install figure export dependencies by default

[jburel]

Install dependencies required to export figure
Figure might not be installed but this should avoid error like ome/docker-example-omero#11

[joshmoore]

In general, 👍 for working around errors for the end users, but I worry about the number of places that we have such hard-coded dependencies. I'd really suggest we hammer out "dependency APIs" like pip install omero-figure[server] that we could re-use everywhere.

[jburel]

@joshmoore I agree about the "dependency APIs". This will need to be prioritised.

[pwalczysko]

I think in order to solve https://forum.image.sc/t/omere-figure-export-pdf-does-not-work/39573/25, we need this PR.

1. The error in the thread (repeating below) can be reproduced, and it seems clear that you cannot really install new packages on the omero-server container as user omero-server (the default user) - there is no clear way how to become root, the password for root is unknown, all I tried failed).

(venv3) bash-4.2$ pip install "reportlab<3.6"
Collecting reportlab<3.6
  Downloading reportlab-3.5.68-cp36-cp36m-manylinux_2_12_x86_64.manylinux2010_x86_64.whl (2.6 MB)
     |################################| 2.6 MB 242 kB/s            
Requirement already satisfied: pillow>=4.0.0 in /opt/omero/server/venv3/lib/python3.6/site-packages (from reportlab<3.6) (8.4.0)
Installing collected packages: reportlab
ERROR: Could not install packages due to an OSError: [Errno 13] Permission denied: '/opt/omero/server/venv3/lib64/python3.6/site-packages/reportlab-3.5.68.dist-info'
Check the permissions.

Edit: The solution is to start the bash for the container already as root, see https://forum.image.sc/t/omere-figure-export-pdf-does-not-work/39573/27

[jburel]

@pwalczysko no longer required to cap reportlab see https://github.com/ome/omero-figure/blob/master/requirements-server.txt

[pwalczysko]

git checkout jburel/figure_deps
docker build -t testjm .

#16 86.56     "msg": "Failed to validate GPG signature for pgdg-redhat-repo-42.0-36PGDG.noarch: Public key for pgdg-redhat-repo-latest.noarchtuwairkh.rpm is not installed"
#16 86.56 }
#16 86.56 
#16 86.56 PLAY RECAP *********************************************************************
#16 86.56 localhost                  : ok=26   changed=14   unreachable=0    failed=1    skipped=22   rescued=0    ignored=0

[joshmoore]

see also ome/ansible-role-postgresql-client#14 (review) perhaps?

[pwalczysko]

@jburel @joshmoore yes, I can see that the build succeeds on the old mac with the amd achitecture. The error #71 (comment) is only happening on the M1.

On the old mac, I am able to run the docker image and connect to the server with insight. Tried to build omero-web in another container and then connect to it, but the omero-web does not see my localhost for some reason.

[pwalczysko]

Okay, so I have now a test run on my M1 mac:

docker build -t testjm .
cd docker-example-omero

• Edit the docker-compose.yml file so that you point to the freshly built testjm image.

...
  omeroserver:
    # This container uses the tag for the latest server release of OMERO 5
    # To upgrade to the next major release, increment the major version number
    image: "testjm"
    environment:
...

• Then just run docker-compose up. Wait for more than 5 mins as the server is slow to start.
• log in to OMERO.web, and start OMERO.figure.
• Observe the Figure_to_pdf.py script is missing.
• Upload it manuall from https://raw.githubusercontent.com/ome/omero-figure/v6.0.1/omero_figure/scripts/omero/figure_scripts/Figure_To_Pdf.py
• create a figure, add labels with italics and bold.
• Export the newly created figure.
• also exec into the server container (built from testjm image) and verify that both reportlab and markdown are installed with latest versions as per pypi

Works fine. Lgtm.