[Gmod-ajax] Trouble behind cherrypy

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[Gmod-ajax] Trouble behind cherrypy

Mariette
Hi,

I'm trying to get jbrowse runing into our website. However it's not working,
I have the jbrowse environement displayed but not annotations and the
seqRef.
Jbrowse can read the refSeq.js and the trackinfo.js but doesn't read the
'seqDir' and
the 'url' fields of these files.
We figured out that the jbrowse sample web site allows to list files
into directories.
Is it required to make jbrowse working ??
The problem is we're using the cherrypy web server which doesn't seems
to allow
files listing, and we're guessing this is the problem ? would that make
sens ??

thanks for your reply,
Jerome


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Re: Trouble behind cherrypy

Giles Velarde-2
Hi,

Perhaps I should respond here because I do use CherryPy for some  
projects, and use JBrowse in another. I would look at

        http://tools.cherrypy.org/wiki/staticdirindex

and see if that helps you (I haven't tried this myself).

That said, why are you deploying JBrowse on CherryPy and not Apache?  
JBrowse needs the web server to only serve static pre-generated JSON  
files, and Apache works perfectly well for that. If the data sets get  
fairly large, you may find any server other than Apache may well  
struggle to cope.

If you need to run some other server-side dynamic pages in Python, you  
can always put CherryPy behind the same Apache server as well. See

        http://tools.cherrypy.org/wiki/BehindApache

for more info.

Regards,
Giles


On 30 Jun 2010, at 14:06, Mariette wrote:

> Hi,
>
> I'm trying to get jbrowse runing into our website. However it's not  
> working,
> I have the jbrowse environement displayed but not annotations and the
> seqRef.
> Jbrowse can read the refSeq.js and the trackinfo.js but doesn't read  
> the
> 'seqDir' and
> the 'url' fields of these files.
> We figured out that the jbrowse sample web site allows to list files
> into directories.
> Is it required to make jbrowse working ??
> The problem is we're using the cherrypy web server which doesn't seems
> to allow
> files listing, and we're guessing this is the problem ? would that  
> make
> sens ??
>
> thanks for your reply,
> Jerome
>
>
> ------------------------------------------------------------------------------
> This SF.net email is sponsored by Sprint
> What will you do first with EVO, the first 4G phone?
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 company registered in England with number 2742969, whose registered
 office is 215 Euston Road, London, NW1 2BE.

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Re: Trouble behind cherrypy

Mariette

Thanks,

I will take a look.  I'm deploying jbrowse on cherrypy
because the application we're developing is deploying
on cherrypy and I want jbrowse to be embeded into
our application. So I don't want jbrowse to be outside
of the application itself.

does it make sense ?

Jerome









Giles Velarde a écrit :

> Hi,
>
> Perhaps I should respond here because I do use CherryPy for some  
> projects, and use JBrowse in another. I would look at
>
> http://tools.cherrypy.org/wiki/staticdirindex
>
> and see if that helps you (I haven't tried this myself).
>
> That said, why are you deploying JBrowse on CherryPy and not Apache?  
> JBrowse needs the web server to only serve static pre-generated JSON  
> files, and Apache works perfectly well for that. If the data sets get  
> fairly large, you may find any server other than Apache may well  
> struggle to cope.
>
> If you need to run some other server-side dynamic pages in Python, you  
> can always put CherryPy behind the same Apache server as well. See
>
> http://tools.cherrypy.org/wiki/BehindApache
>
> for more info.
>
> Regards,
> Giles
>
>
> On 30 Jun 2010, at 14:06, Mariette wrote:
>
>  
>> Hi,
>>
>> I'm trying to get jbrowse runing into our website. However it's not  
>> working,
>> I have the jbrowse environement displayed but not annotations and the
>> seqRef.
>> Jbrowse can read the refSeq.js and the trackinfo.js but doesn't read  
>> the
>> 'seqDir' and
>> the 'url' fields of these files.
>> We figured out that the jbrowse sample web site allows to list files
>> into directories.
>> Is it required to make jbrowse working ??
>> The problem is we're using the cherrypy web server which doesn't seems
>> to allow
>> files listing, and we're guessing this is the problem ? would that  
>> make
>> sens ??
>>
>> thanks for your reply,
>> Jerome
>>
>>
>> ------------------------------------------------------------------------------
>> This SF.net email is sponsored by Sprint
>> What will you do first with EVO, the first 4G phone?
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>> [hidden email]
>> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>>    
>
>
>
>  


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Re: Trouble behind cherrypy

Giles Velarde-2
That does make sense. Will be interesting to see if the cherrypy  
static dir index will work with JBrowse.

