Kepler: Issueshttps://projects.ecoinformatics.org/ecoinfo/https://projects.ecoinformatics.org/ecoinfo/ecoinfo/favicon.ico?14691340362006-01-27T19:25:54ZEcoinformatics Redmine
Redmine Bug #2346 (Resolved): Memory utilization on startup.https://projects.ecoinformatics.org/ecoinfo/issues/23462006-01-27T19:25:54ZKevin Rulandkruland@ku.edu
<p>Current CVS head of kepler (1-27-06): At welcome window, after forced gc,<br />memory usage is 57M. After one empty graph window, memory usage is 65M. After<br />opening second empty graph window, memory usage is 67M.</p> Bug #2320 (Resolved): Cannot run multiple instances of Kepler simultaneously.https://projects.ecoinformatics.org/ecoinfo/issues/23202005-12-16T16:57:58ZKevin Rulandkruland@ku.edu
<p>Because of the internal database (hsqldb), one cannot run two instances of<br />kepler simultaneously. The second instance of kepler started results in a very<br />ugly stacktrace but does not terminate the application. This is an example of<br />the stacktrace:</p>
<p>java.lang.NullPointerException<br /> at org.kepler.objectmanager.cache.CacheUtil.executeSQLCommand(CacheUtil.java:78)<br /> at org.kepler.objectmanager.cache.CacheManager.<init>(CacheManager.java:101)<br /> at org.kepler.objectmanager.cache.CacheManager.getInstance(CacheManager.java:119)<br /> at org.kepler.moml.KSWLibraryBuilder.buildLibrary(KSWLibraryBuilder.java:82)<br /> at ptolemy.vergil.VergilApplication.openLibrary(VergilApplication.java:230)<br /> at<br />ptolemy.vergil.VergilApplication._createDefaultConfiguration(VergilApplication.java:418)<br /> at<br />ptolemy.vergil.VergilApplication._createEmptyConfiguration(VergilApplication.java:439)<br /> at ptolemy.actor.gui.MoMLApplication._parseArgs(MoMLApplication.java:875)<br /> at ptolemy.vergil.VergilApplication._parseArgs(VergilApplication.java:512)<br /> at ptolemy.actor.gui.MoMLApplication.<init>(MoMLApplication.java:208)<br /> at ptolemy.vergil.VergilApplication.<init>(VergilApplication.java:105)<br /> at ptolemy.vergil.VergilApplication$1.run(VergilApplication.java:148)<br /> at java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:178)<br /> at java.awt.EventQueue.dispatchEvent(EventQueue.java:454)<br /> at<br />java.awt.EventDispatchThread.pumpOneEventForHierarchy(EventDispatchThread.java:201)<br /> at<br />java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:151)<br /> at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:145)<br /> at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:137)<br /> at java.awt.EventDispatchThread.run(EventDispatchThread.java:100)<br />java.lang.NullPointerException<br /> at org.kepler.objectmanager.cache.CacheUtil.executeSQLCommand(CacheUtil.java:78)<br /> at org.kepler.objectmanager.cache.CacheManager.<init>(CacheManager.java:101)<br /> at org.kepler.objectmanager.cache.CacheManager.getInstance(CacheManager.java:119)<br /> at org.kepler.moml.KSWLibraryBuilder.buildLibrary(KSWLibraryBuilder.java:82)<br /> at ptolemy.vergil.VergilApplication.openLibrary(VergilApplication.java:230)<br /> at<br />ptolemy.vergil.VergilApplication._createDefaultConfiguration(VergilApplication.java:418)<br /> at<br />ptolemy.vergil.VergilApplication._createEmptyConfiguration(VergilApplication.java:439)<br /> at ptolemy.actor.gui.MoMLApplication._parseArgs(MoMLApplication.java:875)<br /> at ptolemy.vergil.VergilApplication._parseArgs(VergilApplication.java:512)<br /> at ptolemy.actor.gui.MoMLApplication.<init>(MoMLApplication.java:208)<br /> at ptolemy.vergil.VergilApplication.<init>(VergilApplication.java:105)<br /> at ptolemy.vergil.VergilApplication$1.run(VergilApplication.java:148)<br /> at java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:178)<br /> at java.awt.EventQueue.dispatchEvent(EventQueue.java:454)<br /> at<br />java.awt.EventDispatchThread.pumpOneEventForHierarchy(EventDispatchThread.java:201)<br /> at<br />java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:151)<br /> at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:145)<br /> at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:137)<br /> at java.awt.EventDispatchThread.run(EventDispatchThread.java:100)</p>
<p>Here are some possible resolutions:</p>
<p>1) deploy hsqldb as a service and have it run in an independent jvm. Questions:<br /> How is startup managed? Are there any performance or resource constraints?</p>
<p>2) test for another instance of kepler and terminate the second copy with an<br />appropriate error message</p>
<p>3) use a different database system which operates independently from kepler. <br />MySQL is one example. Questions: what are the deployment issues involved here.</p> Bug #2316 (Resolved): Conflicting jars and classpath reductionhttps://projects.ecoinformatics.org/ecoinfo/issues/23162005-12-12T22:57:11ZKevin Rulandkruland@ku.edu
<p>The current collection of jars in the lib/ directory includes many jars which<br />may not be used, many duplicated jars, and probably some conflicting jars. We<br />need to perform analysis to determine the dependencies among the jars and<br />determine which jars are required by which kepler sources (actors and base code).</p> Bug #2278 (Resolved): Fix cache file name clashhttps://projects.ecoinformatics.org/ecoinfo/issues/22782005-11-16T18:21:09ZKevin Rulandkruland@ku.edu
<p>The cache file naming system relies on system date (to millisecond). On faster<br />systems this can cause naming clashes.</p> Bug #2277 (Resolved): Simplify Kar loadinghttps://projects.ecoinformatics.org/ecoinfo/issues/22772005-11-16T18:18:23ZKevin Rulandkruland@ku.edu
<p>For first release, simplify the kar loading process to operate on moml documents<br />only. Each moml file will describe a single actor.</p> Bug #2196 (Resolved): Changes to DarwinCoreDataSource.java DarwinCoreMetaDataSpecification.javahttps://projects.ecoinformatics.org/ecoinfo/issues/21962005-09-13T15:59:39ZKevin Rulandkruland@ku.edu
<p>Multiple changes to these files needed for bug fixing and reducing dependencies<br />on seek classes.</p> Bug #2195 (Resolved): Patch to org.ecoinformatics.seek.datasource. to remove unused importshttps://projects.ecoinformatics.org/ecoinfo/issues/21952005-09-13T15:44:06ZKevin Rulandkruland@ku.edu
<p>The files EcogridDataCacheItem.java, EcogridMetaDataCacheItem.java,<br />EcogridQueryDataCacheItem.java have multiple unused imports which prevent<br />reducing the dependency on the seek jars.</p> Bug #2192 (Resolved): Improve QuickSearch results from Digirhttps://projects.ecoinformatics.org/ecoinfo/issues/21922005-09-08T16:50:04ZKevin Rulandkruland@ku.edu
<p>Implement two improvements to the returned results from Digir QuickSearches.</p>
<p>- Ignore case of scientific name when partitioning records into subsets.<br />- Sort the results by scientific name alphabetically.</p>