You can subscribe to this list here.
2010 |
Jan
|
Feb
|
Mar
|
Apr
|
May
(21) |
Jun
(3) |
Jul
(2) |
Aug
|
Sep
|
Oct
|
Nov
(3) |
Dec
|
---|---|---|---|---|---|---|---|---|---|---|---|---|
2011 |
Jan
|
Feb
(5) |
Mar
|
Apr
|
May
|
Jun
|
Jul
|
Aug
|
Sep
|
Oct
|
Nov
(1) |
Dec
|
From: SourceForge.net <no...@so...> - 2011-11-20 22:34:27
|
Bugs item #3005400, was opened at 2010-05-21 08:40 Message generated for change (Comment added) made by kaiec You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1120046&aid=3005400&group_id=242532 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: Interface (example) Group: Semtinel NetBeans RCP >Status: Closed >Resolution: Fixed Priority: 9 Private: No Submitted By: Kai Eckert (kaiec) Assigned to: Kai Eckert (kaiec) Summary: Population for AnnotationSets fails Initial Comment: At least sometimes, the population of data for the AllAnnotationFrequencyAnalysis fails. Only the table is created. ---------------------------------------------------------------------- >Comment By: Kai Eckert (kaiec) Date: 2011-11-20 14:34 Message: Reworked most parts pf the population algorithm, should be fixed now. ---------------------------------------------------------------------- Comment By: Kai Eckert (kaiec) Date: 2010-05-31 08:41 Message: I hacked a little bit around the population process. ProgressListener are now supported so that at least we can get some feedback, if the population is actually running. I also changed the PersistentAnalysisMapImpl, as there seemed to be a problem with the database table creation, it was created when the first get was invoked, that could in theory be before the population process is started. Now, the population seems to work, if the treeview is used, where the analysis results are not actually used. In the treemap view, there are still problems, so I think this has something todo with the parallel access of the visualisation to the data, before the population is finished properly. So the short message here is: We need a closer look on the whole process, it still is quite buggy... ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1120046&aid=3005400&group_id=242532 |
From: SourceForge.net <no...@so...> - 2011-02-07 15:44:53
|
Bugs item #3175039, was opened at 2011-02-07 15:19 Message generated for change (Settings changed) made by jgansen You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1120046&aid=3175039&group_id=242532 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: None Group: None >Status: Closed >Resolution: Fixed Priority: 5 Private: No Submitted By: Nobody/Anonymous (nobody) Assigned to: J.Gansen (jgansen) Summary: SKOSImporter encounters ClassNotFoundException Initial Comment: When trying to import a local resource with the SKOSImporter an java.lang.ClassNotFoundException is thrown. The Stacktrace is as follows: java.lang.ClassNotFoundException: org.semanticweb.owl.model.OWLOntologyChangeException at java.net.URLClassLoader$1.run(URLClassLoader.java:217) at java.security.AccessController.doPrivileged(Native Method) at java.net.URLClassLoader.findClass(URLClassLoader.java:205) at java.lang.ClassLoader.loadClass(ClassLoader.java:321) at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:294) at java.lang.ClassLoader.loadClass(ClassLoader.java:266) at org.netbeans.ProxyClassLoader.loadClass(ProxyClassLoader.java:252) at java.lang.ClassLoader.loadClass(ClassLoader.java:266) Caused: java.lang.NoClassDefFoundError: org/semanticweb/owl/model/OWLOntologyChangeException at org.semtinel.core.importer.skos.SKOSImporter.init(SKOSImporter.java:80) at org.semtinel.core.importer.skos.SKOSImporter.<init>(SKOSImporter.java:72) at org.semtinel.core.importer.skos.SKOSImportTopComponent$4.run(SKOSImportTopComponent.java:240) ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1120046&aid=3175039&group_id=242532 |
From: SourceForge.net <no...@so...> - 2011-02-07 14:20:45
|
Bugs item #3175039, was opened at 2011-02-07 15:19 Message generated for change (Settings changed) made by jgansen You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1120046&aid=3175039&group_id=242532 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: None Group: None Status: Open Resolution: None Priority: 5 Private: No Submitted By: Nobody/Anonymous (nobody) >Assigned to: J.Gansen (jgansen) Summary: SKOSImporter encounters ClassNotFoundException Initial Comment: When trying to import a local resource with the SKOSImporter an java.lang.ClassNotFoundException is thrown. The Stacktrace is as follows: java.lang.ClassNotFoundException: org.semanticweb.owl.model.OWLOntologyChangeException at java.net.URLClassLoader$1.run(URLClassLoader.java:217) at java.security.AccessController.doPrivileged(Native Method) at java.net.URLClassLoader.findClass(URLClassLoader.java:205) at java.lang.ClassLoader.loadClass(ClassLoader.java:321) at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:294) at java.lang.ClassLoader.loadClass(ClassLoader.java:266) at org.netbeans.ProxyClassLoader.loadClass(ProxyClassLoader.java:252) at java.lang.ClassLoader.loadClass(ClassLoader.java:266) Caused: java.lang.NoClassDefFoundError: org/semanticweb/owl/model/OWLOntologyChangeException at org.semtinel.core.importer.skos.SKOSImporter.init(SKOSImporter.java:80) at org.semtinel.core.importer.skos.SKOSImporter.