Great, we'll upgrade MeV in base after the holidays.
Jari
David Waring wrote:
The MeV people have incorporated the servlet support changes in their
svn repository. So if you want to grab it from sourseforge you could
put it into the Base distribution.
They will likely be incorporating auto-loading features also but
those changes are more complicated and they want to address some
other issues, so that may not happen right away.
On Dec 11, 2008, at 1:31 PM, David Waring wrote:
I have also made another change to my version of Base. My users
wanted real intensities within MeV instead of ratios. But
unfortunately MeV does not support a multi experiment file with
intensities. So I made a modified BioassayExporter and added a new
new FileLoader in MeV based on the TDMS (Stanford) format. I'm going
to see if TIGR is interested in these and my other changes that allow
the data to be loaded automatically skipping the normal dialog.
On Dec 10, 2008, at 1:04 PM, Nicklas Nordborg wrote:
Thanks, this is excellent news!
We were also planning to do this, but there has always been some
other
more important things that had to be done before. It is really nice
that
MeV has been webstart-enabled and can load files from the web. If I
remember correctly the modifications we (Jari) had to do was
related to
make MeV work as a webstart-application and to download the file from
the BASE server. It seems like it is almost possible to use MeV
without
modifications. The first issue can maybe be addressed on the BASE
side
as well. The servlet could be changed to accept query parameters as
part
of the path instead. Eg something like:
http://your.base.server/base2/./mev/export/sessionid/
bioassaysetid
The timeout issue needs to be solved in MeV though.
I have opened a ticket on the BASE plug-ins site:
http://baseplugins.thep.lu.se/ticket/162
If anyone has more information please post comments there
(login=base;
password=base)
/Nicklas
David Waring wrote:
As best I can tell the current version of Base has MeV support built
on Version 4.0.01. The current release version of MeV 4.3.01 is much
improved with a better interface and a more modules. It also has
webstart support built in.
I have installed MeV 4.3 on my Base installation. It required
just a
few tweaks.
Only one change needed to be made in Base code.
launch_mev.jsp had to be changed to include a few more jars and the
arguments are different than the current Base implementation of MeV.
I had to modify two MeV files
FileResourceManager was written to get files via HTTP but choked
when calling a servlet since is was not passing the query piece
of he
URL. That was easily fixed
HTTPDownloader had a 10 second timeout for reading the file I
changed it to 100 seconds.
I will pass the MeV changes on to TIGR and ask them to implement the
since they are relevant to anyone serving data from a servlet
In the mean time I include them here for anyone who wants to build
his own version of MeV
To implement these changes just:
1) download the latest MeV
2) make the changes in the MeV code
3) go to the build_script directory
3) ant build-package
4) ant webstart-package -- you will have to tweak ant to handle the
jar signing
5) change launch_mev.jsp
6) copy all the jars from mev/deploy/webstart/mev/lib/ to the base
mev directory plugins/org/tigr/microarray/mev
Thats it, it does not even require a Base compile or even a server
restart. The only downside is that MeV opens with the the data
loaded
in a dialog box and the users has to select the top-left most data
cell in the table and then click the load box (just like opening a
TDMS file) I've written a work around for this if anyone is
interested.
Changes
here is the diff for
mev/source/org/tigr/microarray/mev/resources/
FileResourceManager.java
252c252,256
File f =
fd.getTempFile(thisDefURL.getPath());
---
String path
= thisDefURL.getPath();
String query
= thisDefURL.getQuery();
if (query !=
null query.length() 0)
path
+= ? + query;
File f =
fd.getTempFile(path);
diff for
mev/source/org/tigr/microarray/mev/resources/HTTPDownloader.java
conn.setReadTimeout(1);
---
conn.setReadTimeout(10);
84c75
conn1.setReadTimeout(1);
---
conn1.setReadTimeout(10);
launch_mev.jsp
replace the jnlp portion with
jnlp spec=1.0
