treebase-guts — Commit and tracker messages

[Treebase-guts] SF.net SVN: treebase:[22] trunk/treebase-core/src/main/perl/dump/sqldump

[<rv...@us...>]

Revision: 22
          http://treebase.svn.sourceforge.net/treebase/?rev=22&view=rev
Author:   rvos
Date:     2009-06-11 05:46:05 +0000 (Thu, 11 Jun 2009)

Log Message:
-----------
Changed arg handling to use Getopt::Long

Modified Paths:
--------------
    trunk/treebase-core/src/main/perl/dump/sqldump

Modified: trunk/treebase-core/src/main/perl/dump/sqldump
===================================================================
--- trunk/treebase-core/src/main/perl/dump/sqldump	2009-06-11 04:02:05 UTC (rev 21)
+++ trunk/treebase-core/src/main/perl/dump/sqldump	2009-06-11 05:46:05 UTC (rev 22)
@@ -2,39 +2,37 @@
 
 use CIPRES::TreeBase::DBIUtil;
 use CIPRES::TreeBase::RecDumper;
-use Getopt::Std;
+use Getopt::Long;
+use Pod::Usage;
+use strict;
 
-# required environment variables:
-# TREEBASE_DB_USER=***
-# TREEBASE_DB_PASS=***
-# TREEBASE_DB_DSN=***
-my %opt = ( 'x' => 0 );
-getopts('x', \%opt) or usage();
+my @tables; # database table to dump out
+my $outhandle = \*STDOUT;     # handle to write dump to
+my $with_progress_meter = 0;  # switch to print a progress meter
+my $with_inserts = 1;         # write insert statements
+my $with_creates = 0;         # write create statements
 
-# database table to dump out, provided as command line argument
-my $table = shift || usage();
+GetOptions(
+	'creates!'  => \$with_creates,
+	'inserts!'  => \$with_inserts,
+	'progress!' => \$with_progress_meter,
+	'user=s'    => \$ENV{'TREEBASE_DB_USER'},
+	'pass=s'    => \$ENV{'TREEBASE_DB_PASS'},
+	'dsn=s'     => \$ENV{'TREEBASE_DB_DSN'},
+	'table=s'   => \@tables,
+	'all'       => sub { @tables = get_all_tables() },
+	'file=s'    => sub {
+		my $file = pop;
+		open my $fh, '>', $file 
+			or die "Couldn't write output file '$file': $!; aborting";
+		$outhandle = $fh;
+	},
+) || pod2usage();
 
-# output file handle, by default to STDOUT, or...
-my $ofh = \*STDOUT;
-
-# ...second command line argument is file name...
-if ( @ARGV ) {
-    my $ofile = shift;
-    
-    # ...try to open a write handle to it...
-    open my($fh), ">", $ofile 
-	or die "Couldn't write output file '$ofile': $!; aborting";
-	
-	# ...and use that...
-    $ofh = $fh;
-}
-
 # create database handle
-my $dbh = CIPRES::TreeBase::DBIUtil->dbh
-  or die "Couldn't connect to database: " . DBI->errstr;
-$dbh->{'RaiseError'} = 1;
+my $dbh = get_handle();
 
-{
+for my $table ( @tables ) {
 	# only using these two functions once, so for clarity as to where they
 	# originate let's use the fully qualified names.
     my @names = CIPRES::TreeBase::DBIUtil::get_colnames($dbh, $table); 
@@ -50,9 +48,13 @@
 	
 	# give dumper the output handle to write to, i.e. either STDOUT
 	# or a file specified on the command line
-    $dumper->set_output($ofh);
+    $dumper->set_output($outhandle);
     
-    {
+    if ( $with_creates ) {
+    	
+    }
+    
+    if ( $with_inserts ) {
     	# get all rows from $table
 		my $q = qq{select * from $table};
 		my $sth = $dbh->prepare($q);
@@ -60,8 +62,8 @@
 		
 		my $row;
 		
-		# if -x is provided, print out progress counter
-		if ( $opt{'x'} ) {
+		# if --progress is provided, print out progress counter
+		if ( $with_progress_meter ) {
 		    my $count = 0;
 		    while ( $row = $sth->fetchrow_arrayref ) {
 				++$count;
@@ -70,7 +72,7 @@
 		    }
 		} 
 		
-		# without -x just dump the records
+		# if --noprogress or default, just dump the records
 		else {
 			while ( $row = $sth->fetchrow_arrayref ) {
 		    	$dumper->rec(@$row);
@@ -81,7 +83,7 @@
 		$sth->finish();
 		
 		# add line break if we're printing a progress counter
-		print STDERR "\n" if $opt{'x'};
+		print STDERR "\n" if $with_progress_meter;
     }
 }
 
@@ -93,3 +95,14 @@
     print "$0 table-name [output_filename]\n";
     exit 1;
 }
+
+sub get_all_tables {
+	
+}
+
+sub get_handle {
+	my $dbh = CIPRES::TreeBase::DBIUtil->dbh
+		or die "Couldn't connect to database: " . DBI->errstr;
+	$dbh->{'RaiseError'} = 1;	
+	return $dbh;
+}


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[Treebase-guts] SF.net SVN: treebase:[21] trunk/treebase-core/src/main/perl/lib/CIPRES/ TreeBase/RecDumper.pm

[<rv...@us...>]

Revision: 21
          http://treebase.svn.sourceforge.net/treebase/?rev=21&view=rev
Author:   rvos
Date:     2009-06-11 04:02:05 +0000 (Thu, 11 Jun 2009)