<init>(SKOSImporter.java:72) at org.semtinel.core.importer.skos.SKOSImportTopComponent$4.run(SKOSImportTopComponent.java:240) ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1120046&aid=3175039&group_id=242532 |
From: SourceForge.net <no...@so...> - 2011-02-07 14:19:48
|
Bugs item #3175039, was opened at 2011-02-07 14:19 Message generated for change (Tracker Item Submitted) made by nobody You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1120046&aid=3175039&group_id=242532 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: None Group: None Status: Open Resolution: None Priority: 5 Private: No Submitted By: Nobody/Anonymous (nobody) Assigned to: Nobody/Anonymous (nobody) Summary: SKOSImporter encounters ClassNotFoundException Initial Comment: When trying to import a local resource with the SKOSImporter an java.lang.ClassNotFoundException is thrown. The Stacktrace is as follows: java.lang.ClassNotFoundException: org.semanticweb.owl.model.OWLOntologyChangeException at java.net.URLClassLoader$1.run(URLClassLoader.java:217) at java.security.AccessController.doPrivileged(Native Method) at java.net.URLClassLoader.findClass(URLClassLoader.java:205) at java.lang.ClassLoader.loadClass(ClassLoader.java:321) at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:294) at java.lang.ClassLoader.loadClass(ClassLoader.java:266) at org.netbeans.ProxyClassLoader.loadClass(ProxyClassLoader.java:252) at java.lang.ClassLoader.loadClass(ClassLoader.java:266) Caused: java.lang.NoClassDefFoundError: org/semanticweb/owl/model/OWLOntologyChangeException at org.semtinel.core.importer.skos.SKOSImporter.init(SKOSImporter.java:80) at org.semtinel.core.importer.skos.SKOSImporter.<init>(SKOSImporter.java:72) at org.semtinel.core.importer.skos.SKOSImportTopComponent$4.run(SKOSImportTopComponent.java:240) ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1120046&aid=3175039&group_id=242532 |
From: SourceForge.net <no...@so...> - 2011-02-04 13:30:33
|
Bugs item #3009363, was opened at 2010-05-31 09:30 Message generated for change (Settings changed) made by jgansen You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1120046&aid=3009363&group_id=242532 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: Interface (example) Group: Semtinel NetBeans RCP >Status: Closed >Resolution: Fixed Priority: 5 Private: No Submitted By: Kai Eckert (kaiec) >Assigned to: J.Gansen (jgansen) Summary: CSV Import/Export Record Source should be Record Set Initial Comment: In the CSV Import(Export Tool, the drop field for record sets is a drop field for record source, while for annotation sets it is correct. This is not critical, as in most cases record sources and sets are identical, but it should nevertheless be changed to record sets. ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1120046&aid=3009363&group_id=242532 |
From: SourceForge.net <no...@so...> - 2011-02-03 12:12:59
|
Bugs item #3109451, was opened at 2010-11-15 11:00 Message generated for change (Settings changed) made by jgansen You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1120046&aid=3109451&group_id=242532 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: None Group: Semtinel Core >Status: Closed >Resolution: Works For Me Priority: 5 Private: No Submitted By: Nobody/Anonymous (nobody) >Assigned to: J.Gansen (jgansen) Summary: Missing indices in db? Initial Comment: On a newly created DB, the import of pubmed records is incredible slow. Probably there is a problem with the indices. ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1120046&aid=3109451&group_id=242532 |
From: SourceForge.net <no...@so...> - 2010-11-24 15:17:11
|
Bugs item #3109449, was opened at 2010-11-15 10:59 Message generated for change (Settings changed) made by jgansen You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1120046&aid=3109449&group_id=242532 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: Interface (example) Group: None >Status: Closed >Resolution: Fixed Priority: 5 Private: No Submitted By: Nobody/Anonymous (nobody) >Assigned to: J.Gansen (jgansen) Summary: Label Record/Annotation Set wrong in Pubmed Search Initial Comment: On tab "import" in Pubmed search, the label is wrong, it should be Annotation Source and Record Source, not Set. ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1120046&aid=3109449&group_id=242532 |
