Open Microscopy Environment

by **phm** » Tue Jun 12, 2018 3:40 pm

kennethgillen wrote:Hi Philippe,

You've truncated the output after bin/omero web start, with `...`, if we can see the entire output, we can look for the openwith.js file being copied.

Also, more than just 10 lines of OMEROweb.log would be useful - perhaps the entire logfile? You can send it to us via our QA system at http://qa.openmicroscopy.org.uk/qa/upload/ if you need a way to transfer larger files.

ls /home/omero/OMERO.py/lib/python/omeroweb/static | grep openwith
return nothing !!!

Apologies - the openwith.js file should be visible further down the filesystem, e.g.

Code: Select all
find /home/omero/OMERO.py/lib/python/omeroweb | grep openwith find /home/omero/OMERO.server/lib/python/omeroweb | grep openwith

And please run them both so we can compare what you had with what you have now.

When it was working, were you still starting OMERO.web from the OMERO.py directory via OMERO.py/bin/omero web start?

Thanks again,

Kenny

Hi Kenny,
Apologies, I found some errors from my part. I was running some commands outside from omerowebenv :evil:

Now I have a web page, but the template is wrong? All omero images are not view.

Code: Select all: omero@omero:~$>OMERO.py/bin/omero web stop Stopping OMERO.web... [OK] OMERO.web WSGI workers (PID 4951) killed. Removed stale /home/omero/OMERO.py/var/django.pid omero@omero:~$>source /home/omero/omerowebvenv/bin/activate (omerowebvenv) omero@omero:~$>sudo rm -rf /tmp/* (omerowebvenv) omero@omero:~$>rm -rf OMERO.py/lib/python/omeroweb/static/* (omerowebvenv) omero@omero:~$>OMERO.py/bin/omero config get omero.mail.config=true omero.mail.host=smtps.college-de-france.fr omero.mail.password=******** omero.mail.username=philippe.mailly@college-de-france omero.web.application_server=wsgi-tcp omero.web.apps=["omero_figure", "omero_iviewer", "omero_fpbioimage"] omero.web.login_logo=https://omero.college-de-france.fr/omero/static/webclient/image/logo_CIRB.jpg omero.web.open_with=[["Image viewer", "webgateway", {"supported_objects": ["image"], "script_url": "webclient/javascript/ome.openwith_viewer.js"}], ["omero_figure", "new_figure", {"supported_objects": ["images"], "target": "_blank", "label": "OMERO.figure"}], ["omero_iviewer", "omero_iviewer_index", {"supported_objects": ["images", "dataset", "well"], "script_url": "omero_iviewer/openwith.js", "label": "OMERO.iviewer"}], ["omero_fpbioimage", "fpbioimage_index", {"supported_objects": ["image"], "script_url": "fpbioimage/openwith.js", "label": "FPBioimage"}]] omero.web.prefix=/omero omero.web.static_url=/omero/static/ 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"}]] omero.web.viewer.view=omero_iviewer.views.index

Code: Select all: (omerowebvenv) omero@omero:~$>OMERO.py/bin/omero config get omero.mail.config=true omero.mail.host=smtps.college-de-france.fr omero.mail.password=******** omero.mail.username=philippe.mailly@college-de-france omero.web.application_server=wsgi-tcp omero.web.apps=["omero_figure", "omero_iviewer", "omero_fpbioimage"] omero.web.login_logo=https://omero.college-de-france.fr/omero/static/webclient/image/logo_CIRB.jpg omero.web.open_with=[["Image viewer", "webgateway", {"supported_objects": ["image"], "script_url": "webclient/javascript/ome.openwith_viewer.js"}], ["omero_figure", "new_figure", {"supported_objects": ["images"], "target": "_blank", "label": "OMERO.figure"}], ["omero_iviewer", "omero_iviewer_index", {"supported_objects": ["images", "dataset", "well"], "script_url": "omero_iviewer/openwith.js", "label": "OMERO.iviewer"}], ["omero_fpbioimage", "fpbioimage_index", {"supported_objects": ["image"], "script_url": "fpbioimage/openwith.js", "label": "FPBioimage"}]] omero.web.prefix=/omero omero.web.static_url=/omero/static/ 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"}]] omero.web.viewer.view=omero_iviewer.views.index