Log Message:
-----------
Formatted source, added closing semicolon to terminate SQL INSERT statements

Modified Paths:
--------------
    trunk/treebase-core/src/main/perl/lib/CIPRES/TreeBase/RecDumper.pm

Modified: trunk/treebase-core/src/main/perl/lib/CIPRES/TreeBase/RecDumper.pm
===================================================================
--- trunk/treebase-core/src/main/perl/lib/CIPRES/TreeBase/RecDumper.pm	2009-06-11 02:10:55 UTC (rev 20)
+++ trunk/treebase-core/src/main/perl/lib/CIPRES/TreeBase/RecDumper.pm	2009-06-11 04:02:05 UTC (rev 21)
@@ -5,12 +5,16 @@
 sub new {
     my $class = shift;
     my %arg = @_;
-    my $fn = $arg{FIELDS} or croak("$class->new: FIELDS required");
-    my $ct = $arg{TYPES} or croak("$class->new: TYPES required");
-    my $tn = uc $arg{TABLE} or croak("$class->new: TABLE required");
-    my $X = my @fieldnames = map uc, @$fn;
-    
-    my $self = { F => \@fieldnames, X => $X, N => $tn, T => $ct };
+    my $fn = $arg{'FIELDS'}   or croak("$class->new: FIELDS required");
+    my $ct = $arg{'TYPES'}    or croak("$class->new: TYPES required");
+    my $tn = uc $arg{'TABLE'} or croak("$class->new: TABLE required");
+    my $X  = my @fieldnames = map uc, @$fn;    
+    my $self = { 
+    	'F' => \@fieldnames, 
+    	'X' => $X, 
+    	'N' => $tn, 
+    	'T' => $ct 
+    };
     bless $self => $class;
     $self->_initialize();
     return $self;
@@ -18,53 +22,54 @@
 
 sub set_output {
     my ($self, $fh) = @_;
-    $self->{OUT} = $fh;
+    $self->{'OUT'} = $fh;
 }
 
 sub _initialize {
     my $self = shift;
     my $fieldlist = join ", ", @{$self->{F}}; 
     # Need to escape certain field names here
-    $self->{PREFIX} = qq{INSERT INTO $self->{N} ($fieldlist) VALUES (};
-    $self->{SUFFIX} = qq{)\n};
+    $self->{'PREFIX'} = qq{INSERT INTO $self->{N} ($fieldlist) VALUES (};
+    $self->{'SUFFIX'} = qq{);\n}; # XXX added closing semicolon
     return;
 }
 
 # Format data into an insert statement and return (or write) the result
 sub rec {
-  my $self = shift;
-  @_ > @{$self->{F}} 
-    and croak("rec: too many items (expected $self->{X})");
-  @_ < @{$self->{F}}
-    and croak("rec: too few items (expected $self->{X})");
-
-  @_ = $self->quote_data(@_);
-
-  my $values = join ", ", @_;
-  my $insert = $self->{PREFIX} . $values . $self->{SUFFIX};
-  return print {$self->{OUT}} $insert if $self->{OUT};
-  return $insert;
+	my $self = shift;
+	@_ > @{$self->{F}} 
+		and croak("rec: too many items (expected $self->{X})");
+	@_ < @{$self->{F}}
+		and croak("rec: too few items (expected $self->{X})");
+	
+	@_ = $self->quote_data(@_);
+	
+	my $values = join ", ", @_;
+	my $insert = $self->{'PREFIX'} . $values . $self->{'SUFFIX'};
+	return print {$self->{'OUT'}} $insert if $self->{'OUT'};
+	return $insert;
 }
 
 # XXX UNFINISHED !!!!
 sub quote_data {
     my $self = shift;
     my @d = @_;
-    for my $i (0 .. $#{$self->{F}}) {
-	my $t = $self->{T}[$i];
-	local *_ = \$d[$i];
-	$_ = "NULL", next unless defined;
-
-	if ($t eq "CHAR" || $t eq "VARCHAR") {
-	    s/'/''/g;
-	    $_ = "'$_'";
-	} elsif ($t =~ /^(BIG|SMALL|)INT$/ || $t eq "INTEGER" 
-		 || $t eq "DOUBLE") {
-	    # do nothing
-	} else {
-	    croak("Unknown field type '$t'; aborting");
+	for my $i (0 .. $#{$self->{F}}) {
+		my $t = $self->{T}[$i];
+		local *_ = \$d[$i];
+		$_ = "NULL", next unless defined;
+	
+		if ($t eq "CHAR" || $t eq "VARCHAR") {
+		    s/'/''/g;
+		    $_ = "'$_'";
+		} 
+		elsif ($t =~ /^(BIG|SMALL|)INT$/ || $t eq 'INTEGER' || $t eq 'DOUBLE') {
+		    # do nothing
+		} 
+		else {
+		    croak("Unknown field type '$t'; aborting");
+		}
 	}
-    }
 
     return @d;
 }


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[Treebase-guts] SF.net SVN: treebase:[19] trunk/treebase-core/src/main/perl/dump/sqldump

[<rv...@us...>]

Revision: 19
          http://treebase.svn.sourceforge.net/treebase/?rev=19&view=rev
Author:   rvos
Date:     2009-06-11 01:37:41 +0000 (Thu, 11 Jun 2009)

Log Message:
-----------
Added clarifying comments on sqldump script.

