Figure and PDF export

[phm]

Could you also tell which 404 we are talking about exactly? Is that omero.web grey page?

What is the output of

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curl -I https://omero.college-de-france.fr/omero

Ola

Hi Ola

It's the blank page as

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Not Found

The requested URL /omero/webclient/login/ was not found on this server.

Apache/2.2.15 (CentOS) Server at omero.college-de-france.fr Port 443



[root@omero omero]# curl -I https://omero.college-de-france.fr/omero

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curl: (60) Peer certificate cannot be authenticated with known CA certificates
More details here: http://curl.haxx.se/docs/sslcerts.html

curl performs SSL certificate verification by default, using a "bundle"
of Certificate Authority (CA) public keys (CA certs). If the default
bundle file isn't adequate, you can specify an alternate file
using the --cacert option.
If this HTTPS server uses a certificate signed by a CA represented in
the bundle, the certificate verification probably failed due to a
problem with the certificate (it might be expired, or the name might
not match the domain name in the URL).
If you'd like to turn off curl's verification of the certificate, use
the -k (or --insecure) option.


Philippe

[kennethgillen]

Hi Kenneth,
these are files that you want.

Hi Philippe,

I noticed from a previous post, and your latest error message, you no longer use nginx. The config files you previously sent in this thread were the nginx config - could you please attach the Apache config files that you are using, as well as the latest logfiles from Apache.

** Note: not necessary, of course, if you actually should be using NGINX as per Ola's post above.

Thanks

[atarkowska]

Philippe, I would like to poin that in http://www.openmicroscopy.org/community ... =40#p16404 you asked about help in upgrading to OMERO 5.2 and you switched to use NGINX as you had issues with apache. If this has changed since Nov 2015 you should point it in the beggingin of your question that you changed webserver. My impresison is that you are still using NGINX as your omero confing and web config say so. I would recommand you to turn off apache and start nginx

For the future you may want to uninstall apache permanently!

Ola

[phm]

Philippe, I would like to poin that in http://www.openmicroscopy.org/community ... =40#p16404 you asked as about help to upgrade to OMERO 5.2 and you switched to use NGINX as you had issues with apache. If this has changed since Nov 2015 you should point it in the beggingin of your question that you changed webserver. My impresison is that you are still using NGINX as your omero confing and web config say so. I would recommand you to turn off apache and start nginx

For the future you may want to uninstall apache permanently!

Ola

Hi Ola
Sorry for the confusion.
I stopped and removed apache and started nginx. Now the omero is web working. However the pdf export return always the same message :

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Traceback (most recent call last):
  File "./script", line 1716, in <module>
    runScript()
  File "./script", line 1703, in runScript
    fileAnnotation = export_figure(conn, scriptParams)
  File "./script", line 1660, in export_figure
    return figExport.buildFigure()
  File "./script", line 688, in buildFigure
    self.add_panels_to_page(panels_json, imageIds, page)
  File "./script", line 1343, in add_panels_to_page
    image, pilImg = self.drawPanel(panel, page, i)
  File "./script", line 1166, in drawPanel
    self.pasteImage(pilImg, imgName, panel, page, dpi)
  File "./script", line 1452, in pasteImage
    pilImg.save(imgName)
  File "/opt/rh/python27/root/usr/lib64/python2.7/site-packages/PIL/Image.py", line 1665, in save
    save_handler(self, fp, filename)
  File "/opt/rh/python27/root/usr/lib64/python2.7/site-packages/PIL/TiffImagePlugin.py", line 1320, in _save
    offset = ifd.save(fp)
  File "/opt/rh/python27/root/usr/lib64/python2.7/site-packages/PIL/TiffImagePlugin.py", line 608, in save
    if len(data) <= 4:
TypeError: object of type 'int' has no len()


Philippe

[wmoore]

Hi Philippe,

You're seeing this error: https://github.com/python-pillow/Pillow/issues/1524 which I've only seen with Pillow 3.0.0. I just tried this on my Mac and reproduced the same error. However, if you use Pillow 2.9 then this should work fine.

Regards,

Will

[atarkowska]

Philippe, Will originally pointed to insall Pillow 3.3.0 but this version may not be compativle with numpy. Please make sure you install 2.9, see https://trello.com/c/jZjPZf8K/637-attri ... te-tobytes

Please remember to follow viewtopic.php?f=4&t=8083&start=20#p17322

Ola

[phm]

Philippe, Will originally pointed to insall Pillow 3.3.0 but this version may not be compativle with numpy. Please make sure you install 2.9, see https://trello.com/c/jZjPZf8K/637-attri ... te-tobytes

Please remember to follow viewtopic.php?f=4&t=8083&start=20#p17322

Ola

Hi Ola,
Pillow 3.30 was installed on the server, so I removed Pillow, but how to install Pillow 2.9 ?
pip install Pillow install the 3.30 version and pip install Pillow-2.9 could not find the version

Philippe

[kennethgillen]

Using whichever method you found to install/uninstall inside the Python instance your OMERO is using..

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pip install Pillow<3.0

Cheers,

Kenny

** Note: above should be

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pip install "Pillow<3.0"

[phm]

Using whichever method you found to install/uninstall inside the Python instance your OMERO is using..

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pip install Pillow<3.0

Cheers,

Kenny

Hi Kenneth

Thank, however in Centos the good syntax is :
pip install Pillow==2.90

But after restarted the web server the error for pdf export in Figures is the same....

Philippe

[wmoore]

Hi Philippe,

Are you sure you're still seeing this error:

Code: Select all

packages/PIL/TiffImagePlugin.py", line 608, in save
    if len(data) <= 4:
TypeError: object of type 'int' has no len()


If so, then it seems that you're somehow still running Pillow 3.0 since Pillow 2.9 doesn't have that code at line 608: https://github.com/python-pillow/Pillow ... in.py#L608