Opened 14 years ago
Closed 14 years ago
#222 closed task (fixed)
Utility for transfering file between BASE and a GenePattern server
Reported by: | Nicklas Nordborg | Owned by: | Nicklas Nordborg |
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Priority: | critical | Milestone: | ZZ GenePattern integration v1.0 |
Component: | net.sf.basedb.genepattern | Keywords: | |
Cc: |
Description
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.
Change History (8)
comment:1 Changed 14 years ago by
Status: | new → assigned |
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comment:2 Changed 14 years ago by
comment:3 Changed 14 years ago by
(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.
comment:4 Changed 14 years ago by
comment:5 Changed 14 years ago by
(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
comment:6 Changed 14 years ago by
comment:7 Changed 14 years ago by
(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.
comment:8 Changed 14 years ago by
Resolution: | → fixed |
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Status: | assigned → closed |
(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).