search from OMERO.insight

[bhcho]

Hi Josh and Jmarie,

I'm not sure who is right.
jmarie says it has sort of limitation in search functionality and Josh says the external xml file is queriable for search as long as it is linked to an image.
But Josh, I already linked that external file to an image and tried to search by query from OMERO.insight (and failed).

BK

[jmoore]

BK,

can you try to reproduce with the code snippet I pasted and see if you get any results? If not, then both the code and Insight are showing the same results (which is expected) and it probably has something to do with your indexer. This may be one of the bugs I've recently fixed like http://trac.openmicroscopy.org.uk/omero/ticket/2982. If not, then something else is going on and we'll need to evaluate further.

~Josh.

[bhcho]

Hi J,

I just followed the snippet and I got something strange.
the created image id and the searched image id are different.
I guess the searched image id is the one I already linked with the same external xml file before.


Anyway,
what should I do with my indexer?
Do I need to update my OMERO server with a build version?

BK

[jmoore]

Hi BK,

I was working in a clean environment. In your case, search.byFullText may well return more than one image with the value. You'll most likely need to use:

Code: Select all

ids = [x.id.val for x in search.results()]
if i.id.val in ids:
    print "Found image ", i.id.val


Cheers,
~Josh

[bhcho]

Hi, Josh,

the problem is that I can't get any retrieved image from OMERO.insight (4.2.0 release version).
what should I do to see the retrieved images?
Do I need to update a build version of both OMERO server and clients ?
If so, could you please direct me to the link to the build version?

Best,
BK

[jmoore]

BK,

Remember the reason I was asking you to try out the snippet was so that I could know what exactly it is you need to do next:

can you try to reproduce with the code snippet I pasted and see if you get any results? If not, then both the code and Insight are showing the same results (which is expected) and it probably has something to do with your indexer. This may be one of the bugs I've recently fixed like http://trac.openmicroscopy.org.uk/omero/ticket/2982. If not, then something else is going on and we'll need to evaluate further.

Would you mind modifying the Python script as specified or examine the return value of "search.results()" manually and see whether or not you are getting the intended image back?

Thanks!
~Josh

[bhcho]

Hi Josh,

I followed your last snippet and I retrieved nothing.
when I see the "ids" from below, it's just the other image ID as i described before.

Code: Select all

ids = [x.id.val for x in search.results()]
if i.id.val in ids:
    print "Found image ", i.id.val

[jmoore]

Ok, thanks for the info, BK.

Then it does look like the issue is the indexer. Could you try a 4.2.1-DEV download which we are also currently testing:

• http://hudson.openmicroscopy.org.uk/job/OMERO-trunk/1132/artifact/trunk/target/OMERO.server-4.2.1-DEV-r8376-trunk1132.zip
• http://hudson.openmicroscopy.org.uk/job/INSIGHT/1882/ (choose your proper platform)

and let us know how it goes.

Cheers,
~Josh.

[bhcho]

Hi Josh,

could you tell me or direct me to the link how to install safely and stably upgrade my server/clients with the build version?
I dont want to frustrate myself.

BK

[jmoore]

Hi BK,

the upgrade process for 4.2.0 to 4.2.1 has not yet been added to:
http://www.openmicroscopy.org/site/support/omero4/server/upgrade
as we're still in the last stages of testing.

That being said, other than the configuration you performed on your 4.2.0 server (stored in etc/grid/config.xml, which you can copy over or recreate) there should be nothing significant you need to do other than unpack the zip and run bin/omero admin start. If you are using OMERO.web, it will need special handling.

For example, the script we use internally is:

Code: Select all

DIR=$1
DJANGO_PID="$HOME/OMERO-CURRENT/var/django.pid"

OMERO-CURRENT/bin/omero admin status --nodeonly && OMERO-CURRENT/bin/omero admin stop
if [ -e $DJANGO_PID ]; then
        kill `cat $DJANGO_PID`
fi
rm -f OMERO-CURRENT
rm -f $HOME/web-log/*.log
ln -s $DIR OMERO-CURRENT
cd OMERO-CURRENT
cp $HOME/config.xml etc/grid
bin/omero admin start

#WEB
chmod 755 var
mkdir var/lib
cp $HOME/custom_settings.py var/lib/custom_settings.py
python var/lib/custom_settings.py
bin/omero web syncmedia
bin/omero web start


Alternatively, you can keep an eye on the /support/omero4/server/upgrade page (or CC yourself on #3184) for the formal instructions.We'll do what we can to help you with the QA builds, but as a pre-release user we need your help as least as much as you need ours.

Cheers,
~Josh.