If it doesn't, then I would suggest writing a mock-index controller in  
CherryPy yourself, essentially returning the same thing that JBrowse  
is expecting. In theory, all you would have to do is write an exposed  
method that lists the contents of a directory, formatting this  
appropriately, and map it to requests that the JBrowse javascript is  
making.

Regards,
Giles

On 30 Jun 2010, at 15:37, Mariette wrote:

>
> Thanks,
>
> I will take a look.  I'm deploying jbrowse on cherrypy
> because the application we're developing is deploying
> on cherrypy and I want jbrowse to be embeded into
> our application. So I don't want jbrowse to be outside
> of the application itself.
>
> does it make sense ?
>
> Jerome
>
>
>
>
>
>
>
>
>
> Giles Velarde a écrit :
>> Hi,
>>
>> Perhaps I should respond here because I do use CherryPy for some  
>> projects, and use JBrowse in another. I would look at
>>
>> http://tools.cherrypy.org/wiki/staticdirindex
>>
>> and see if that helps you (I haven't tried this myself).
>>
>> That said, why are you deploying JBrowse on CherryPy and not  
>> Apache?  JBrowse needs the web server to only serve static pre-
>> generated JSON  files, and Apache works perfectly well for that. If  
>> the data sets get  fairly large, you may find any server other than  
>> Apache may well  struggle to cope.
>>
>> If you need to run some other server-side dynamic pages in Python,  
>> you  can always put CherryPy behind the same Apache server as well.  
>> See
>>
>> http://tools.cherrypy.org/wiki/BehindApache
>>
>> for more info.
>>
>> Regards,
>> Giles
>>
>>
>> On 30 Jun 2010, at 14:06, Mariette wrote:
>>
>>
>>> Hi,
>>>
>>> I'm trying to get jbrowse runing into our website. However it's  
>>> not  working,
>>> I have the jbrowse environement displayed but not annotations and  
>>> the
>>> seqRef.
>>> Jbrowse can read the refSeq.js and the trackinfo.js but doesn't  
>>> read  the
>>> 'seqDir' and
>>> the 'url' fields of these files.
>>> We figured out that the jbrowse sample web site allows to list files
>>> into directories.
>>> Is it required to make jbrowse working ??
>>> The problem is we're using the cherrypy web server which doesn't  
>>> seems
>>> to allow
>>> files listing, and we're guessing this is the problem ? would  
>>> that  make
>>> sens ??
>>>
>>> thanks for your reply,
>>> Jerome
>>>
>>>
>>> ------------------------------------------------------------------------------
>>> This SF.net email is sponsored by Sprint
>>> What will you do first with EVO, the first 4G phone?
>>> Visit sprint.com/first -- http://p.sf.net/sfu/sprint-com-first
>>> _______________________________________________
>>> Gmod-ajax mailing list
>>> [hidden email]
>>> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>>>
>>
>>
>>
>>
>



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 Limited, a charity registered in England with number 1021457 and a
 company registered in England with number 2742969, whose registered
 office is 215 Euston Road, London, NW1 2BE.

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Re: Trouble behind cherrypy

Mitch Skinner
In reply to this post by Mariette
JBrowse doesn't use the directory listings; when JBrowse gets a file
from the server it's through a direct link (or a URL template, in some
places).

It's harder to debug if I can't see the app, but my first guess would be
that it has something to do with relative URLs.  refSeq.js and
trackInfo.js both contain URLs relative to the directory containing the
jbrowse index.html file.

That's assuming that you're using the default index.html file.  Are you
doing that, or are you doing something else?

There's a setting (the "dataRoot" parameter to the Browser javascript
object constructor) that makes the root of those relative URLs
configurable, but because of a recent exchange on the gmod-ajax list I'm
looking at changing how that works.  If you've got a non-default
directory setup I'd be interested to know how you have things laid out,
so that we can make sure that setting works correctly for everyone.

