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
>
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