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omero figure

General user discussion about using the OMERO platform to its fullest. Please ask new questions at https://forum.image.sc/tags/omero
Please note:
Historical discussions about OMERO. Please look for and ask new questions at https://forum.image.sc/tags/omero

There are workflow guides for various OMERO functions on our help site - http://help.openmicroscopy.org

You should find answers to any basic questions about using the clients there.
Post a reply

omero figure

Postby LeroyAlex » Fri Dec 19, 2014 10:38 am

Hi,

Since the begining of the week, i can't export my works in pdf.
I can see the creating pdf process but i dont get the download button when it's done.

Here the log when i stop/restart omero web + admin diagnostics:
Code: Select all
C:\OMERO.server>bin\omero web stop
Stopping OMERO.web... DEVELOPMENT: You will have to kill processes by hand!

C:\OMERO.server>bin\omero web start
INFO:__main__:Application Starting...
INFO:root:Processing custom settings for module omeroweb.settings
DEBUG:omeroweb.settings:UPGRADES_URL = 'http://upgrade.openmicroscopy.org.uk/' (
source:default)
DEBUG:omeroweb.settings:ADMINS = [] (source:default)
DEBUG:omeroweb.settings:ALLOWED_HOSTS = [u'*'] (source:default)
DEBUG:omeroweb.settings:APPLICATION_SERVER = 'development' (source:omero.web.app
lication_server)
DEBUG:omeroweb.settings:APPLICATION_SERVER_HOST = '0.0.0.0' (source:default)
DEBUG:omeroweb.settings:APPLICATION_SERVER_MAX_REQUESTS = 400 (source:default)
DEBUG:omeroweb.settings:APPLICATION_SERVER_PORT = '4080' (source:default)
DEBUG:omeroweb.settings:ADDITIONAL_APPS = [u'tagsearch', u'autotag', u'figure']
(source:omero.web.apps)
DEBUG:omeroweb.settings:CACHES = {u'default': {u'BACKEND': u'django.core.cache.b
ackends.dummy.DummyCache'}} (source:default)
DEBUG:omeroweb.settings:DATABASES = {} (source:default)
DEBUG:omeroweb.settings:DEBUG = True (source:omero.web.debug)
DEBUG:omeroweb.settings:EMAIL_HOST = None (source:default)
DEBUG:omeroweb.settings:EMAIL_HOST_PASSWORD = u'********************' (source:de
fault)
DEBUG:omeroweb.settings:EMAIL_HOST_USER = None (source:default)
DEBUG:omeroweb.settings:EMAIL_PORT = None (source:default)
DEBUG:omeroweb.settings:EMAIL_SUBJECT_PREFIX = '[OMERO.web] ' (source:default)
DEBUG:omeroweb.settings:EMAIL_USE_TLS = False (source:default)
DEBUG:omeroweb.settings:FORCE_SCRIPT_NAME = None (source:default)
DEBUG:omeroweb.settings:INDEX_TEMPLATE = None (source:default)
DEBUG:omeroweb.settings:LOGDIR = 'C:/OMERO.server/var/log' (source:default)
DEBUG:omeroweb.settings:LOGIN_LOGO = None (source:default)
DEBUG:omeroweb.settings:LOGIN_VIEW = 'weblogin' (source:default)
DEBUG:omeroweb.settings:NANOXML_JAR = 'nanoxml.jar' (source:default)
DEBUG:omeroweb.settings:OPEN_ASTEX_MAX_SIDE = 400 (source:default)
DEBUG:omeroweb.settings:OPEN_ASTEX_MAX_VOXELS = 27000000 (source:default)
DEBUG:omeroweb.settings:OPEN_ASTEX_MIN_SIDE = 20 (source:default)
DEBUG:omeroweb.settings:PING_INTERVAL = 60000 (source:default)
DEBUG:omeroweb.settings:PUBLIC_CACHE_ENABLED = False (source:default)
DEBUG:omeroweb.settings:PUBLIC_CACHE_KEY = u'********************' (source:defau
lt)
DEBUG:omeroweb.settings:PUBLIC_CACHE_TIMEOUT = 86400 (source:default)
DEBUG:omeroweb.settings:PUBLIC_ENABLED = False (source:default)
DEBUG:omeroweb.settings:PUBLIC_PASSWORD = u'********************' (source:defaul
t)
DEBUG:omeroweb.settings:PUBLIC_SERVER_ID = 1 (source:default)
DEBUG:omeroweb.settings:PUBLIC_URL_FILTER = <_sre.SRE_Pattern object at 0x0369F6
38> (source:default)
DEBUG:omeroweb.settings:PUBLIC_USER = None (source:default)
DEBUG:omeroweb.settings:SCRIPTS_TO_IGNORE = [u'\\omero\\figure_scripts\\Movie_Fi
gure.py', u'\\omero\\figure_scripts\\Split_View_Figure.py', u'\\omero\\figure_sc
ripts\\Thumbnail_Figure.py', u'\\omero\\figure_scripts\\ROI_Split_Figure.py', u'
\\omero\\export_scripts\\Make_Movie.py', u'\\omero\\setup_scripts\\FLIM_initiali
se.py', u'\\omero\\import_scripts\\Populate_ROI.py'] (source:default)
DEBUG:omeroweb.settings:SEND_BROKEN_LINK_EMAILS = True (source:default)
DEBUG:omeroweb.settings:SERVER_EMAIL = None (source:default)
DEBUG:omeroweb.settings:SERVER_LIST = [[u'localhost', 4064, u'omero']] (source:d
efault)
DEBUG:omeroweb.settings:SESSION_COOKIE_AGE = 86400 (source:default)
DEBUG:omeroweb.settings:SESSION_ENGINE = 'omeroweb.filesessionstore' (source:def
ault)
DEBUG:omeroweb.settings:SESSION_EXPIRE_AT_BROWSER_CLOSE = True (source:default)
DEBUG:omeroweb.settings:STATIC_URL = '/static/' (source:default)
DEBUG:omeroweb.settings:STATICFILES_DIRS = [] (source:default)
DEBUG:omeroweb.settings:TEMPLATE_DIRS = [] (source:default)
DEBUG:omeroweb.settings:CENTER_PLUGINS = [[u'Auto Tag', u'autotag/auto_tag_init.
js.html', u'auto_tag_panel']] (source:omero.web.ui.center_plugins)
DEBUG:omeroweb.settings:UI_MENU_DROPDOWN = {u'ALL': u'All members', u'COLLEAGUES
': u'Members', u'LEADERS': u'Owners'} (source:default)
DEBUG:omeroweb.settings:RIGHT_PLUGINS = [[u'Acquisition', u'webclient/data/inclu
des/right_plugin.acquisition.js.html', u'metadata_tab'], [u'Preview', u'webclien
t/data/includes/right_plugin.preview.js.html', u'preview_tab']] (source:default)

