giffordlabcvr / gluetools Goto Github PK

I tried to preview the NCBI importer actions but encountered an IO_ERROR. I am behand a firewall and need to go via a proxy so that is a potenial cause. Can be reproduced locally with:

GLUE> project hev
GLUE> module ncbiHevImporter
GLUE> preview --detailed
14:19:18.767 GlueException WARNING: NcbiImporterException.IO_ERROR supplied args: 1, required args: 2
14:19:18.771 GlueException WARNING: Wrong number of error arguments for IO_ERROR in NcbiImporterException, args: [eSearch]
Error: IO_ERROR[eSearch]
Cause: Network is unreachable (connect failed)
Mode path: /project/hev/module/ncbiHevImporter

GLUE version 0.1.121, OS Linux Ubuntu 16.04.2 LTS, openjdk version "1.8.0_131"

Upon trying to tab complete 'create alignment':
Mode path: /project/ERV
Option load-save-path: /Users/tristandennis/DIGS/ctl
GLUE> create alignment 12:05:13.614 CommandCompleter WARNING: Failed to instantiate command completer class uk.ac.gla.cvr.gluetools.core.command.project.CreateAlignmentCommand.Completer
12:05:13.615 CommandCompleter WARNING: java.lang.NoSuchMethodException: uk.ac.gla.cvr.gluetools.core.command.project.CreateAlignmentCommand$Completer.()
12:05:13.894 CommandCompleter WARNING: Failed to instantiate command completer class uk.ac.gla.cvr.gluetools.core.command.project.CreateAlignmentCommand.Completer
12:05:13.894 CommandCompleter WARNING: java.lang.NoSuchMethodException: uk.ac.gla.cvr.gluetools.core.command.project.CreateAlignmentCommand$Completer.(

GLUE> import source LTR/
Exception in thread "main" org.apache.cayenne.CayenneRuntimeException: [v.3.1 Sep 20 2014 14:06:21] Commit Exception
at org.apache.cayenne.access.DataContext.flushToParent(DataContext.java:845)
at org.apache.cayenne.access.DataContext.commitChanges(DataContext.java:756)
at uk.ac.gla.cvr.gluetools.core.command.CommandContext.commit(CommandContext.java:137)
at uk.ac.gla.cvr.gluetools.core.command.project.ImportSourceCommand.execute(ImportSourceCommand.java:148)
at uk.ac.gla.cvr.gluetools.core.command.project.ImportSourceCommand.execute(ImportSourceCommand.java:31)
at uk.ac.gla.cvr.gluetools.core.console.Console.executeTokenStrings(Console.java:176)
at uk.ac.gla.cvr.gluetools.core.console.Console.executeTokenStrings(Console.java:127)
at uk.ac.gla.cvr.gluetools.core.console.Console.handleLine(Console.java:117)
at uk.ac.gla.cvr.gluetools.core.console.Console.handleInteractiveLine(Console.java:91)
at uk.ac.gla.cvr.gluetools.core.console.Console.interactiveSession(Console.java:378)
at uk.ac.gla.cvr.gluetools.core.console.Console.main(Console.java:296)
Caused by: java.sql.BatchUpdateException: Duplicate entry 'LTR' for key 'PRIMARY'
at com.mysql.jdbc.PreparedStatement.executeBatchSerially(PreparedStatement.java:1819)
at com.mysql.jdbc.PreparedStatement.executeBatch(PreparedStatement.java:1281)
at org.apache.cayenne.access.jdbc.BatchAction.runAsBatch(BatchAction.java:143)
at org.apache.cayenne.access.jdbc.BatchAction.performAction(BatchAction.java:83)
at org.apache.cayenne.access.DataNodeQueryAction.runQuery(DataNodeQueryAction.java:87)
at org.apache.cayenne.access.DataNode.performQueries(DataNode.java:280)
at org.apache.cayenne.access.DataDomainFlushAction.runQueries(DataDomainFlushAction.java:233)
at org.apache.cayenne.access.DataDomainFlushAction.flush(DataDomainFlushAction.java:154)
at org.apache.cayenne.access.DataDomain.onSyncFlush(DataDomain.java:853)
at org.apache.cayenne.access.DataDomain$2.transform(DataDomain.java:817)
at org.apache.cayenne.access.DataDomain.runInTransaction(DataDomain.java:877)
at org.apache.cayenne.access.DataDomain.onSyncNoFilters(DataDomain.java:814)
at org.apache.cayenne.access.DataDomain$DataDomainSyncFilterChain.onSync(DataDomain.java:1031)
at org.apache.cayenne.access.DataDomain.onSync(DataDomain.java:785)
at org.apache.cayenne.access.DataContext.flushToParent(DataContext.java:817)
... 10 more
Caused by: com.mysql.jdbc.exceptions.jdbc4.MySQLIntegrityConstraintViolationException: Duplicate entry 'LTR' for key 'PRIMARY'
at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62)
at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
at java.lang.reflect.Constructor.newInstance(Constructor.java:422)
at com.mysql.jdbc.Util.handleNewInstance(Util.java:389)
at com.mysql.jdbc.Util.getInstance(Util.java:372)
at com.mysql.jdbc.SQLError.createSQLException(SQLError.java:973)
at com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:3835)
at com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:3771)
at com.mysql.jdbc.MysqlIO.sendCommand(MysqlIO.java:2435)
at com.mysql.jdbc.MysqlIO.sqlQueryDirect(MysqlIO.java:2582)
at com.mysql.jdbc.ConnectionImpl.execSQL(ConnectionImpl.java:2535)
at com.mysql.jdbc.PreparedStatement.executeInternal(PreparedStatement.java:1911)
at com.mysql.jdbc.PreparedStatement.executeUpdate(PreparedStatement.java:2145)
at com.mysql.jdbc.PreparedStatement.executeBatchSerially(PreparedStatement.java:1777)
... 24 more