Regards,
Mitch

On 06/30/2010 06:06 AM, Mariette wrote:

> Hi,
>
> I'm trying to get jbrowse runing into our website. However it's not working,
> I have the jbrowse environement displayed but not annotations and the
> seqRef.
> Jbrowse can read the refSeq.js and the trackinfo.js but doesn't read the
> 'seqDir' and
> the 'url' fields of these files.
> We figured out that the jbrowse sample web site allows to list files
> into directories.
> Is it required to make jbrowse working ??
> The problem is we're using the cherrypy web server which doesn't seems
> to allow
> files listing, and we're guessing this is the problem ? would that make
> sens ??
>
> thanks for your reply,
> Jerome
>
> ------------------------------------------------------------------------------
> This SF.net email is sponsored by Sprint
> What will you do first with EVO, the first 4G phone?
> Visit sprint.com/first -- http://p.sf.net/sfu/sprint-com-first
> _______________________________________________
> Gmod-ajax mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>    


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Re: Trouble behind cherrypy

Mitch Skinner
On 06/30/2010 04:44 PM, Mitch Skinner wrote:
> There's a setting (the "dataRoot" parameter to the Browser javascript
> object constructor)
>    

I forgot to add, there's a bit of documentation on those parameters here:

http://jbrowse.org/docs/jbrowse-jsdoc/symbols/Browser.html

Mitch

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Re: Trouble behind cherrypy

Mariette
In reply to this post by Mitch Skinner

Thanks Mitch for your reply,

it's working the probleme was coming from the path of the 'seqDir'
and the path of the  'url' fields which were not absolute from the
calling page.

Thanks again,
Jerome






Mitch Skinner a écrit :

> JBrowse doesn't use the directory listings; when JBrowse gets a file
> from the server it's through a direct link (or a URL template, in some
> places).
>
> It's harder to debug if I can't see the app, but my first guess would be
> that it has something to do with relative URLs.  refSeq.js and
> trackInfo.js both contain URLs relative to the directory containing the
> jbrowse index.html file.
>
> That's assuming that you're using the default index.html file.  Are you
> doing that, or are you doing something else?
>
> There's a setting (the "dataRoot" parameter to the Browser javascript
> object constructor) that makes the root of those relative URLs
> configurable, but because of a recent exchange on the gmod-ajax list I'm
> looking at changing how that works.  If you've got a non-default
> directory setup I'd be interested to know how you have things laid out,
> so that we can make sure that setting works correctly for everyone.
>
> Regards,
> Mitch
>
> On 06/30/2010 06:06 AM, Mariette wrote:
>  
>> Hi,
>>
>> I'm trying to get jbrowse runing into our website. However it's not working,
>> I have the jbrowse environement displayed but not annotations and the
>> seqRef.
>> Jbrowse can read the refSeq.js and the trackinfo.js but doesn't read the
>> 'seqDir' and
>> the 'url' fields of these files.
>> We figured out that the jbrowse sample web site allows to list files
>> into directories.
>> Is it required to make jbrowse working ??
>> The problem is we're using the cherrypy web server which doesn't seems
>> to allow
>> files listing, and we're guessing this is the problem ? would that make
>> sens ??
>>
>> thanks for your reply,
>> Jerome
>>
>> ------------------------------------------------------------------------------
>> This SF.net email is sponsored by Sprint
>> What will you do first with EVO, the first 4G phone?
>> Visit sprint.com/first -- http://p.sf.net/sfu/sprint-com-first
>> _______________________________________________
>> Gmod-ajax mailing list
>> [hidden email]
>> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>>    
>>    
>
>
> ------------------------------------------------------------------------------
> This SF.net email is sponsored by Sprint
> What will you do first with EVO, the first 4G phone?
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>  


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Re: Trouble behind cherrypy

Mariette
In reply to this post by Mitch Skinner

Hi Mitch,

so I'm getting further thanks for your help.
To explain you how we configure our site : we have multiple users, each
with his own directory.
This directory is not seen by our web server (which is cherrypy). So far
what we're doing is
to put the refSeq.js and the trackInfo.js in the user/project directory
so this file is taken in
consideration when looking at the user quota (required for our site). To
do so we basicly
have a dinamic link which return the right refSeq.js/trackInfo.js files
considering the authentified
user.