From: SourceForge.net <no...@so...> - 2010-11-15 11:08:02
|
Bugs item #3109449, was opened at 2010-11-15 09:59 Message generated for change (Tracker Item Submitted) made by nobody You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1120046&aid=3109449&group_id=242532 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: Interface (example) Group: None Status: Open Resolution: None Priority: 5 Private: No Submitted By: Nobody/Anonymous (nobody) Assigned to: Nobody/Anonymous (nobody) Summary: Label Record/Annotation Set wrong in Pubmed Search Initial Comment: On tab "import" in Pubmed search, the label is wrong, it should be Annotation Source and Record Source, not Set. ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1120046&aid=3109449&group_id=242532 |
From: SourceForge.net <no...@so...> - 2010-11-15 10:00:38
|
Bugs item #3109451, was opened at 2010-11-15 10:00 Message generated for change (Tracker Item Submitted) made by nobody You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1120046&aid=3109451&group_id=242532 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: None Group: Semtinel Core Status: Open Resolution: None Priority: 5 Private: No Submitted By: Nobody/Anonymous (nobody) Assigned to: Nobody/Anonymous (nobody) Summary: Missing indices in db? Initial Comment: On a newly created DB, the import of pubmed records is incredible slow. Probably there is a problem with the indices. ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1120046&aid=3109451&group_id=242532 |
From: SourceForge.net <no...@so...> - 2010-07-07 02:20:16
|
Bugs item #3010108, was opened at 2010-06-01 21:50 Message generated for change (Comment added) made by sf-robot You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1120046&aid=3010108&group_id=242532 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: Interface (example) Group: Semtinel NetBeans RCP >Status: Closed Resolution: Later Priority: 1 Private: No Submitted By: Alexander Hanschke (alexhanschke) Assigned to: Alexander Hanschke (alexhanschke) Summary: InPhOImporter encounters ArrayIndexOutOfBoundsException Initial Comment: When importing the resource http://inpho.cogs.indiana.edu/owl/db-arch_20100601.owl an ArrayIndexOutOfBoundsException is thrown - the Stacktrace is as follows: org.h2.jdbc.JdbcSQLException: Allgemeiner Fehler: java.lang.ArrayIndexOutOfBoundsException: 0 General error: java.lang.ArrayIndexOutOfBoundsException: 0 [50000-107] at org.h2.message.Message.getSQLException(Message.java:103) at org.h2.message.Message.convert(Message.java:274) at org.h2.table.TableData.addRow(TableData.java:135) at org.h2.command.dml.Insert.update(Insert.java:96) at org.h2.command.CommandContainer.update(CommandContainer.java:71) at org.h2.command.Command.executeUpdate(Command.java:207) at org.h2.jdbc.JdbcPreparedStatement.execute(JdbcPreparedStatement.java:173) at org.semtinel.core.data.hibernate.SchemeInserterImpl.insertConcept(SchemeInserterImpl.java:243) at org.semtinel.core.importer.inpho.InPhOImporter.mapConceptURIsToConceptIDsForOntology(InPhOImporter.java:175) at org.semtinel.core.importer.inpho.InPhOImporter.process(InPhOImporter.java:152) at org.semtinel.core.importer.inpho.InPhOImporterTopComponent$4.run(InPhOImporterTopComponent.java:207) at java.lang.Thread.run(Thread.java:619) Caused by: java.lang.ArrayIndexOutOfBoundsException: 0 at org.h2.util.IntArray.add(IntArray.java:43) at org.h2.index.BtreeNode.add(BtreeNode.java:102) at org.h2.index.BtreeIndex.add(BtreeIndex.java:223) at org.h2.table.TableData.addRow(TableData.java:117) ... 9 more Caused: java.lang.RuntimeException: SQL Error at org.semtinel.core.data.hibernate.SchemeInserterImpl.insertConcept(SchemeInserterImpl.java:251) at org.semtinel.core.importer.inpho.InPhOImporter.mapConceptURIsToConceptIDsForOntology(InPhOImporter.java:175) at org.semtinel.core.importer.inpho.InPhOImporter.process(InPhOImporter.java:152) at org.semtinel.core.importer.inpho.InPhOImporterTopComponent$4.run(InPhOImporterTopComponent.java:207) [catch] at java.lang.Thread.run(Thread.java:619) ---------------------------------------------------------------------- >Comment By: SourceForge Robot (sf-robot) Date: 2010-07-07 02:20 Message: This Tracker item was closed automatically by the system. It was previously set to a Pending status, and the original submitter did not respond within 14 days (the time period specified by the administrator of this Tracker). ---------------------------------------------------------------------- Comment By: Alexander Hanschke (alexhanschke) Date: 2010-06-22 22:14 Message: Problem did not last after full rebuild of Semtinel from source. Further observation may be necessary. ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1120046&aid=3010108&group_id=242532 |
