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 <[email protected] > <mailto:[email protected]>>: > > 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 > <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". > > 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 > <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 > [email protected] <mailto:[email protected]> > http://www.compbio.dundee.ac.uk/mailman/listinfo/jalview-dev > > > > > _______________________________________________ > Jalview-dev mailing list > [email protected] > http://www.compbio.dundee.ac.uk/mailman/listinfo/jalview-dev > _______________________________________________ Jalview-dev mailing list [email protected] http://www.compbio.dundee.ac.uk/mailman/listinfo/jalview-dev