Modified Paths:
--------------
    trunk/treebase-core/src/main/perl/dump/sqldump

Modified: trunk/treebase-core/src/main/perl/dump/sqldump
===================================================================
--- trunk/treebase-core/src/main/perl/dump/sqldump	2009-05-29 22:52:00 UTC (rev 18)
+++ trunk/treebase-core/src/main/perl/dump/sqldump	2009-06-11 01:37:41 UTC (rev 19)
@@ -1,58 +1,87 @@
 #!/usr/bin/perl
 
-use CIPRES::TreeBase::DBIUtil qw(get_colnames get_coltypes);
+use CIPRES::TreeBase::DBIUtil;
 use CIPRES::TreeBase::RecDumper;
 use Getopt::Std;
 
-my %opt = ('x' => 0);
+my %opt = ( 'x' => 0 );
 getopts('x', \%opt) or usage();
 
+# database table to dump out, provided as command line argument
 my $table = shift || usage();
+
+# output file handle, by default to STDOUT, or...
 my $ofh = \*STDOUT;
-if (@ARGV) {
+
+# ...second command line argument is file name...
+if ( @ARGV ) {
     my $ofile = shift;
+    
+    # ...try to open a write handle to it...
     open my($fh), ">", $ofile 
 	or die "Couldn't write output file '$ofile': $!; aborting";
+	
+	# ...and use that...
     $ofh = $fh;
 }
 
+# create database handle
 my $dbh = CIPRES::TreeBase::DBIUtil->dbh
   or die "Couldn't connect to database: " . DBI->errstr;
-$dbh->{RaiseError} = 1;
+$dbh->{'RaiseError'} = 1;
 
 {
-    my @names = get_colnames($dbh, $table);
-    my @types = get_coltypes($dbh, $table);
-    my $dumper = 
-	CIPRES::TreeBase::RecDumper->new(
-	    FIELDS => \@names,
-	    TYPES  => \@types,
-	    TABLE  => $table
-	) or die "??";
+	# only using these two functions once, so for clarity as to where they
+	# originate let's use the fully qualified names.
+    my @names = CIPRES::TreeBase::DBIUtil::get_colnames($dbh, $table); 
+    my @types = CIPRES::TreeBase::DBIUtil::get_coltypes($dbh, $table);
+    
+    # instantiate a RecDumper object, which will format a row-as-array
+    # into an insert statement
+    my $dumper = CIPRES::TreeBase::RecDumper->new(
+	    'FIELDS' => \@names,
+	    'TYPES'  => \@types,
+	    'TABLE'  => $table
+	) or die "Couldn't instantiate CIPRES::TreeBase::RecDumper";
+	
+	# give dumper the output handle to write to, i.e. either STDOUT
+	# or a file specified on the command line
     $dumper->set_output($ofh);
     
     {
-	my $q = qq{select * from $table};
-	my $sth = $dbh->prepare($q);
-	$sth->execute();
-	
-	my $row;
-	if ($opt{x}) {
-	    my $count = 0;
-	    while ($row = $sth->fetchrow_arrayref) {
-		++$count;
-		$dumper->rec(@$row);
-		print STDERR "\r$count" if $count % 1000 == 0;
-	    }
-	} else {
-	    $dumper->rec(@$row) while $row = $sth->fetchrow_arrayref;
-	}
-	
-	$sth->finish();
-	print STDERR "\n" if $opt{x};
+    	# get all rows from $table
+		my $q = qq{select * from $table};
+		my $sth = $dbh->prepare($q);
+		$sth->execute();
+		
+		my $row;
+		
+		# if -x is provided, print out progress counter
+		if ( $opt{'x'} ) {
+		    my $count = 0;
+		    while ( $row = $sth->fetchrow_arrayref ) {
+				++$count;
+				$dumper->rec(@$row);
+				print STDERR "\r$count" if $count % 1000 == 0;
+		    }
+		} 
+		
+		# without -x just dump the records
+		else {
+			while ( $row = $sth->fetchrow_arrayref ) {
+		    	$dumper->rec(@$row);
+			}
+		}
+		
+		# finish the statement handler
+		$sth->finish();
+		
+		# add line break if we're printing a progress counter
+		print STDERR "\n" if $opt{'x'};
     }
 }
 
+# disconnect from database
 $dbh->disconnect;
 exit 0;
 


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[Treebase-guts] SF.net SVN: treebase:[20] trunk/treebase-core/src/main/perl/dump/sqldump

[<rv...@us...>]

Revision: 20
          http://treebase.svn.sourceforge.net/treebase/?rev=20&view=rev
Author:   rvos
Date:     2009-06-11 02:10:55 +0000 (Thu, 11 Jun 2009)

Log Message:
-----------
Added clarifying comments on sqldump script.

Modified Paths:
--------------
    trunk/treebase-core/src/main/perl/dump/sqldump

Modified: trunk/treebase-core/src/main/perl/dump/sqldump
===================================================================
--- trunk/treebase-core/src/main/perl/dump/sqldump	2009-06-11 01:37:41 UTC (rev 19)
+++ trunk/treebase-core/src/main/perl/dump/sqldump	2009-06-11 02:10:55 UTC (rev 20)
@@ -4,6 +4,10 @@
 use CIPRES::TreeBase::RecDumper;
 use Getopt::Std;
 
+# required environment variables:
+# TREEBASE_DB_USER=***
+# TREEBASE_DB_PASS=***
+# TREEBASE_DB_DSN=***
 my %opt = ( 'x' => 0 );
 getopts('x', \%opt) or usage();
 


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[Treebase-guts] [ treebase-Bugs-2798604 ] no block of taxa could be created from a MrBayes .con tree

[SourceForge.net <no...@so...>]

Bugs item #2798604, was opened at 2009-05-29 23:21
Message generated for change (Tracker Item Submitted) made by blaiseli
You can respond by visiting: 
https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=2798604&group_id=248804

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: data
Group: None
Status: Open
Priority: 5
Private: No
Submitted By: Blaise Li (blaiseli)
Assigned to: Mark Dominus (mjdominus)
Summary: no block of taxa could be created from a MrBayes .con tree

Initial Comment:
The upoad of the attached file fails: it says it cannot generate a block of taxa. This is either a bug or a strong limitation: the file contains a nexus tree obtained from MrBayes; it should not be so special.

