gmod-ajax

[Gmod-ajax] Feature Mark Up

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

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

Re: [Gmod-ajax] Feature Mark Up

[Andrew U. <and...@gm...>]

Hi Steve (et al)...

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.

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.

Cheers,


Andrew


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
>
> -------------------------------------------------------------------------
> Using Tomcat but need to do more? Need to support web services, security?
> Get stuff done quickly with pre-integrated technology to make your job easier
> Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo
> http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&dat=121642
> _______________________________________________
> Gmod-ajax mailing list
> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>

Re: [Gmod-ajax] Feature Mark Up

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

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
>>
>>-------------------------------------------------------------------------
>>Using Tomcat but need to do more? Need to support web services, security?
>>Get stuff done quickly with pre-integrated technology to make your job easier
>>Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo
>>http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&dat=121642
>>_______________________________________________
>>Gmod-ajax mailing list
>>Gmo...@li...
>>https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>>
> 
> 
> -------------------------------------------------------------------------
> Using Tomcat but need to do more? Need to support web services, security?
> Get stuff done quickly with pre-integrated technology to make your job easier
> Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo
> http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&dat=121642
> _______________________________________________
> Gmod-ajax mailing list
> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
> 

Re: [Gmod-ajax] Feature Mark Up

[Andrew U. <and...@gm...>]

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
> >>
> >>-------------------------------------------------------------------------
> >>Using Tomcat but need to do more? Need to support web services, security?
> >>Get stuff done quickly with pre-integrated technology to make your job easier
> >>Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo
> >>http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&dat=121642
> >>_______________________________________________
> >>Gmod-ajax mailing list
> >>Gmo...@li...
> >>https://lists.sourceforge.net/lists/listinfo/gmod-ajax
> >>
> >
> >
> > -------------------------------------------------------------------------
> > Using Tomcat but need to do more? Need to support web services, security?
> > Get stuff done quickly with pre-integrated technology to make your job easier
> > Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo
> > http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&dat=121642
> > _______________________________________________
> > Gmod-ajax mailing list
> > Gmo...@li...
> > https://lists.sourceforge.net/lists/listinfo/gmod-ajax
> >
>
> -------------------------------------------------------------------------
> Using Tomcat but need to do more? Need to support web services, security?
> Get stuff done quickly with pre-integrated technology to make your job easier
> Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo
> http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&dat=121642
> _______________________________________________
> Gmod-ajax mailing list
> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>

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
>>>>

Re: [Gmod-ajax] Feature Mark Up

[Andrew U. <and...@gm...>]

Hi Steve...

Yep, it works and looks good, you should check it in.  The only issue
I see is that the window scrolls back to top whenever the pop up menu
fires... maybe it has to do with its positioning in the DOM, I'm not
sure... it should be a child of outerDivMain, I think, not the entire
document.  But I'd have to play with it to figure it out.

We were thinking about having the pop up menu behave a little
differently - it shoud pop up after hovering over a feature for a
fraction of a second or so, then disappear when dragging starts.  The
reason for this is that single-clicking should be reserved for other
things, such as dragging or maybe drawing a little box or something to
select features, etc. (this will come later, it's not well-defined at
the moment).  Also, double-clicking to center should be unhindered by
a menu popping up after the first click, but I think that can be taken
care of by cancelling the results of a single-click event if a
double-click comes in... somehow.

I also see that double-clicking to center (on the main view cell, not
the ruler cell) is broken now, but I think I know why and I can fix it
when the code is in CVS.

Next comes the figuring out how to populate the pop up menu with
relevant info...

Thanks!


