Re: [Gmod-ajax] Feature Mark Up

[Steve T. <st...@mo...>]

Hi Andrew,

> 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.
> 

We have worked out what the problem is and it is down to some configuration issues set up by the Oxford IT service which I won't go into since it's so bizarre (unless you're *really* interested :-)).
http will work in a day or so but in the meantime have a look on our test server. This *should* work...

http://jenna.molbiol.ox.ac.uk/gbrowse/TiledImage/ecoli/prototype_gbrowse.html

I have also added a js pop-up based on one that was originally developed by Sylvain Gaillard and Gaëtan Droc.

If it all works your end I will check it in.

Cheers,

Steve
> 
> 
> 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
>>>>