----------------------------------------------------------------------

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[Treebase-guts] [ treebase-Bugs-2797430 ] Password hashing

[SourceForge.net <no...@so...>]

Bugs item #2797430, was opened at 2009-05-27 11:08
Message generated for change (Tracker Item Submitted) made by mjdominus
You can respond by visiting: 
https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=2797430&group_id=248804

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
Priority: 7
Private: No
Submitted By: Mark Dominus (mjdominus)
Assigned to: Nobody/Anonymous (nobody)
Summary: Password hashing

Initial Comment:
Passwords are stored in the USER table of the database in plain text.

They should be hashed instead.


----------------------------------------------------------------------

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[Treebase-guts] [ treebase-Bugs-2796466 ] no matrix page???

[SourceForge.net <no...@so...>]

Bugs item #2796466, was opened at 2009-05-25 15:01
Message generated for change (Comment added) made by rvos
You can respond by visiting: 
https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=2796466&group_id=248804

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including the initial issue submission, for this request,
not just the latest update.
Category: None
Group: None
>Status: Closed
Priority: 9
Private: No
Submitted By: Rutger Vos (rvos)
>Assigned to: Rutger Vos (rvos)
Summary: no matrix page???

Initial Comment:
http://8ball.sdsc.edu:6666/treebase-web/search/study/study/matrix.html?matrixid=3447&id=2162

----------------------------------------------------------------------

>Comment By: Rutger Vos (rvos)
Date: 2009-05-25 22:37

Message:
Fixed as per revision 6497 (typo in jsp)

----------------------------------------------------------------------

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[Treebase-guts] [ treebase-Bugs-2796466 ] no matrix page???

[SourceForge.net <no...@so...>]

Bugs item #2796466, was opened at 2009-05-25 15:01
Message generated for change (Tracker Item Submitted) made by rvos
You can respond by visiting: 
https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=2796466&group_id=248804

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
Priority: 9
Private: No
Submitted By: Rutger Vos (rvos)
Assigned to: Nobody/Anonymous (nobody)
Summary: no matrix page???

Initial Comment:
http://8ball.sdsc.edu:6666/treebase-web/search/study/study/matrix.html?matrixid=3447&id=2162

----------------------------------------------------------------------

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[Treebase-guts] [ treebase-Bugs-2782675 ] Deleting a tree block throws LockAcquisitionException

[SourceForge.net <no...@so...>]

Bugs item #2782675, was opened at 2009-04-28 08:09
Message generated for change (Comment added) made by rvos
You can respond by visiting: 
https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=2782675&group_id=248804

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including the initial issue submission, for this request,
not just the latest update.
Category: data
Group: piel
Status: Open
Priority: 4
Private: No
Submitted By: Rutger Vos (rvos)
Assigned to: Mark Dominus (mjdominus)
Summary: Deleting a tree block throws LockAcquisitionException

Initial Comment:
Deleting a tree block with only two trees started to take forever but then finished with an uncaught exception (attached below).

