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// >>> >>> >>> 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); ###
Re: [basedb-devel] MeV
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// >> >> >> 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 >>
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// > > > 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 >> >> > codebase="http://<%=serverName%>:<%=serverPort%><%=serverPath%>/ >> plugins/org/tigr/microarray/mev" >> version="4.0"> >> >> >> MeV: MultiExperiment Viewer >> http://www.tm4.org >> http://www.tm4.org"/> >> >> >> >> >> >> >> >>
Re: [basedb-devel] MeV
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// 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 > >codebase="http://<%=serverName%>:<%=serverPort%><%=serverPath%>/ > plugins/org/tigr/microarray/mev" > version="4.0"> > > > MeV: MultiExperiment Viewer > http://www.tm4.org > http://www.tm4.org"/> > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > >
[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 MeV: MultiExperiment Viewer http://www.tm4.org http://www.tm4.org"/> http://java.sun.com/products/autodl/j2se"/> -fileType tdms -fileUrl http://<%=serverName%>:<%=serverPort%><%=serverPath%>/ plugins/org/tigr/microarray/mev/export?ID=<%=SessionID% >&bioassayset_id=<%=bioassaysetId%> -- 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. Join us at MIX09 to help pave the way to the Next Web now. Learn more and register at http://ad.doubleclick.net/clk;208669438;13503038;i?http://2009.visitmix.com/ ___ basedb-devel mailing list basedb-devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/basedb-devel
Re: [basedb-devel] MEV can't open data files
Hi Nicklas, thank you for your response. Nicklas Nordborg ha scritto: > Ilenia Zara wrote: > > [...] > Please check Tomcat's log file if you can find any error message there. > From the catalina.out file: java.sql.SQLException: Incorrect key file for table '/tmp/#sql_6a9c_0.MYI'; try to repair it at com.mysql.jdbc.SQLError.createSQLException(SQLError.java:946) at com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:2934) at com.mysql.jdbc.MysqlIO.sendCommand(MysqlIO.java:1616) at com.mysql.jdbc.ServerPreparedStatement.serverExecute(ServerPreparedStatement.java:1230) at com.mysql.jdbc.ServerPreparedStatement.executeInternal(ServerPreparedStatement.java:740) at com.mysql.jdbc.PreparedStatement.executeQuery(PreparedStatement.java:1428) at com.mchange.v2.c3p0.impl.NewProxyPreparedStatement.executeQuery(NewProxyPreparedStatement.java:76) at net.sf.basedb.core.QueryExecutor$FutureResultSet.call(QueryExecutor.java:180) at net.sf.basedb.core.QueryExecutor$FutureResultSet.call(QueryExecutor.java:168) at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:303) at java.util.concurrent.FutureTask.run(FutureTask.java:138) at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:885) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:907) at java.lang.Thread.run(Thread.java:619) > >> The problem doesn't occur with any of my test raw bioassays as long as I >> use them in groups of less than 13 raw bioassays. >> > > This could be some memory-related problem... but I think BASE should be > able to handle a lot more than 12 bioassays without problems. > > Just some month ago we noted that the default settings of MySQL has > changed and in order to not run into memory problems you have to set > useServerPrepStmts=true in the db.url setting in base.config. See > http://base.thep.lu.se/ticket/953 > Yes, when I worked with BASE 2.5.x , I didn't have any problem with the export of a root bioassayset with more than 12 raw bioassays on MeV. Now with BASE 2.6.2 using the same files and base configuration I can't export the root bioassayset even if I set useServerPrepStmts=true in the db.url. I tried to set useServerPrepStmts=false and modify the 'innodb_buffer_pool_size' and 'innodb_additional_mem_pool_size' variables on mysql and it works, but it's not the solution... Do you have any suggestions? Thank you, Ilenia > /Nicklas > > - > This SF.net email is sponsored by the 2008 JavaOne(SM) Conference > Don't miss this year's exciting event. There's still time to save $100. > Use priority code J8TL2D2. > http://ad.doubleclick.net/clk;198757673;13503038;p?http://java.sun.com/javaone > ___ > basedb-devel mailing list > basedb-devel@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/basedb-devel > - This SF.net email is sponsored by the 2008 JavaOne(SM) Conference Don't miss this year's exciting event. There's still time to save $100. Use priority code J8TL2D2. http://ad.doubleclick.net/clk;198757673;13503038;p?http://java.sun.com/javaone ___ basedb-devel mailing list basedb-devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/basedb-devel
Re: [basedb-devel] MEV can't open data files
Ilenia Zara wrote: > Hi All, > > I read the ticket 996 (http://base.thep.lu.se/ticket/996) and I have a > similar problem. > I have an experiment with 16 raw bioassays on MG_U74Av2. > If I export a root bioassayset with more than 12 raw bioassays on MeV, > the "Slide data loading" window is stopping at 0% with the error > message: "TDMS Load Error" - "There is no spot data available". I don't think it is the same error since it is giving an error message. This probably happens because there was some other kind of problem. Please check Tomcat's log file if you can find any error message there. > The problem doesn't occur with any of my test raw bioassays as long as I > use them in groups of less than 13 raw bioassays. This could be some memory-related problem... but I think BASE should be able to handle a lot more than 12 bioassays without problems. Just some month ago we noted that the default settings of MySQL has changed and in order to not run into memory problems you have to set useServerPrepStmts=true in the db.url setting in base.config. See http://base.thep.lu.se/ticket/953 /Nicklas - This SF.net email is sponsored by the 2008 JavaOne(SM) Conference Don't miss this year's exciting event. There's still time to save $100. Use priority code J8TL2D2. http://ad.doubleclick.net/clk;198757673;13503038;p?http://java.sun.com/javaone ___ basedb-devel mailing list basedb-devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/basedb-devel
[basedb-devel] MEV can't open data files
Hi All, I read the ticket 996 (http://base.thep.lu.se/ticket/996) and I have a similar problem. I have an experiment with 16 raw bioassays on MG_U74Av2. If I export a root bioassayset with more than 12 raw bioassays on MeV, the "Slide data loading" window is stopping at 0% with the error message: "TDMS Load Error" - "There is no spot data available". The problem doesn't occur with any of my test raw bioassays as long as I use them in groups of less than 13 raw bioassays. I don't know if this is the same problem. I'm using BASE 2.6.2. I hope this is helpful. Best regards, Ilenia - This SF.net email is sponsored by the 2008 JavaOne(SM) Conference Don't miss this year's exciting event. There's still time to save $100. Use priority code J8TL2D2. http://ad.doubleclick.net/clk;198757673;13503038;p?http://java.sun.com/javaone ___ basedb-devel mailing list basedb-devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/basedb-devel
