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