Importing 'public' images from OMERO5.server to ImageJ

[tohsato]

We are hoping to allow any user to import images, which are managed by 'public user' on our OMERO.server (ver. 5.0.0, http://ssbd.qbic.riken.jp/omero/), into ImageJ via a plugin such as Bio-Formats Remote Importer and OMERO.insight without use of a password. Our configuration currently allows to access by OMERO.insight, but requires a password.
Does anyone have any suggestions?
Yukako.

[jburel]

Dear Yukako

A possible solution will be to start OMERO.insight from the webclient using Webstart and pass the session ID.
That option will require to adjust OMERO.insight to accept sessionID instead of user/password: this should be pretty straightforward, the second change is to pass parameters to OMERO.insight when launched via Webstart.

Cheers
Jmarie

[wmoore]

Another alternative might be to allow web users to simply upload images as attachments (E.g. to a Dataset) then have a server-side script which periodically uses the command-line importer to import the images into the appropriate Dataset.

This would remove the need for users to use Insight, although they'd need alternative instructions on how to upload images.
Also the command-line importer would need to handle import failures in some way - might need some supervision.

Just a thought!

[tohsato]

Dear Jmarie and Wmoore,

Thanks for your advices.

I would like to choice the 1st solution (adjustment of OMERO.insight).
Does such case I need to edit and compile the source of OMERO.server ?

However, I failed the compilation from the source using Java 1.7.0_45,
Python 2.6.6, and ICE3.4 on RedHat 6, even though binary OMERO.server ran properly
under the same conditions.

Code: Select all

$ git clone --recursive git://github.com/openmicroscopy/openmicroscopy
$ cd openmicroscopy
$./build.py
...
BUILD FAILED
/OMERO/openmicroscopy/build.xml:191: The following error occurred while executing this line:
/OMERO/openmicroscopy/components/antlib/resources/global.xml:411: The following error occurred while executing this line:
/OMERO/openmicroscopy/components/blitz/build.xml:28: The following error occurred while executing this line:
/OMERO/openmicroscopy/components/blitz/build.xml:212: The following error occurred while executing this line:
/OMERO/openmicroscopy/components/antlib/resources/global.xml:554: exec returned: 2

Best regards,
Yukako

[manics]

Hi Yukako

Could you paste or attach your entire build error? I think you're probably missing some build dependencies which are in addition to those required to run the server. On RHEL6 these include the java-1.7.0-openjdk-devel ice-python-devel ice-java-devel python-genshi packages (amongst others), if you show us the full error it should become clearer.

The other thing to beware of is which branch you're building. If you want to modify a server from the 5.0 series you'll need to check out the dev_5_0 branch, by default you'll check out our development branch.

Simon

[manics]

For RHEL/CentOS 6 you might also need to install python-setuptools and set the SLICEPATH environment variable:

Code: Select all

sudo yum -y install git java-1.7.0-openjdk-devel \
    ice-servers ice-python-devel ice-java-devel ice-c++-devel \
    python-genshi python-setuptools
export SLICEPATH=/usr/share/Ice-X.X.X/slice
./build.py


[tohsato]

Hi Simon and Manics,

Thanks! I successed to compile! My failure caused by loss of python-genshi and
and undefined SLICEPATH.

Next I will edit /components/insight/SRC/org/openmicroscopy/shoola/*.java
to implement a connection between ImageJ and OMERO.insight using session ID.

Please allow me to ask some questions if I am stuck the editing.

Thanks,
Yukako

[mtbc]

Dear Yukako,

I am glad to hear of your success, thank you for letting us know. We will be glad to answer any further questions you have on how to achieve this link with OMERO. Do also let us know if any of the existing developer documentation is unclear.

Cheers,
Mark

[tohsato]

Dear all,

Sorry to get straight to the point but could you tell me
how can I add the OMERO.insight function into source-compiled OMERO.server?

I could not find "Launch OMERO.insight via Java Web start" button on Webclient
and "/dist/lib/insight/" folder in source's directories
(Ver. 5.0.0/web-downloaded, 5.0.3/web-downloaded, and 5.1.0/git-clone).

I tried './build.py build-insight' and successed, but did not appear those.

Best regards,
Yukako.

[manics]

Hi Yukako

To get Insight working via webstart you'll have to run './build.py release-webstart=signed' after './build.py', but be aware you'll have to modify your Java security settings to allow self-signed webstart applications to run (our releases are signed with our own code-signing certificate from a recognised certificate authority). Alternatively you could run './build.py release-clients', then unzip and run Insight from the command line.

Simon