Uncaught Exception Encountered
org.hibernate.exception.LockAcquisitionException: could not execute native bulk manipulation query at org.hibernate.exception.SQLStateConverter.convert(SQLStateConverter.java:82) at org.hibernate.exception.JDBCExceptionHelper.convert(JDBCExceptionHelper.java:43) at org.hibernate.engine.query.NativeSQLQueryPlan.performExecuteUpdate(NativeSQLQueryPlan.java:174) at org.hibernate.impl.SessionImpl.executeNativeUpdate(SessionImpl.java:1163) at org.hibernate.impl.SQLQueryImpl.executeUpdate(SQLQueryImpl.java:334) at org.cipres.treebase.dao.jdbc.PhyloTreeJDBC.deletePhyloTreeNodeSQL(PhyloTreeJDBC.java:70) at org.cipres.treebase.dao.tree.PhyloTreeDAO.realDelete(PhyloTreeDAO.java:176) at org.cipres.treebase.dao.tree.PhyloTreeDAO.deleteTreeBlock(PhyloTreeDAO.java:201) at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25) at java.lang.reflect.Method.invoke(Method.java:585) at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:304) at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:182) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:149) at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:106) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:171) at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:204) at $Proxy65.deleteTreeBlock(Unknown Source) at org.cipres.treebase.web.controllers.DeleteATreeBlockController.onSubmit(DeleteATreeBlockController.java:106) at org.springframework.web.servlet.mvc.SimpleFormController.processFormSubmission(SimpleFormController.java:267) at org.springframework.web.servlet.mvc.CancellableFormController.processFormSubmission(CancellableFormController.java:140) at org.springframework.web.servlet.mvc.AbstractFormController.handleRequestInternal(AbstractFormController.java:265) at org.springframework.web.servlet.mvc.AbstractController.handleRequest(AbstractController.java:153) at org.springframework.web.servlet.mvc.SimpleControllerHandlerAdapter.handle(SimpleControllerHandlerAdapter.java:48) at org.springframework.web.servlet.DispatcherServlet.doDispatch(DispatcherServlet.java:858) at org.springframework.web.servlet.DispatcherServlet.doService(DispatcherServlet.java:792) at org.springframework.web.servlet.FrameworkServlet.processRequest(FrameworkServlet.java:476) at org.springframework.web.servlet.FrameworkServlet.doPost(FrameworkServlet.java:441) at javax.servlet.http.HttpServlet.service(HttpServlet.java:710) at javax.servlet.http.HttpServlet.service(HttpServlet.java:803) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:269) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188) at org.displaytag.filter.ResponseOverrideFilter.doFilter(ResponseOverrideFilter.java:125) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:215) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188) at org.springframework.orm.hibernate3.support.OpenSessionInViewFilter.doFilterInternal(OpenSessionInViewFilter.java:198) at org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:75) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:215) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188) at com.opensymphony.module.sitemesh.filter.PageFilter.parsePage(PageFilter.java:119) at com.opensymphony.module.sitemesh.filter.PageFilter.doFilter(PageFilter.java:55) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:215) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188) at org.acegisecurity.util.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:264) at org.acegisecurity.intercept.web.FilterSecurityInterceptor.invoke(FilterSecurityInterceptor.java:107) at org.acegisecurity.intercept.web.FilterSecurityInterceptor.doFilter(FilterSecurityInterceptor.java:72) at org.acegisecurity.util.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:274) at org.acegisecurity.ui.ExceptionTranslationFilter.doFilter(ExceptionTranslationFilter.java:110) at org.acegisecurity.util.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:274) at org.acegisecurity.wrapper.SecurityContextHolderAwareRequestFilter.doFilter(SecurityContextHolderAwareRequestFilter.java:81) at org.acegisecurity.util.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:274) at org.acegisecurity.ui.AbstractProcessingFilter.doFilter(AbstractProcessingFilter.java:217) at org.acegisecurity.util.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:274) at org.acegisecurity.context.HttpSessionContextIntegrationFilter.doFilter(HttpSessionContextIntegrationFilter.java:191) at org.acegisecurity.util.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:274) at org.acegisecurity.util.FilterChainProxy.doFilter(FilterChainProxy.java:148) at org.acegisecurity.util.FilterToBeanProxy.doFilter(FilterToBeanProxy.java:90) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:215) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188) at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:213) at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:174) at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:127) at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:117) at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:108) at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:174) at org.apache.coyote.http11.Http11Processor.process(Http11Processor.java:874) at org.apache.coyote.http11.Http11BaseProtocol$Http11ConnectionHandler.processConnection(Http11BaseProtocol.java:665) at org.apache.tomcat.util.net.PoolTcpEndpoint.processSocket(PoolTcpEndpoint.java:528) at org.apache.tomcat.util.net.LeaderFollowerWorkerThread.runIt(LeaderFollowerWorkerThread.java:81) at org.apache.tomcat.util.threads.ThreadPool$ControlRunnable.run(ThreadPool.java:689) at java.lang.Thread.run(Thread.java:595) Caused by: com.ibm.db2.jcc.b.SqlException: DB2 SQL error: SQLCODE: -911, SQLSTATE: 40001, SQLERRMC: 2 at com.ibm.db2.jcc.b.id.e(id.java:1640) at com.ibm.db2.jcc.c.fb.t(fb.java:748) at com.ibm.db2.jcc.c.fb.l(fb.java:398) at com.ibm.db2.jcc.c.fb.a(fb.java:64) at com.ibm.db2.jcc.c.s.a(s.java:48) at com.ibm.db2.jcc.c.xb.c(xb.java:266) at com.ibm.db2.jcc.b.jd.ab(jd.java:1684) at com.ibm.db2.jcc.b.jd.a(jd.java:2253) at com.ibm.db2.jcc.b.jd.W(jd.java:537) at com.ibm.db2.jcc.b.jd.executeUpdate(jd.java:520) at com.mchange.v2.c3p0.impl.NewProxyPreparedStatement.executeUpdate(NewProxyPreparedStatement.java:105) at org.hibernate.engine.query.NativeSQLQueryPlan.performExecuteUpdate(NativeSQLQueryPlan.java:165) ... 69 more Cookies: itemToHighlight=[http%3A//8ball.sdsc.edu%3A6666/treebase-web/user/treeBlockList.html] JSESSIONID=[4F285F84FEA3650D68B71E616273E85D] __utma=[60813167.1783846415.1214875683.1214875683.1239852153.2] __utmz=[60813167.1239852153.2.1.utmccn]


----------------------------------------------------------------------

>Comment By: Rutger Vos (rvos)
Date: 2009-05-14 21:49

Message:
I can't re-create this exception.

----------------------------------------------------------------------

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[Treebase-guts] [ treebase-Bugs-2790248 ] Taxon Blocks duplicated in analysis download from

[SourceForge.net <no...@so...>]

Bugs item #2790248, was opened at 2009-05-11 19:11
Message generated for change (Comment added) made by rvos
You can respond by visiting: 
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Category: data
Group: None
>Status: Closed
Priority: 3
Private: No
Submitted By: William Piel (sfrgpiel)
>Assigned to: Rutger Vos (rvos)
Summary: Taxon Blocks duplicated in analysis download from

Initial Comment:
When you click on http://8ball.sdsc.edu:6666/treebase-web/search/downloadAnAnalysisStep.html?analysisid=2022 to download an analysis, two identical TAXA blocks, each with the same title, are included in the nexus file. This is confusing to Mesquite, which doesn't know which goes with which. Please have the nexus written with only one TAXA block shared by both CHARACTER and TREE blocks. 