Right now we have a problem with the link 'url' and 'seqDir' path as
they have to be relative
to the web page where jbrowse is built.
How can we do to direct those links to our user directory ?? any idea ?

hope it make sense,
Jerome




Mitch Skinner a écrit :

> JBrowse doesn't use the directory listings; when JBrowse gets a file
> from the server it's through a direct link (or a URL template, in some
> places).
>
> It's harder to debug if I can't see the app, but my first guess would
> be that it has something to do with relative URLs.  refSeq.js and
> trackInfo.js both contain URLs relative to the directory containing
> the jbrowse index.html file.
>
> That's assuming that you're using the default index.html file.  Are
> you doing that, or are you doing something else?
>
> There's a setting (the "dataRoot" parameter to the Browser javascript
> object constructor) that makes the root of those relative URLs
> configurable, but because of a recent exchange on the gmod-ajax list
> I'm looking at changing how that works.  If you've got a non-default
> directory setup I'd be interested to know how you have things laid
> out, so that we can make sure that setting works correctly for everyone.
>
> Regards,
> Mitch
>
> On 06/30/2010 06:06 AM, Mariette wrote:
>> Hi,
>>
>> I'm trying to get jbrowse runing into our website. However it's not
>> working,
>> I have the jbrowse environement displayed but not annotations and the
>> seqRef.
>> Jbrowse can read the refSeq.js and the trackinfo.js but doesn't read the
>> 'seqDir' and
>> the 'url' fields of these files.
>> We figured out that the jbrowse sample web site allows to list files
>> into directories.
>> Is it required to make jbrowse working ??
>> The problem is we're using the cherrypy web server which doesn't seems
>> to allow
>> files listing, and we're guessing this is the problem ? would that make
>> sens ??
>>
>> thanks for your reply,
>> Jerome
>>
>> ------------------------------------------------------------------------------
>>
>> This SF.net email is sponsored by Sprint
>> What will you do first with EVO, the first 4G phone?
>> Visit sprint.com/first -- http://p.sf.net/sfu/sprint-com-first
>> _______________________________________________
>> Gmod-ajax mailing list
>> [hidden email]
>> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>>    
>


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Re: Trouble behind cherrypy

Mariette

Hi everyone,
I have a last question conserning jbrowse, I saw in the doc it is
pssobile to provide to the jbrowse instance the seqRef.js and
the trakInfo.js

*params*
    a dictionary with the following keys:

        * |containerID| - ID of the HTML element that contains the browser
        * |refSeqs| - list of reference sequence information items
          (usually from refSeqs.js)
        * |trackData| - list of track data items (usually from trackInfo.js)
        * |dataRoot| - (optional) URL prefix for the data directory
        * |browserRoot| - (optional) URL prefix for the browser code
        * |tracks| - (optional) comma-delimited string containing
          initial list of tracks to view
        * |location| - (optional) string describing the initial location
        * |defaultTracks| - (optional) comma-delimited string containing
          initial list of tracks to view if there are no cookies and no
          "tracks" parameter
        * |defaultLocation| - (optional) string describing the initial
          location if there are no cookies and no "location" parameter

However I'd like to give it whenever I want so jbrowse take in
consideration different tracks/seqs files without reloading the
page. How could that be done ??

I basicly want to do that because in our application users are allowed
to delete/add/modify 'annotations' so I'd like to update the view
when such actions are performed without reloading the web page (so
.js files cannot be reloaded).

Thanks for your answer,
Jerome







Mariette a écrit :

