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(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> >>>> >>>> >>>> >>>> >>>> -------------------------------------------------------------------- >>>> - >>>> --------- >>>> SF.Net email is Sponsored by MIX09, March 18-20, 2009 in Las >>>> Vegas, Nevada. >>>> The future of the web can't happen without you. 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