msaviewer - next steps

jalviewcrowdadmin · 28 October 2014 14:53

Hi Sebastian.

Tochukwu - our newest Jalview developer, has just started looking at creating an msaviewer export. He's not had much experience with working with bioinformatics web resources so I'd really appreciate it if you could give him a brief tour of the msaviewer web examples. It would also be good to know exactly what is considered 'BioJS best practice' for deploying the msaviewer so we can make sure any pages generated by Jalview aren't going to break when BioJS or msaviewer is updated in the future.

From our side, we'd really like it if MSA viewer could provide a link to post data to the www.jalview.org/services/launchApp service so any data in an MSA viewer could be opened in the Jalview Desktop. I've got a feeling the easiest way to do this robustly is to look at creating an HTTP api for the desktop so javascript code on the web page can launch an instance of Jalview that listens on a localhost port, and posts JSON to it. Otherwise, we'd have to work out how to either get Jalview to extract the data from the page where msaviewer is deployed, or stash the data in msaviewer somewhere and then pass the URL to Jalview via it's servlet JNLP launch mechanism so it can load it. Any thoughts/strong opinions about the easiest way to proceed ?

Jim.

sebi · 29 October 2014 03:53

Hi Jim,

sorry for being so unresponsive.

has just started looking at creating an msaviewer export.

Wow great. I started to create a GFF and Annotation parser for the Jalview format, but then completely run short of time.
(I did start my own naive and unfinished patch)

So again I am super sorry and will get more involved in #1541.

http://issues.jalview.org/browse/JAL-1541

a brief tour of the msaviewer web examples

Project website (interactive example): http://biojs-msa.org/
Integration in Galaxy: https://github.com/greenify/tools-iuc/tree/master/visualizations/biojs-msa

More examples: http://workmen.biojs.net/demo/biojs-vis-msa
MSA-Wiki: Home · wilzbach/msa Wiki · GitHub

@Tochukwu: I hope this you. Don't hesitate to contact me if you have questions.

It would also be good to know exactly what is considered 'BioJS best practice' [...] aren't going to break

Tough question. JavaScript is a rapidly changing language, but what will never change for the msaviewer is that:

* the msaviewer is assumed to parse the input file(s) asynchronously
(those parsers are independent packages and unlikely to change)
* it is loaded into one div element
* one constructs an msaviewer instance with this DOM element
* it uses require to inject the component code
* one has to call `render` to draw the MSA on the page

The additional configuration options the MSA receives are likely to change.

From our side, we'd really like it if MSA viewer could provide a link to post data to the www.jalview.org/services/launchApp service so any data in an MSA viewer could be opened in the Jalview Desktop. [..] creating an HTTP api for the desktop

As soon as I will find a bit of "leisure", I will definitely add the "'View in Jalview' link".

github.com/wilzbach/msa

'View in Jalview' link for an MSA view

opened 04:59PM - 16 Sep 14 UTC

closed 04:05AM - 19 Nov 14 UTC

foreveremain

It would be really useful to have a 'launch in Jalview' view for msa-viewer, tha…t passed URLs to the jalview launch service that allowed someone to open the alignmment + annotation shown in an MSA view as a Jalview session: Service URL: http://www.jalview.org/services/launchApp Available servlet parameters (please URLEncode): open=<alignment file URL> jvm-max-heap=heap size in M or G features maps to '-features' treeFile maps to '-tree' tree maps to '-tree' annotations maps to '-annotations' colour maps to '-colour'

Any thoughts/strong opinions

+1 for the HTTP API. I don't it is possible for Jalview to parse the msaviewer page.
Currently everything is loaded asynchronously, so just saving the URL in the msaviewer would avoid the effort for you to write an HTTP API.
(Anyway an POST API seems way more flexible than using GET parameters)

Best,

Seb

···

On 2014-10-28 15:53, Jim Procter wrote:

Hi Sebastian.

