Open Microscopy Environment

Hi,

we are new to OMERO and in the testing phase now . (So pretty much newbs.)
We are testing with the OMERO virtual appliance and I have one question.
After importing some CZI’s with OMERO.insight we connect via OMERO.web. Everything works fine.
My question is regarding to that files tree in the OMERO.web:

https://www.dropbox.com/s/xa823h58u6usg ... o_tree.PNG

How can I read out the Information of that tree (which files have been uploaded) for let’s say using it for a python oad ??

Kind regards,
Flaviu

Hi Flaviu

I'm not sure what you mean by "Python oad". You can easily get a list of images in a dataset in Python if you know the Dataset ID (given in the right hand panel of OMERO.web). For example, using the OMERO IPython shell:

Code: Select all

$ bin/omero shell --login
Previously logged in to octopus:4064 as user-1
Server: [octopus]
Username: [user-1]
Password:
Created session ba7a4cfb-2ede-4eab-8115-7d41f3d77c5d (user-1@octopus:4064). Idle timeout: 10.0 min. Current group: private-1
Python 2.7.7 (default, Jun  2 2014, 18:55:26)
Type "copyright", "credits" or "license" for more information.

IPython 2.1.0 -- An enhanced Interactive Python.
?         -> Introduction and overview of IPython's features.
%quickref -> Quick reference.
help      -> Python's own help system.
object?   -> Details about 'object', use 'object??' for extra details.

In [1]: import omero, omero.gateway

In [2]: conn=omero.gateway.BlitzGateway(client_obj=client)

In [3]: dataset=conn.getObject('Dataset',4709)

In [4]: images=list(dataset.listChildren())

In [5]: images
Out[5]:
[<_ImageWrapper id=50243>,
<_ImageWrapper id=50244>,
<_ImageWrapper id=50245>,
<_ImageWrapper id=50246>,
<_ImageWrapper id=50247>,
<_ImageWrapper id=50248>]


Thanks for your answer I think it will help me out

I have a second question regarding the dropbox function:
Let’s say I drop a CZI in to the dropbox folder. (OMERO takes it in and let the CZI in the folder).
What happens if I open the CZI from the dropbox folder let’s say with Fiji do some work on it an overwrite it? Will it be uploaded into OMERO as a new file? Will nothing happen?

Thanks

Flaviu wrote:I have a second question regarding the dropbox function:
Let’s say I drop a CZI in to the dropbox folder. (OMERO takes it in and let the CZI in the folder).
What happens if I open the CZI from the dropbox folder let’s say with Fiji do some work on it an overwrite it? Will it be uploaded into OMERO as a new file? Will nothing happen?

If you modify a file which is under /OMERO/DropBox then very likely it will be re-imported as a new image, though this is somewhat platform-specific. In general, you should consider the DropBox directory a write-once location. If you need this "edit-in-place" type of functionality, then see our In-place import documentation. But be careful: even then, modifying the files in place can lead to strange behavior.

Cheers,
~Josh

Hi all,
We tested out the dropbox function and everything worked fine. Every Image I copied into the /home/omero/OMERO.data/DropBox debian folder automatically appears in the web application. For testing we used the OMERO virtual appliance. So a virtual machine with the Oracle VirtualBox.

But now a problem appeared.

I wanted to use the Shared Folder function from VirtualBox Manager for the dropbox folder. So in settings, Shared Folders I set a Windows (7, 64bit) folder. After starting the virtual machine I typed in the command: mount –t vboxsf share mount_point. For “share” the name of the Windows folder, for “mount_point” the debian omero dp folder (/home/omero/OMERO.data/DropBox/Name). But now the dropbox functionality seems not to work anymore.

Any idea what I am doing wrong?

Kind regards

Hi Flaviu,

Under https://www.openmicroscopy.org/site/support/omero5/sysadmins/dropbox.html#prerequisites, the third bullet point states:

The filesystem which OMERO.dropbox watches must be local to the given operating system. Watching a network-attached share (NAS) is strictly *not* supported.

Based on your findings, I would guess that a vboxsf mount is working similarly to NAS and therefore no notifications are being received. Could you zip up the following files from your server and upload them either here or to http://qa.openmicroscopy.org.uk/qa/upload/?

• var/log/DropBox.log
• var/log/FileServer.log
• var/log/master.err
• var/log/master.out
• var/log/MonitorServer.log

Thanks,
~Josh

I've uploaded the file here.

Thanks for the logs, Flaviu.

The processes do seem generally healthy so my assumption is very much that Virtual Box is simply not producing notification events for file changes to this mount. In which case, I don't think this is going to be a viable DropBox setup. Sorry.

Regards,
~Josh

So it is not possible to use dropbox via Virtual Box ?? e.g. copy an image into a windows 7 dp folder -> Image appears in omero.web ??

Have you tried setting up a share the other way around, i.e. creating a shared folder inside the VirtualBox image and mounting that from your host? (this is just an idea, I haven't actually tried it).