DEBUG:omeroweb.settings:TOP_LINKS = [[u'Tag Search', u'tagsearch'], [u'Figure',
u'figure_index']] (source:omero.web.ui.top_links)
DEBUG:omeroweb.settings:VIEWER_INITIAL_ZOOM_LEVEL = None (source:default)
DEBUG:omeroweb.settings:WEBGATEWAY_CACHE = None (source:default)
DEBUG:omeroweb.settings:WEBSTART_CLASS = 'org.openmicroscopy.shoola.Main' (sourc
e:default)
DEBUG:omeroweb.settings:WEBSTART_HEAP = '1024m' (source:default)
DEBUG:omeroweb.settings:WEBSTART_HOMEPAGE = 'http://www.openmicroscopy.org' (sou
rce:default)
DEBUG:omeroweb.settings:WEBSTART_HOST = 'localhost' (source:default)
DEBUG:omeroweb.settings:WEBSTART_ICON = 'webstart/img/icon-omero-insight.png' (s
ource:default)
DEBUG:omeroweb.settings:WEBSTART_JAR = 'omero.insight.jar' (source:default)
DEBUG:omeroweb.settings:WEBSTART_PORT = '4064' (source:default)
DEBUG:omeroweb.settings:WEBSTART_TEMPLATE = None (source:default)
DEBUG:omeroweb.settings:WEBSTART_TITLE = 'OMERO.insight' (source:default)
DEBUG:omeroweb.settings:WEBSTART_VENDOR = 'The Open Microscopy Environment' (sou
rce:default)
DEBUG:omeroweb.settings:Attempting to import additional app settings for app: ta
gsearch
DEBUG:omeroweb.settings:Couldn't import settings from app: tagsearch
DEBUG:omeroweb.settings:Attempting to import additional app settings for app: au
totag
INFO:root:Processing custom settings for module autotag.settings
DEBUG:omeroweb.settings:Attempting to import additional app settings for app: fi
gure
INFO:root:Processing custom settings for module figure.settings
DEBUG:omeroweb.settings:INSTALLED_APPS=[('django.contrib.staticfiles', 'django.c
ontrib.auth', 'django.contrib.contenttypes', 'django.contrib.sessions', 'django.
contrib.sites', 'omeroweb.feedback', 'omeroweb.webadmin', 'omeroweb.webclient',
'omeroweb.webgateway', 'omeroweb.webtest', 'omeroweb.webredirect', 'omeroweb.web
start', u'omeroweb.tagsearch', u'omeroweb.autotag', u'omeroweb.figure')]