From: SourceForge.net <no...@so...> - 2010-07-04 22:35:11
|
Bugs item #3005154, was opened at 2010-05-21 10:26 Message generated for change (Settings changed) made by alexhanschke You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1120046&aid=3005154&group_id=242532 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: Interface (example) Group: Semtinel NetBeans RCP >Status: Closed >Resolution: Fixed Priority: 5 Private: No Submitted By: Nobody/Anonymous (nobody) Assigned to: Alexander Hanschke (alexhanschke) Summary: Buttons disabled in STW Import Initial Comment: In STW Importer, after selecting the input files, the button "Finish" is disabled. A workaround is to cancel the dialog and open it again. Now the formerly selected input files are still avilable and "Finish" can be pressed. But of course, that is not desirable. ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1120046&aid=3005154&group_id=242532 |
From: SourceForge.net <no...@so...> - 2010-06-22 22:14:07
|
Bugs item #3010108, was opened at 2010-06-01 23:50 Message generated for change (Comment added) made by alexhanschke You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1120046&aid=3010108&group_id=242532 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: Interface (example) Group: Semtinel NetBeans RCP >Status: Pending >Resolution: Later >Priority: 1 Private: No Submitted By: Alexander Hanschke (alexhanschke) Assigned to: Alexander Hanschke (alexhanschke) Summary: InPhOImporter encounters ArrayIndexOutOfBoundsException Initial Comment: When importing the resource http://inpho.cogs.indiana.edu/owl/db-arch_20100601.owl an ArrayIndexOutOfBoundsException is thrown - the Stacktrace is as follows: org.h2.jdbc.JdbcSQLException: Allgemeiner Fehler: java.lang.ArrayIndexOutOfBoundsException: 0 General error: java.lang.ArrayIndexOutOfBoundsException: 0 [50000-107] at org.h2.message.Message.getSQLException(Message.java:103) at org.h2.message.Message.convert(Message.java:274) at org.h2.table.TableData.addRow(TableData.java:135) at org.h2.command.dml.Insert.update(Insert.java:96) at org.h2.command.CommandContainer.update(CommandContainer.java:71) at org.h2.command.Command.executeUpdate(Command.java:207) at org.h2.jdbc.JdbcPreparedStatement.execute(JdbcPreparedStatement.java:173) at org.semtinel.core.data.hibernate.SchemeInserterImpl.insertConcept(SchemeInserterImpl.java:243) at org.semtinel.core.importer.inpho.InPhOImporter.mapConceptURIsToConceptIDsForOntology(InPhOImporter.java:175) at org.semtinel.core.importer.inpho.InPhOImporter.process(InPhOImporter.java:152) at org.semtinel.core.importer.inpho.InPhOImporterTopComponent$4.run(InPhOImporterTopComponent.java:207) at java.lang.Thread.run(Thread.java:619) Caused by: java.lang.ArrayIndexOutOfBoundsException: 0 at org.h2.util.IntArray.add(IntArray.java:43) at org.h2.index.BtreeNode.add(BtreeNode.java:102) at org.h2.index.BtreeIndex.add(BtreeIndex.java:223) at org.h2.table.TableData.addRow(TableData.java:117) ... 9 more Caused: java.lang.RuntimeException: SQL Error at org.semtinel.core.data.hibernate.SchemeInserterImpl.insertConcept(SchemeInserterImpl.java:251) at org.semtinel.core.importer.inpho.InPhOImporter.mapConceptURIsToConceptIDsForOntology(InPhOImporter.java:175) at org.semtinel.core.importer.inpho.InPhOImporter.process(InPhOImporter.java:152) at org.semtinel.core.importer.inpho.InPhOImporterTopComponent$4.run(InPhOImporterTopComponent.java:207) [catch] at java.lang.Thread.run(Thread.java:619) ---------------------------------------------------------------------- >Comment By: Alexander Hanschke (alexhanschke) Date: 2010-06-23 00:14 Message: Problem did not last after full rebuild of Semtinel from source. Further observation may be necessary. ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1120046&aid=3010108&group_id=242532 |
From: SourceForge.net <no...@so...> - 2010-06-22 22:05:05
|
Bugs item #3005362, was opened at 2010-05-21 16:37 Message generated for change (Comment added) made by alexhanschke You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1120046&aid=3005362&group_id=242532 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: Interface (example) Group: Semtinel NetBeans RCP >Status: Closed >Resolution: Fixed Priority: 5 Private: No Submitted By: Kai Eckert (kaiec) Assigned to: Alexander Hanschke (alexhanschke) Summary: Threading for statistics import Initial Comment: The CSV statistics importer freezes the GUI, it need to be pushed to a background thread. ---------------------------------------------------------------------- >Comment By: Alexander Hanschke (alexhanschke) Date: 2010-06-23 00:05 Message: Should be fixed with rev e044b1354628372fb372b23d7d8b817dbf1e7ec0 ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1120046&aid=3005362&group_id=242532 |