> Hi Mitch,
>
> so I'm getting further thanks for your help.
> To explain you how we configure our site : we have multiple users, each
> with his own directory.
> This directory is not seen by our web server (which is cherrypy). So far
> what we're doing is
> to put the refSeq.js and the trackInfo.js in the user/project directory
> so this file is taken in
> consideration when looking at the user quota (required for our site). To
> do so we basicly
> have a dinamic link which return the right refSeq.js/trackInfo.js files
> considering the authentified
> user.
>
> Right now we have a problem with the link 'url' and 'seqDir' path as
> they have to be relative
> to the web page where jbrowse is built.
> How can we do to direct those links to our user directory ?? any idea ?
>
> hope it make sense,
> Jerome
>
>
>
>
> Mitch Skinner a écrit :
>  
>> JBrowse doesn't use the directory listings; when JBrowse gets a file
>> from the server it's through a direct link (or a URL template, in some
>> places).
>>
>> It's harder to debug if I can't see the app, but my first guess would
>> be that it has something to do with relative URLs.  refSeq.js and
>> trackInfo.js both contain URLs relative to the directory containing
>> the jbrowse index.html file.
>>
>> That's assuming that you're using the default index.html file.  Are
>> you doing that, or are you doing something else?
>>
>> There's a setting (the "dataRoot" parameter to the Browser javascript
>> object constructor) that makes the root of those relative URLs
>> configurable, but because of a recent exchange on the gmod-ajax list
>> I'm looking at changing how that works.  If you've got a non-default
>> directory setup I'd be interested to know how you have things laid
>> out, so that we can make sure that setting works correctly for everyone.
>>
>> Regards,
>> Mitch
>>
>> On 06/30/2010 06:06 AM, Mariette wrote:
>>    
>>> Hi,
>>>
>>> I'm trying to get jbrowse runing into our website. However it's not
>>> working,
>>> I have the jbrowse environement displayed but not annotations and the
>>> seqRef.
>>> Jbrowse can read the refSeq.js and the trackinfo.js but doesn't read the
>>> 'seqDir' and
>>> the 'url' fields of these files.
>>> We figured out that the jbrowse sample web site allows to list files
>>> into directories.
>>> Is it required to make jbrowse working ??
>>> The problem is we're using the cherrypy web server which doesn't seems
>>> to allow
>>> files listing, and we're guessing this is the problem ? would that make
>>> sens ??
>>>
>>> thanks for your reply,
>>> Jerome
>>>
>>> ------------------------------------------------------------------------------
>>>
>>> This SF.net email is sponsored by Sprint
>>> What will you do first with EVO, the first 4G phone?
>>> Visit sprint.com/first -- http://p.sf.net/sfu/sprint-com-first
>>> _______________________________________________
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>>> [hidden email]
>>> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>>>    
>>>      
>
>
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Re: Trouble behind cherrypy

Ian Holmes
Jerome, there is currently no way to do this but it is on our to-do
list. Ian


Mariette wrote:

> Hi everyone,
> I have a last question conserning jbrowse, I saw in the doc it is
> pssobile to provide to the jbrowse instance the seqRef.js and
> the trakInfo.js
>
> *params*
>     a dictionary with the following keys:
>
>         * |containerID| - ID of the HTML element that contains the browser
>         * |refSeqs| - list of reference sequence information items
>           (usually from refSeqs.js)
>         * |trackData| - list of track data items (usually from trackInfo.js)
>         * |dataRoot| - (optional) URL prefix for the data directory
>         * |browserRoot| - (optional) URL prefix for the browser code
>         * |tracks| - (optional) comma-delimited string containing
>           initial list of tracks to view