0 static files copied, 903 unmodified.
Starting OMERO.web... INFO:__main__:Application Starting...
INFO:root:Processing custom settings for module omeroweb.settings
DEBUG:omeroweb.settings:UPGRADES_URL = 'http://upgrade.openmicroscopy.org.uk/' (
source:default)
DEBUG:omeroweb.settings:ADMINS = [] (source:default)
DEBUG:omeroweb.settings:ALLOWED_HOSTS = [u'*'] (source:default)
DEBUG:omeroweb.settings:APPLICATION_SERVER = 'development' (source:omero.web.app
lication_server)
DEBUG:omeroweb.settings:APPLICATION_SERVER_HOST = '0.0.0.0' (source:default)
DEBUG:omeroweb.settings:APPLICATION_SERVER_MAX_REQUESTS = 400 (source:default)
DEBUG:omeroweb.settings:APPLICATION_SERVER_PORT = '4080' (source:default)
DEBUG:omeroweb.settings:ADDITIONAL_APPS = [u'tagsearch', u'autotag', u'figure']
(source:omero.web.apps)
DEBUG:omeroweb.settings:CACHES = {u'default': {u'BACKEND': u'django.core.cache.b
ackends.dummy.DummyCache'}} (source:default)
DEBUG:omeroweb.settings:DATABASES = {} (source:default)
DEBUG:omeroweb.settings:DEBUG = True (source:omero.web.debug)
DEBUG:omeroweb.settings:EMAIL_HOST = None (source:default)
DEBUG:omeroweb.settings:EMAIL_HOST_PASSWORD = u'********************' (source:de
fault)
DEBUG:omeroweb.settings:EMAIL_HOST_USER = None (source:default)
DEBUG:omeroweb.settings:EMAIL_PORT = None (source:default)
DEBUG:omeroweb.settings:EMAIL_SUBJECT_PREFIX = '[OMERO.web] ' (source:default)
DEBUG:omeroweb.settings:EMAIL_USE_TLS = False (source:default)
DEBUG:omeroweb.settings:FORCE_SCRIPT_NAME = None (source:default)
DEBUG:omeroweb.settings:INDEX_TEMPLATE = None (source:default)
DEBUG:omeroweb.settings:LOGDIR = 'C:/OMERO.server/var/log' (source:default)
DEBUG:omeroweb.settings:LOGIN_LOGO = None (source:default)
DEBUG:omeroweb.settings:LOGIN_VIEW = 'weblogin' (source:default)
DEBUG:omeroweb.settings:NANOXML_JAR = 'nanoxml.jar' (source:default)
DEBUG:omeroweb.settings:OPEN_ASTEX_MAX_SIDE = 400 (source:default)
DEBUG:omeroweb.settings:OPEN_ASTEX_MAX_VOXELS = 27000000 (source:default)
DEBUG:omeroweb.settings:OPEN_ASTEX_MIN_SIDE = 20 (source:default)
DEBUG:omeroweb.settings:PING_INTERVAL = 60000 (source:default)
DEBUG:omeroweb.settings:PUBLIC_CACHE_ENABLED = False (source:default)
DEBUG:omeroweb.settings:PUBLIC_CACHE_KEY = u'********************' (source:defau
lt)
DEBUG:omeroweb.settings:PUBLIC_CACHE_TIMEOUT = 86400 (source:default)
DEBUG:omeroweb.settings:PUBLIC_ENABLED = False (source:default)
DEBUG:omeroweb.settings:PUBLIC_PASSWORD = u'********************' (source:defaul
t)
DEBUG:omeroweb.settings:PUBLIC_SERVER_ID = 1 (source:default)
DEBUG:omeroweb.settings:PUBLIC_URL_FILTER = <_sre.SRE_Pattern object at 0x036C76
38> (source:default)
DEBUG:omeroweb.settings:PUBLIC_USER = None (source:default)
DEBUG:omeroweb.settings:SCRIPTS_TO_IGNORE = [u'\\omero\\figure_scripts\\Movie_Fi
gure.py', u'\\omero\\figure_scripts\\Split_View_Figure.py', u'\\omero\\figure_sc
ripts\\Thumbnail_Figure.py', u'\\omero\\figure_scripts\\ROI_Split_Figure.py', u'
\\omero\\export_scripts\\Make_Movie.py', u'\\omero\\setup_scripts\\FLIM_initiali
se.py', u'\\omero\\import_scripts\\Populate_ROI.py'] (source:default)
DEBUG:omeroweb.settings:SEND_BROKEN_LINK_EMAILS = True (source:default)
DEBUG:omeroweb.settings:SERVER_EMAIL = None (source:default)
DEBUG:omeroweb.settings:SERVER_LIST = [[u'localhost', 4064, u'omero']] (source:d
efault)
DEBUG:omeroweb.settings:SESSION_COOKIE_AGE = 86400 (source:default)
DEBUG:omeroweb.settings:SESSION_ENGINE = 'omeroweb.filesessionstore' (source:def
ault)
DEBUG:omeroweb.settings:SESSION_EXPIRE_AT_BROWSER_CLOSE = True (source:default)
DEBUG:omeroweb.settings:STATIC_URL = '/static/' (source:default)
DEBUG:omeroweb.settings:STATICFILES_DIRS = [] (source:default)
DEBUG:omeroweb.settings:TEMPLATE_DIRS = [] (source:default)
DEBUG:omeroweb.settings:CENTER_PLUGINS = [[u'Auto Tag', u'autotag/auto_tag_init.
js.html', u'auto_tag_panel']] (source:omero.web.ui.center_plugins)
DEBUG:omeroweb.settings:UI_MENU_DROPDOWN = {u'ALL': u'All members', u'COLLEAGUES
': u'Members', u'LEADERS': u'Owners'} (source:default)
DEBUG:omeroweb.settings:RIGHT_PLUGINS = [[u'Acquisition', u'webclient/data/inclu
des/right_plugin.acquisition.js.html', u'metadata_tab'], [u'Preview', u'webclien
t/data/includes/right_plugin.preview.js.html', u'preview_tab']] (source:default)

