Open Microscopy Environment

Hi guys,

after installing the new omero iviewer on my server

i am getting this error when i am opening it

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Page not found (404)
Request Method:   GET
Request URL:   https://omero-cai.hhu.de/iviewer/151/?dataset=151
Using the URLconf defined in omeroweb.urls, Django tried these URL patterns, in this order:
^(?i)figure/
^(?i)omero_webtagging_tagsearch/
^(?i)fpbioimage/
^(?i)gallery/
^(?i)mapr/
^(?i)omero_webtagging_autotag/
^(?i)iviewer/ ^/?$ [name='omero_iviewer_index']
^(?i)iviewer/ ^persist_rois/?$ [name='omero_iviewer_persist_rois']
^(?i)iviewer/ ^image_data/(?P<image_id>[0-9]+)/$ [name='omero_iviewer_image_data']
^(?i)iviewer/ ^save_projection/?$ [name='omero_iviewer_save_projection']
^(?i)iviewer/ ^well_images/?$ [name='omero_iviewer_well_images']
^favicon\.ico$
^(?i)webgateway/
^(?i)webadmin/
^(?i)webclient/
^(?i)url/
^(?i)feedback/
^(?i)api/
^index/$ [name='webindex_custom']
^$ [name='index']
^static\/(?P<path>.*)$
The current URL, iviewer/151/, didn't match any of these.

my url looks like : https://omero-cai.hhu.de/iviewer/153/?dataset=151

i think the porblem with the porduced url, becasue it not similar to any of the recent one

anyway i tried to wirte a valid url like : https://omero-cai.hhu.de/iviewer/?image=151
but i am getting white page nothing inside

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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.new_user_group=default
omero.ldap.password=**************
omero.ldap.referral=follow
omero.ldap.sync_on_login=false
omero.ldap.urls=ldap://ldaps.ad.hhu.de:389
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.web.application_server=wsgi-tcp
omero.web.apps=["omero_figure", "omero_webtagging_tagsearch", "omero_fpbioimage", "omero_gallery", "omero_mapr", "omero_webtagging_autotag", "omero_iviewer"]
omero.web.debug=true
omero.web.mapr.config=[{"menu": "key1", "config": {"default": ["Key1"], "all": ["Key1", "Key2"], "ns": ["openmicroscopy.org/mapr/key1"], "label": "Key1"}}]
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_fpbioimage", "fpbioimage_index", {"supported_objects": ["image"], "script_url": "fpbioimage/openwith.js", "label": "FPBioimage"}], ["omero_iviewer", "omero_iviewer_index", {"supported_objects": ["images", "dataset", "well"], "script_url": "omero_iviewer/openwith.js", "label": "OMERO.iviewer"}]]
omero.web.ui.center_plugins=[["Auto Tag", "omero_webtagging_autotag/auto_tag_init.js.html", "auto_tag_panel"]]
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"], ["Gallery", "webgallery_index", {"target": "_blank", "title": "Open Gallery in new tab"}], ["mapr", {"query_string": {"experimenter": -1}, "viewname": "maprindex_key1"}, {"title": "Key1 browser"}]]


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OMERO Diagnostics 5.3.5-ice36-b73
================================================================================
       
WARNING:omero.util.UpgradeCheck:UPGRADE AVAILABLE:Please upgrade to 5.4.0. See http://downloads.openmicroscopy.org/latest/omero for the latest version.