From: SourceForge.net <no...@so...> - 2010-06-01 21:50:25
|
Bugs item #3010108, was opened at 2010-06-01 23:50 Message generated for change (Tracker Item Submitted) made by alexhanschke You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1120046&aid=3010108&group_id=242532 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: Interface (example) Group: Semtinel NetBeans RCP Status: Open Resolution: None Priority: 2 Private: No Submitted By: Alexander Hanschke (alexhanschke) Assigned to: Alexander Hanschke (alexhanschke) Summary: InPhOImporter encounters ArrayIndexOutOfBoundsException Initial Comment: When importing the resource http://inpho.cogs.indiana.edu/owl/db-arch_20100601.owl an ArrayIndexOutOfBoundsException is thrown - the Stacktrace is as follows: org.h2.jdbc.JdbcSQLException: Allgemeiner Fehler: java.lang.ArrayIndexOutOfBoundsException: 0 General error: java.lang.ArrayIndexOutOfBoundsException: 0 [50000-107] at org.h2.message.Message.getSQLException(Message.java:103) at org.h2.message.Message.convert(Message.java:274) at org.h2.table.TableData.addRow(TableData.java:135) at org.h2.command.dml.Insert.update(Insert.java:96) at org.h2.command.CommandContainer.update(CommandContainer.java:71) at org.h2.command.Command.executeUpdate(Command.java:207) at org.h2.jdbc.JdbcPreparedStatement.execute(JdbcPreparedStatement.java:173) at org.semtinel.core.data.hibernate.SchemeInserterImpl.insertConcept(SchemeInserterImpl.java:243) at org.semtinel.core.importer.inpho.InPhOImporter.mapConceptURIsToConceptIDsForOntology(InPhOImporter.java:175) at org.semtinel.core.importer.inpho.InPhOImporter.process(InPhOImporter.java:152) at org.semtinel.core.importer.inpho.InPhOImporterTopComponent$4.run(InPhOImporterTopComponent.java:207) at java.lang.Thread.run(Thread.java:619) Caused by: java.lang.ArrayIndexOutOfBoundsException: 0 at org.h2.util.IntArray.add(IntArray.java:43) at org.h2.index.BtreeNode.add(BtreeNode.java:102) at org.h2.index.BtreeIndex.add(BtreeIndex.java:223) at org.h2.table.TableData.addRow(TableData.java:117) ... 9 more Caused: java.lang.RuntimeException: SQL Error at org.semtinel.core.data.hibernate.SchemeInserterImpl.insertConcept(SchemeInserterImpl.java:251) at org.semtinel.core.importer.inpho.InPhOImporter.mapConceptURIsToConceptIDsForOntology(InPhOImporter.java:175) at org.semtinel.core.importer.inpho.InPhOImporter.process(InPhOImporter.java:152) at org.semtinel.core.importer.inpho.InPhOImporterTopComponent$4.run(InPhOImporterTopComponent.java:207) [catch] at java.lang.Thread.run(Thread.java:619) ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1120046&aid=3010108&group_id=242532 |
From: SourceForge.net <no...@so...> - 2010-05-31 15:41:11
|
Bugs item #3005400, was opened at 2010-05-21 17:40 Message generated for change (Comment added) made by kaiec You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1120046&aid=3005400&group_id=242532 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: Interface (example) Group: Semtinel NetBeans RCP Status: Open Resolution: None Priority: 9 Private: No Submitted By: Kai Eckert (kaiec) Assigned to: Kai Eckert (kaiec) Summary: Population for AnnotationSets fails Initial Comment: At least sometimes, the population of data for the AllAnnotationFrequencyAnalysis fails. Only the table is created. ---------------------------------------------------------------------- Comment By: Kai Eckert (kaiec) Date: 2010-05-31 17:41 Message: I hacked a little bit around the population process. ProgressListener are now supported so that at least we can get some feedback, if the population is actually running. I also changed the PersistentAnalysisMapImpl, as there seemed to be a problem with the database table creation, it was created when the first get was invoked, that could in theory be before the population process is started. Now, the population seems to work, if the treeview is used, where the analysis results are not actually used. In the treemap view, there are still problems, so I think this has something todo with the parallel access of the visualisation to the data, before the population is finished properly. So the short message here is: We need a closer look on the whole process, it still is quite buggy... ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1120046&aid=3005400&group_id=242532 |