----------------------------------------------------------------------

>Comment By: Rutger Vos (rvos)
Date: 2009-05-14 21:45

Message:
Analysis steps are now serialized to nexus as follows: two taxa blocks are
created, one containing all taxon labels in all input data objects, and one
containing all taxon labels in all output data objects. The data objects
(trees, matrices) reference these respective taxa blocks, depending on
whether they're input or output data.

----------------------------------------------------------------------

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[Treebase-guts] [ treebase-Bugs-2785695 ] NCHAR=NULL in morphological downloaded datasets

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Bugs item #2785695, was opened at 2009-05-02 17:20
Message generated for change (Comment added) made by rvos
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Category: data
Group: None
>Status: Closed
Priority: 5
Private: No
Submitted By: William Piel (sfrgpiel)
>Assigned to: Rutger Vos (rvos)
Summary: NCHAR=NULL in morphological downloaded datasets

Initial Comment:
In test matrix M4232 and submission id S2424, the reconstructed matrices have "NCHAR=NULL" when they should have a real number, e.g. "NCHAR=98"

----------------------------------------------------------------------

>Comment By: Rutger Vos (rvos)
Date: 2009-05-14 21:39

Message:
As of revision 6485, morphological matrices correctly display their nchar
when serialized to reconstituted nexus files.

----------------------------------------------------------------------

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[Treebase-guts] [ treebase-Bugs-2791028 ] software commands field too short

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Bugs item #2791028, was opened at 2009-05-13 06:24
Message generated for change (Tracker Item Submitted) made by rvos
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Category: data
Group: None
Status: Open
Priority: 4
Private: No
Submitted By: Rutger Vos (rvos)
Assigned to: Mark Dominus (mjdominus)
Summary: software commands field too short

Initial Comment:
The field for software commands cannot contain long commands blocks (data access error thrown).

----------------------------------------------------------------------

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[Treebase-guts] [ treebase-Bugs-2790234 ] Uncaught Exception when trying to edit a taxon label

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Bugs item #2790234, was opened at 2009-05-11 18:41
Message generated for change (Comment added) made by rvos
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Category: None
Group: None
>Status: Closed
Priority: 5
Private: No
Submitted By: William Piel (sfrgpiel)
>Assigned to: Rutger Vos (rvos)
Summary: Uncaught Exception when trying to edit a taxon label

Initial Comment:
Following this:

http://8ball.sdsc.edu:6666/treebase-web/user/editTaxonLabel.html?taxonlabelid=237198

Caused the (attached) "Uncaught Exception Encountered". 



----------------------------------------------------------------------

>Comment By: Rutger Vos (rvos)
Date: 2009-05-13 04:24

Message:
Some dependencies for hibernate had gone missing during the last rebuild. A
clean build of the war resolved the issue: the taxon label editor now comes
up correctly.

----------------------------------------------------------------------

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[Treebase-guts] [ treebase-Bugs-2790244 ] Uncaught Exception Encountered when searching on a matrix.

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Bugs item #2790244, was opened at 2009-05-11 19:04
Message generated for change (Settings changed) made by rvos
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Category: ui
Group: None
>Status: Closed
Priority: 5
Private: No
Submitted By: William Piel (sfrgpiel)
>Assigned to: Rutger Vos (rvos)
Summary: Uncaught Exception Encountered when searching on a matrix.

Initial Comment:

Clicked the Matrix tab, typed in M391, clicked Matrix ID, then got a big Uncaught Exception barf.

http://8ball.sdsc.edu:6666/treebase-web/search/matrixSearch.html


----------------------------------------------------------------------

>Comment By: Rutger Vos (rvos)
Date: 2009-05-13 04:22

Message:
Some hibernate dependencies had gone missing during the last rebuild on
8ball. A clean rebuild of the war fixed the issue - the search now returns
one matrix.

----------------------------------------------------------------------

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[Treebase-guts] [ treebase-Bugs-2790269 ] Email Confirmation for New Users

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Bugs item #2790269, was opened at 2009-05-11 15:59
Message generated for change (Tracker Item Submitted) made by sfrgpiel
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Category: ui
Group: None
Status: Open
Priority: 1
Private: No
Submitted By: William Piel (sfrgpiel)
Assigned to: Nobody/Anonymous (nobody)
Summary: Email Confirmation for New Users

Initial Comment:
Hilmar and Todd at NESCent were surprised that we do not have an email-confirmation step for new users. This is probably a good feature to have, but is not critical so I gave it a low priority. 

----------------------------------------------------------------------

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[Treebase-guts] [ treebase-Bugs-2790248 ] Taxon Blocks duplicated in analysis download from

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Bugs item #2790248, was opened at 2009-05-11 15:11
Message generated for change (Tracker Item Submitted) made by sfrgpiel
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Category: data
Group: None
Status: Open
Priority: 3
Private: No
Submitted By: William Piel (sfrgpiel)
Assigned to: Mark Dominus (mjdominus)
Summary: Taxon Blocks duplicated in analysis download from

Initial Comment:
When you click on http://8ball.sdsc.edu:6666/treebase-web/search/downloadAnAnalysisStep.html?analysisid=2022 to download an analysis, two identical TAXA blocks, each with the same title, are included in the nexus file. This is confusing to Mesquite, which doesn't know which goes with which. Please have the nexus written with only one TAXA block shared by both CHARACTER and TREE blocks. 