>         * |location| - (optional) string describing the initial location
>         * |defaultTracks| - (optional) comma-delimited string containing
>           initial list of tracks to view if there are no cookies and no
>           "tracks" parameter
>         * |defaultLocation| - (optional) string describing the initial
>           location if there are no cookies and no "location" parameter
>
> However I'd like to give it whenever I want so jbrowse take in
> consideration different tracks/seqs files without reloading the
> page. How could that be done ??
>
> I basicly want to do that because in our application users are allowed
> to delete/add/modify 'annotations' so I'd like to update the view
> when such actions are performed without reloading the web page (so
> .js files cannot be reloaded).
>
> Thanks for your answer,
> Jerome
>
>
>
>
>
>
>
> Mariette a écrit :
>> Hi Mitch,
>>
>> so I'm getting further thanks for your help.
>> To explain you how we configure our site : we have multiple users, each
>> with his own directory.
>> This directory is not seen by our web server (which is cherrypy). So far
>> what we're doing is
>> to put the refSeq.js and the trackInfo.js in the user/project directory
>> so this file is taken in
>> consideration when looking at the user quota (required for our site). To
>> do so we basicly
>> have a dinamic link which return the right refSeq.js/trackInfo.js files
>> considering the authentified
>> user.
>>
>> Right now we have a problem with the link 'url' and 'seqDir' path as
>> they have to be relative
>> to the web page where jbrowse is built.
>> How can we do to direct those links to our user directory ?? any idea ?
>>
>> hope it make sense,
>> Jerome
>>
>>
>>
>>
>> Mitch Skinner a écrit :
>>  
>>> JBrowse doesn't use the directory listings; when JBrowse gets a file
>>> from the server it's through a direct link (or a URL template, in some
>>> places).
>>>
>>> It's harder to debug if I can't see the app, but my first guess would
>>> be that it has something to do with relative URLs.  refSeq.js and
>>> trackInfo.js both contain URLs relative to the directory containing
>>> the jbrowse index.html file.
>>>
>>> That's assuming that you're using the default index.html file.  Are
>>> you doing that, or are you doing something else?
>>>
>>> There's a setting (the "dataRoot" parameter to the Browser javascript
>>> object constructor) that makes the root of those relative URLs
>>> configurable, but because of a recent exchange on the gmod-ajax list
>>> I'm looking at changing how that works.  If you've got a non-default
>>> directory setup I'd be interested to know how you have things laid
>>> out, so that we can make sure that setting works correctly for everyone.
>>>
>>> Regards,
>>> Mitch
>>>
>>> On 06/30/2010 06:06 AM, Mariette wrote:
>>>    
>>>> Hi,
>>>>
>>>> I'm trying to get jbrowse runing into our website. However it's not
>>>> working,
>>>> I have the jbrowse environement displayed but not annotations and the
>>>> seqRef.
>>>> Jbrowse can read the refSeq.js and the trackinfo.js but doesn't read the
>>>> 'seqDir' and
>>>> the 'url' fields of these files.
>>>> We figured out that the jbrowse sample web site allows to list files
>>>> into directories.
>>>> Is it required to make jbrowse working ??
>>>> The problem is we're using the cherrypy web server which doesn't seems
>>>> to allow
>>>> files listing, and we're guessing this is the problem ? would that make
>>>> sens ??
>>>>
>>>> thanks for your reply,
>>>> Jerome
>>>>
>>>> ------------------------------------------------------------------------------
>>>>
>>>> This SF.net email is sponsored by Sprint
>>>> What will you do first with EVO, the first 4G phone?
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>>>>    
>>>>      
>>
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>
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Re: Trouble behind cherrypy