Code: Select all: (omerowebvenv) omero@omero:~$>OMERO.py/bin/omero web start Copying '/usr/lib/python2.7/site-packages/omero_figure/static/figure/figure.js' Copying '/usr/lib/python2.7/site-packages/omero_figure/static/figure/templates.js' Copying '/usr/lib/python2.7/site-packages/omero_figure/static/figure/3rdparty/json2.js' Copying '/usr/lib/python2.7/site-packages/omero_figure/static/figure/3rdparty/backbone-1.0.0.js' Copying '/usr/lib/python2.7/site-packages/omero_figure/static/figure/3rdparty/underscore-1.3.3.js' Copying '/usr/lib/python2.7/site-packages/omero_figure/static/figure/3rdparty/bootstrap-colorpicker/css/bootstrap-colorpicker.min.css' Copying '/usr/lib/python2.7/site-packages/omero_figure/static/figure/3rdparty/bootstrap-colorpicker/css/bootstrap-colorpicker.css' Copying '/usr/lib/python2.7/site-packages/omero_figure/static/figure/3rdparty/bootstrap-colorpicker/img/bootstrap-colorpicker/alpha.png' Copying '/usr/lib/python2.7/site-packages/omero_figure/static/figure/3rdparty/bootstrap-colorpicker/img/bootstrap-colorpicker/hue.png' Copying '/usr/lib/python2.7/site-packages/omero_figure/static/figure/3rdparty/bootstrap-colorpicker/img/bootstrap-colorpicker/hue-horizontal.png' Copying '/usr/lib/python2.7/site-packages/omero_figure/static/figure/3rdparty/bootstrap-colorpicker/img/bootstrap-colorpicker/alpha-horizontal.png' Copying '/usr/lib/python2.7/site-packages/omero_figure/static/figure/3rdparty/bootstrap-colorpicker/img/bootstrap-colorpicker/saturation.png' Copying '/usr/lib/python2.7/site-packages/omero_figure/static/figure/3rdparty/bootstrap-colorpicker/js/bootstrap-colorpicker.min.js' Copying '/usr/lib/python2.7/site-packages/omero_figure/static/figure/3rdparty/bootstrap-colorpicker/js/bootstrap-colorpicker.js' Copying '/usr/lib/python2.7/site-packages/omero_figure/static/figure/3rdparty/raphael-2.1.2/raphael.js' Copying 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'/usr/lib/python2.7/site-packages/omero_fpbioimage/static/fpbioimage/FPBioimage/FPBioimage.data.unityweb' Copying '/usr/lib/python2.7/site-packages/omero_fpbioimage/static/fpbioimage/FPBioimage/full.png' Copying '/usr/lib/python2.7/site-packages/omero_fpbioimage/static/fpbioimage/FPBioimage/FPBioimage.json' Copying '/usr/lib/python2.7/site-packages/omero_fpbioimage/static/fpbioimage/FPBioimage/FPBioimage.asm.memory.unityweb' Copying '/usr/lib/python2.7/site-packages/omero_fpbioimage/static/fpbioimage/FPBioimage/FPBioimage.asm.framework.unityweb' Copying '/usr/lib/python2.7/site-packages/omero_fpbioimage/static/fpbioimage/FPBioimage/download.js' Copying '/usr/lib/python2.7/site-packages/omero_fpbioimage/static/fpbioimage/FPBioimage/FPProgress.js' Copying '/usr/lib/python2.7/site-packages/omero_fpbioimage/static/fpbioimage/FPBioimage/logo.png' Copying '/usr/lib/python2.7/site-packages/omero_fpbioimage/static/fpbioimage/FPBioimage/FPLoader.js' Copying '/usr/lib/python2.7/site-packages/omero_fpbioimage/static/fpbioimage/FPBioimage/empty.png' Copying '/home/omero/OMERO.py/lib/python/omeroweb/feedback/static/feedback/css/layout.css' Copying '/home/omero/OMERO.py/lib/python/omeroweb/webadmin/static/webadmin/css/chosen.css' Copying '/home/omero/OMERO.py/lib/python/omeroweb/webadmin/static/webadmin/css/dusty.css' Copying '/home/omero/OMERO.py/lib/python/omeroweb/webadmin/static/webadmin/css/drivespace.css' Copying '/home/omero/OMERO.py/lib/python/omeroweb/webadmin/static/webadmin/css/picklist.css' Copying '/home/omero/OMERO.py/lib/python/omeroweb/webadmin/static/webadmin/image/active.png' Copying '/home/omero/OMERO.py/lib/python/omeroweb/webadmin/static/webadmin/image/ldap.png' Copying '/home/omero/OMERO.py/lib/python/omeroweb/webadmin/static/webadmin/image/frame_edit.png' Copying '/home/omero/OMERO.py/lib/python/omeroweb/webadmin/static/webadmin/image/edit.png' Copying 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'/home/omero/OMERO.py/lib/python/omeroweb/webclient/static/webclient/image/comment/comment_repeater_rev.png' Copying '/home/omero/OMERO.py/lib/python/omeroweb/webclient/static/webclient/image/comment/comment_repeater.png' Copying '/home/omero/OMERO.py/lib/python/omeroweb/webclient/static/webclient/image/comment/comment_cap_rev.png' Copying '/home/omero/OMERO.py/lib/python/omeroweb/webclient/static/webclient/image/comment/comment_foot.png' Copying '/home/omero/OMERO.py/lib/python/omeroweb/webclient/static/webclient/image/help/basket1.gif' Copying '/home/omero/OMERO.py/lib/python/omeroweb/webclient/static/webclient/image/menu/import.png' Copying '/home/omero/OMERO.py/lib/python/omeroweb/webclient/static/webclient/image/menu/share.png' Copying '/home/omero/OMERO.py/lib/python/omeroweb/webclient/static/webclient/image/menu/history.png' Copying '/home/omero/OMERO.py/lib/python/omeroweb/webclient/static/webclient/image/menu/menu_with_import.png' Copying 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'/home/omero/OMERO.py/lib/python/omeroweb/webclient/static/webclient/javascript/ome.openwith_viewer.js' Copying '/home/omero/OMERO.py/lib/python/omeroweb/webclient/static/webclient/javascript/jquery.form-3.51.js' Copying '/home/omero/OMERO.py/lib/python/omeroweb/webclient/static/webclient/javascript/jquery.jstree.ometools_plugin.js' Copying '/home/omero/OMERO.py/lib/python/omeroweb/webclient/static/webclient/javascript/jquery.jstree.locate_plugin.js' Copying '/home/omero/OMERO.py/lib/python/omeroweb/webclient/static/webclient/javascript/jquery.infieldlabel-0.1.js' Copying '/home/omero/OMERO.py/lib/python/omeroweb/webclient/static/webclient/javascript/jquery.jstree.fields_plugin.js' Copying '/home/omero/OMERO.py/lib/python/omeroweb/webclient/static/webclient/javascript/ome.chgrp.js' Copying '/home/omero/OMERO.py/lib/python/omeroweb/webclient/static/webclient/javascript/jquery.jstree.omecut_plugin.js' Copying '/home/omero/OMERO.py/lib/python/omeroweb/webclient/static/webclient/javascript/ome.right_panel_customanns_pane.js' Copying '/home/omero/OMERO.py/lib/python/omeroweb/webclient/static/webclient/javascript/ome.right_panel_mapanns_pane.js' Copying '/home/omero/OMERO.py/lib/python/omeroweb/webclient/static/webclient/javascript/ome.make_movie.js' Copying '/home/omero/OMERO.py/lib/python/omeroweb/webclient/static/webclient/javascript/jquery.jstree.conditionalselect_plugin.js' Copying '/home/omero/OMERO.py/lib/python/omeroweb/webclient/static/webclient/javascript/jquery.jstree.truncatetext_plugin.js' Copying '/home/omero/OMERO.py/lib/python/omeroweb/webclient/static/webclient/javascript/ome.right_panel_fileanns_pane.js' Copying '/home/omero/OMERO.py/lib/python/omeroweb/webclient/static/webclient/javascript/ome.thumbnail_figure.js' Copying '/home/omero/OMERO.py/lib/python/omeroweb/webclient/static/webclient/javascript/jquery.editinplace-0.1.2.js' Copying '/home/omero/OMERO.py/lib/python/omeroweb/webclient/static/webclient/javascript/ome.tree.js' Copying '/home/omero/OMERO.py/lib/python/omeroweb/webclient/static/webclient/javascript/ome.right_panel_ratings_pane.js' Copying '/home/omero/OMERO.py/lib/python/omeroweb/webclient/static/webclient/javascript/jquery.jstree.pagination_plugin.js' Copying '/home/omero/OMERO.py/lib/python/omeroweb/webclient/static/webclient/javascript/ome.right_panel_tags_pane.js' Copying '/home/omero/OMERO.py/lib/python/omeroweb/webclient/static/webclient/javascript/modernizr-2.5.3.js' Copying '/home/omero/OMERO.py/lib/python/omeroweb/webclient/static/webclient/javascript/ome.split_view_figure.js' Copying '/home/omero/OMERO.py/lib/python/omeroweb/webclient/static/webclient/javascript/ome.webclient.actions.js' Copying '/home/omero/OMERO.py/lib/python/omeroweb/webclient/static/webclient/javascript/ome.tagging_form.js' Copying '/home/omero/OMERO.py/lib/python/omeroweb/webclient/static/webclient/javascript/ie8_pngfix/supersleight-min.js' Copying '/home/omero/OMERO.py/lib/python/omeroweb/webclient/static/webclient/javascript/slider/range.js' Copying '/home/omero/OMERO.py/lib/python/omeroweb/webclient/static/webclient/javascript/slider/slider.js' Copying '/home/omero/OMERO.py/lib/python/omeroweb/webclient/static/webclient/javascript/slider/timer.js' Post-processed 'omeroweb.viewer.min.css' as 'omeroweb.viewer.min.css' Post-processed 'omeroweb.viewer.min.js' as 'omeroweb.viewer.min.js' 380 static files copied to '/home/omero/OMERO.py/lib/python/omeroweb/static', 2 post-processed. Clearing expired sessions. This may take some time... [OK] Starting OMERO.web... [OK]