----------------------------------------------------------------------

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[Treebase-guts] [ treebase-Bugs-2790244 ] Uncaught Exception Encountered when searching on a matrix.

[SourceForge.net <no...@so...>]

Bugs item #2790244, was opened at 2009-05-11 15:04
Message generated for change (Tracker Item Submitted) made by sfrgpiel
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Category: ui
Group: None
Status: Open
Priority: 5
Private: No
Submitted By: William Piel (sfrgpiel)
Assigned to: Nobody/Anonymous (nobody)
Summary: Uncaught Exception Encountered when searching on a matrix.

Initial Comment:

Clicked the Matrix tab, typed in M391, clicked Matrix ID, then got a big Uncaught Exception barf.

http://8ball.sdsc.edu:6666/treebase-web/search/matrixSearch.html


----------------------------------------------------------------------

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[Treebase-guts] [ treebase-Bugs-2790234 ] Uncaught Exception when trying to edit a taxon label

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Bugs item #2790234, was opened at 2009-05-11 14:41
Message generated for change (Tracker Item Submitted) made by sfrgpiel
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Category: None
Group: None
Status: Open
Priority: 5
Private: No
Submitted By: William Piel (sfrgpiel)
Assigned to: Nobody/Anonymous (nobody)
Summary: Uncaught Exception when trying to edit a taxon label

Initial Comment:
Following this:

http://8ball.sdsc.edu:6666/treebase-web/user/editTaxonLabel.html?taxonlabelid=237198

Caused the (attached) "Uncaught Exception Encountered". 



----------------------------------------------------------------------

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[Treebase-guts] [ treebase-Bugs-2789158 ] Problems when linking to external taxonomy

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Bugs item #2789158, was opened at 2009-05-08 15:01
Message generated for change (Tracker Item Submitted) made by esterb
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Category: data
Group: None
Status: Open
Priority: 5
Private: No
Submitted By: Ester Gaya (esterb)
Assigned to: Mark Dominus (mjdominus)
Summary: Problems when linking to external taxonomy

Initial Comment:
Hi, 

I am just submitting a DNA matrix and when I am having problems when trying to link to taxonomy. I may be doing something wrong...
If it finds a NamebankID from UBio or NCBI no problem, but if I have to add the taxon id by hand, the 'no association' button is checked by default and even if I add the id number below and I update it, it appears an error message (I attached it as a doc file below). I can't find a way to unclick the 'no association' button. Then it appears this message for all the taxa I couldn't link:  an unsuccesful attempt has been made to link this to the external taxonomy

Also, another question, it is really painful to link specimen by specimen to its taxonomy. I have several specimens from the same species and I have been able to figure out a way to link that species at once, without having to do it one by one. It can be very painful for a population level study. Is there a way to do it?

Thank you

----------------------------------------------------------------------

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[Treebase-guts] [ treebase-Bugs-2712234 ] Taxon label editor displays wrong items

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Bugs item #2712234, was opened at 2009-03-25 13:47
Message generated for change (Comment added) made by mjdominus
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Category: ui
Group: piel
>Status: Closed
Priority: 8
Private: No
Submitted By: Mark Dominus (mjdominus)
Assigned to: Mark Dominus (mjdominus)
Summary: Taxon label editor displays wrong items

Initial Comment:
BP reports that during taxon validation, 
> When I follow one of the "validate by hand" links, I see a list like this one for Actinomucor elegans: but it list three identical items to
> choose from, each having identical ncbi_taxids. We should never really see a list of multiple hits each with the same ncbi_taxid, but 
> we can see multiple hits on the same ubio_namebankid. 

(See http://8ball.sdsc.edu:6666/treebase-web/user/editTaxonLabel.html?taxonlabelid=237178 ; a copy of the HTML file is attached)


----------------------------------------------------------------------

>Comment By: Mark Dominus (mjdominus)
Date: 2009-05-08 09:45

Message:
Piel did not reply to my request for signoff two weeks ago, so I am closing
this.


----------------------------------------------------------------------

Comment By: Mark Dominus (mjdominus)
Date: 2009-04-22 15:09

Message:
I rebuilt the TI database; I believe it is complete and correct now.

I am awaiting confirmation from Bill to close this.

----------------------------------------------------------------------

Comment By: Rutger Vos (rvos)
Date: 2009-04-02 02:11

Message:
Unfortunately, the taxon label editor actually displays the *right* items.
Namely, there are three taxon variants with the same name, namebankID and
NCBI taxon ID in the database:

 Actinomucor elegans, (Internal ID: 894, uBio: 2832730, NCBI: 64647)
 Actinomucor elegans, (Internal ID: 546683, uBio: 2832730, NCBI: 64647)
 Actinomucor elegans, (Internal ID: 554383, uBio: 2832730, NCBI: 64647)

It seems to me that the only way in which this issue can be resolved is by
re-validating the loaded taxon, taxonvariant and taxonlabel data and
collapsing such duplicates.

As per revision 6373, the duplicates are shown, e.g. see
http://8ball.sdsc.edu:6666/treebase-web/user/editTaxonLabel.html?taxonlabelid=237178

----------------------------------------------------------------------

Comment By: Mark Dominus (mjdominus)
Date: 2009-03-25 14:18

Message:
Also there is a lower-priority component to this bug; see #2712268

----------------------------------------------------------------------

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[Treebase-guts] [ treebase-Bugs-2712291 ] Display matrix IDs for unnamed matrices

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Bugs item #2712291, was opened at 2009-03-25 18:19
Message generated for change (Comment added) made by rvos
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Category: ui
Group: easy
>Status: Closed
Priority: 4
Private: No
Submitted By: Mark Dominus (mjdominus)
>Assigned to: Rutger Vos (rvos)
Summary: Display matrix IDs for unnamed matrices

Initial Comment:
BP says:
> (3)- when a user selects, say, "Matrix" as the dataype for a step, he 
> then sees a list of all matrices and has to pick one or more to include 
> with the analysis step. If the matrices don't have names or titles, they 
> appear as blank rows. Please add a matrix ID column so that even 
> matrices without names can be identified by the user. 

