Hi, Olivier Lefevre wrote: > I am not having much luck installing that plugin. It wants you to > run updatedb.sh. When I do that it says "Building database", which > is alarming in and of itself since that suggests it is rebuilding > the db from scratch, which begs the question of whether it is > possible to install that plugin on a "live", already populated > base instance: I don't want it to throw out all the existing data.
The standard route to make changes to the database is to use the updatedb.sh script. You can run the updatedb.sh script as many times you like, it will only make changes if needed. If you follow the instructions that came with the Illumina package, i.e., http://baseplugins.thep.lu.se/browser/plugins/base2/net.sf.basedb.illumina/tags/1.3/INSTALL for the 1.3 release, it should install cleanly. Maybe the issue is to run the updatedb.sh script? You should simply run it like prompt> cd /path/to/base/bin prompt> ./updatedb.sh password This should finish cleanly with output similar to the listing below. If you have another root-userid than 'root' on your base installation you should run updatedb.sh like the below line. root-userid is the refering to BASE root-userid. prompt> ./updatedb.sh root-userid password If I use the wrong userid or password I get a message indicating just that. Proper userid/password combination gives [0%] --System information----------------------------- BASE : 2.12.1pre Database : jdbc:mysql://localhost/base2?characterEncoding=UTF-8&useCursorFetch=true&defaultFetchSize=100&useServerPrepStmts=true Dialect : org.hibernate.dialect.MySQLInnoDBDialect JDBC : com.mysql.jdbc.Driver; version 5.1 Java : Java(TM) SE Runtime Environment; 1.6.0_07-b06-153; Apple Inc. OS : Mac OS X; x86_64; 10.5.7 ------------------------------------------------- [0%] Building database...................... [30%] Database built successfully. [35%] Initialising database... [36%] --Creating quota types... [37%] --Creating quota... [38%] --Creating roles... [39%] --Creating users... [40%] --Creating groups... [41%] --Creating keys... [42%] --Creating units... [43%] --Creating protocol types... [44%] --Creating hardware types... [45%] --Creating hardware... [46%] --Creating software types... [47%] --Creating software... [48%] --Creating directories... [49%] --Creating file types... [50%] --Creating MIME types... [51%] --Creating plate geometries... [52%] --Creating plate mappings... [53%] --Creating labels... [54%] --Creating annotation types... [56%] --Creating clients... [57%] --Creating plugin definitions... [58%] --Creating example plugin configurations... [59%] --Creating formulas... [60%] --Creating job agents... [61%] --Creating data file types... [62%] --Creating platforms... [63%] --Creating news... [70%] Database initialised successfully. [75%] Updating database... [90%] Database updated successfully. [95%] Installing web application... [100%] Web application installed successfully. This was generated on a live installation (well tomcat is not running but otherwise a real live mysql database) > > But that's not the worst of of it. It immediately complains of > "APPARENT DEADLOCK!!!" (twice) and also (many times) of "Access > denied for user 'base2user'@'localhost' (using password: YES)", > which is baffling since I supplied the correct uid and pwd at > the command line when starting the script. Finally it gives up. > > Can anyone make a suggestion? Can you send the output of ./updatedb.sh Cheers, Jari ------------------------------------------------------------------------------ Crystal Reports - New Free Runtime and 30 Day Trial Check out the new simplified licensing option that enables unlimited royalty-free distribution of the report engine for externally facing server and web deployment. http://p.sf.net/sfu/businessobjects _______________________________________________ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject "unsubscribe" to basedb-users-requ...@lists.sourceforge.net
