[ome-devel] questions about OMERO

[Jason Swedlow]

Hi Curtis-

Thanks for the feedback.

On 19 Feb 2007, at 21:48, Curtis Rueden wrote:

> Hi,
>
> With Chris's help, I was able to get OMERO working pretty well -- it
> was largely an issue of documentation. To anyone else installing
> OMERO, I suggest following the "manual install" instructions, and
> ignoring the "quick install" option. As time allows, we plan to
> investigate implementation of a "Download from OMERO" plugin for
> ImageJ as part of our plugin suite.

OK, sounds cool.  We'll work on the docs to make sure they are as  
clear as possible.

Many of your questions regard functionality that is planned-- see  
http://cvs.openmicroscopy.org.uk/tiki/tiki-index.php?page=Feb+2007+Mtg 
+Agenda+and+Notes  Note that these are getting turned into real  
Roadmaps on the trac sites over the next few days.

>
> I do have some questions about the system, though:
>
> 1) Can OMERO export original files with no programming (e.g., from
> OMERO.insight)? If not, is this functionality planned? We would like
> to start by using OMERO as a "smart file server," with the ability to
> freely download original files from the database for use in external
> applications.

OMERO.insight doesn't support this functionality mostly because that  
kind of functionality wouldn't work for our users-- the files are  
just too big.  Obviously, we wanted to leverage the image server and  
rendering engine.  We do support uploading original files into the  
server, although we've currently turned that functionality off until  
we get a better idea of requirements.  We'll discuss it and let you  
know.  No, we will not  RECREATE proprietary file formats, but we are  
working on exporting OME-TIFF.

>
> 2) Is there currently a way to view all associated metadata for an
> Image -- such as a list of linked structures as in OME's web
> interface, or perhaps an XML view? It would be useful to get a nice,
> neat view of an Image's relevant metadata within OMERO.insight.
>

Working on that-- the key is the nice, neat part.  What's shown in  
insight is very limited-- deliberately.  We'll get there, but we want  
to display what people most often use.

> 3) Is there a command-line or other automation-friendly importer for
> OMERO? It would be helpful for some acquisition systems -- the
> acquired data could be uploaded to a dedicated machine (probably the
> OMERO server machine), which would perform an automated import.

Batch import from the server is coming.  It is obviously a critical  
functionality, although when we have polled our users, they want  
both.  We are getting there.

>
> 4) Is there a timeline for OMERO being able to import OME-TIFF and
> OME-XML, or some subset thereof?

Once we get a few things in Bio-Formats ironed out, it will be added,  
for sure, probably in 3.0-Beta2.

> It seems like the ability to freely
> handle OME-XML could be very useful for exchanging data between OME
> and OMERO. I suppose there is a sticking point with custom
> SemanticTypes, but I don't know enough about OMERO's architecture to
> have a feel for how difficult a problem that poses.

Probably a significant one, at least for someone wanting to do an  
automatic data model update (a la OME Server).  We want to make sure  
we have the steps necessary to do this correctly sorted out and doc'd  
before we release this.  However, we do have a tool that transfers  
data from an OME to an OMERO database (and only sees core OME  
types).  It has not been updated and is out of step with  
OMERO-3.0Beta1.  We want t have a better solution to interoperability  
and are discussing that right now (I need some time on the phone with  
Ilya, if I could just get a few moments...).

Thanks for your comments.  Always welcome.

Cheers,

Jason


>
> Thanks,
> Curtis
>
> On 2/9/07, Chris Allan <callan at blackcat.ca> wrote:
>>
>> On 8 Feb 2007, at 17:11, Curtis Rueden wrote:
>>
>>> Hi,
>>
>> Hi Curtis.
>>
>>>
>>> I installed OMERO today, but am having problems getting it to work.
>>>
>>> I am running Ubuntu 6.06 "Dapper" with PostgreSQL 8.0.7 and Java
>>> 1.5.0_06.
>>>
>>> For the OMERO server, I followed the installation instructions on  
>>> the
>>> OmeroLinuxInstallHowto tiki page. A few notes:
>>> * The -R and -S flags are not valid for createuser on my system,  
>>> so I
>>> left them off.
>>> * I told createuser that the "omero" user should not have permission
>>> to create additional users.
>>> * I eventually figured out that you must update the
>>> etc/local.properties file to reflect the chosen password for the
>>> "omero" postgres user. The "Quick Install" instructions do not  
>>> mention
>>> it.
>>
>> http://cvs.openmicroscopy.org.uk/tiki/tiki-index.php?
>> page=OmeroLinuxInstallHowto
>>
>> Just assuming you're using this documentation page. If you're not, is
>> there somewhere else you retrieved the information from Curtis?
>>
>>
>> The Quick Install assumes that you're going to use "omero"/"omero" as
>> your database user and password, it states:
>>
>> * NOTE: For a Quick Install it is assumed that you will follow the
>> examples laid out here with an password of omero for the omero
>> database user.
>>
>>
>> If you want to change these settings you must follow the "Manual
>> Install" instructions, where it states:
>>
>> * Edit the etc/local.properties file in the OMERO distribution based
>> upon your database user and password choices.
>>
>>
>> Happy to modify the text and/or make it more explicit (Font size 32
>> maybe? :)). Thoughts?
>>
>>
>> So, have you followed the "Manual Install" instructions? As you've
>> changed the local.properties file, you must:
>>
>> export JBOSS_HOME=~/Desktop/omero-3.0-Beta1/jboss-4.0.4.GA
>> java omero update deploy
>>
>> (These instructions are in the "Reconfiguration" section of the
>> Install document)
>>
>> You can confirm proper deployment by examining the $JBOSS_HOME/ 
>> server/
>> default/deploy directory.
>>
>>>
>>
>> ...snip...
>>
>>> 10:33:53,199 WARN  [SettingsFactory] Could not obtain connection
>>> metadata
>>> org.jboss.util.NestedSQLException: Could not create connection; -
>>> nested throwable: (org.jboss.resource.JBossResourceException:
>>> Apparently wrong driver class specified for URL: class:
>>> org.postgresql.Driver, url: jdbc:postgresql://localhost/omero3); -
>>> nested throwable: (org.jboss.resource.JBossResourceException: Could
>>> not create connection; - nested throwable:
>>> (org.jboss.resource.JBossResourceException: Apparently wrong driver
>>> class specified for URL: class: org.postgresql.Driver, url:
>>> jdbc:postgresql://localhost/omero3))
>>>   at org.jboss.resource.adapter.jdbc.WrapperDataSource.getConnection
>>> (WrapperDataSource.java:94)
>>> ---
>>>
>>> Are these messages normal, or is something wrong with my
>>> configuration?
>>
>> Yes, it's normal.
>>
>> ...snip...
>>
>>>
>>> Any advice?
>>
>> See above.
>>
>>>
>>> -Curtis
>>
>> Ciao.
>>
>> -Chris
>>
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