Open Microscopy Environment

Hi OMERO team,


after installing Omero figure, i tried to Export a PDF, but the issue is that no download button was showed (Blue button)

note that if i go to Activity list in WebCleint i can see the PDF file and download it

my config is:

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Omero.ldap.sync_on_login=false
ldap.base=dc=ad,dc=hhu,dc=de
omero.data.dir=/mnt/ExtVol/OMERO
omero.db.name=omero_database
omero.db.pass=********
omero.db.user=omero_user
omero.jvmcfg.append=-Dcom.sun.jndi.ldap.connect.pool.timeout=500
omero.ldap.base=dc=ad,dc=hhu,dc=de
omero.ldap.config=true
omero.ldap.group_filter=(&(cn=CAi_*)(memberof=cn=CAi_Allgemein,OU=FileShares,OU=Zentrum für Informations- und Medientechnologie,OU=Heinrich-Heine-Universität,dc=ad,dc=hhu,dc=de))
omero.ldap.group_mapping=name=cn
omero.ldap.new_user_group=:filtered_dn_attribute:memberOf
omero.ldap.password=********
omero.ldap.referral=follow
omero.ldap.sync_on_login=true
omero.ldap.urls=ldap://ldaps.ad.hhu.de:389
omero.ldap.user_filter=(memberof:1.2.840.113556.1.4.1941:=cn=CAi_Allgemein,OU=FileShares,OU=Zentrum für Informations- und Medientechnologie,OU=Heinrich-Heine-Universität,dc=ad,dc=hhu,dc=de)
omero.ldap.user_mapping=omeName=sAMAccountName,firstName=givenName,lastName=sn,email=mail
omero.ldap.username=SVC_Omero
omero.mail.config=true
omero.mail.host=mail.hhu.de
omero.new_user_group=:query:(member=Q049Q0FpX0NBaSxPVT1GaWxlU2hhcmVzLE9VPVplbnRydW0gZsO8ciBJbm)
omero.web.application_server=wsgi-tcp
omero.web.apps=["omero_figure", "omero_webtagging_tagsearch"]
omero.web.debug=false
omero.web.open_with=[["Image viewer", "webindex", {"supported_objects": ["image"], "script_url": "webclient/javascript/ome.openwith_viewer.js"}], ["omero_figure", "new_figure", {"supported_objects": ["images"], "target": "_blank", "label": "OMERO.figure"}]]
omero.web.ui.top_links=[["Data", "webindex", {"title": "Browse Data via Projects, Tags etc"}], ["History", "history", {"title": "History"}], ["Help", "http://help.openmicroscopy.org/", {"target": "new", "title": "Open OMERO user guide in a new tab"}], ["Figure", "figure_index", {"target": "_blank", "title": "Open Figure in new tab"}], ["Tag Search", "tagsearch"]]


bin/omero admin diagnostics

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================================================================================
OMERO Diagnostics 5.3.2-ice36-b62
================================================================================
       
Commands:   java -version                  1.8.0     (/usr/bin/java)
Commands:   python -V                      2.7.5     (/usr/bin/python)
Commands:   icegridnode --version          3.6.3     (/usr/bin/icegridnode)
Commands:   icegridadmin --version         3.6.3     (/usr/bin/icegridadmin)
Commands:   psql --version                 9.4.11    (/usr/bin/psql)

Server:     icegridnode                    running
Server:     Blitz-0                        active (pid = 2313, enabled)
Server:     DropBox                        active (pid = 2319, enabled)
Server:     FileServer                     active (pid = 2323, enabled)
Server:     Indexer-0                      active (pid = 2336, enabled)
Server:     MonitorServer                  active (pid = 2338, enabled)
Server:     OMERO.Glacier2                 active (pid = 2346, enabled)
Server:     OMERO.IceStorm                 active (pid = 2357, enabled)
Server:     PixelData-0                    active (pid = 2352, enabled)
Server:     Processor-0                    active (pid = 2381, enabled)
Server:     Tables-0                       active (pid = 2387, enabled)
Server:     TestDropBox                    inactive (enabled)

Log dir:    /home/omero/OMERO.server-5.3.2-ice36-b62/var/log exists
Log files:  Blitz-0.log                    140.0 MB      errors=330  warnings=838
Log files:  DropBox.log                    90.0 KB       errors=35   warnings=38 
Log files:  FileServer.log                 14.0 KB     
Log files:  Indexer-0.log                  1.0 MB        errors=32   warnings=69 
Log files:  MonitorServer.log              42.0 KB     
Log files:  OMEROweb.lock                  0.0 KB       
Log files:  OMEROweb.log                   2.0 MB        errors=90   warnings=322
Log files:  PixelData-0.log                653.0 KB      errors=28   warnings=63 
Log files:  Processor-0.log                3.0 MB        errors=150  warnings=304
Log files:  Tables-0.log                   572.0 KB      errors=144  warnings=295
Log files:  TestDropBox.log                n/a
Log files:  master.err                     79.0 KB       errors=36   warnings=72 
Log files:  master.out                     81.0 KB     
Log files:  Total size                     149.33 MB


