? biomart-plib/BioMart/Configuration/BooleanListFilter.pm
? biomart-plib/BioMart/Dataset/TextIndex.pm
Index: biomart-plib/BioMart/Configurator.pm
===================================================================
RCS file: /cvsroot/CVSmaster/biomart-plib/BioMart/Configurator.pm,v
retrieving revision 1.16.2.3
diff -r1.16.2.3 Configurator.pm
195c195,196
< my $sql = "SELECT compressed_xml FROM ".$dataSet->schema."."."meta_configuration
---
> #dgg-badgz# my $sql = "SELECT compressed_xml FROM ".$dataSet->schema."."."meta_configuration "..
> my $sql = "SELECT xml FROM ".$dataSet->schema."."."meta_configuration
200c201
< my $xml = Compress::Zlib::memGunzip($$row[0]) ;
---
> my $xml = $$row[0]; #dgg-badgz# Compress::Zlib::memGunzip($$row[0]) ;
205a207,210
> # dgg patch for bad xml.gz tripping XML::Parser
> $xml =~ s,\\\\015\\\\012,\n,g; #? or s,\\015\\012,\n,g;
> warn "DEBUG.dgg: bad xml? [".substr($xml,0,200)."]\n" if($dataSetName =~ /fly|flstructure/);
>
Index: biomart-plib/BioMart/Initializer.pm
===================================================================
RCS file: /cvsroot/CVSmaster/biomart-plib/BioMart/Initializer.pm,v
retrieving revision 1.24.2.6
diff -r1.24.2.6 Initializer.pm
355a356,357
> # dgg patch for bad xml.gz tripping XML::Parser
> $xml =~ s,\\\\015\\\\012,\n,g;
Index: biomart-plib/BioMart/Dataset/TableSet.pm
===================================================================
RCS file: /cvsroot/CVSmaster/biomart-plib/BioMart/Dataset/TableSet.pm,v
retrieving revision 1.11.2.3
diff -r1.11.2.3 TableSet.pm
669c669,670
< # warn ($sql);
---
> ## dgg;
> warn ("DEBUG.tableset sql=\n ".$sql."\n");
787c788,789
< # warn ($sql);
---
> ## dgg;
> warn ("DEBUG.count sql=\n ".$sql."\n");
Index: biomart-plib/BioMart/Dataset/GenomicSequence/DNAAdaptor.pm
===================================================================
RCS file: /cvsroot/CVSmaster/biomart-plib/BioMart/Dataset/GenomicSequence/DNAAdaptor.pm,v
retrieving revision 1.1.1.1
diff -r1.1.1.1 DNAAdaptor.pm
167c167,169
<
---
> #dgg.debug# or env DBI_TRACE=1 perl ... # problem is/was missing schemaprefix. for pgsql opt dbtable
> warn "seq.sql=".$sth->{Statement}." w/ $coord, $len, $chunkStart, $chr\n";
>
Index: conf/SiteDefs.pm
===================================================================
RCS file: /cvsroot/CVSmaster/biomart-web/conf/Attic/SiteDefs.pm,v
retrieving revision 1.8.2.4
diff -r1.8.2.4 SiteDefs.pm
97c97,100
< $ENSEMBL_PORT = 9999;
---
> ## $ENSEMBL_PORT = 9999;
> ## http://lynx.bio.indiana.edu:7991/
> ## http://chipmunk.bio.indiana.edu:7992/
> $ENSEMBL_PORT = 7992;
118c121,122
< $ENSEMBL_ACCESSLOG = $ENSEMBL_SERVERROOT.'/logs/access_log ensembl_extended';
---
> ##$ENSEMBL_ACCESSLOG = $ENSEMBL_SERVERROOT.'/logs/access_log ensembl_extended';
> $ENSEMBL_ACCESSLOG = $ENSEMBL_SERVERROOT.'/logs/access_log combined';
Index: modules/Apache/EnsEMBL/Handlers.pm
===================================================================
RCS file: /cvsroot/CVSmaster/biomart-web/modules/Apache/EnsEMBL/Handlers.pm,v
retrieving revision 1.1.1.1
diff -r1.1.1.1 Handlers.pm
32c32
< $TT = ( $TT + $TT<<15 ) & 0xffffffff;
---
> $TT = ( $TT + $TT << 15 ) & 0xffffffff;
Index: perl/multi/martview
===================================================================
RCS file: /cvsroot/CVSmaster/biomart-web/perl/multi/martview,v
retrieving revision 1.98.2.30
diff -r1.98.2.30 martview
78a79,93
> use constant DEBUG => 0; # dgg
> # dgg DEBUG where is print output going???
