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(10000);
---
> conn.setReadTimeout(100000);
84c75
< conn1.setReadTimeout(10000);
---
> conn1.setReadTimeout(100000);
####################################
launch_mev.jsp
replace the jnlp portion with
<jnlp spec="1.0"
codebase="http://<%=serverName%>:<%=serverPort%><%=serverPath%>/
plugins/org/tigr/microarray/mev"
version="4.0">
<information>
<title>MeV: MultiExperiment Viewer</title>
<vendor>http://www.tm4.org</vendor>
<homepage href="http://www.tm4.org"/>
</information>
<security>
<all-permissions/>
</security>
<resources>
<jar href="mev-base.jar"/>
<jar href="HTTPClient.jar"/>
<jar href="JSciCore.jar"/>
<jar href="JSciPartial.jar"/>
<jar href="Text_JDBC30.jar"/>
<jar href="args4j-2.0.9.jar"/>
<jar href="base64.jar"/>
<jar href="colt.jar"/>
<jar href="comcgh.jar"/>
<jar href="commons-net-1.4.1.jar"/>
<jar href="dialogHelp.jar"/>
<jar href="educgh.jar"/>
<jar href="ftpbean.jar"/>
<jar href="goose.jar"/>
<jar href="images.jar"/>
<jar href="j3daudio.jar"/>
<jar href="j3dcore.jar"/>
<jar href="j3dutils.jar"/>
<jar href="jai_codec.jar"/>
<jar href="jai_core.jar"/>
<jar href="jama.jar"/>
<jar href="jaxp.jar"/>
<jar href="jbcl.jar"/>
<jar href="jconn2.jar"/>
<jar href="jdom-1.0.jar"/>
<jar href="jfreechart-0.9.20.jar"/>
<jar href="jfreechart-common-0.9.5.jar"/>
<jar href="jsch-0.1.39.jar"/>
<jar href="mail.jar"/>
<jar href="mev-algorithm-impl.jar"/>
<jar href="mev-algorithm-support.jar"/>
<jar href="mev-gui-impl.jar"/>
<jar href="mev-gui-support.jar"/>
<jar href="mev-util.jar"/>
<jar href="normalization.jar"/>
<jar href="piccolo.jar"/>
<jar href="piccolox.jar"/>
<jar href="servlet.jar"/>
<jar href="soap.jar"/>
<jar href="swing-layout-1.0.1.jar"/>
<jar href="swingx-2006_10_27.jar"/>
<jar href="tar.jar"/>
<jar href="vecmath.jar"/>
<jar href="weka.jar"/>
<jar href="xerces.jar"/>
<jar href="xml-apis.jar"/>
<extension name="others" href="others.jsp"/>
<j2se version="1.5.0+"
max-heap-size="512M"
href="http://java.sun.com/products/autodl/j2se"/>
</resources>
<application-desc main-class="org.tigr.microarray.mev.TMEV">
<argument>-fileType</argument>
<argument>tdms</argument>
<argument>-fileUrl</argument>
<argument>http://<%=serverName%>:<%=serverPort%><%=serverPath%>/
plugins/org/tigr/microarray/mev/export?ID=<%=SessionID%
>&bioassayset_id=<%=bioassaysetId%></argument>
</application-desc>
</jnlp>
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