Tochukwu - our newest Jalview developer, has just started looking at creating an msaviewer export. He's not had much experience with working with bioinformatics web resources so I'd really appreciate it if you could give him a brief tour of the msaviewer web examples. It would also be good to know exactly what is considered 'BioJS best practice' for deploying the msaviewer so we can make sure any pages generated by Jalview aren't going to break when BioJS or msaviewer is updated in the future.

From our side, we'd really like it if MSA viewer could provide a link to post data to the www.jalview.org/services/launchApp service so any data in an MSA viewer could be opened in the Jalview Desktop. I've got a feeling the easiest way to do this robustly is to look at creating an HTTP api for the desktop so javascript code on the web page can launch an instance of Jalview that listens on a localhost port, and posts JSON to it. Otherwise, we'd have to work out how to either get Jalview to extract the data from the page where msaviewer is deployed, or stash the data in msaviewer somewhere and then pass the URL to Jalview via it's servlet JNLP launch mechanism so it can load it. Any thoughts/strong opinions about the easiest way to proceed ?

Jim.

darolmar · 29 October 2014 07:45

Hi,

I would suggest to include a summary of this discussion at wiki. In this way, other people interested will have access to the info. I also have a little experience with bioSW so, probably, I’m not the right person to do such a summary but I’ll be glad to help as much as I can.

Thanks so much in advance.

Cheers,

David

···

2014-10-29 4:53 GMT+01:00 Sebastian Wilzbach <sebi@wilzbach.me>:

Hi Jim,

sorry for being so unresponsive.

has just started looking at creating an msaviewer export.

Wow great. I started to create a GFF and Annotation parser for the Jalview format, but then completely run short of time.
(I did start my own naive and unfinished patch)

https://github.com/greenify/biojs-io-gff
https://github.com/greenify/biojs-io-annots

So again I am super sorry and will get more involved in #1541.

http://issues.jalview.org/browse/JAL-1541

a brief tour of the msaviewer web examples

Project website (interactive example): http://biojs-msa.org/
Integration in Galaxy: https://github.com/greenify/tools-iuc/tree/master/visualizations/biojs-msa

More examples: http://workmen.biojs.net/demo/biojs-vis-msa
MSA-Wiki: https://github.com/greenify/biojs-vis-msa/wiki

@Tochukwu: I hope this you. Don’t hesitate to contact me if you have questions.

It would also be good to know exactly what is considered ‘BioJS best practice’ […] aren’t going to break

Tough question. JavaScript is a rapidly changing language, but what will never change for the msaviewer is that:

the msaviewer is assumed to parse the input file(s) asynchronously
(those parsers are independent packages and unlikely to change)

it is loaded into one div element

one constructs an msaviewer instance with this DOM element

it uses require to inject the component code

one has to call render to draw the MSA on the page

The additional configuration options the MSA receives are likely to change.

From our side, we’d really like it if MSA viewer could provide a link to post data to the www.jalview.org/services/launchApp service so any data in an MSA viewer could be opened in the Jalview Desktop. […] creating an HTTP api for the desktop

As soon as I will find a bit of “leisure”, I will definitely add the “‘View in Jalview’ link”.

https://github.com/greenify/biojs-vis-msa/issues/64

Any thoughts/strong opinions

+1 for the HTTP API. I don’t it is possible for Jalview to parse the msaviewer page.
Currently everything is loaded asynchronously, so just saving the URL in the msaviewer would avoid the effort for you to write an HTTP API.
(Anyway an POST API seems way more flexible than using GET parameters)

Best,

Seb

On 2014-10-28 15:53, Jim Procter wrote:

Hi Sebastian.

Tochukwu - our newest Jalview developer, has just started looking at creating an msaviewer export. He’s not had much experience with working with bioinformatics web resources so I’d really appreciate it if you could give him a brief tour of the msaviewer web examples. It would also be good to know exactly what is considered ‘BioJS best practice’ for deploying the msaviewer so we can make sure any pages generated by Jalview aren’t going to break when BioJS or msaviewer is updated in the future.