Andrew


On 11/15/06, Steve Taylor <st...@mo...> wrote:
> 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=3DU000=
96%3A1..10000
> >
> > works just fine.  This one:
> >
> > https://slave.molbiol.ox.ac.uk/gbrowse/TiledImage/ecoli/prototype_gbrow=
se.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 configurati=
on 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 Ga=EBtan 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 som=
eone 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 prob=
lems? Again the URLs to try are:
> >>
> >>Ajax Gbrowse
> >>http://slave.molbiol.ox.ac.uk/gbrowse/TiledImage/ecoli/prototype_gbrows=
e.html
> >>
> >>Original Gbrowse
> >>http://gbrowse.molbiol.ox.ac.uk/cgi-bin/gbrowse/coli_demo/?name=3DU0009=
6%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 t=
he 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 (fr=
om the js library Prototype).
> >>>>
> >>>>You can see what it looks like on:
> >>>>
> >>>>http://slave.molbiol.ox.ac.uk/gbrowse/TiledImage/ecoli/prototype_gbro=
wse.html
> >>>>
> >>>>Try dragging and clicking on features.
> >>>>
> >>>>Advantages of current implementation
> >>>>-----------------------------------
> >>>>- should work on all browsers and doesn't require any fancy javascrip=
t
> >>>>- 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 upd=
ates
> >>>>
> >>>>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 p=
retty 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=3DU00096%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
> >>>>
>
> -------------------------------------------------------------------------
> Take Surveys. Earn Cash. Influence the Future of IT
> Join SourceForge.net's Techsay panel and you'll get the chance to share y=
our
> opinions on IT & business topics through brief surveys - and earn cash
> http://www.techsay.com/default.php?page=3Djoin.php&p=3Dsourceforge&CID=3D=
DEVDEV
> _______________________________________________
> Gmod-ajax mailing list
> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>

Re: [Gmod-ajax] Feature Mark Up

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

Hi Andrew,

>
>Yep, it works and looks good, you should check it in.  The only issue
>I see is that the window scrolls back to top whenever the pop up menu
>fires... maybe it has to do with its positioning in the DOM, I'm not
>sure... it should be a child of outerDivMain, I think, not the entire
>document.  But I'd have to play with it to figure it out.
>
>  
>
I hadn't noticed that. I'll have a look.

>We were thinking about having the pop up menu behave a little
>differently - it shoud pop up after hovering over a feature for a
>fraction of a second or so, then disappear when dragging starts.  The
>reason for this is that single-clicking should be reserved for other
>things, such as dragging or maybe drawing a little box or something to
>select features, etc. (this will come later, it's not well-defined at
>the moment).  Also, double-clicking to center should be unhindered by
>a menu popping up after the first click, but I think that can be taken
>care of by cancelling the results of a single-click event if a
>double-click comes in... somehow.
>  
>
I had it set on mouseover as you described and it felt not quite right 
for some reason but having a pop up on a hover is how we use the cgi 
GBrowse and it works great. We can try out a few options and see what's 
best and I think you are right about keeping the click events free. A 
rubber banding mechanism might be a good idea in the future to zoom in, 
for example.

>I also see that double-clicking to center (on the main view cell, not
>the ruler cell) is broken now, but I think I know why and I can fix it
>when the code is in CVS.
>
>  
>

Ok will check it in.

>Next comes the figuring out how to populate the pop up menu with
>relevant info...
>  
>
Yep. This is more tricky... I think we should try and use as many 
'official' GBrowse calls as possible to ensure future compatibility. I 
wonder if Lincoln or Scott (if they are reading this) could offer any 
advice?
Cheers,

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.
>>>
>>>      
>>>
>>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
>>>>>>
>>>>>>            
>>>>>>
>>-------------------------------------------------------------------------
>>Take Surveys. Earn Cash. Influence the Future of IT
>>Join SourceForge.net's Techsay panel and you'll get the chance to share your
>>opinions on IT & business topics through brief surveys - and earn cash
>>http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDEV
>>_______________________________________________
>>Gmod-ajax mailing list
>>Gmo...@li...
>>https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>>
>>    
>>
>
>-------------------------------------------------------------------------
>Take Surveys. Earn Cash. Influence the Future of IT
>Join SourceForge.net's Techsay panel and you'll get the chance to share your
>opinions on IT & business topics through brief surveys - and earn cash
>http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDEV
>_______________________________________________
>Gmod-ajax mailing list
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>https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>
>  
>

Re: [Gmod-ajax] Feature Mark Up

[Mitch S. <li...@ar...>]

On Wed, 2006-11-15 at 20:47 +0000, Stephen Taylor wrote:
> I had it set on mouseover as you described and it felt not quite right 
> for some reason but having a pop up on a hover is how we use the cgi 
> GBrowse and it works great. We can try out a few options and see what's 
> best and I think you are right about keeping the click events free. A 
> rubber banding mechanism might be a good idea in the future to zoom in, 
> for example.

Clearly I'm coming into this discussion half-way, so maybe you've
already talked about this, but -

The pop up menu seems pretty much like a regular context menu that would
be shown on a right-click.  I know dojo has a widget for this; not sure
about prototype or prototype-based js libs.  It sounds fairly
straightforward to roll this bit of functionality on your own, though:
http://lab.artlung.com/oncontextmenu/
The Dojo version does do some extra work to support Opera and Konqueror
which apparently don't have this natively.  Of course, this leaves the
left-click open for dragging or selection.

