Re: [basedb-devel] MeV
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
Re: [basedb-devel] MeV
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 codebase=http://%=serverName%:%=serverPort%%=serverPath%/ plugins/org/tigr/microarray/mev version=4.0 information titleMeV: MultiExperiment Viewer/title vendorhttp://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/
[basedb-devel] MeV
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 codebase=http://%=serverName%:%=serverPort%%=serverPath%/ plugins/org/tigr/microarray/mev version=4.0 information titleMeV: MultiExperiment Viewer/title vendorhttp://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+