From: SourceForge.net <no...@so...> - 2010-05-31 07:30:09
|
Bugs item #3009363, was opened at 2010-05-31 09:30 Message generated for change (Tracker Item Submitted) made by kaiec You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1120046&aid=3009363&group_id=242532 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: Interface (example) Group: Semtinel NetBeans RCP Status: Open Resolution: None Priority: 5 Private: No Submitted By: Kai Eckert (kaiec) Assigned to: Alexander Hanschke (alexhanschke) Summary: CSV Import/Export Record Source should be Record Set Initial Comment: In the CSV Import(Export Tool, the drop field for record sets is a drop field for record source, while for annotation sets it is correct. This is not critical, as in most cases record sources and sets are identical, but it should nevertheless be changed to record sets. ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1120046&aid=3009363&group_id=242532 |
From: SourceForge.net <no...@so...> - 2010-05-21 15:40:45
|
Bugs item #3005400, was opened at 2010-05-21 17:40 Message generated for change (Tracker Item Submitted) made by kaiec You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1120046&aid=3005400&group_id=242532 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: Interface (example) Group: Semtinel NetBeans RCP Status: Open Resolution: None Priority: 9 Private: No Submitted By: Kai Eckert (kaiec) Assigned to: Kai Eckert (kaiec) Summary: Population for AnnotationSets fails Initial Comment: At least sometimes, the population of data for the AllAnnotationFrequencyAnalysis fails. Only the table is created. ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1120046&aid=3005400&group_id=242532 |
From: SourceForge.net <no...@so...> - 2010-05-21 14:37:20
|
Bugs item #3005362, was opened at 2010-05-21 16:37 Message generated for change (Tracker Item Submitted) made by kaiec You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1120046&aid=3005362&group_id=242532 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: Interface (example) Group: Semtinel NetBeans RCP Status: Open Resolution: None Priority: 5 Private: No Submitted By: Kai Eckert (kaiec) Assigned to: Alexander Hanschke (alexhanschke) Summary: Threading for statistics import Initial Comment: The CSV statistics importer freezes the GUI, it need to be pushed to a background thread. ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1120046&aid=3005362&group_id=242532 |
From: SourceForge.net <no...@so...> - 2010-05-21 14:28:13
|
Bugs item #3005352, was opened at 2010-05-21 16:28 Message generated for change (Tracker Item Submitted) made by kaiec You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1120046&aid=3005352&group_id=242532 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: Interface (example) Group: Semtinel NetBeans RCP Status: Open Resolution: None Priority: 6 Private: No Submitted By: Kai Eckert (kaiec) Assigned to: Alexander Hanschke (alexhanschke) Summary: Statistics Import creates Annotation Set instead of Source Initial Comment: Newly imported annotation data are available as annotation sources. For the statistics data import, a set is directly created, instead of the annotation source. ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1120046&aid=3005352&group_id=242532 |
From: SourceForge.net <no...@so...> - 2010-05-21 14:15:55
|
Bugs item #3005342, was opened at 2010-05-21 16:15 Message generated for change (Tracker Item Submitted) made by kaiec You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1120046&aid=3005342&group_id=242532 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: None Group: None Status: Open Resolution: None Priority: 2 Private: No Submitted By: Kai Eckert (kaiec) Assigned to: Alexander Hanschke (alexhanschke) Summary: LazyInitializationException while population is running Initial Comment: See stack trace below. This is caused by the current database setup: H2 is in embedded mode and allows only one concurrent access. The hibernate session is disconnected while another thread (in this case population) runs directly on the database. If you now reload the visualisation or do something else that causes Semtinel to access the data, this exception is thrown. Stacktrace: org.hibernate.LazyInitializationException: failed to lazily initialize a collection of role: org.semtinel.core.data.hibernate.ConceptImpl.narrower, session is disconnected at org.hibernate.collection.AbstractPersistentCollection.throwLazyInitializationException(AbstractPersistentCollection.java:358) at org.hibernate.collection.AbstractPersistentCollection.throwLazyInitializationExceptionIfNotConnected(AbstractPersistentCollection.java:353) at