Hi, Unfortunately I am away with a poor connection to the Internet. I have a couple of pointers:
1) Look at how the MeV plug-in does. The plug-in downloads data from a BASE server using a download. MeV is a Java web start application where essential parameters are communicated through the jnlp file. See - http://trac.thep.lu.se/trac/basehacks/wiki/MeV for info on needed MeV changes such as auto download of data from BASE - http://base.thep.lu.se/browser/trunk/www/plugins/org/tigr/microarray/mev (the JSP files) for implementation of dynamic jnlp file creation. 2) BASE supports filedownload through a servlet (I cannot remember the details but studying the MeV example above should reveal it). 3) In the web services client http://baseplugins.thep.lu.se/wiki/se.lu.thep.webservices_clients there is downloads of cel/cdf files. Hope this helps you in your quest of improving BASE. Cheers, Jari Peter Mertens wrote: > Hi, > > instead of using a plugin i want to create my own base webservice. > > This service is almost working, except for one point. Where i want to get > the url where the data files are located. > > So, i can get the project, experiment and the data from the experiment. > Now > i want to send all information about the data:name, id, description and > the > url where the client, calling the service, can download the files from. > > What i tried is: > > public String getCelFiles(int experimentId) > { > Experiment experiment = experimentVector.get(experimentId-1); > > System.out.println("RawBioAssays of exp: "+experiment.getName()); > > ItemResultIterator<RawBioAssay> rawBioAssays; > > String rbas = "<RawBioAssays>"; > > try > { > dc = sc.newDbControl(); > > ItemQuery<RawBioAssay> query = experiment.getRawBioAssays(); > System.out.println("nr of raw bioassays: "+query.count(dc)); > > rawBioAssays = query.iterate(dc); > > if (rawBioAssays != null) > { > RawBioAssay item = null; > String name = ""; > String loc =""; > String url =""; > int id=0; > File file = null; > String path = ""; > > while (rawBioAssays.hasNext()) > { > item = rawBioAssays.next(); > name = item.getName(); > > rbas += "<RawBioAssay>"; > rbas += "<Name>"+name+"</Name>"; > > id = item.getId(); > file = Affymetrix.getCelFile(item); > path = file.getPath().toString(); > > rbas += "<Id>"+id+"</Id>"; > > loc = HTML.urlEncode(path); > url = fileUrl+"-"+sessionId+"-"+loc; > > rbas += "<Url>"+url+"</Url>"; > rbas += "</RawBioAssay>"; > } > > } > dc.close(); > > } > catch(Exception e) > { > System.out.println("e:"+e); > } > rbas += "</RawBioAssays>"; > > return rbas; > } > > This returns a the string: > <RawBioAssays><RawBioAssay><Name>1.1_2</Name><Id>90</Id><Url> > http://nbx8.nugo.org/nutriBASE/filemanager/files/view/-42d47d6797b7b05c-/home/PeterMertens/raw+data/test/1.1_2.CEL > </Url></RawBioAssay><RawBioAssay><Name>1.2</Name><Id>92</Id><Url> > http://nbx8.nugo.org/nutriBASE/filemanager/files/view/-42d47d6797b7b05c-/home/PeterMertens/raw+data/test/1.2.CEL > </Url></RawBioAssay></RawBioAssays> > > If i try to download the files (while the session is still active) using > the > url's i get a http 500 response. > I suppose that the part /filemanager/files/view/ is not correct since the > fileview.jsp is not loaded, but i don't have a clue how to do it > correctly. > > A possible solution would be to download the files to a folder in the > webserver's directory and than ... . This is not a very nice solution for > this problem so i hope somebody can help getting the url of the files on > the > base server. > > thanks, > > Peter > > > > > 2007/9/27, Nicklas Nordborg <[EMAIL PROTECTED]>: >> >> Peter Mertens wrote: >> > Dear list, >> > >> > i'm working on a plugin that gives the possibility to run the analysis >> > on another machine (not the one base is installed on). >> >> Have you checked out the possiblitity to use Job agents? They can be >> used to execute any plug-in on a different server. See >> http://base.thep.lu.se/chrome/site/trunk/html/admindoc/plugin_installation/plugins.jobagents.html >> >> for more information. >> >> > In order to download the files (cel and cdf) over http, i need the to >> > retrieve the URL's. >> > Can somebody tell me how to get this? >> >> The file URL depends on the sesssion ID of the logged in user. Plug-ins >> are executed in a different session with a different ID, so I am not >> sure it will work since the web server may know about the session ID >> used by the plug-in. It is not possible for the plug-in to get the >> session ID for the user. In fact, the user may already have logged out >> before the plug-in is executed. >> >> I think it is better if your plug-in call File.getDownloadStream() >> and copies the file to the machine where you are going to run the >> analysis program. >> >> > In the documentation i found that all files have method "getLocation". >> > But it is not mentioned what kind of location this is. >> > Also the code of this method did not tell me more. >> >> This method can return 3 different values: OFFLINE, PRIMARY and >> SECONDARY. If it returns OFFLINE the file is not stored at all on the >> BASE server. The SECONDARY location is a backup location and the file >> can't be accessed. You should check that the getLocation() method >> returns PRIMARY or you can't use the file. >> >> /Nicklas >> >> ------------------------------------------------------------------------- This SF.net email is sponsored by: Splunk Inc. Still grepping through log files to find problems? Stop. Now Search log events and configuration files using AJAX and a browser. Download your FREE copy of Splunk now >> http://get.splunk.com/ _______________________________________________ basedb-devel mailing list basedb-devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/basedb-devel