Code: Select all: (omerowebvenv) omero@omero:~$>find /home/omero/OMERO.py/lib/python/omeroweb | grep openwith /home/omero/OMERO.py/lib/python/omeroweb/static/omero_iviewer/openwith.js /home/omero/OMERO.py/lib/python/omeroweb/static/webclient/image/icon_openwith_toolbar.png /home/omero/OMERO.py/lib/python/omeroweb/static/webclient/image/icon_openwith.png /home/omero/OMERO.py/lib/python/omeroweb/static/webclient/javascript/ome.openwith_viewer.js /home/omero/OMERO.py/lib/python/omeroweb/static/fpbioimage/openwith.js /home/omero/OMERO.py/lib/python/omeroweb/webclient/static/webclient/image/icon_openwith_toolbar.png /home/omero/OMERO.py/lib/python/omeroweb/webclient/static/webclient/image/icon_openwith.png /home/omero/OMERO.py/lib/python/omeroweb/webclient/static/webclient/javascript/ome.openwith_viewer.js (omerowebvenv) omero@omero:~$>find /home/omero/OMERO.server/lib/python/omeroweb | grep openwith /home/omero/OMERO.server/lib/python/omeroweb/static/webclient/image/icon_openwith_toolbar.png /home/omero/OMERO.server/lib/python/omeroweb/static/webclient/image/icon_openwith.png /home/omero/OMERO.server/lib/python/omeroweb/static/webclient/javascript/ome.openwith_viewer.js /home/omero/OMERO.server/lib/python/omeroweb/webclient/static/webclient/image/icon_openwith_toolbar.png /home/omero/OMERO.server/lib/python/omeroweb/webclient/static/webclient/image/icon_openwith.png /home/omero/OMERO.server/lib/python/omeroweb/webclient/static/webclient/javascript/ome.openwith_viewer.js

