Error when exporting pdf from omero.figure

When I try to export at figure as a PDF in omero.figure, I get the following error:

Markdown not installed. See https://pypi.python.org/pypi/Markdown
Reportlab not installed.
Traceback (most recent call last):
File “./script”, line 2325, in
run_script()
File “./script”, line 2311, in run_script
file_annotation = export_figure(conn, script_params)
File “./script”, line 2267, in export_figure
return fig_export.build_figure()
File “./script”, line 941, in build_figure
self.create_figure()
File “./script”, line 1788, in create_figure
“Need to install https://bitbucket.org/rptlab/reportlab”)
ImportError: Need to install https://bitbucket.org/rptlab/reportlab

However, I do have both Markdown and Reportlab are installed on my computer:

Daniels-iMac:~ danielhoops$ pip list
DEPRECATION: Python 2.7 reached the end of its life on January 1st, 2020. Please upgrade your Python as Python 2.7 is no longer maintained. A future version of pip will drop support for Python 2.7. More details about Python 2 support in pip, can be found at https://pip.pypa.io/en/latest/development/release-process/#python-2-support
Package Version


Markdown 3.1.1
reportlab 3.5.42

#I removed the other packages that were listed for brevity.

Also, that error regarding Python 2.7 may be relevant. I also have Python 3.8.2 installed, however the error still appears, and pip is installed within the Python 2.7 directory.

I’m on a Mac running OS 10.15.3

Hi,

What version of OMERO are you running?
OMERO 5.6.0 requires python3 (3.6 or 3.7).

Do you have separate python virtual environments for the OMERO.server and OMERO.web installs?

You need to make sure that reportlab is installed in the same python environment where the server is running, since it is the OMERO.sever that runs the figure export script. You don’t need reportlab for the OMERO.figure app installed in the OMERO.web deployment.

Hope that helps,

Will.

Hi Will,

I appreciate your quick response. Unfortunately I’m not sure exactly what you mean, but here’s my best stab at it.

For the desktop app, Omero.insight, I’m running version 5.5.9. As for the server, I’m currently using a trial licence and server ome-demoserver.openmicroscopy.org. My user name is DanielHoops and I’m accessing OMERO.web through Safari, if that helps.

Thanks and sorry again that I can’t answer your questions more directly.

Dan

Hi Dan,

Ah, Sorry, that error is entirely our fault. We need to install reportlab on the demo server. You don’t need to have it installed anywhere on your machine.

We’ll look into fixing that ASAP. Thanks for the feedback.

Will.

1 Like

In the meantime, you can choose to export figures as TIFF images, as long as they are single page figures (multi-page figures will try to create a zip that contains a PDF info page).

Will.

Thanks! I really appreciate your help. I’ll use the TIFF option as a stop-gap in the mean time, while I wait to be able to download the PDF.

Thanks again!

Dan

It seems to be fixed. Thanks again!