org.hibernate.collection.AbstractPersistentCollection.readSize(AbstractPersistentCollection.java:97) at org.hibernate.collection.PersistentBag.size(PersistentBag.java:225) at org.semtinel.core.visuals.treemap.ConceptTreemapData.getTMSizeMetric(ConceptTreemapData.java:128) at org.kaiec.treemap.layout.SquarifiedLayout.Layout(SquarifiedLayout.java:103) at org.kaiec.treemap.layout.SquarifiedLayout.layoutrow(SquarifiedLayout.java:185) at org.kaiec.treemap.layout.SquarifiedLayout.squarify(SquarifiedLayout.java:132) at org.kaiec.treemap.layout.SquarifiedLayout.squarify(SquarifiedLayout.java:127) at org.kaiec.treemap.layout.SquarifiedLayout.squarify(SquarifiedLayout.java:127) at org.kaiec.treemap.layout.SquarifiedLayout.squarify(SquarifiedLayout.java:127) at org.kaiec.treemap.layout.SquarifiedLayout.squarify(SquarifiedLayout.java:127) at org.kaiec.treemap.layout.SquarifiedLayout.Layout(SquarifiedLayout.java:111) at org.kaiec.treemap.layout.SquarifiedLayout.layoutrow(SquarifiedLayout.java:193) at org.kaiec.treemap.layout.SquarifiedLayout.squarify(SquarifiedLayout.java:132) at org.kaiec.treemap.layout.SquarifiedLayout.squarify(SquarifiedLayout.java:127) at org.kaiec.treemap.layout.SquarifiedLayout.squarify(SquarifiedLayout.java:127) at org.kaiec.treemap.layout.SquarifiedLayout.squarify(SquarifiedLayout.java:127) at org.kaiec.treemap.layout.SquarifiedLayout.squarify(SquarifiedLayout.java:127) at org.kaiec.treemap.layout.SquarifiedLayout.Layout(SquarifiedLayout.java:111) at org.kaiec.treemap.CalculationThread.run(CalculationThread.java:46) ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1120046&aid=3005342&group_id=242532 |
From: SourceForge.net <no...@so...> - 2010-05-21 13:49:13
|
Bugs item #3005171, was opened at 2010-05-21 10:56 Message generated for change (Settings changed) made by kaiec You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1120046&aid=3005171&group_id=242532 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: None Group: None Status: Open Resolution: None Priority: 5 Private: No Submitted By: Nobody/Anonymous (nobody) >Assigned to: Alexander Hanschke (alexhanschke) Summary: GenericJDBCException after thesaurus import Initial Comment: While importing the RVK, I clicked through the overview. After the import finished according to the progress bar, an error popped up, see stacktrace below. The RVK was imported, afterwards, the database contained 797613 concepts. There are 797612 broader_narrower relations, so that seems to be quite complete. Labels and Notations are also available. So probably, only the overview functionality was affected by the error, but nevertheless... Stacktrace: org.hibernate.exception.GenericJDBCException: could not execute query at org.hibernate.exception.SQLStateConverter.handledNonSpecificException(SQLStateConverter.java:103) at org.hibernate.exception.SQLStateConverter.convert(SQLStateConverter.java:91) at org.hibernate.exception.JDBCExceptionHelper.convert(JDBCExceptionHelper.java:43) at org.hibernate.loader.Loader.doList(Loader.java:2216) at org.hibernate.loader.Loader.listIgnoreQueryCache(Loader.java:2104) at org.hibernate.loader.Loader.list(Loader.java:2099) at org.hibernate.loader.criteria.CriteriaLoader.list(CriteriaLoader.java:94) at org.hibernate.impl.SessionImpl.list(SessionImpl.java:1569) at org.hibernate.impl.CriteriaImpl.list(CriteriaImpl.java:283) at org.semtinel.core.data.hibernate.CoreManagerImpl.getAnnotationSources(CoreManagerImpl.java:222) at org.semtinel.core.overview.OverviewChildFactory.createKeys(OverviewChildFactory.java:76) at org.openide.nodes.AsynchChildren.run(AsynchChildren.java:147) at org.openide.util.RequestProcessor$Task.run(RequestProcessor.java:572) at org.openide.util.RequestProcessor$Processor.run(RequestProcessor.java:997) Caused by: org.h2.jdbc.JdbcSQLException: Zeitüberschreitung beim Versuch die Tabelle CONCEPTSCHEME zu sperren Timeout trying to lock table CONCEPTSCHEME; SQL statement: select this_.id as id13_3_, this_.conceptScheme_id as conceptS3_13_3_, this_.name as name13_3_, conceptsch2_.id as id1_0_, conceptsch2_.topConcept_id as topConcept3_1_0_, conceptsch2_.uri as uri1_0_, conceptimp3_.id as id0_1_, conceptimp3_.conceptScheme_id as conceptS3_0_1_, conceptimp3_.uri as uri0_1_, conceptsch4_.id as id1_2_, conceptsch4_.topConcept_id as topConcept3_1_2_, conceptsch4_.uri as uri1_2_ from AnnotationSource this_ left outer join ConceptScheme conceptsch2_ on this_.conceptScheme_id=conceptsch2_.id left outer join Concept conceptimp3_ on conceptsch2_.topConcept_id=conceptimp3_.id left outer join ConceptScheme conceptsch4_ on conceptimp3_.conceptScheme_id=conceptsch4_.id [50200-107] at org.h2.message.Message.getSQLException(Message.java:103) at