From our side, we’d really like it if MSA viewer could provide a link to post data to the www.jalview.org/services/launchApp service so any data in an MSA viewer could be opened in the Jalview Desktop. I’ve got a feeling the easiest way to do this robustly is to look at creating an HTTP api for the desktop so javascript code on the web page can launch an instance of Jalview that listens on a localhost port, and posts JSON to it. Otherwise, we’d have to work out how to either get Jalview to extract the data from the page where msaviewer is deployed, or stash the data in msaviewer somewhere and then pass the URL to Jalview via it’s servlet JNLP launch mechanism so it can load it. Any thoughts/strong opinions about the easiest way to proceed ?

Jim.

Jalview-dev mailing list
Jalview-dev@jalview.org
http://www.compbio.dundee.ac.uk/mailman/listinfo/jalview-dev

sebi · 1 December 2014 11:00

Hi all,

this just a short update that I found my own "workaround" to send user data to Jalview (until there is a Jalview POST webservice).
You can test this with these steps:

1) Open biojs-msa.org/app
2) Drop in any FASTA / Clustal file from your desktop
3) Click "Export to Jalview"

If someone is interested, here is the code [1].

I would suggest to include a summary of this discussion at wiki

I would be glad to help there, but I couldn't find an appropriate place in the Jalview wiki.

Best,

Seb

[1] https://github.com/greenify/biojs-vis-msa/blob/master/src/utils/export.coffee

···

On 2014-10-29 08:45, David Roldán Martínez wrote:

Hi,

I would suggest to include a summary of this discussion at wiki. In this way, other people interested will have access to the info. I also have a little experience with bioSW so, probably, I'm not the right person to do such a summary but I'll be glad to help as much as I can.

Thanks so much in advance.

Cheers,
   David

2014-10-29 4:53 GMT+01:00 Sebastian Wilzbach <sebi@wilzbach.me <mailto:sebi@wilzbach.me>>:

    Hi Jim,

    sorry for being so unresponsive.

    > has just started looking at creating an msaviewer export.

    Wow great. I started to create a GFF and Annotation parser for the Jalview format, but then completely run short of time.
    (I did start my own naive and unfinished patch)

    GitHub - biojs-io/biojs-io-gff: A GFF (General feature format) parser
    GitHub - wilzbach/msa-annots: Jalview annotation parser

    So again I am super sorry and will get more involved in #1541.

    http://issues.jalview.org/browse/JAL-1541

    > a brief tour of the msaviewer web examples

    Project website (interactive example): http://biojs-msa.org/
    Integration in Galaxy: https://github.com/greenify/tools-iuc/tree/master/visualizations/biojs-msa

    More examples: http://workmen.biojs.net/demo/biojs-vis-msa
    MSA-Wiki: Home · wilzbach/msa Wiki · GitHub

    @Tochukwu: I hope this you. Don't hesitate to contact me if you have questions.

    > It would also be good to know exactly what is considered 'BioJS best practice' [...] aren't going to break

    Tough question. JavaScript is a rapidly changing language, but what will never change for the msaviewer is that:

    * the msaviewer is assumed to parse the input file(s) asynchronously
    (those parsers are independent packages and unlikely to change)
    * it is loaded into one div element
    * one constructs an msaviewer instance with this DOM element
    * it uses require to inject the component code
    * one has to call `render` to draw the MSA on the page

    The additional configuration options the MSA receives are likely to change.

    > From our side, we'd really like it if MSA viewer could provide a link to post data to the www.jalview.org/services/launchApp <http://www.jalview.org/services/launchApp> service so any data in an MSA viewer could be opened in the Jalview Desktop. [..] creating an HTTP api for the desktop

    As soon as I will find a bit of "leisure", I will definitely add the "'View in Jalview' link".

