Hi Hee Shin,I'm not sure I understand; where you able to make Apollo connect to Chado or not? It sounds like you just edited some sample data? Or is saving the edits back to Chado the problem?
Scott On Jun 25, 2009, at 5:10 PM, heekim wrote:
Thank you! I download the old version, it reads Chado well now. While i read Using Apollo to edit annotations in the user guide. It doesn't mention about editing on Apollo-Chado.It is possible to edit annotations on Apollo-Chado, which is my currentsetup.Actually, this is what my boss wants to do because she understood in thisway. Please let me know. Hee Shin Scott Cain-4 wrote:Hi Hee Shin, I cc'ed this to the Apollo mailing list because I don't know the answer either. I can see several Apollo packages that are marked"hidden" in the sourceforge download admin page, but it's not clear to me which one would be the previous version; I guessed 1.10.0, but thatisn't available. Scott On Jun 25, 2009, at 3:48 PM, heekim wrote:I would like to use more stable version. Would please how to download the previous version. I couldn't find in the sourceforge.net. I only see 1.11.0. Thak you. Hee Shin Jonathan Crabtree-4 wrote:Hi Hee, This is a known bug in Apollo 1.11.0. I've committed a patch for it to CVS (see revision 1.7 of DNAUtils.java), but it hasn't made its way into a new release yet: http://gmod.cvs.sourceforge.net/viewvc/gmod/apollo/src/java/org/bdgp/util/DNAUtils.java?view=log You may want to join the Apollo mailing list if you have not already done so, so that you can see the ongoing discussion on this topic. In brief, this is not the only problem with the 1.11.0 release and judging by the CVS logs I think Ed (the main Apollo developer) is busy ironing out the rest of them as we speak. You may want to consider waiting for the next release, downgrading to a previous release, or running off the CVS HEAD, depending on your inclination and time constraints... Jonathan On Thu, Jun 25, 2009 at 2:36 PM, heekim <[email protected]> wrote:in the debugging mode, i was able to catch what to do. I made progress. I had another error that I dont understand. it says, "FATAL: Exception in Apollo.mainRun() thread java.lang.IllegalArgumentException: Could not find complement for 'N'" this is my setup,I created the instance called "beetle" which inherited RiceInstance.<chadodb> <name>BeetleBase Chado KSU server</name> <adapter>apollo.dataadapter.chado.jdbc.PostgresChadoAdapter</ adapter> <url>jdbc:postgresql://xxx.xxx.xxx.xxx:5432/ BeetleBase3_Hans_Marce</url> <dbName>BeetleBase3_Hans_Marce</dbName> <dbUser>postgres</dbUser> <dbInstance>beetle</dbInstance> <style>gff3.style</style> <!-- <sequenceTypes> <type>gene</type> <type>golden_path_region</type> </sequenceTypes> --> </chadodb> Thank you. Hee Shin Scott Cain-4 wrote:Hi Hee Shin, You can turn on debugging by changing 'INFO' to 'DEBUG' in thelog4j.properties file in the conf directory. Please try again withdebugging turned on so we can see the complete list of steps that Apollo goes through. Also, there have been some reports about problems with the most recent release of Apollo when it comes to use with Chado (v 1.11). You might want to try version 1.10 as well. Scott On Fri, Jun 19, 2009 at 5:21 PM, heekim<[email protected]> wrote:Hi, I am modifying chado-adapter.xml to adopt Apollo to Chado. However, whenever I define <dbInstance>beetle</dbInstance>, it showsanerror; FATAL: Failed to read config file conf/apollo.cfg. I also tried it with/without <chadoInstance id="beetle">, however, it still have the same error. I hope that I can adopt Apollo to Chado. Thank you. Hee Shin -- View this message in context:http://www.nabble.com/problem-of-adopting-Apollo-to-Chado-tp24119004p24119004.htmlSent from the gmod-schema mailing list archive at Nabble.com.------------------------------------------------------------------------------Are you an open source citizen? Join us for the Open Source Bridgeconference! Portland, OR, June 17-19. 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Register today!http://ad.doubleclick.net/clk;215844324;13503038;v?http://opensourcebridge.org_______________________________________________ Gmod-schema mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/gmod-schema-- View this message in context: http://www.nabble.com/problem-of-adopting-Apollo-to-Chado-tp24119004p24208792.html Sent from the gmod-schema mailing list archive at Nabble.com. ------------------------------------------------------------------------------ _______________________________________________ Gmod-schema mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/gmod-schema------------------------------------------------------------------------------ _______________________________________________ Gmod-schema mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/gmod-schema-- View this message in context: http://www.nabble.com/problem-of-adopting-Apollo-to-Chado-tp24119004p24209921.html Sent from the gmod-schema mailing list archive at Nabble.com. ------------------------------------------------------------------------------ _______________________________________________ Gmod-schema mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/gmod-schema----------------------------------------------------------------------- Scott Cain, Ph. D. scott at scottcain dot net GMOD Coordinator (http://gmod.org/) 216-392-3087 Ontario Institute for Cancer Research ------------------------------------------------------------------------------ _______________________________________________ Gmod-schema mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/gmod-schema-- View this message in context: http://www.nabble.com/problem-of-adopting-Apollo-to-Chado-tp24119004p24211158.html Sent from the gmod-schema mailing list archive at Nabble.com. ------------------------------------------------------------------------------ _______________________________________________ Gmod-schema mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/gmod-schema
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