Re: [Gmod-ajax] Feature Mark Up

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Hi Steve...

I found the problem.  Everywhere, including "prototype_gbrowse.html",
your URLs should be "https", not "http"... on a whim I portscanned
{slave,gbrowse}.molbiol.ox.ac.uk and noticed port 80 is closed, but
443 is open... or at least for U.S.-originating packets.

So this one:

https://gbrowse.molbiol.ox.ac.uk/cgi-bin/gbrowse/coli_demo/?name=U00096%3A1..10000

works just fine.  This one:

https://slave.molbiol.ox.ac.uk/gbrowse/TiledImage/ecoli/prototype_gbrowse.html

seems to load the XHTML, but nothing else.  The problem seems to be
that the XHTML has "http" instead of "https" for the JavaScript
library URLs, so I can't load the JavaScript libraries.  If the URLs
for libraries were changed to something like:

https://slave.molbiol.ox.ac.uk/gbrowse/TiledImage/client/View.js

then they would load.

I guess there is some firewall config causing this problem... although
I'm puzzled why it works for someone from Australia but not the U.S.

Cheers,

Andrew

On 11/14/06, Steve Taylor <st...@mo...> wrote:
> Hi Andrew,
> >
> > This sounds like excellent news, thanks!  But, I'm getting timed-out
> > loading both pages you linked to... can you let us know when they're
> > back up?  I would love to take a look.
> >
>
> Hmmm. I have tested both here and they work reasonably quickly although are more slow to load than the original AjaxGBrowse...I also got a got someone to test in Australia and he said it loaded ok
> though slightly more slowly.
>
> Can you try again please? Has anyone else on the list had time out problems? Again the URLs to try are:
>
> Ajax Gbrowse
> http://slave.molbiol.ox.ac.uk/gbrowse/TiledImage/ecoli/prototype_gbrowse.html
>
> Original Gbrowse
> http://gbrowse.molbiol.ox.ac.uk/cgi-bin/gbrowse/coli_demo/?name=U00096%3A1..10000
>
> > You should commit the code to CVS... I've also made a few changes
> > across the server-side code (including generate-tiles) to test
> > on-demand tile rendering, which will be useful for large genomes, and
> > to fix some stupid bugs left in TiledImage, etc. from back in the day
> > (e.g. database connections not hanging up), which you probably noticed
> > and fixed by now also.  Once your code is in, I'll merge in my
> > changes.
> >
> > Just to let everyone know about the "render on demand" stuff... the
> > idea is that we still fill a database with primitives, but only render
> > tiles as they are request by user (they are also saved, so no need to
> > re-render unless the underlying data changes, so we'll have some sort
> > of "dirty tile" flag or some such).
> >
> > This will enable people to put up large genomes without pre-rendering
> > all the tiles.  Currently, the rendering step is the major limiting
> > factor (my benchmarks show around 90% of the actual generate-tiles.pl
> > time is spent on database lookup of primitives).  For example, Dmel
> > arm 4 takes a full day to render on our 24-CPU cluster, but only an
> > hour of that time is spent filling the database.
> >
> > I'm trying a few things to optimize this right now, including the
> > on-demand rendering, and I'll keep the list updated once I get
> > somewhere (the things I'm trying can be found on
> > http://biowiki.org/view/GBrowse/WishList under the "rendering
> > optimizations" sublist).  I think we could seriously reduce the
> > fill/access time, but until then, on-demand rendering will at least
> > make large genomes feasible.
> >
>
> Sounds good. Look forward to seeing that!
>
> Steve
> >
> >
> > On 11/13/06, Steve Taylor <st...@mo...> wrote:
> >
> >>Hi,
> >>
> >>I thought I'd send this to open up the discussions on the new list!:-)
> >>
> >>I haven't checked in this code yet but I have modified generate-tiles.pm and BatchTilesImage.pm to allow marking up of the features in each of the tiles using client side image maps. We may want to
> >>change this later to do CSS maps but that would be only a small code modification. It basically generates an html file per tile with an inlined image and the appropriate map coordinates. The browser
> >>XMLHttpRequests the data over when it needs to using Ajax.Updater (from the js library Prototype).
> >>
> >>You can see what it looks like on:
> >>
> >>http://slave.molbiol.ox.ac.uk/gbrowse/TiledImage/ecoli/prototype_gbrowse.html
> >>
> >>Try dragging and clicking on features.
> >>
> >>Advantages of current implementation
> >>-----------------------------------
> >>- should work on all browsers and doesn't require any fancy javascript
> >>- will support polygons, ellipses etc
> >>- allows distribution on different servers for tiles
> >>
> >>Disadvantages of implementation
> >>-------------------------------
> >>- all html per tile currently generated server side (not sure if this is an advantage or disadvantage at this stage) but may be a pain to do updates
> >>
> >>Obviously where javascript:alert('Active image map') you should have the relevant details of the feature and a nicer pop up. The js alerts are pretty annoying at the moment when dragging! I intend to
> >>put js pop ups similar to the ones we have at http://gbrowse.molbiol.ox.ac.uk/cgi-bin/gbrowse/coli_demo/?name=U00096%3A1..10000.
> >>
> >>Let me know what you think. I will check it in if people think it is worthwhile at this stage.
> >>
> >>Regards,
> >>
> >>Steve
> >>------------------------------------------------------------------
> >>Head of Computational Biology Research Group
> >>Medical Sciences Division
> >>Weatherall Institute of Molecular Medicine/Sir William Dunn School
> >>Oxford University
> >>Tel: +44 (0)1865 (2)22640 (WIMM - Monday to Wednesday)
> >>Tel: +44 (0)1865 (2)85732 (Dunn - Thursday to Friday)
> >>Web: http://www.compbio.ox.ac.uk
> >>
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