    'View in Jalview' link for an MSA view · Issue #64 · wilzbach/msa · GitHub

    > Any thoughts/strong opinions

    +1 for the HTTP API. I don't it is possible for Jalview to parse the msaviewer page.
    Currently everything is loaded asynchronously, so just saving the URL in the msaviewer would avoid the effort for you to write an HTTP API.
    (Anyway an POST API seems way more flexible than using GET parameters)

    Best,

    Seb

    On 2014-10-28 15:53, Jim Procter wrote:
    > Hi Sebastian.
    >
    > Tochukwu - our newest Jalview developer, has just started looking at creating an msaviewer export. He's not had much experience with working with bioinformatics web resources so I'd really appreciate it if you could give him a brief tour of the msaviewer web examples. It would also be good to know exactly what is considered 'BioJS best practice' for deploying the msaviewer so we can make sure any pages generated by Jalview aren't going to break when BioJS or msaviewer is updated in the future.
    >
    > From our side, we'd really like it if MSA viewer could provide a link to post data to the www.jalview.org/services/launchApp <http://www.jalview.org/services/launchApp> service so any data in an MSA viewer could be opened in the Jalview Desktop. I've got a feeling the easiest way to do this robustly is to look at creating an HTTP api for the desktop so javascript code on the web page can launch an instance of Jalview that listens on a localhost port, and posts JSON to it. Otherwise, we'd have to work out how to either get Jalview to extract the data from the page where msaviewer is deployed, or stash the data in msaviewer somewhere and then pass the URL to Jalview via it's servlet JNLP launch mechanism so it can load it. Any thoughts/strong opinions about the easiest way to proceed ?
    >
    > Jim.

    _______________________________________________
    Jalview-dev mailing list
    Jalview-dev@jalview.org <mailto:Jalview-dev@jalview.org>
    http://www.compbio.dundee.ac.uk/mailman/listinfo/jalview-dev

_______________________________________________
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Jalview-dev@jalview.org
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j_procter · 1 December 2014 12:08

Thanks for this Seb.

I know the lack of direct POSTing to Jalview is frustrating... this is a must for v2.9..

On loading biojs-msa.org/app and trying the 'Export to jalview' function I get a dialog telling me that the sequences were not imported via URL, however you have a mechanism for publishing the file to the web with the option below 'Publish to the web' - would it be posible to perform that function first and then send the URL to the servlet ?

Jim.
ps. nice to see all the sequence logo calculation functions appearing! You've already gone beyond what Jalview provides there At the moment, the biggest issue I see with the viewer are the menu controls.. they're just plain ugly :q (sorry - no offence intended!)

···

On 01/12/2014 11:00, Sebastian Wilzbach wrote:

this just a short update that I found my own "workaround" to send user data to Jalview (until there is a Jalview POST webservice).
You can test this with these steps:

1) Open biojs-msa.org/app
2) Drop in any FASTA / Clustal file from your desktop
3) Click "Export to Jalview"

If someone is interested, here is the code [1].

I would suggest to include a summary of this discussion at wiki

I would be glad to help there, but I couldn't find an appropriate place in the Jalview wiki.

Best,

Seb

[1] https://github.com/greenify/biojs-vis-msa/blob/master/src/utils/export.coffee

On 2014-10-29 08:45, David Roldán Martínez wrote:

Hi,

I would suggest to include a summary of this discussion at wiki. In this way, other people interested will have access to the info. I also have a little experience with bioSW so, probably, I'm not the right person to do such a summary but I'll be glad to help as much as I can.

Thanks so much in advance.

Cheers,
    David

2014-10-29 4:53 GMT+01:00 Sebastian Wilzbach <sebi@wilzbach.me <mailto:sebi@wilzbach.me>>:

     Hi Jim,

     sorry for being so unresponsive.

     > has just started looking at creating an msaviewer export.