Mariette

Thanks for this answer.
Do you think this fonctionnality will be coming up soon ?

Jerome



Ian Holmes a écrit :

> Jerome, there is currently no way to do this but it is on our to-do
> list. Ian
>
>
> Mariette wrote:
>  
>> Hi everyone,
>> I have a last question conserning jbrowse, I saw in the doc it is
>> pssobile to provide to the jbrowse instance the seqRef.js and
>> the trakInfo.js
>>
>> *params*
>>     a dictionary with the following keys:
>>
>>         * |containerID| - ID of the HTML element that contains the browser
>>         * |refSeqs| - list of reference sequence information items
>>           (usually from refSeqs.js)
>>         * |trackData| - list of track data items (usually from trackInfo.js)
>>         * |dataRoot| - (optional) URL prefix for the data directory
>>         * |browserRoot| - (optional) URL prefix for the browser code
>>         * |tracks| - (optional) comma-delimited string containing
>>           initial list of tracks to view
>>         * |location| - (optional) string describing the initial location
>>         * |defaultTracks| - (optional) comma-delimited string containing
>>           initial list of tracks to view if there are no cookies and no
>>           "tracks" parameter
>>         * |defaultLocation| - (optional) string describing the initial
>>           location if there are no cookies and no "location" parameter
>>
>> However I'd like to give it whenever I want so jbrowse take in
>> consideration different tracks/seqs files without reloading the
>> page. How could that be done ??
>>
>> I basicly want to do that because in our application users are allowed
>> to delete/add/modify 'annotations' so I'd like to update the view
>> when such actions are performed without reloading the web page (so
>> .js files cannot be reloaded).
>>
>> Thanks for your answer,
>> Jerome
>>
>>
>>
>>
>>
>>
>>
>> Mariette a écrit :
>>    
>>> Hi Mitch,
>>>
>>> so I'm getting further thanks for your help.
>>> To explain you how we configure our site : we have multiple users, each
>>> with his own directory.
>>> This directory is not seen by our web server (which is cherrypy). So far
>>> what we're doing is
>>> to put the refSeq.js and the trackInfo.js in the user/project directory
>>> so this file is taken in
>>> consideration when looking at the user quota (required for our site). To
>>> do so we basicly
>>> have a dinamic link which return the right refSeq.js/trackInfo.js files
>>> considering the authentified
>>> user.
>>>
>>> Right now we have a problem with the link 'url' and 'seqDir' path as
>>> they have to be relative
>>> to the web page where jbrowse is built.
>>> How can we do to direct those links to our user directory ?? any idea ?
>>>
>>> hope it make sense,
>>> Jerome
>>>
>>>
>>>
>>>
>>> Mitch Skinner a écrit :
>>>  
>>>      
>>>> JBrowse doesn't use the directory listings; when JBrowse gets a file
>>>> from the server it's through a direct link (or a URL template, in some
>>>> places).
>>>>
>>>> It's harder to debug if I can't see the app, but my first guess would
>>>> be that it has something to do with relative URLs.  refSeq.js and
>>>> trackInfo.js both contain URLs relative to the directory containing
>>>> the jbrowse index.html file.
>>>>
>>>> That's assuming that you're using the default index.html file.  Are
>>>> you doing that, or are you doing something else?
>>>>
>>>> There's a setting (the "dataRoot" parameter to the Browser javascript
>>>> object constructor) that makes the root of those relative URLs
>>>> configurable, but because of a recent exchange on the gmod-ajax list
>>>> I'm looking at changing how that works.  If you've got a non-default
>>>> directory setup I'd be interested to know how you have things laid
>>>> out, so that we can make sure that setting works correctly for everyone.
>>>>
>>>> Regards,
>>>> Mitch
>>>>
>>>> On 06/30/2010 06:06 AM, Mariette wrote:
>>>>    
>>>>        
>>>>> Hi,
>>>>>
>>>>> I'm trying to get jbrowse runing into our website. However it's not
>>>>> working,
>>>>> I have the jbrowse environement displayed but not annotations and the
>>>>> seqRef.
>>>>> Jbrowse can read the refSeq.js and the trackinfo.js but doesn't read the
>>>>> 'seqDir' and
>>>>> the 'url' fields of these files.
>>>>> We figured out that the jbrowse sample web site allows to list files
>>>>> into directories.
>>>>> Is it required to make jbrowse working ??
>>>>> The problem is we're using the cherrypy web server which doesn't seems
>>>>> to allow
>>>>> files listing, and we're guessing this is the problem ? would that make
>>>>> sens ??
>>>>>
>>>>> thanks for your reply,
>>>>> Jerome
>>>>>
>>>>> ------------------------------------------------------------------------------
>>>>>
>>>>> This SF.net email is sponsored by Sprint
>>>>> What will you do first with EVO, the first 4G phone?
>>>>> Visit sprint.com/first -- http://p.sf.net/sfu/sprint-com-first
>>>>> _______________________________________________
>>>>> Gmod-ajax mailing list
>>>>> [hidden email]
>>>>> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>>>>>    
>>>>>      
>>>>>          
>>> ------------------------------------------------------------------------------
>>> This SF.net email is sponsored by Sprint
>>> What will you do first with EVO, the first 4G phone?
>>> Visit sprint.com/first -- http://p.sf.net/sfu/sprint-com-first
>>> _______________________________________________
>>> Gmod-ajax mailing list
>>> [hidden email]
>>> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>>>  
>>>      
>> ------------------------------------------------------------------------------
>> This SF.net email is sponsored by Sprint
>> What will you do first with EVO, the first 4G phone?
>> Visit sprint.com/first -- http://p.sf.net/sfu/sprint-com-first
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>>    
>
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Re: Trouble behind cherrypy