org.h2.message.Message.getSQLException(Message.java:114) at org.h2.message.Message.getSQLException(Message.java:77) at org.h2.table.TableData.doLock(TableData.java:430) at org.h2.table.TableData.lock(TableData.java:369) at org.h2.table.TableFilter.lock(TableFilter.java:107) at org.h2.table.TableFilter.lock(TableFilter.java:109) at org.h2.command.dml.Select.queryWithoutCache(Select.java:548) at org.h2.command.dml.Query.query(Query.java:233) at org.h2.command.CommandContainer.query(CommandContainer.java:81) at org.h2.command.Command.executeQueryLocal(Command.java:141) at org.h2.command.Command.executeQuery(Command.java:122) at org.h2.jdbc.JdbcPreparedStatement.executeQuery(JdbcPreparedStatement.java:96) at org.hibernate.jdbc.AbstractBatcher.getResultSet(AbstractBatcher.java:186) at org.hibernate.loader.Loader.getResultSet(Loader.java:1787) at org.hibernate.loader.Loader.doQuery(Loader.java:674) at org.hibernate.loader.Loader.doQueryAndInitializeNonLazyCollections(Loader.java:236) at org.hibernate.loader.Loader.doList(Loader.java:2213) ... 10 more ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1120046&aid=3005171&group_id=242532 |
From: SourceForge.net <no...@so...> - 2010-05-21 13:49:13
|
Bugs item #3005154, was opened at 2010-05-21 10:26 Message generated for change (Settings changed) made by kaiec You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1120046&aid=3005154&group_id=242532 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: Interface (example) Group: Semtinel NetBeans RCP Status: Open Resolution: None Priority: 5 Private: No Submitted By: Nobody/Anonymous (nobody) >Assigned to: Alexander Hanschke (alexhanschke) Summary: Buttons disabled in STW Import Initial Comment: In STW Importer, after selecting the input files, the button "Finish" is disabled. A workaround is to cancel the dialog and open it again. Now the formerly selected input files are still avilable and "Finish" can be pressed. But of course, that is not desirable. ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1120046&aid=3005154&group_id=242532 |
From: SourceForge.net <no...@so...> - 2010-05-21 13:48:47
|
Bugs item #3005177, was opened at 2010-05-21 11:01 Message generated for change (Settings changed) made by kaiec You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1120046&aid=3005177&group_id=242532 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: None Group: None >Status: Closed >Resolution: Fixed Priority: 5 Private: No Submitted By: Kai Eckert (kaiec) >Assigned to: Kai Eckert (kaiec) Summary: New bugs should be emailed to developers... Initial Comment: That would be great! ---------------------------------------------------------------------- Comment By: Kai Eckert (kaiec) Date: 2010-05-21 14:05 Message: Maybe now it is even working :-) ---------------------------------------------------------------------- Comment By: Kai Eckert (kaiec) Date: 2010-05-21 13:55 Message: Now we have two mailing lists for that, semtinel-bugs and semtinel-features. They are read only! ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1120046&aid=3005177&group_id=242532 |
From: SourceForge.net <no...@so...> - 2010-05-21 13:48:20
|
Bugs item #3005270, was opened at 2010-05-21 14:07 Message generated for change (Settings changed) made by kaiec You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1120046&aid=3005270&group_id=242532 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: None Group: None >Status: Closed >Resolution: Fixed Priority: 5 Private: No Submitted By: Kai Eckert (kaiec) >Assigned to: Kai Eckert (kaiec) Summary: bugs-mailinglist still not working Initial Comment: strange ---------------------------------------------------------------------- Comment By: Kai Eckert (kaiec) Date: 2010-05-21 14:20 Message: now it works a little... ---------------------------------------------------------------------- Comment By: Kai Eckert (kaiec) Date: 2010-05-21 14:13 Message: Next try ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1120046&aid=3005270&group_id=242532 |
From: SourceForge.net <no...@so...> - 2010-05-21 13:48:20
|
Bugs item #3005277, was opened at 2010-05-21 14:23 Message generated for change (Settings changed) made by kaiec You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1120046&aid=3005277&group_id=242532 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: Interface (example) Group: Semtinel NetBeans RCP >Status: Closed >Resolution: Fixed Priority: 5 Private: No Submitted By: Alexander Hanschke (alexhanschke) >Assigned to: Kai Eckert (kaiec) Summary: testing bug ml, again... Initial Comment: hello world ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1120046&aid=3005277&group_id=242532 |