DEBUG:omeroweb.settings:TOP_LINKS = [[u'Tag Search', u'tagsearch'], [u'Figure',
u'figure_index']] (source:omero.web.ui.top_links)
DEBUG:omeroweb.settings:VIEWER_INITIAL_ZOOM_LEVEL = None (source:default)
DEBUG:omeroweb.settings:WEBGATEWAY_CACHE = None (source:default)
DEBUG:omeroweb.settings:WEBSTART_CLASS = 'org.openmicroscopy.shoola.Main' (sourc
e:default)
DEBUG:omeroweb.settings:WEBSTART_HEAP = '1024m' (source:default)
DEBUG:omeroweb.settings:WEBSTART_HOMEPAGE = 'http://www.openmicroscopy.org' (sou
rce:default)
DEBUG:omeroweb.settings:WEBSTART_HOST = 'localhost' (source:default)
DEBUG:omeroweb.settings:WEBSTART_ICON = 'webstart/img/icon-omero-insight.png' (s
ource:default)
DEBUG:omeroweb.settings:WEBSTART_JAR = 'omero.insight.jar' (source:default)
DEBUG:omeroweb.settings:WEBSTART_PORT = '4064' (source:default)
DEBUG:omeroweb.settings:WEBSTART_TEMPLATE = None (source:default)
DEBUG:omeroweb.settings:WEBSTART_TITLE = 'OMERO.insight' (source:default)
DEBUG:omeroweb.settings:WEBSTART_VENDOR = 'The Open Microscopy Environment' (sou
rce:default)
DEBUG:omeroweb.settings:Attempting to import additional app settings for app: ta
gsearch
DEBUG:omeroweb.settings:Couldn't import settings from app: tagsearch
DEBUG:omeroweb.settings:Attempting to import additional app settings for app: au
totag
INFO:root:Processing custom settings for module autotag.settings
DEBUG:omeroweb.settings:Attempting to import additional app settings for app: fi
gure
INFO:root:Processing custom settings for module figure.settings
DEBUG:omeroweb.settings:INSTALLED_APPS=[('django.contrib.staticfiles', 'django.c
ontrib.auth', 'django.contrib.contenttypes', 'django.contrib.sessions', 'django.
contrib.sites', 'omeroweb.feedback', 'omeroweb.webadmin', 'omeroweb.webclient',
'omeroweb.webgateway', 'omeroweb.webtest', 'omeroweb.webredirect', 'omeroweb.web
start', u'omeroweb.tagsearch', u'omeroweb.autotag', u'omeroweb.figure')]
Validating models...

