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You are here: Home Community Minutes Meetings November 2011 Dundee Developers' Meeting BlitzGateway discussion

BlitzGateway discussion

Participants: Simone Leo (CRS4), Luca Lianas (CRS4), Gianmauro Cuccuru (CRS4), Chris Allan (OMERO), Carlos Neves (OMERO), Scott Littlewood (OMERO), Aleksandra Tarkowska (OMERO)

The purpose of the discussion was to introduce CRS4 development team to new changes in and check how does it fit to their existing project. It also allows OMERO Python team to get brief overview of integration with system handling both genetic and clinical data for large scale population.


  • Luca briefly presented omero.model extensions.

  • Luca: We are planning to have automatic generator from archetypes to omero.model. We use clinical data for our tables. Every object inside the system has an action, it is operation that creates the object in the system. This kind of action can be define as operation that runs on top of the object and modify it. Actions object describe how to perform the action. Different actions based on different targets. If I want to retrieve how the object was produced, I can follow link back from object through the action to target.

  • Chris: How many unique types do you have? Luca: About 90. They are populated by tool called Galaxy.

  • Chris: What is VID?

  • Luca: We put global identifier for every object VID, is a hex value prefixed by V0. It is generated with uuid module from python.

  • Luca: We have a proxy class (ProxyCore in that access the proxy to handles connection the omero server. Then we use meta classes to give the common functions.

  • Chris: BlitzObject interrogates the runtime omero object and looks what fields are in that object. You could slot in the BlitzObjectWrappers without any changes. Because does find_all_by_query you would need to redundant client services, apart from specific things for your app.

  • Ola: How do you set up OMERO accounts and manage permissions?

  • Luca: We have various users to access various data. We use existing Django Permission mechanism. We have our own Django database build on top of Django Admin framework. We have two different type of users, those who have only access to web app as well as those who needs access OMERO directly.

  • Luca: We have our own small authentication app.

  • Josh (from feather discussion): in order to solve the authentication issues you could either try to write your own Password Provider calling external authentication resources (your Django auth) and plug it into OMERO or use LDAP for both OMERO and web app.

  • Chris: How we can access your code in svn?

  • Simone: We could move this to external subversion.

  • Chris:It would be good to bring those things together, because now we have 4 different implementation of the same thing like OMERO.tables.

  • Simone: We faced issues with OMERO.session lifetime.

  • Chris: Which OMERO version do you use?

  • Luca: 4.3.2

  • Chris: Keep in mind that there were bug in Ice. We fixed it in 4.3.0? We noticed in Java some objects are not exactly clean up. In action with large number of objects we faced garbage collection issues. Would be good to have a usecase specifying creation of object, we will be able to find what is happened and improve it for you.

Actions agreed upon:

  • CRS4 will adopt BlitzGateway connection wrapper as well as BlitzObjectWrappers and its extensions with the existing code.
  • CRS4 will make their source code available to OMERO team.
  • OMERO python team will investigate existing usecases of OMERO.tables across various python applications and define collective ways of working with tables.
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