[Pipet Devel] While you're in CVS...

J.W. Bizzaro bizzaro at geoserve.net
Mon Dec 20 12:52:11 EST 1999

Brad Chapman wrote:
>         I have done some actual coding (woo-hoo!) on some of the
> filesystem/container stuff we were talking about and just committed it to
> cvs in a brand new directory: loci-file.


> 5. Click okay, and the program will write out a file 'XMLoutput.xml'
> containing the directory substructure modelled as an XML-type document.
> 6. Click on File and Exit in the main window, since that's all it does.
> 7. Check out XMLoutput.xml and see if it accurately represents the filesystem.

The XML looks decent to me.

I'd suggest looking at the 'xmllib' module that actually comes with Python. 
We probably should use it (an althernative is Gnome's LibXML) for all of our
XML work.  Of course it'll save quite a bit of coding for reading and (I
think) writing XML.  Look at 'xmlparse.py' (bottom half of file) in the
loci-core module for an example of its use in parsing.

There is one catch to 'file2XML.py': It recursively descends subdirectories,
which is not needed (it's neat that you made it do that though).  A container
only needs to know the contents (types, etc.) of its top level directory. 
Only if you DnD a 'sub-container'/subdirectory out of the list, will the
contents of the subdir need to be known: That's when a new container,
containing the subdirectory, is made.

> time with it. Please let me know if I messed up the cvs commit or if
> anything else is horrible wrong and I'll try to fix it.

The only 'problem' we're having with making new directories via CVS is that
the ownership is by default username.username.  It needs to be username.cvs. 
I can fix that as root, and any user can fix it, by going to


and typing

    $ chown -R .cvs <modulename>

I already did that for loci-file, but if you make a new directory in
loci-file, you need to check that it is set to group cvs (and that it is group
read/writable).  Otherwise, another user will get a 'permission denied' error
doing a checkout.

>         WRT all of the discussion on the list--these are my quick thoughts
> on the loci as Apache type filesystem stuff:
> 1. As much as I hate config files, we probably need a loci.conf file to
> specify things like $LOCI_ROOT and private and public directories.

We need to define all sorts of settings anyway.  Maybe we'll use XML.

> I think
> instead of having specific defined directories for public and private, we
> should just take the Apache-type approach and specifically specify private
> directories within the $LOCI_ROOT file system. Although I could really care
> less where Loci is on my file system, people, in general, like to have
> control over the location of their programs and will probably want to
> specify it.

So all of $LOCI_ROOT is public unless otherwise specified?  I'd agree if the
rest of the filesystem was _privately_ accessible.

For example, most binaries are installed to


If $LOCI_ROOT were set to


All those lovely bioinformatics apps in /usr/bin/ would be inaccessible, even
privately :-(

> 2. How are we going to deal with security issues surrounding programs? Will
> all programs running under Loci need to be located within the $LOCI_ROOT
> filesystem? If so, will they all need to be in a specific directory
> ($LOCI_ROOT/bin?) like cgi-scripts in apache? I really know nothing about
> security so I'm just throwing out an idea.

Pretty much what I addressed above.  You wouldn't have access to /usr/bin/
unless you used symlinks, which is a possibility.

I'm not a security guru myself, but some on this list seem to know quite a
bit.  Perhaps someone should be appointed 'Security Guru'.  Any volunteers?

> Oh, and Jeff--with the new snapshot I lost the nice scrollbars that I had
> previously. So now I can move loci off the desktop and they just end up
> disappearing instead of the desktop scrolling.

Are you sure the Workspace scrolled automatically when you dragged a locus?  I
never added that functionality.

Scrollbars are there but only show up when the window is smaller than the
Workspace.  Try resizing the window.

> I like the new direction it
> is going though, and will be excited to see some loci inside loci!

Me too ;-)

                      |           J.W. Bizzaro           |
                      |                                  |
                      | http://bioinformatics.org/~jeff/ |
                      |                                  |
                      |           THE OPEN LAB           |
                      |    Open Source Bioinformatics    |
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                      |    http://bioinformatics.org/    |

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