Exception in thread "main" org.apache.cayenne.validation.ValidationException: [v.3.1 Sep 20 2014 14:06:21] Validation failures: Validation failure for uk.ac.gla.cvr.gluetools.core.datamodel.seqOrigData.SeqOrigData.packedData: "packedData" is required.
Validation failure for uk.ac.gla.cvr.gluetools.core.datamodel.seqOrigData.SeqOrigData.packedData: "packedData" is required.
at org.apache.cayenne.access.ObjectStoreGraphDiff.validateAndCheckNoop(ObjectStoreGraphDiff.java:111)
at org.apache.cayenne.access.DataContext.flushToParent(DataContext.java:806)
at org.apache.cayenne.access.DataContext.commitChanges(DataContext.java:756)
at uk.ac.gla.cvr.gluetools.core.command.CommandContext.commit(CommandContext.java:137)
at uk.ac.gla.cvr.gluetools.core.command.project.ImportSequenceCommand.execute(ImportSequenceCommand.java:59)
at uk.ac.gla.cvr.gluetools.core.command.project.ImportSequenceCommand.execute(ImportSequenceCommand.java:20)
at uk.ac.gla.cvr.gluetools.core.console.Console.executeTokenStrings(Console.java:176)
at uk.ac.gla.cvr.gluetools.core.console.Console.executeTokenStrings(Console.java:127)
at uk.ac.gla.cvr.gluetools.core.console.Console.handleLine(Console.java:117)
at uk.ac.gla.cvr.gluetools.core.console.Console.handleInteractiveLine(Console.java:91)
at uk.ac.gla.cvr.gluetools.core.console.Console.interactiveSession(Console.java:378)
at uk.ac.gla.cvr.gluetools.core.console.Console.main(Console.java:296)

I'm not sure if this is really a problem but after run file hcvProject.glue had completed with OK, I typed in quit and got this:

GLUE> quit
OK
Exception in thread "main" org.apache.cayenne.CayenneRuntimeException: [v.3.1.1 Apr 29 2016 12:50:34] Error invoking event method shutdown
        at org.apache.cayenne.di.spi.ScopeEventBinding.onScopeEvent(ScopeEventBinding.java:67)
        at org.apache.cayenne.di.spi.DefaultScope.postScopeEvent(DefaultScope.java:145)
        at org.apache.cayenne.di.spi.DefaultScope.shutdown(DefaultScope.java:75)
        at org.apache.cayenne.di.spi.DefaultInjector.shutdown(DefaultInjector.java:138)
        at org.apache.cayenne.configuration.CayenneRuntime.shutdown(CayenneRuntime.java:166)
        at uk.ac.gla.cvr.gluetools.core.GluetoolsEngine.dispose(GluetoolsEngine.java:195)
        at uk.ac.gla.cvr.gluetools.core.GluetoolsEngine.shutdown(GluetoolsEngine.java:189)
        at uk.ac.gla.cvr.gluetools.core.console.Console.shutdown(Console.java:571)
        at uk.ac.gla.cvr.gluetools.core.console.Console.main(Console.java:385)
Caused by: java.lang.reflect.InvocationTargetException
        at sun.reflect.GeneratedMethodAccessor3.invoke(Unknown Source)
        at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
        at java.lang.reflect.Method.invoke(Method.java:498)
        at org.apache.cayenne.di.spi.ScopeEventBinding.onScopeEvent(ScopeEventBinding.java:61)
        ... 8 more
Caused by: org.apache.cayenne.CayenneRuntimeException: [v.3.1.1 Apr 29 2016 12:50:34] Error while shutting down
        at org.apache.cayenne.conn.PoolManager.beforeScopeEnd(PoolManager.java:236)
        at org.apache.cayenne.configuration.server.DelegatingDataSourceFactory.shutdown(DelegatingDataSourceFactory.java:76)
        ... 12 more

After native installation (http://glue-tools.cvr.gla.ac.uk/#/installation), when I built the example project, it gave an error:

Exception at line 241 of glue/exampleAlignmentTree.glue
Invoked from line 53 of exampleProject.glue
Error: Linking / constraining reference must not be one of the selected source members.

I have checked the versions of mysql and java, as well as installation of blast+/ mafft/ raxml, and found they all worked well.

Thank you!

GLUE> create source MGRV2
Exception in thread "main" org.apache.cayenne.CayenneRuntimeException: [v.3.1 Sep 20 2014 14:06:21] Commit Exception
at org.apache.cayenne.access.DataContext.flushToParent(DataContext.java:845)
at org.apache.cayenne.access.DataContext.commitChanges(DataContext.java:756)
at uk.ac.gla.cvr.gluetools.core.command.CommandContext.commit(CommandContext.java:137)
at uk.ac.gla.cvr.gluetools.core.command.project.CreateSourceCommand.execute(CreateSourceCommand.java:46)
at uk.ac.gla.cvr.gluetools.core.command.project.CreateSourceCommand.execute(CreateSourceCommand.java:19)
at uk.ac.gla.cvr.gluetools.core.console.Console.executeTokenStrings(Console.java:176)
at uk.ac.gla.cvr.gluetools.core.console.Console.executeTokenStrings(Console.java:127)
at uk.ac.gla.cvr.gluetools.core.console.Console.handleLine(Console.java:117)
at uk.ac.gla.cvr.gluetools.core.console.Console.handleInteractiveLine(Console.java:91)
at uk.ac.gla.cvr.gluetools.core.console.Console.interactiveSession(Console.java:378)
at uk.ac.gla.cvr.gluetools.core.console.Console.main(Console.java:296)
Caused by: java.sql.BatchUpdateException: Duplicate entry 'MGRV2' for key 'PRIMARY'
at com.mysql.jdbc.PreparedStatement.executeBatchSerially(PreparedStatement.java:1819)
at com.mysql.jdbc.PreparedStatement.executeBatch(PreparedStatement.java:1281)
at org.apache.cayenne.access.jdbc.BatchAction.runAsBatch(BatchAction.java:143)
at org.apache.cayenne.access.jdbc.BatchAction.performAction(BatchAction.java:83)
at org.apache.cayenne.access.DataNodeQueryAction.runQuery(DataNodeQueryAction.java:87)
at org.apache.cayenne.access.DataNode.performQueries(DataNode.java:280)
at org.apache.cayenne.access.DataDomainFlushAction.runQueries(DataDomainFlushAction.java:233)
at org.apache.cayenne.access.DataDomainFlushAction.flush(DataDomainFlushAction.java:154)
at org.apache.cayenne.access.DataDomain.onSyncFlush(DataDomain.java:853)
at org.apache.cayenne.access.DataDomain$2.transform(DataDomain.java:817)
at org.apache.cayenne.access.DataDomain.runInTransaction(DataDomain.java:877)
at org.apache.cayenne.access.DataDomain.onSyncNoFilters(DataDomain.java:814)
at org.apache.cayenne.access.DataDomain$DataDomainSyncFilterChain.onSync(DataDomain.java:1031)
at org.apache.cayenne.access.DataDomain.onSync(DataDomain.java:785)
at org.apache.cayenne.access.DataContext.flushToParent(DataContext.java:817)
... 10 more
Caused by: com.mysql.jdbc.exceptions.jdbc4.MySQLIntegrityConstraintViolationException: Duplicate entry 'MGRV2' for key 'PRIMARY'
at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62)
at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
at java.lang.reflect.Constructor.newInstance(Constructor.java:422)
at com.mysql.jdbc.Util.handleNewInstance(Util.java:389)
at com.mysql.jdbc.Util.getInstance(Util.java:372)
at com.mysql.jdbc.SQLError.createSQLException(SQLError.java:973)
at com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:3835)
at com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:3771)
at com.mysql.jdbc.MysqlIO.sendCommand(MysqlIO.java:2435)
at com.mysql.jdbc.MysqlIO.sqlQueryDirect(MysqlIO.java:2582)
at com.mysql.jdbc.ConnectionImpl.execSQL(ConnectionImpl.java:2535)
at com.mysql.jdbc.PreparedStatement.executeInternal(PreparedStatement.java:1911)
at com.mysql.jdbc.PreparedStatement.executeUpdate(PreparedStatement.java:2145)
at com.mysql.jdbc.PreparedStatement.executeBatchSerially(PreparedStatement.java:1777)