Philippe

by **kennethgillen** » Tue Jun 12, 2018 4:32 pm

Hi Philippe,

Now I have a web page, but the template is wrong? All omero images are not view.

Could you please send us

OMEROweb.log file, either the whole file, zipped, or the last several hundred lines.
Screenshot showing what you're seeing

Many thanks,

Kenny

by **phm** » Wed Jun 13, 2018 8:00 am

kennethgillen wrote:Hi Philippe,

Now I have a web page, but the template is wrong? All omero images are not view.

Could you please send us

OMEROweb.log file, either the whole file, zipped, or the last several hundred lines.
Screenshot showing what you're seeing

Many thanks,

Kenny

Hi Kenny,
Here the log and snapshot.
Thanks
Philippe

by **kennethgillen** » Fri Jun 15, 2018 3:18 pm

Hi Philippe,

In the OMEROweb.log we can only see a png, personal32.png, as an error.

Your screenshot shows many more files, including the .CSS, as missing.

Your browser's developer toolbar and server's NGINX logs should show you more 404 errors than just this file.

If they do, can you please send them to us as well?

There's certainly a mismatch between what's being requested and failing in the OMEROweb.log and how OMERO.web and NGINX are configured.

Hopefully we can track it down.

Many thanks,

Kenny

by **phm** » Mon Jun 18, 2018 8:37 am

kennethgillen wrote:Hi Philippe,

In the OMEROweb.log we can only see a png, personal32.png, as an error.

Your screenshot shows many more files, including the .CSS, as missing.

Your browser's developer toolbar and server's NGINX logs should show you more 404 errors than just this file.

If they do, can you please send them to us as well?

There's certainly a mismatch between what's being requested and failing in the OMEROweb.log and how OMERO.web and NGINX are configured.

Hopefully we can track it down.

Many thanks,

Kenny

Hi Kenny,
In my browser's developer toolbar I found that all images from OMERO are missing but not my as logo image. In fact if I look in omeroweb static folder in OMERO.py the webgateway folder is missing ????
I copied the webgateway from OMERO.server to the OMERO.py folder and now I have the good images for the log page, but when I got the next page some menu locations are wrong and when I click in Data menu it go back to the login page.
I copied the 3rdparty also, then I can log and use the omero pages !

Thanks
Philippe

by **kennethgillen** » Tue Jun 19, 2018 10:24 am

Hi Philippe,

"I copied the 3rdparty also, then I can log and use the omero pages !"

Does that mean your OMERO.web is happy and working fully again?

Many thanks,

Kenny

by **phm** » Thu Jun 28, 2018 11:58 am

kennethgillen wrote:Hi Philippe,

"I copied the 3rdparty also, then I can log and use the omero pages !"

Does that mean your OMERO.web is happy and working fully again?

Many thanks,

Kenny

Hi Kenny,
Yes all functionalities are working.
Philippe

Open Microscopy Environment

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Re: Iviewer and fpbioimage web apps

Re: Iviewer and fpbioimage web apps

Re: Iviewer and fpbioimage web apps

Re: Iviewer and fpbioimage web apps

Re: Iviewer and fpbioimage web apps

Re: Iviewer and fpbioimage web apps

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