Ian Holmes
It's hard to say; we're doing some refactoring now and it might "fall out" of that..
Sorry I cannot be more specific at this stage. Certainly what you ask for is a common request from people using jbrowse as part of a repository-type system, so I expect we would have this within the year, but don't hold me to it

Sent from my iPad

On Jul 12, 2010, at 12:57 AM, Mariette <[hidden email]> wrote:

>
> Thanks for this answer.
> Do you think this fonctionnality will be coming up soon ?
>
> Jerome
>
>
>
> Ian Holmes a écrit :
>> Jerome, there is currently no way to do this but it is on our to-do
>> list. Ian
>>
>>
>> Mariette wrote:
>>  
>>> Hi everyone,
>>> I have a last question conserning jbrowse, I saw in the doc it is
>>> pssobile to provide to the jbrowse instance the seqRef.js and
>>> the trakInfo.js
>>>
>>> *params*
>>>    a dictionary with the following keys:
>>>
>>>        * |containerID| - ID of the HTML element that contains the browser
>>>        * |refSeqs| - list of reference sequence information items
>>>          (usually from refSeqs.js)
>>>        * |trackData| - list of track data items (usually from trackInfo.js)
>>>        * |dataRoot| - (optional) URL prefix for the data directory
>>>        * |browserRoot| - (optional) URL prefix for the browser code
>>>        * |tracks| - (optional) comma-delimited string containing
>>>          initial list of tracks to view
>>>        * |location| - (optional) string describing the initial location
>>>        * |defaultTracks| - (optional) comma-delimited string containing
>>>          initial list of tracks to view if there are no cookies and no
>>>          "tracks" parameter
>>>        * |defaultLocation| - (optional) string describing the initial
>>>          location if there are no cookies and no "location" parameter
>>>
>>> However I'd like to give it whenever I want so jbrowse take in
>>> consideration different tracks/seqs files without reloading the
>>> page. How could that be done ??
>>>
>>> I basicly want to do that because in our application users are allowed
>>> to delete/add/modify 'annotations' so I'd like to update the view
>>> when such actions are performed without reloading the web page (so
>>> .js files cannot be reloaded).
>>>
>>> Thanks for your answer,
>>> Jerome
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>> Mariette a écrit :
>>>    
>>>> Hi Mitch,
>>>>
>>>> so I'm getting further thanks for your help.
>>>> To explain you how we configure our site : we have multiple users, each with his own directory.
>>>> This directory is not seen by our web server (which is cherrypy). So far what we're doing is
>>>> to put the refSeq.js and the trackInfo.js in the user/project directory so this file is taken in
>>>> consideration when looking at the user quota (required for our site). To do so we basicly
>>>> have a dinamic link which return the right refSeq.js/trackInfo.js files considering the authentified
>>>> user.
>>>>
>>>> Right now we have a problem with the link 'url' and 'seqDir' path as they have to be relative
>>>> to the web page where jbrowse is built.
>>>> How can we do to direct those links to our user directory ?? any idea ?
>>>>
>>>> hope it make sense,
>>>> Jerome
>>>>
>>>>
>>>>
>>>>
>>>> Mitch Skinner a écrit :
>>>>        
>>>>> JBrowse doesn't use the directory listings; when JBrowse gets a file from the server it's through a direct link (or a URL template, in some places).
>>>>>
>>>>> It's harder to debug if I can't see the app, but my first guess would be that it has something to do with relative URLs.  refSeq.js and trackInfo.js both contain URLs relative to the directory containing the jbrowse index.html file.
>>>>>
>>>>> That's assuming that you're using the default index.html file.  Are you doing that, or are you doing something else?
>>>>>
>>>>> There's a setting (the "dataRoot" parameter to the Browser javascript object constructor) that makes the root of those relative URLs configurable, but because of a recent exchange on the gmod-ajax list I'm looking at changing how that works.  If you've got a non-default directory setup I'd be interested to know how you have things laid out, so that we can make sure that setting works correctly for everyone.
>>>>>
>>>>> Regards,
>>>>> Mitch
>>>>>
>>>>> On 06/30/2010 06:06 AM, Mariette wrote:
>>>>>            
>>>>>> Hi,
>>>>>>
>>>>>> I'm trying to get jbrowse runing into our website. However it's not working,
>>>>>> I have the jbrowse environement displayed but not annotations and the
>>>>>> seqRef.
>>>>>> Jbrowse can read the refSeq.js and the trackinfo.js but doesn't read the
>>>>>> 'seqDir' and
>>>>>> the 'url' fields of these files.
>>>>>> We figured out that the jbrowse sample web site allows to list files
>>>>>> into directories.
>>>>>> Is it required to make jbrowse working ??
>>>>>> The problem is we're using the cherrypy web server which doesn't seems
>>>>>> to allow
>>>>>> files listing, and we're guessing this is the problem ? would that make
>>>>>> sens ??
>>>>>>
>>>>>> thanks for your reply,
>>>>>> Jerome
>>>>>>
>>>>>> ------------------------------------------------------------------------------
>>>>>> This SF.net email is sponsored by Sprint
>>>>>> What will you do first with EVO, the first 4G phone?
>>>>>> Visit sprint.com/first -- http://p.sf.net/sfu/sprint-com-first
>>>>>> _______________________________________________
>>>>>> Gmod-ajax mailing list
>>>>>> [hidden email]
>>>>>> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>>>>>>                  
>>>> ------------------------------------------------------------------------------
>>>> This SF.net email is sponsored by Sprint
>>>> What will you do first with EVO, the first 4G phone?
>>>> Visit sprint.com/first -- http://p.sf.net/sfu/sprint-com-first
>>>> _______________________________________________
>>>> Gmod-ajax mailing list
>>>> [hidden email]
>>>> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>>>>        
>>> ------------------------------------------------------------------------------
>>> This SF.net email is sponsored by Sprint
>>> What will you do first with EVO, the first 4G phone?
>>> Visit sprint.com/first -- http://p.sf.net/sfu/sprint-com-first
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>>
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