Open Microscopy Environment

Hi,

during exporting a PDF, the lastest GIT version of OMERO.figure fails with:

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Figure.pdf
Invalid parameters: VALUE LIST for "Export_Option": None not in ['PDF', 'PDF_IMAGES']


Downloading a stable release verison from http://downloads.openmicroscopy.org/figure/1.0.0/figure-1.0.0.zip and reverting back to that version was also impossible because of a "403 Forbidden" web server error.

Cheers,

Tristan

Hi Tristan,

as reported in our mailing lists, our downloads resources are currently unavailable. An email will be sent when the issues are solved on our side.

Back to your issues, please be aware that the development version of the OMERO.figure source code has not been validated by a full QA process and should not be considered as production-quality.
Assuming you have cloned the Git repository, you should be able to checkout the 1.0.0 tag of the application using:

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git checkout v1.0.0


Best,
Sebastien

http://lists.openmicroscopy.org.uk/pipe ... 03198.html
http://lists.openmicroscopy.org.uk/pipe ... 05063.html

Hi Tristan,

Do you have all the latest web changes as well as the PDF script changes?
You are seeing this error because the PDF script adds an extra parameter but this hasn't been supplied by the views.py (see https://github.com/will-moore/figure/pull/55).
Updating everything in the app to the latest 'develop' branch changes and restarting web should fix this problem.

However, reverting to the 1.0.0 script should also fix that issue (although not guaranteed to work if you have more recent changes to the web code).

As Sebastien said, although the "develop" branch of figure should work, it certainly hasn't had the full testing of a proper release, so should only be used for testing, not production.

Cheers,

Will.

Hi Will & Sebastien,

prior to this error I did a "git pull" to update to the newest version. This should have included the Figure_to_PDF.py.

Meanwhile, I updated our OMERO installation from 5.0.6 to 5.0.8 and reverted to Figure 1.0.0, replacing the Figure_to_PDF.py with omero script replace etc.

Now the PDF export works, but I do not get the standard A4 page display. There is only a grey background. Going to Page Setup... in the Menu does nothing, but I can add images that appear as empty blue rectangle.

Any ideas?

Cheers,

Tristan

EDIT: Ok, so if I add an image (using its ID), the blue frame will appear (with correct dimensions) int he middle of the grey background, but with no content. The image, however, will still be displayed in the most top left corner if I scroll to the left and to the top.

Hi Tristan,

I'm not sure what error you're seeing but I'm guessing you've still got something out of sync.
Maybe the size or page-count of the figure is breaking with the earlier version of the app?

If you restart web server, refresh the base /figure/ page and create a new figure, do you see a problem?

Hopefully that's all that's needed. Let me know if that doesn't work,

Cheers,

Will.

Hi Will,

I tried restarting the whole OMERO system including web, but as expected this did not change anything about the output. I still see only the grey background, added images are displayed frame-only without any contents and certain menu items under "File" do not work (e.g. Page Setup).

I included a screenshot of the problem with a newly created figure (Browser Cache has been cleared completely, server was restarted previously).

Figure worked flawlessly for a long while with the latest HEAD versions from Git, I'm not sure what led to these issues. Any more ideas?

[img]figure_issue.jpg[/img]

Hi Tristan,

Ok, just to be clear, you've now reverted to OMERO.figure 1.0.0?
I just tried $ git checkout v1.0.0 on my local install, then refreshed /figure/ and added a new image and it this appears to be OK.

It seems that either your templates.js file or figure.css are wrong, causing the mis-localisation of the image panel.
If you right-click on the page, then "Inspect Element" you should be able to see the DOM hierarchy (see screenshot of me doing this).

body > main > div id='canvas_wrapper' > article > div id='paper' > div class='imagePanel' > div > img

The div id='paper' should correspond to the white page (that is missing in your screen-shot).

You could also try to click on the 'Console' tab in the developer tools and refresh the page to see if there are any errors.

Hope that gives us some clues,

Will.

Hi Will,

sorry for the slow communication. Yes, I reverted to 1.0.0.0. When inspecting the DOM hierarchy I found that the id="paper" div is much too large. The code reads as follows:

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<div id="paper" style="width: 612px; height: 792px; left: 4694px; top: 3604px;"><div class="imagePanel" style="top: 267.315068493151px; left: 178px; width: 256px; height: 256px;">    <!-- The content of <div class='imagePanel'> for each panel -->
    <div class="imgContainer">
        <img class="img_panel" src="/omero/webgateway/render_image/544/27/0/?c=1|109:765.25$00FF00,2|168.35:1388.8875$FF0000,3|116.5:611.625$FFFF00&amp;m=c" style="left: 0px; top: 0px; width: 256px; height: 256px; -webkit-transform-origin: 50% 50% 0px; transform-origin: 50% 50% 0px; -webkit-transform: rotate(0deg); transform: rotate(0deg);">
    </div>
</div></div>


The console lists no errors on reload apart from a missing favicon.ico.

Hi Tristan,

As far as I can see, the DOM elements you've pasted there are the same as mine, with:

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<div id="paper" style="width: 612px; height: 792px; left: 4694px; top: 3604px;">


If this still isn't visible on your screen then something else must be messing it up.

I'm not sure I can suggest anything else, but if you want to e-mail me with a url and some guest login that I can access your OMERO.figure, then I can take a look at that myself?

Cheers,

Will.

Hi Will,

thanks for the offer, I sent you a private message on this board with a test user account and some images to work with.

Regards,

Tristan