----------------------------------------------------------------------

>Comment By: Rutger Vos (rvos)
Date: 2009-05-08 00:25

Message:
As of revision 6461, matrices now have a default title ("Matrix" + ID), so
there are no blank rows.

----------------------------------------------------------------------

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[Treebase-guts] [ treebase-Bugs-2787987 ] Discard All button in tree topologies takes you to trees tab

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Bugs item #2787987, was opened at 2009-05-06 17:57
Message generated for change (Comment added) made by rvos
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Category: ui
Group: piel
>Status: Closed
Priority: 3
Private: No
Submitted By: William Piel (sfrgpiel)
>Assigned to: Rutger Vos (rvos)
Summary: Discard All button in tree topologies takes you to trees tab

Initial Comment:
Clicking the "Discard All Results" button in the "Tree Topologies" tab takes the user to the "Trees" tab when it should stay in the same tab.

----------------------------------------------------------------------

>Comment By: Rutger Vos (rvos)
Date: 2009-05-08 00:23

Message:
As of 6461, modifying the tree search results list (discarding some or all
results) on the topology page now returns the user to the topology search
tab, not the tree search tab.

----------------------------------------------------------------------

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[Treebase-guts] [ treebase-Bugs-2712294 ] Display tree IDs for unnamed trees

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Bugs item #2712294, was opened at 2009-03-25 18:20
Message generated for change (Comment added) made by rvos
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Category: ui
Group: easy
>Status: Closed
Priority: 4
Private: No
Submitted By: Mark Dominus (mjdominus)
>Assigned to: Rutger Vos (rvos)
Summary: Display tree IDs for unnamed trees

Initial Comment:
BP says:
> (4)- when a user selects, say, "Tree" or "Tree Block" as the dataype for 
> a step, he then sees a list of all trees and has to pick one or more to 
> include with the analysis step. If the trees don't have names or titles, 
> they appear as blank rows. Please add a tree ID column so that even 
> trees without names can be identified by the user. 

----------------------------------------------------------------------

>Comment By: Rutger Vos (rvos)
Date: 2009-05-07 23:56

Message:
As of revision 6460, trees and tree blocks now have a default return value
for the "title" field: the local class name + the object id, e.g.
PhyloTree1231. This means that the list of available input/output data now
always at least have the title column populated. This fix is also useful
for nexus file generation, where heretofore the "TITLE=foo;" token was
sometimes empty.

----------------------------------------------------------------------

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[Treebase-guts] [ treebase-Bugs-2683594 ] More download opportunities

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Bugs item #2683594, was opened at 2009-03-11 18:55
Message generated for change (Comment added) made by rvos
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Category: ui
Group: piel
>Status: Closed
Priority: 4
Private: No
Submitted By: Mark Dominus (mjdominus)
Assigned to: Rutger Vos (rvos)
Summary: More download opportunities

Initial Comment:
BP says:  -- We need easier and more immediate ways of downloading nexus files. Under the Matrix tab, it would be good to have a download icon on each row (which downloads only that matrix). Also, on the Study summery page, for each analysis it would be good to have a download icon (which downloads a Mesquite-compatible nexus file with character blocks for all associated matrices a tree block with all associated trees).



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>Comment By: Rutger Vos (rvos)
Date: 2009-05-07 22:51

Message:
As of revision 6457, individual analysis steps can be downloaded as
reconstituted nexus files, including all their input and output data.
(Matrices and trees could already be downloaded.)

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Comment By: Rutger Vos (rvos)
Date: 2009-03-19 07:32

Message:
Working on this. Have added download buttons to the tree search results
list.

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https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=2683594&group_id=248804

[Treebase-guts] [ treebase-Bugs-2785703 ] CHARSTATELABELS missing in continuous data

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Bugs item #2785703, was opened at 2009-05-02 13:32
Message generated for change (Comment added) made by sfrgpiel
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including the initial issue submission, for this request,
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Category: data
Group: None
Status: Open
Priority: 5
Private: No
Submitted By: William Piel (sfrgpiel)
Assigned to: Mark Dominus (mjdominus)
Summary: CHARSTATELABELS missing in continuous data

Initial Comment:
Uploading a continuous dataset that has CHARSTATELABELS fails to store the CHARSTATELABELS and fails to reconstruct them in the downloaded/reconstructed file. Continuous characters do not have state labels, but they have the names/title of characters. Compare the attached data-in vs the data-out to see what has failed to be captured.

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Comment By: William Piel (sfrgpiel)
Date: 2009-05-07 07:56

Message:
Technically it's probably true that we should use CHARLABELS over
CHARSTATELABELS, but since Mesquite uses CHARSTATELABELS, I'm inclined to
follow their lead. (see the 01-editContinuous.nex tutorial file in the
Mesquite distribution). 

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Comment By: Rutger Vos (rvos)
Date: 2009-05-07 05:16

Message:
Shouldn't we be using CHARLABELS, not CHARSTATELABELS, for continuous
matrices?

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