Maybe people aren't terribly used to web apps providing their own
context menus yet, but I've seen this in Yahoo's new mail app (with
accelerator keys, even!), and it fits pretty well with general desktop
UI habits.

Mitch

Re: [Gmod-ajax] Feature Mark Up

[Scott C. <ca...@cs...>]

On Wed, 2006-11-15 at 20:47 +0000, Stephen Taylor wrote:
> Hi Andrew,
> >Next comes the figuring out how to populate the pop up menu with
> >relevant info...
> > =20
> >
> Yep. This is more tricky... I think we should try and use as many=20
> 'official' GBrowse calls as possible to ensure future compatibility. I=20
> wonder if Lincoln or Scott (if they are reading this) could offer any=20
> advice?
>=20
The GBrowse cgi doesn't expose much in terms of fundamentals that one
could use for populating popup menus with data.  Currently, people who
use popups with gbrowse create all of the data up front and encode it in
javascript elements in the imagemap.  I suppose that works fine from a
cgi point of view, but is not as appropriate for an ajax application (is
it?).  So if we want to make it work in an 'ajaxy' way, we'll need
either to expand the api of the gbrowse cgi, or create another cgi for
serving up xml for requests like that.

If you want to see an example of how people are currently generating
popups, you can look at this example:

http://www.plasmodb.org/cgi-bin/gbrowse/plasmodb/?start=3D101357;stop=3D121=
356;ref=3DMAL12;width=3D800;version=3D100;label=3DAnnotatedGenes-SyntenySpa=
nsVivaxMC-SyntenyGenesVivaxMC;id=3D9cf36ae32368b7ec3e3c516c08c358d4

which is done with this conf file:

http://gmod.cvs.sourceforge.net/gmod/Generic-Genome-Browser/contrib/SynView=
/gbrowse.conf/plasmodb.conf?revision=3D1.1.2.1&view=3Dmarkup&pathrev=3Dgbro=
wse-session

Scott

--=20
------------------------------------------------------------------------
Scott Cain, Ph. D.                                         ca...@cs...
GMOD Coordinator (http://www.gmod.org/)                     216-392-3087
Cold Spring Harbor Laboratory

Re: [Gmod-ajax] Feature Mark Up

[Ian H. <ih...@be...>]

Chris Mungall mentioned something a while back about some sort of  
universal markup language he & Seth had specced out for GO. He also  
suggested some kind of protocol for publishing feature annotations in  
a sort of universal ontology framework.

Chris, are you on this list? it'd be good to get these & related  
ideas in more concrete form...

As well as rich pop-up info, we need to develop client-server  
protocols for (i) search and (ii) annotation upload.


On Nov 16, 2006, at 8:46 AM, Scott Cain wrote:

> On Wed, 2006-11-15 at 20:47 +0000, Stephen Taylor wrote:
>> Hi Andrew,
>>> Next comes the figuring out how to populate the pop up menu with
>>> relevant info...
>>>
>>>
>> Yep. This is more tricky... I think we should try and use as many
>> 'official' GBrowse calls as possible to ensure future  
>> compatibility. I
>> wonder if Lincoln or Scott (if they are reading this) could offer any
>> advice?
>>
> The GBrowse cgi doesn't expose much in terms of fundamentals that one
> could use for populating popup menus with data.  Currently, people who
> use popups with gbrowse create all of the data up front and encode  
> it in
> javascript elements in the imagemap.  I suppose that works fine from a
> cgi point of view, but is not as appropriate for an ajax  
> application (is
> it?).  So if we want to make it work in an 'ajaxy' way, we'll need
> either to expand the api of the gbrowse cgi, or create another cgi for
> serving up xml for requests like that.
>
> If you want to see an example of how people are currently generating
> popups, you can look at this example:
>
> http://www.plasmodb.org/cgi-bin/gbrowse/plasmodb/? 
> start=101357;stop=121356;ref=MAL12;width=800;version=100;label=Annotat 
> edGenes-SyntenySpansVivaxMC- 
> SyntenyGenesVivaxMC;id=9cf36ae32368b7ec3e3c516c08c358d4
>
> which is done with this conf file:
>
> http://gmod.cvs.sourceforge.net/gmod/Generic-Genome-Browser/contrib/ 
> SynView/gbrowse.conf/plasmodb.conf? 
> revision=1.1.2.1&view=markup&pathrev=gbrowse-session
>
> Scott
>
> -- 
> ---------------------------------------------------------------------- 
> --
> Scott Cain, Ph. D.                                          
> ca...@cs...
> GMOD Coordinator (http://www.gmod.org/)                      
> 216-392-3087
> Cold Spring Harbor Laboratory
> ---------------------------------------------------------------------- 
> ---
> Take Surveys. Earn Cash. Influence the Future of IT
> Join SourceForge.net's Techsay panel and you'll get the chance to  
> share your
> opinions on IT & business topics through brief surveys - and earn cash
> http://www.techsay.com/default.php? 
> page=join.php&p=sourceforge&CID=DEVDEV________________________________ 
> _______________
> Gmod-ajax mailing list
> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax

Re: [Gmod-ajax] Feature Mark Up

[Scott C. <ca...@cs...>]

Actually, what I wrote before isn't quite correct; while the gbrowse cgi
doesn't server up raw information, other cgis in the gbrowse
distribution can.  You can get both DAS1 and biomoby, though I don't
know that much the details of what the streams look like (DAS2 is XML, I
don't think DAS1 is).  It is possible that javascript client-side code
is already written for these services, I just don't know about it.

Scott


On Thu, 2006-11-16 at 09:54 -0800, Ian Holmes wrote:
> Chris Mungall mentioned something a while back about some sort of =20
> universal markup language he & Seth had specced out for GO. He also =20
> suggested some kind of protocol for publishing feature annotations in =20
> a sort of universal ontology framework.
>=20
> Chris, are you on this list? it'd be good to get these & related =20
> ideas in more concrete form...
>=20
> As well as rich pop-up info, we need to develop client-server =20
> protocols for (i) search and (ii) annotation upload.
>=20
>=20
> On Nov 16, 2006, at 8:46 AM, Scott Cain wrote:
>=20
> > On Wed, 2006-11-15 at 20:47 +0000, Stephen Taylor wrote:
> >> Hi Andrew,
> >>> Next comes the figuring out how to populate the pop up menu with
> >>> relevant info...
> >>>
> >>>
> >> Yep. This is more tricky... I think we should try and use as many
> >> 'official' GBrowse calls as possible to ensure future =20
> >> compatibility. I
> >> wonder if Lincoln or Scott (if they are reading this) could offer any
> >> advice?
> >>
> > The GBrowse cgi doesn't expose much in terms of fundamentals that one
> > could use for populating popup menus with data.  Currently, people who
> > use popups with gbrowse create all of the data up front and encode =20
> > it in
> > javascript elements in the imagemap.  I suppose that works fine from a
> > cgi point of view, but is not as appropriate for an ajax =20
> > application (is
> > it?).  So if we want to make it work in an 'ajaxy' way, we'll need
> > either to expand the api of the gbrowse cgi, or create another cgi for
> > serving up xml for requests like that.
> >
> > If you want to see an example of how people are currently generating
> > popups, you can look at this example:
> >
> > http://www.plasmodb.org/cgi-bin/gbrowse/plasmodb/?=20
> > start=3D101357;stop=3D121356;ref=3DMAL12;width=3D800;version=3D100;labe=
l=3DAnnotat=20
> > edGenes-SyntenySpansVivaxMC-=20
> > SyntenyGenesVivaxMC;id=3D9cf36ae32368b7ec3e3c516c08c358d4
> >
> > which is done with this conf file:
> >
> > http://gmod.cvs.sourceforge.net/gmod/Generic-Genome-Browser/contrib/=20
> > SynView/gbrowse.conf/plasmodb.conf?=20
> > revision=3D1.1.2.1&view=3Dmarkup&pathrev=3Dgbrowse-session
> >
> > Scott
> >
> > --=20
> > ----------------------------------------------------------------------=20
> > --
> > Scott Cain, Ph. D.                                         =20
> > ca...@cs...
> > GMOD Coordinator (http://www.gmod.org/)                     =20
> > 216-392-3087
> > Cold Spring Harbor Laboratory
> > ----------------------------------------------------------------------=20
> > ---
> > Take Surveys. Earn Cash. Influence the Future of IT
> > Join SourceForge.net's Techsay panel and you'll get the chance to =20
> > share your
> > opinions on IT & business topics through brief surveys - and earn cash
> > http://www.techsay.com/default.php?=20
> > page=3Djoin.php&p=3Dsourceforge&CID=3DDEVDEV___________________________=
_____=20
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Scott Cain, Ph. D.                                         ca...@cs...
GMOD Coordinator (http://www.gmod.org/)                     216-392-3087
Cold Spring Harbor Laboratory

