• OMERO.server 5.6.14-ice36 and earlier include the KeyVal_from_csv.py
• OMERO.server 5.6.15-ice36 no longer includes KeyVal_from_csv.py which has been renamed in Key-value pair scripts enhancement #216 but includes its new incarnation Import_from_csv.py

I then tried for fun to install the omero-scripts package in the server and web venv and for both installations it did not automatically import/overwrite the older present scripts. I don't know if this is intended or not.

This is expected. Although omero-scripts is maintained as a Python package, the OMERO script service uses $OMERODIR/lib/scripts/ as its source of truth. Note this directory can contain symlinks from another location like a Python virtual environment.

In the end, I just simply did upload the new scripts manually. But for new users this might be a bit of a hurdle already. An automatic distribution as indicated in the README.md is preferable.

Absolutely, there should be no need for users to upload new scripts manually. New releases of omero-scripts should end up bundled in the following OMERO.server release.

Upon reading this repos README.md, it says

All scripts (e.g. *.py) present in the directory will be automatically distributed with all binary builds.

At least from my side, the usage of automatically is possibly misleading here. Distributing new scripts in the OMERO binary builds effectively means updating https://github.com/ome/openmicroscopy/blob/27b69ac69788e990c72b3ee0d5ff896a123abf84/etc/omero.properties#L253. Releasing omero-scripts to PyPI still requires a manual process (described in https://github.com/ome/omero-scripts?tab=readme-ov-file#release-process) but there is some automation to update etc/omero.properties following a PyPI release. I would say there is definitely a process for updating the OMERO.server scripts even if it's not fully automated.

[JensWendt]

ahhhh, I have v5.6.14, so right before the change.

But this seems a bit odd, as I was installing it on 22nd May with

$VENV_SERVER/bin/pip install omero-server
$SERVER=https://downloads.openmicroscopy.org/omero/5.6/server-ice36.zip
$wget $SERVER -O OMERO.server-ice36.zip

which I assumed would get me the latest version.
But Dominik Lindner announced 5.6.15 on image.sc on April 7th, so it was out for some time already.
Checking omero-server on pypi it's even only at 0.4.0 ?! The GitHub repo releases even jump from 5.6.12 directly to 5.7.0. I am a bit confused how would I know which is the most recent omero-server What determines the version, the python package or the artifact from the website?

@sbesson okay, I kind of expected omero-scripts to behave like that, I just wanted to try it out, as I was unsure if this was maybe something new that I missed.

I couldn't quite follow the automation processed you are describing. But assuming someone would update their omero-server would they "automatically" get the new KV-scripts and remove the old ones?

[sbesson]

You're correct, the redirect is still pointing to 5.6.14

% curl -IL https://downloads.openmicroscopy.org/omero/5.6
HTTP/1.1 302 Moved Temporarily
Server: nginx/1.28.0
Date: Thu, 05 Jun 2025 09:09:58 GMT
Content-Type: text/html
Content-Length: 145
Location: https://downloads.openmicroscopy.org/omero/5.6.14
Connection: keep-alive
Strict-Transport-Security: max-age=31536000; includeSubDomains
X-Frame-Options: SAMEORIGIN

HTTP/1.1 301 Moved Permanently
Server: nginx/1.28.0
Date: Thu, 05 Jun 2025 09:09:58 GMT
Content-Type: text/html
Content-Length: 169
Location: https://downloads.openmicroscopy.org/omero/5.6.14/
Connection: keep-alive
Strict-Transport-Security: max-age=31536000; includeSubDomains
X-Frame-Options: SAMEORIGIN

HTTP/1.1 200 OK
Server: nginx/1.28.0
Date: Thu, 05 Jun 2025 09:09:59 GMT
Content-Type: text/html
Connection: keep-alive
Strict-Transport-Security: max-age=31536000; includeSubDomains
X-Frame-Options: SAMEORIGIN

Checking omero-server on pypi it's even only at 0.4.0 ?! The GitHub repo releases even jump from 5.6.12 directly to 5.7.0. I am a bit confused how would I know which is the most recent omero-server What determines the version, the python package or the artifact from the website?

Your confusion is legitimate since "OMERO server" is unfortunately extremely overloaded and there are at least 3 related but different concepts:

• the Java library published as org.openmicroscopy:omero-server and which source code is available at https://github.com/ome/omero-server. This contains a lot of the logic used by the server for handling authentication, permissions...
• the Python library published as https://pypi.org/project/omero-server and which source code is at https://github.com/ome/omero-cli-server/. This is largely a meta-package aggregating all the Python libraries required to start and configure the server i.e. omero-py, tables, omero-certificates
• the OMERO.server binary available from https://github.com/ome/openmicroscopy/releases. This bundl includes all the Java libraries, including the omero-server.jar, the configuration for running the OMERO services using IceGridAdmin, the SQL schemas for the OMERO database amongst others

There is likely a case for distinguishing these concepts but this will require a backwards-incompatible naming change.
To your questions, release announcements made at https://www.openmicroscopy.org/announcements/ usually reflect the apparition of a new binary under https://github.com/ome/openmicroscopy/releases (mirrored under https://downloads.openmicroscopy.org/omero/) so this would be the source of truth.

[jburel]

We will look into the redirect problem since that should have been done automatically