Mus.Zeta.txt

Tried to compute an alignment of ERV sequences using the blast aligner module:

GLUE> compute alignment Mus.Zeta blastAligner
13:29:26.349 ComputeAlignmentCommand FINEST: Searching for members to align
13:29:26.369 ComputeAlignmentCommand FINEST: Found 36 members to align
Exception in thread "main" java.lang.NullPointerException
at uk.ac.gla.cvr.gluetools.core.command.project.ComputeAlignmentCommand.applyMemberAlignedSegments(ComputeAlignmentCommand.java:196)
at uk.ac.gla.cvr.gluetools.core.command.project.ComputeAlignmentCommand.getBatchResult(ComputeAlignmentCommand.java:134)
at uk.ac.gla.cvr.gluetools.core.command.project.ComputeAlignmentCommand.getAllAlignResults(ComputeAlignmentCommand.java:112)
at uk.ac.gla.cvr.gluetools.core.command.project.ComputeAlignmentCommand.execute(ComputeAlignmentCommand.java:96)
at uk.ac.gla.cvr.gluetools.core.command.project.ComputeAlignmentCommand.execute(ComputeAlignmentCommand.java:50)
at uk.ac.gla.cvr.gluetools.core.console.Console.executeTokenStrings(Console.java:176)
at uk.ac.gla.cvr.gluetools.core.console.Console.executeTokenStrings(Console.java:127)
at uk.ac.gla.cvr.gluetools.core.console.Console.handleLine(Console.java:117)
at uk.ac.gla.cvr.gluetools.core.console.Console.handleInteractiveLine(Console.java:91)
at uk.ac.gla.cvr.gluetools.core.console.Console.interactiveSession(Console.java:377)
at uk.ac.gla.cvr.gluetools.core.console.Console.main(Console.java:296)

GLUE then exits to shell

I've been working through the example project and some of the other virus projects. My version (the precompiled version) always seems to get stuck when importing alignments.

In the example project, I get an error after this command:
module unconstrainedAlignmentImporter import AL_UNCONSTRAINED -f alignments/SmithAlignment_23_1_2016_modified.fna

With the output:
[Fatal Error] :1:1: Premature end of file.
Error: XML parse exception: Premature end of file.
Cause: Premature end of file.

I'm running it on a mac with java 1.8.0_172 and MySQL 8.0.13

Thanks!

This is not urgent for me, but just a thought on interoperability between complementary tools. MicroReact accepts a newick tree and a CSV with matching IDs and metadata for interactive viewing in a web browser.