0 errors found
December 19, 2014 - 11:27:55
Django version 1.6, using settings 'omeroweb.settings'
Starting development server at http://0.0.0.0:4080/
Quit the server with CTRL-BREAK.
Cancelled
Terminer le programme de commandes (O/N) ? 0


C:\OMERO.server>bin\omero admin diagnostics

================================================================================

OMERO Diagnostics 5.0.5-ice34-b47
================================================================================


WARNING:omero.util.UpgradeCheck:UPGRADE AVAILABLE:Please upgrade to 5.0.6 See ht
tp://trac.openmicroscopy.org.uk/omero for the latest version

Commands:   java -version                  1.7.0     (C:\Program Files\Java\jdk1
.7.0_71\bin\java.EXE)
Commands:   python -V                      2.6.6     (C:\Python26\python.EXE)
Commands:   icegridnode --version          3.4.2     (C:\Program Files (x86)\Zer
oC\Ice-3.4.2\bin\icegridnode.EXE)
Commands:   icegridadmin --version         3.4.2     (C:\Program Files (x86)\Zer
oC\Ice-3.4.2\bin\icegridadmin.EXE)
Commands:   psql --version                 not found

Server:     icegridnode                    running
Server:     Blitz-0                        active (pid = 2136, enabled)
Server:     DropBox                        inactive (disabled)
Server:     FileServer                     active (pid = 2264, enabled)
Server:     Indexer-0                      active (pid = 2272, enabled)
Server:     MonitorServer                  inactive (disabled)
Server:     OMERO.Glacier2                 active (pid = 2296, enabled)
Server:     OMERO.IceStorm                 active (pid = 2320, enabled)
Server:     PixelData-0                    active (pid = 2304, enabled)
Server:     Processor-0                    active (pid = 2336, enabled)
Server:     Tables-0                       inactive (disabled)
Server:     TestDropBox                    inactive (enabled)
Server:     OMERO.master                   active (running as LocalSystem)

OMERO:      SSL port                       4064
OMERO:      TCP port                       4063

Log dir:    C:\OMERO.server\var\log        exists

Log files:  Blitz-0.log                    495.0 MB      errors=951  warnings=99
090
Log files:  DropBox.log                    7.0 KB        errors=30   warnings=0

Log files:  FileServer.log                 3.0 KB
Log files:  Indexer-0.log                  1.0 MB        errors=0    warnings=6

Log files:  MonitorServer.log              9.0 KB        errors=20   warnings=0

Log files:  OMEROweb.log                   415.0 KB      errors=1    warnings=0

Log files:  OMEROweb_request.log           0.0 KB
Log files:  PixelData-0.log                724.0 KB      errors=15   warnings=23
6
Log files:  Processor-0.log                778.0 KB      errors=42   warnings=16

Log files:  Tables-0.log                   n/a
Log files:  TestDropBox.log                n/a
Log files:  master.err                     0.0 KB
Log files:  master.out                     0.0 KB
Log files:  Total size                     498.58 MB