Re: [Gmod-ajax] Feature Mark Up

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

Hi,

Been away for a few days but I have committed the code now. To get the required mark up you will have to run generate-tiles.pl which will generate html files containing the image map data in the same 
dir as the .png files. Currently, all the mouse over events are also stored in the html too. Yuk. This is a pretty low tech way of doing things and not very desirable in the long run esp. when we 
start populating it with real data... I tried to set mouseovers the on the fly using Ajax.Updater/onSuccess but had some problems that were related to caching (I think). I am sure Andrew would be able 
to fix this extremely quickly.

I have added a new var called htmlFiles in ViewerComponent.js. Setting this to 1 causes the browser to update the divs by pulling in the html, setting it to 0 means it uses the old style of specifying 
the path of the local image src.  htmlFiles default is 1 so if you do a cvs update and haven't run generate-tiles.pl remember to change it to 0.

> Actually, what I wrote before isn't quite correct; while the gbrowse cgi
> doesn't server up raw information, other cgis in the gbrowse
> distribution can.  You can get both DAS1 and biomoby, though I don't
> know that much the details of what the streams look like (DAS2 is XML, I
> don't think DAS1 is).  It is possible that javascript client-side code
> is already written for these services, I just don't know about it.
> 

Gbrowse Moby certainly looks like it could be a viable solution. In theory it seems to have in its favour that it should be straightforward to GET the data via a URL...

Cheers,

Steve


> Scott
> 
> 
> On Thu, 2006-11-16 at 09:54 -0800, Ian Holmes wrote:
> 
>>Chris Mungall mentioned something a while back about some sort of  
>>universal markup language he & Seth had specced out for GO. He also  
>>suggested some kind of protocol for publishing feature annotations in  
>>a sort of universal ontology framework.
>>
>>Chris, are you on this list? it'd be good to get these & related  
>>ideas in more concrete form...
>>
>>As well as rich pop-up info, we need to develop client-server  
>>protocols for (i) search and (ii) annotation upload.
>>
>>
>>On Nov 16, 2006, at 8:46 AM, Scott Cain wrote:
>>
>>
>>>On Wed, 2006-11-15 at 20:47 +0000, Stephen Taylor wrote:
>>>
>>>>Hi Andrew,
>>>>
>>>>>Next comes the figuring out how to populate the pop up menu with
>>>>>relevant info...
>>>>>
>>>>>
>>>>
>>>>Yep. This is more tricky... I think we should try and use as many
>>>>'official' GBrowse calls as possible to ensure future  
>>>>compatibility. I
>>>>wonder if Lincoln or Scott (if they are reading this) could offer any
>>>>advice?
>>>>
>>>
>>>The GBrowse cgi doesn't expose much in terms of fundamentals that one
>>>could use for populating popup menus with data.  Currently, people who
>>>use popups with gbrowse create all of the data up front and encode  
>>>it in
>>>javascript elements in the imagemap.  I suppose that works fine from a
>>>cgi point of view, but is not as appropriate for an ajax  
>>>application (is
>>>it?).  So if we want to make it work in an 'ajaxy' way, we'll need
>>>either to expand the api of the gbrowse cgi, or create another cgi for
>>>serving up xml for requests like that.
>>>
>>>If you want to see an example of how people are currently generating
>>>popups, you can look at this example:
>>>
>>>http://www.plasmodb.org/cgi-bin/gbrowse/plasmodb/? 
>>>start=101357;stop=121356;ref=MAL12;width=800;version=100;label=Annotat 
>>>edGenes-SyntenySpansVivaxMC- 
>>>SyntenyGenesVivaxMC;id=9cf36ae32368b7ec3e3c516c08c358d4
>>>
>>>which is done with this conf file:
>>>
>>>http://gmod.cvs.sourceforge.net/gmod/Generic-Genome-Browser/contrib/ 
>>>SynView/gbrowse.conf/plasmodb.conf? 
>>>revision=1.1.2.1&view=markup&pathrev=gbrowse-session
>>>
>>>Scott
>>>
>>>-- 
>>>---------------------------------------------------------------------- 
>>>--
>>>Scott Cain, Ph. D.                                          
>>>ca...@cs...
>>>GMOD Coordinator (http://www.gmod.org/)                      
>>>216-392-3087
>>>Cold Spring Harbor Laboratory
>>>----------------------------------------------------------------------