Environment:OMERO_HOME=(unset)             
Environment:OMERO_NODE=(unset)             
Environment:OMERO_MASTER=(unset)           
Environment:OMERO_USERDIR=(unset)         
Environment:OMERO_TMPDIR=(unset)           
Environment:PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/root/bin
Environment:PYTHONPATH=(unset)             
Environment:ICE_HOME=(unset)               
Environment:LD_LIBRARY_PATH=(unset)       
Environment:DYLD_LIBRARY_PATH=(unset)     

OMERO SSL port:4064                           
OMERO TCP port:4063                           
OMERO data dir:'/mnt/ExtVol/OMERO'            Exists? True   Is writable? True
OMERO temp dir:'/home/omero/omero/tmp'        Exists? True   Is writable? True   (Size: 0)

JVM settings: Blitz-${index}                -Xmx1255m -XX:MaxPermSize=1g -XX:+IgnoreUnrecognizedVMOptions
JVM settings: Indexer-${index}              -Xmx837m -XX:MaxPermSize=1g -XX:+IgnoreUnrecognizedVMOptions
JVM settings: PixelData-${index}            -Xmx1255m -XX:MaxPermSize=1g -XX:+IgnoreUnrecognizedVMOptions
JVM settings: Repository-${index}           -Xmx837m -XX:MaxPermSize=1g -XX:+IgnoreUnrecognizedVMOptions

OMERO.web status... [RUNNING] (PID 1126)
Django version: 1.8.18


if you want some logs let me know, which files, i have to upload it

cheers
Saleh

Hi Saleh,

Did you upload the omero-server-side figure export script?

cf "Enabling figure export" at https://pypi.python.org/pypi/omero-figure

You can double check if the script is there via the OMERO cli:

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bash-4.2$ ~/OMERO.web/bin/omero script list | grep Figure_To_Pdf
Using session x-x-x-x-x (kenny@omeroserver:4064). Idle timeout: 10 min. Current group: My Group
2635123 | /omero/figure_scripts/Figure_To_Pdf.py

Hi Kenny,

my script listed under OMERO.server Not under OMERO.web , is it ok so ?!!

bin/omero script list | grep Figure_To_Pdf
Using session bb428a37-a1e2-47c0-9950-792e518d7631 (saleht@localhost:4064). Idle timeout: 10 min. Current group: MyGroup
15901 | /omero/figure_scripts/Figure_To_Pdf.py

Hi Saleh,

Okay - it's good that you can download the PDFs via `activities` - that rules out a problem with the plugin.

I've never come across the download button not appearing in the UI before - so it would be good to know the following:

* Browser and browser version
* OS/Platform of client
* Figure version

And of course, have you tried in a different browser, in a private-browsing session?

Best,

Kenny

Hi kenny,

my OMERO.figure version is 3.0.0

actually i test it with many browsers
Ubuntu 17.04 with Mozilla v 54.0 (x64)
Ubuntu 17.04 with chrome v 58
Debian 8.7 with Mozilla v 45
Windows10 Mozilla v 54
Windows10 INTERNET Explorer

And of course, have you tried in a different browser, in a private-browsing session?

yes i did

Regards
Saleh

Hi Saleh,

I'm afraid there's not much at least I can think of to debug this.

You may as well try upgrading figure to the latest version, though I don't expect it'll fix your problem.

Then next thing I would do after upgrading figure, with no OMERO.web expert around, is to fire up "developer tools" in your web browser of choice and start checking for things like javascript errors or missing images or similar.

Hopefully someone else in the community can recognise this one and take up the thread.

Cheers,

Kenny

And just a quick follow up:

my script listed under OMERO.server Not under OMERO.web , is it ok so ?!!

No. We will also need to address why why you aren't seeing the script from the web UI. Questions that come to mind:

* When you say "OMERO.server" do you mean from `bin/omero script list`?
* You were testing both with the same user?
* Your OMERO.web is only configured to talk to one OMERO.server, correct?


Cheers,
~Josh.

Dear Josh,

my script listed under OMERO.server Not under OMERO.web , is it ok so ?!!



No. We will also need to address why why you aren't seeing the script from the web UI. Questions that come to mind:

No. i can see the the script from Web UI,

When you say "OMERO.server" do you mean from `bin/omero script list`?

yes if i did /home/omero/OMERO.server/bin/omero script list, i can see Figure To Pdf.py listed

Dear Kenny,

yes yesterday i check Web conosole in my web browser, after pressing Export button, i am getting
an Error :

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Empty string passed to getElementById()
XML Parsing Error: not well-formed
Location: https://omero-cai.hhu.de/figure/make_web_figure/
Line Number 1, Column 1:  make_web_figure:1:1

        .

and i note that if i press Export with empty page, i am getting this red error button, maybe this will help

cheers
Saleh

Dear Saleh

We are still investigating the issue but the red triangle button is expected when you click export on an empty panel

Cheers
Jmarie