Environment:OMERO_HOME=(unset)
Environment:OMERO_NODE=(unset)
Environment:OMERO_MASTER=(unset)
Environment:OMERO_TEMPDIR=(unset)
Environment:PATH=C:\Python26;C:\Python26\Scripts;C:\Windows\system32;C:\Windows;
C:\Windows\System32\Wbem;C:\Windows\System32\WindowsPowerShell\v1.0\;C:\Program
Files (x86)\ZeroC\Ice-3.4.2\bin;C:\Program Files\Java\jdk1.7.0_71\bin;
Environment:PYTHONPATH=C:\Program Files (x86)\ZeroC\Ice-3.4.2\python
Environment:ICE_HOME=(unset)
Environment:LD_LIBRARY_PATH=(unset)
Environment:DYLD_LIBRARY_PATH=(unset)

OMERO data dir: 'E:\\Omero-data\\OMERO' Exists? True    Is writable? True
OMERO temp dir: 'C:\Users\aleroy\AppData\Roaming\omero\tmp'     Exists? True
Is writable? True   (Size: 0)
OMERO.web status... DEVELOPMENT: You will have to check status by hand!



Only thing suspicious i see is the you will have to check status by hand...?

Best,

Alex.
LeroyAlex
 
Posts: 50
Joined: Sun Oct 19, 2014 4:19 pm
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Re: omero figure

Postby manics » Fri Dec 19, 2014 3:06 pm

Hi Alex

Have you recently changed your server configuration, or updated your system? It looks like you're running the OMERO.web development server, this is fine for testing but not recommended for production use.

Simon
User avatar
manics
Team Member
 
Posts: 261
Joined: Mon Oct 08, 2012 11:01 am
Location: Dundee
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Re: omero figure

Postby LeroyAlex » Mon Jan 05, 2015 10:09 am

No, no update or anything else but i came back to a "restoration point".
I did this many times and never had problems before though.
LeroyAlex
 
Posts: 50
Joined: Sun Oct 19, 2014 4:19 pm
Top

Re: omero figure

Postby wmoore » Tue Jan 06, 2015 1:21 pm

Hi Alex,

I'm afraid the error handling for PDF generation scripts is not very good within OMERO.figure yet, but if you go to the main webclient UI, and click on the "Activities" icon (to the left of the search field in the top header) then this should list any PDF figure scripts you've recently run, and you'll have access to error or info logs there.
Hope that gets you something useful.
One possibly is "No Processor Available" https://trac.openmicroscopy.org.uk/ome/ticket/8266
where the solution is to simply restart with:

Code: Select all
$ bin/omero admin ice "server stop Processor-0"


Let us know if that's not the issue,

Cheers,
Will.
User avatar
wmoore
Team Member
 
Posts: 674
Joined: Mon May 18, 2009 12:46 pm
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Re: omero figure

Postby LeroyAlex » Mon Jan 12, 2015 3:41 pm

Srry for the late answer.
Indeed, it was the no processor available error, and i fixed it with the command line you gave in your post.
I'm grateful, thank you.

Best,

Alex.
LeroyAlex
 
Posts: 50
Joined: Sun Oct 19, 2014 4:19 pm
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Re: omero figure

Postby saleht » Wed Jul 05, 2017 7:37 am

Hi guys,

i have same issue, after pressing Export button, No download button appear, but if i checked activity list, i can see my pdf and able to download it. how can i solve this issue, or at least trace it, i check Blizlog file it has no enough info
even i did
Code: Select all
bin/omero admin ice "server stop Processor-0"

i reboot the server nothing helped Me :(
any help, i will be glad :)))

cheers Saleh
Last edited by saleht on Wed Jul 05, 2017 9:02 am, edited 1 time in total.
saleht
 
Posts: 96
Joined: Wed Nov 16, 2016 1:06 pm
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Re: omero figure

Postby jmoore » Wed Jul 05, 2017 8:18 am

Saleh,

do you mind not re-using this old thread? Let's start a new one and include the relevant logs as well as `admin diagnostics` etc.

Thanks.
~Josh.
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jmoore
Site Admin
 
Posts: 1591
Joined: Fri May 22, 2009 1:29 pm
Location: Germany
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Re: omero figure

Postby saleht » Wed Jul 05, 2017 9:02 am

Hi josh,

i will do it :)
saleht
 
Posts: 96
Joined: Wed Nov 16, 2016 1:06 pm
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