[MOBY-dev] FYI: Search function on MOBY Web site gives "404 Not Found" error...

[Frank Gibbons]

Martin,

At 10:34 AM 2/10/2006, you wrote:
>If this error would be the only missing link/feature in the Biomoby doc, I
>would shut up... But I must admit that Mark's previous documentation (API
>in one long page) was not that great but much better. Proof? If I need to
>look at it I am still using my local copy of his page because the new
>pages simply are not linked together.

I'm not sure what you mean - the pages of the API are linked, at least to 
the extent that the older single-page document was linked. In addition, 
there's a table of contents on the right-hand side of each page, so you 
don't have to back-track to find what you need. I think this version makes 
it easier to see what is known, but I'm open to the idea that it might not 
work for everyone. Certainly, if you're looking for something to print out, 
then having one long page is better.

>BTW, the checkbot on the page
>ttp://biomoby.open-bio.org/CVS_CONTENT/moby-live/Docs/MOBY-S_API/index_API.html
>reports 26 missing links (from 58; ratio 44%).

I wasn't familiar with checkbot, but found its homepage from google. 
Unfortunately, checkbot's homepage is down (the irony is killing me ;-D. 
Could you send a list of the broken links, Martin? I'll be happy to fix them.

>Could somebody remind me who has access to the pages - is it possible to
>correct it in a CVS?

As far as possible, it is all under CVS. Only the front page, and the pages 
linked to from the bar at the top, are not under CVS. I think the entire 
website's contents should be under CVS, so that any one of us could set up 
a complete mirror site. Basically, whatever is shown on the website as 
having an URL containing CVS_CONTENT is accessible in CVS. The website is 
updated from CVS every few hours. I encourage every developer to get in 
there, and add links to things as they see fit. The docs you check out 
under CVS also link to the biomoby.org website, where possible, so you can 
start at your local docs, but surf to biomoby.org seamlessly.

As for the search function, I pointed out that it was broken about a month 
ago. Does anyone know if it ever worked? In other words, is it simply a 
case of some pointers being broken, and if we reset them, everything will 
work again? Or, if it never worked in the first place, is it more of a 
black-box, where we don't know what's wrong, or how long it might take to fix?

Just as much as the code, perhaps even more so since much of it is 
language-independent, the documentation should be the work of all 
developers. I know that few people particularly enjoy writing docs, and 
certainly there are no kudos for doing it, compared to writing code. To my 
mind, having a single long page of almost plain text is not a particularly 
easy way for a newbie to get to learn how MOBY works. That's more who I 
felt we should be aiming for - put it all out there, make it as easy to 
find as possible. But you know, perhaps we need both, I'm open to that. We 
could have a rule in the makefile/build.xml to paste all the pages together 
into a single document for people who prefer to navigate MOBY like that.

-Frank

PhD, Computational Biologist,
Harvard Medical School BCMP/SGM-322, 250 Longwood Ave, Boston MA 02115, USA.
Tel: 617-432-3555       Fax: 
617-432-3557       http://llama.med.harvard.edu/~fgibbons