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 = 8070, enabled)
Server:     DropBox                        active (pid = 8086, enabled)
Server:     FileServer                     active (pid = 8094, enabled)
Server:     Indexer-0                      active (pid = 8095, enabled)
Server:     MonitorServer                  active (pid = 8098, enabled)
Server:     OMERO.Glacier2                 active (pid = 8102, enabled)
Server:     OMERO.IceStorm                 active (pid = 8126, enabled)
Server:     PixelData-0                    active (pid = 8099, enabled)
Server:     Processor-0                    active (pid = 8114, enabled)
Server:     Tables-0                       active (pid = 8139, enabled)
Server:     TestDropBox                    inactive (enabled)

Log dir:    /home/omero/OMERO.server-5.3.5-ice36-b73/var/log exists
Log files:  Blitz-0.log                    71.0 MB       errors=3    warnings=72 
Log files:  DropBox.log                    29.0 KB       errors=0    warnings=11 
Log files:  FileServer.log                 3.0 KB       
Log files:  Indexer-0.log                  182.0 KB      errors=0    warnings=2   
Log files:  MonitorServer.log              15.0 KB     
Log files:  OMEROweb.lock                  0.0 KB       
Log files:  OMEROweb.log                   1.0 MB        errors=60   warnings=225
Log files:  PixelData-0.log                88.0 KB     
Log files:  Processor-0.log                1.0 MB        errors=0    warnings=2   
Log files:  Tables-0.log                   18.0 KB       errors=0    warnings=2   
Log files:  TestDropBox.log                n/a
Log files:  master.err                     43.0 KB       errors=11   warnings=19 
Log files:  master.out                     0.0 KB       
Log files:  Total size                     74.45 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/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/home/cai/.local/bin:/home/cai/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: 189193472)

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... [RU

any suggestions ??

cheers, Saleh

Hi Saleh,

Do you still have the command-line you ran to install iviewer?

e.g. did you run the command listed https://pypi.python.org/pypi/omero-iviewer/ e.g.

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pip install -U omero-iviewer

Thanks,

Kenny

yes i did
i sent my logs also

Hi Saleh

I have re-installed the latest released version of iviewer on our server
and I could not reproduce your issue.
The url looks like

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iviewer/?images=4600&dataset=340

when I open it using the open_with option
which is the expected format.

Could it be that you have 2 versions of iviewer installed?
Will you be able to check?

Cheers
Jmarie

Hi again,

i was busy with somehting else, but i still have same issue.

i noticed that if i used the link which hast the following format

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iviewer/?images=153&dataset=151

works,

and the generated link after opening the iviewer 0.3 using open with is

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https://omero-cai.hhu.de/iviewer/151/?dataset=151

and they are not the same.

who responsable to generate the link during opening iviewer, i think openwith.js

cheers, Saleh

Hi Salah,

I suspect your browser has cached the /static/omero_iviewer/openwith.js.
You could try in a different browser or use "private" mode where you haven't already cached this.

Or you could open that url and check whether the js you get at /static/omero_iviewer/openwith.js is showing the latest version at https://github.com/ome/omero-iviewer/bl ... penwith.js
Try a refresh of this if it's not showing the latest.

Hopefully that's all that's needed?

Regards,
Will.

However, I realised that the AJAX requests to load the openwith.js is adding a cache-busting querystring, eg.
/static/omero_iviewer/openwith.js?_=1508504343120
So that should be enough to avoid caching issues.

Let us know how you get on.
Cheers,

Will

Hi Will,

Just a quick "me too'. On one of my installations I get the exact same behavior as @saleht. The generated URL is malformed in the exact same way. Coming in with a different browser or even a different machine doesn't help so it's something subtle in OMERO.web itself. Indeed probably something left behind from an older version of iviewer. Mine is on 5.4.0.

Cheers,
- Damir

Hi Will,
Following your lead to look at /static/omero_iviewer/openwith.js in the lib/python/omeroweb, I see that the version I have there is completely different from the version in the 0.3.0 package. I guess that during the startup of OMERO.web, it did not copy all the static files from the iviewer 0.3.0 package into that location but kept the older versions that were there from the 0.2.0 version.
So that brings up the question: how can you force it to copy those static files over again? Will it work to just do:
cd ~omero/OMERO.{server or py}/lib/python/omeroweb/static
rm -rf omero_iviewer

Thanks,
- Damir

Hi Will & Damir,


i did what Damir mention about -delete omero-iviewer from static folder-
it works now

thx for you both 4 your support
cheers, Saleh