Utility for transfering file between BASE and a GenePattern server

[Nicklas Nordborg]

It is not possible to send URL:s to the GenePattern server in the same way as we do for MeV. The reason is that a single session is locked to the user's IP number and this is probably not the same as the IP for the GenePattern server.

So we need a utility that moves file from BASE to a temporary working directory and then a servlet that can serve files from this directory to the GenePattern server. Each job should have a separate working directory and if possible we should lock access to this directory to the IP number of the current GenePattern server. The result files will also be downloaded to this directory and then transfered back to BASE.

When the job has completed the temporary working directory should be deleted.

[Nicklas Nordborg]

(In [1107]) References #222: Utility for transfering file between BASE and a GenePattern server

The basic functionality is now in place, including a hard-coded test servlet. To make sure everything is working properly we need to start with the prototype plug-in (#218).

[Nicklas Nordborg]

(In [1109]) References #222: Utility for transfering file between BASE and a GenePattern server

Added support for downloading files. The files are downloaded to a temporary working directory and exposed as InputStream/OutputStream objects since that suits the BASE API better. I first tried to use JobResult.getURLForFileName() but that issues a request outside the web services session and only results in downloading a HTML page asking for a login/password.

[Nicklas Nordborg]

(In [1116]) References #222 and #229. File transfer gateway now uses the new wrappers.

[Nicklas Nordborg]

(In [1127]) References #222: Utility for transfering file between BASE and a GenePattern server

Now uses the alternate servlet mapping as implemented in ​http://base.thep.lu.se/ticket/1333

[Nicklas Nordborg]

(In [1128]) References #222, #218, #229. Several changes just to make things work.

[Nicklas Nordborg]

(In [1129]) References #222: Utility for transfering file between BASE and a GenePattern server

Separated adding and copying of files to two separate steps. Added a convenience method for downloading a file and reading it into a string.