     Wow great. I started to create a GFF and Annotation parser for the Jalview format, but then completely run short of time.
     (I did start my own naive and unfinished patch)

     GitHub - biojs-io/biojs-io-gff: A GFF (General feature format) parser
     GitHub - wilzbach/msa-annots: Jalview annotation parser

     So again I am super sorry and will get more involved in #1541.

     http://issues.jalview.org/browse/JAL-1541

     > a brief tour of the msaviewer web examples

     Project website (interactive example): http://biojs-msa.org/
     Integration in Galaxy: https://github.com/greenify/tools-iuc/tree/master/visualizations/biojs-msa

     More examples: http://workmen.biojs.net/demo/biojs-vis-msa
     MSA-Wiki: Home · wilzbach/msa Wiki · GitHub

     @Tochukwu: I hope this you. Don't hesitate to contact me if you have questions.

     > It would also be good to know exactly what is considered 'BioJS best practice' [...] aren't going to break

     Tough question. JavaScript is a rapidly changing language, but what will never change for the msaviewer is that:

     * the msaviewer is assumed to parse the input file(s) asynchronously
     (those parsers are independent packages and unlikely to change)
     * it is loaded into one div element
     * one constructs an msaviewer instance with this DOM element
     * it uses require to inject the component code
     * one has to call `render` to draw the MSA on the page

     The additional configuration options the MSA receives are likely to change.

     > From our side, we'd really like it if MSA viewer could provide a link to post data to the www.jalview.org/services/launchApp <http://www.jalview.org/services/launchApp> service so any data in an MSA viewer could be opened in the Jalview Desktop. [..] creating an HTTP api for the desktop

     As soon as I will find a bit of "leisure", I will definitely add the "'View in Jalview' link".

     'View in Jalview' link for an MSA view · Issue #64 · wilzbach/msa · GitHub

     > Any thoughts/strong opinions

     +1 for the HTTP API. I don't it is possible for Jalview to parse the msaviewer page.
     Currently everything is loaded asynchronously, so just saving the URL in the msaviewer would avoid the effort for you to write an HTTP API.
     (Anyway an POST API seems way more flexible than using GET parameters)

     Best,

     Seb

     On 2014-10-28 15:53, Jim Procter wrote:
     > Hi Sebastian.
     >
     > Tochukwu - our newest Jalview developer, has just started looking at creating an msaviewer export. He's not had much experience with working with bioinformatics web resources so I'd really appreciate it if you could give him a brief tour of the msaviewer web examples. It would also be good to know exactly what is considered 'BioJS best practice' for deploying the msaviewer so we can make sure any pages generated by Jalview aren't going to break when BioJS or msaviewer is updated in the future.
     >
     > From our side, we'd really like it if MSA viewer could provide a link to post data to the www.jalview.org/services/launchApp <http://www.jalview.org/services/launchApp> service so any data in an MSA viewer could be opened in the Jalview Desktop. I've got a feeling the easiest way to do this robustly is to look at creating an HTTP api for the desktop so javascript code on the web page can launch an instance of Jalview that listens on a localhost port, and posts JSON to it. Otherwise, we'd have to work out how to either get Jalview to extract the data from the page where msaviewer is deployed, or stash the data in msaviewer somewhere and then pass the URL to Jalview via it's servlet JNLP launch mechanism so it can load it. Any thoughts/strong opinions about the easiest way to proceed ?
     >
     > Jim.

     _______________________________________________
     Jalview-dev mailing list
     Jalview-dev@jalview.org <mailto:Jalview-dev@jalview.org>
     http://www.compbio.dundee.ac.uk/mailman/listinfo/jalview-dev

_______________________________________________
Jalview-dev mailing list
Jalview-dev@jalview.org
http://www.compbio.dundee.ac.uk/mailman/listinfo/jalview-dev

_______________________________________________
Jalview-dev mailing list
Jalview-dev@jalview.org
http://www.compbio.dundee.ac.uk/mailman/listinfo/jalview-dev