[Pipet Devel] New piper version + docs

J.W. Bizzaro bizzaro at geoserve.net
Fri Jun 9 23:17:14 EDT 2000

Brad Chapman wrote:

> This version is quite changed from the
> past ones since we are now using CORBA for communication between the
> user interface and the definition layer. Excitement abounds!


BTW, do you want the sockets API to be phased out?

> This
> change-over has resulted in some loss of functionality from the socket
> version as a result. What works right now is addition, deletion,
> connection and disconnection of loci, basically. The container widget
> stuff hasn't been changed over yet (mainly because I'm not sure how to
> do it with the new system.)

There was quite a bit of confusion between you and me about how to implement
this container.  I eventually wanted to make container == workspace of
unconnected loci, and we argued about that for a while.

I still want container == workspace (network) of unconnected loci (nodes) for
MOST types of containers.  But, a database "container" is a special case,
particularly since there are so many database "items" to consider (we can't
make one node per database item when some databases are huge).  So, perhaps
databases should not be workspaces but instead treated like any other external

>     There are also a ton of other changes, including a switch to use
> the most recent 4DOM. This switch involves a lot of changes in
> namespaces, since 4DOM is going to become the default DOM for python,
> so it has now taken the xml.dom namespace over. So you'll need to have
> this version, and also need to be careful when installing it to blast
> away the PyXML version of xml.dom.

Do they still use "node" in the namespace?

>     Thanks to Jeff's keen eye, I also fixed some install bugs (and
> hopefully didn't add any more), and I added an extra target
> --with-piperhome=/a/different/path/to/put/piper, so that people can
> put the libraries in one place and the scripts to run it in another
> (and add version numbers).


>     I also updated the dl documentation and added two new docs, "How
> to Plug a Program into Piper"

Super.  But maybe this should be part of the BL or PL docs.

> and "How to write a UI for Piper."

And this should be part of the UIL docs.  Jeez Brad, now you're doing our work
for us ;-)

> My
> idea is that we can use these as a starting point to get more docs and
> firm up our ideas about how to do things. In the user interface one, I
> tried to address some of the points Deanne and Jeff raised on the list
> in their disccusion on peep about how to talk to the dl. I would
> really like to hear feedback on these docs so we can make them better.
> These are just my attempts to do this from a marathon session of doc
> writing. The html versions of these docs are in the distribution, and
> pdf versions are at the university of georgia site.

Cooooowel.  I'll check it out.

>     I'm very excited, as this is taken us much closer to getting
> piper integrated with Overflow--we've even got Overflow node types
> being loaded up (now we just need a little GUI to go with 'em).

*tries to sneak out of room without being noticed*

Seriously, my (and our) goal is to make BL and PL network design and operation
almost identical from the user's point of view.

So, when do we want to put the Piper source on our sourceforge system?

                      |           J.W. Bizzaro           |
                      |                                  |
                      | http://bioinformatics.org/~jeff/ |
                      |                                  |
                      |        BIOINFORMATICS.ORG        |
                      |           The Open Lab           |
                      |                                  |
                      |    http://bioinformatics.org/    |

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