[Fuge-devel] FuGE Hibernate Toolkit Version 1.0-SNAPSHOT

[Allyson Lister]

Hi all,

I've committed the first version of the hibernate stk. Yippee!

Docs at: http://fuge.sourceforge.net/stks/hibernate-stk/

There are a few things people should know about this:

URGENT

• There is a problem where the many-2-many relationship between Software and Equipment is not getting filled. I have posted to the Andromda forum, but without luck. For full details of this failure, please see that post: http://galaxy.andromda.org/forum/viewtopic.php?t=5837 . Does anyone have any ideas? In the meantime, all code will work without exceptions, but you lose all links that would normally be held in that table. There is a unit test which, if you run, will fail and illustrates the problem. You would also see the problem with the XmlDbRoundtripTest unit test, if I didn't purposefully remove those parts of the XML before comparison so that any other unknown errors would be displayed. Comparing the two XML files would result in missing equipment references in Software, and vice versa.
  

IMPORTANT

• Documentation is still fairly sparse. I'll continue working on it. Particularly, there is nothing in the docs yet regarding how to show MagicDraw where the andromda zips are.
  
• We need a location to host a maven repository of our STK jars. In this way (for instance), people using the hibernate stk can use the xsd stk jars without having to download and install the xsd stk themselves. I am happy to be the one who maintains this repo, but I have no physical location to put it. Many SF projects seem to use their public html space, but I know that SF frowns on the upload of any third-party jars to its website, as their licensing status may be unclear. Is there anyone who would mind hosting the FuGE maven repository?
• There is another limitation of one of the Unit tests that is run: I call it the AccessRight Chicken and the Egg problem. Full details of this are available on: http://fuge.sourceforge.net/stks/hibernate-stk/fuge-hibernate-books/fuge-hibernate/access-rights.html. If anyone has any ideas for possible solutions, that would be great.
  

OF LESS IMMEDIATE IMPORT

• There has been quite a bit of discussion on the list about which license to use: I have chosen MIT, as that seems to have been the consensus, but others can still speak up! The full text of the license, as it appears within the java documents, is as follows. I'm a little worried that I got the authors right - is the copyright really owned by the PSI and MGED society? Shouldn't the authors be FuGE developers, or the authors found in the documents, or something similar?
  

/**
 * Copyright Notice
 *
 * The MIT License
 *
 * Copyright (c) 2008 2007-8 Proteomics Standards Initiative / Microarray and Gene Expression Data Society
 *
 * Permission is hereby granted, free of charge, to any person obtaining a copy
 * of this software and associated documentation files (the "Software"), to deal
 * in the Software without restriction, including without limitation the rights
 * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
 * copies of the Software, and to permit persons to whom the Software is
 * furnished to do so, subject to the following conditions:
 *
 * The above copyright notice and this permission notice shall be included in
 * all copies or substantial portions of the Software.
 *
 * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
 * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
 * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
 * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
 * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
 * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
 * THE SOFTWARE.
 *
 * Acknowledgements
 *  The authors wish to thank the Proteomics Standards Initiative for
 *  the provision of infrastructure and expertise in the form of the PSI
 *  Document Process that has been used to formalise this document.
 */


--
Thanks,
Allyson :)

Allyson Lister
Research Associate
Centre for Integrated Systems Biology for Ageing and Nutrition
Newcastle University
http://www.cisban.ac.uk
School of Computing Science
Newcastle University
Newcastle upon Tyne, NE1 7RU

[Allyson Lister]

Hi all,

Michael had a problem sending this mail to the list - so, I've copied it in here myself, with my reply inline. thanks! :)

From: Miller, Michael D (Rosetta)
Sent: Monday, July 21, 2008 9:38 AM
To: 'fuge-...@lists.sourceforge.net'
Subject: RE: [Fuge-devel] FuGE Hibernate Toolkit Version 1.0-SNAPSHOT

hi allyson,

terrific job.

"There is a problem where the many-2-many relationship between Software and Equipment is not getting filled"

one of the very pragmatic things i did here with our customized version of the MAGEstk was to write code that automatically ran that did anything that wasn't done by the automatic generation.  so, in a sense, the code is still all automatically generated but some small pieces were not generic.  certainly not ideal but then everything worked out of the box.

That's an interesting point. I'm not sure where in the autogenerated code the session.flush() should go - I suspect directly after the loading of any software with an equipment ref, or vice versa. I still haven't heard from the Andromda forums - I may re-post to the hibernate section, as I'm not getting any joy from the spring section, but I'm not sure that would help. I suppose I could write a script that makes the appropriate change... I'll have a think about this. Thanks for the idea!
 

"There is another limitation of one of the Unit tests that is run: I call it the AccessRight Chicken and the Egg problem."

i take it these unit tests are automatically generated?  for unit tests i think you can feel free to use them as a start in cases like this and hand write an addition to it that makes sure the test runs as desired, which is more or less what you've done.

As far as I know, andromda can't generate unit tests? Maybe it can... Anyway, these tests are hand-written to illustrate a problem. Yeah, I agree that it is only the limitation of the unit test that would make this error appear, and for now I am ignoring it, so it's not a high priority... thanks!

Allyson :)

cheers,
michael