> # print qq(Content-Type: text/html
> #
> #
> # DEBUG: dgg test output
> # );
> ## need this, cant find why dang mod_perl Apache print override is not sending output to browser
> sub print {
> print @_;
> # my $r = Apache->request;
> # $r->print( @_);
> # #CORE::print STDERR "ApachePrint: ",@_,"\n";
> }
>
90c105
< #warn("#######1 $$ ENTERING MARTVIEW AT ".localtime(time));
---
> warn("#######1 $$ ENTERING MARTVIEW AT ".localtime(time));
115c130
< print( get_suspend_page() );
---
> martview::print( get_suspend_page() );
125a141,148
> # if(DEBUG){
> # print STDERR "\n#--- CGI Vars IN:\n";
> # my $cg= new CGI;
> # my $params = $cg->Vars;
> # foreach my $k (keys %$params) { print STDERR " $k=".$params->{$k}."; "; }
> # print STDERR "\n";
> # }
>
206c229
< print qq(Content-Type: text/html
---
> martview::print qq(Content-Type: text/html
225a249
> warn "##dgg martview printpage\n";
245c269,271
< print $CGI->header;
---
> martview::print $CGI->header;
> # martview::print " DEBUG *** dgg HERE
\n";
>
249a276
> #warn "##dgg martview before ens-render\n";
265c292,293
< print ensembl_page_header(%header_opts);
---
> #warn "##dgg martview enspagehead\n";
> martview::print ensembl_page_header(%header_opts);
289,290c317,320
< print $content;
< print ensembl_page_footer;
---
> #warn "##dgg martview print content, len=",length($content),"\n";
> open(WP,">$SiteDefs::ENSEMBL_SERVERROOT/htdocs/martpage.html");print WP $content; close(WP);
> martview::print $content;
> martview::print ensembl_page_footer;
292a323
> #warn "##dgg martview exit\n";
323,325c354,356
< print $page->http_header;
< print $page->start_html;
< print ensembl_navigation_table(
---
> martview::print $page->http_header;
> martview::print $page->start_html;
> martview::print ensembl_navigation_table(
364c395
< # warn( 'Got from cache: ', join( ', ', @cache_location ) );
---
> warn( 'Got from cache: ', join( ', ', @cache_location ) );
433c464
< #return $output;
---
> return $output;
840a872,879
>
> ## dgg here; want multi-select lists;
> if ($filter->name() =~ /multi/) { # fixme
> $entry->set_cgi_multiple(1);
> $entry->set_cgi_size(5);
> }
> ##
>
922a962,969
>
> ## dgg here; want multi-select lists;
> if ($filter->name() =~ /multi/) { # fixme
> $entry->set_cgi_multiple(1);
> $entry->set_cgi_size(5);
> }
> ##
>
1643a1691
>
1649a1698,1709
> #dgg debug where is multiselect list ?
> my @debugallvals= @values; # $CGI->param( $dataSetName.'_'. $entry->name );
> my @debugfilt= $CGI->param( $dataSetName.'_'. $entry->name.'_filter' );
> my @debuglist= $CGI->param( $dataSetName.'_'. $name.'_list' ); #NOTE $name not entry.name
> warn("DEBUG.in1 ",$dataSetName,'_',$entry->name," vals=",@debugallvals,"\n") if DEBUG;
> warn("DEBUG.in1 _list ",@debuglist," \n") if DEBUG;
> warn("DEBUG.in1 _filters ",@debugfilt," \n") if DEBUG;
> # DEBUG.in1 sce3b_id_list_filters vals=Excluded
> # DEBUG.in1 _list
> # DEBUG.in1 _filter binding_site_sgd_bool << here, need @array
>
>
1717a1778,1779
>
>
1719a1782,1819
>
> ### dgg; need patch here? YES for multiselect list
> ## but boolfilter doesnt support multi-list; how to do?
> ## need to query->addFilter( join( ' OR ', @ entries ) );
> ## SEE BELOW; need this code twice ...
>
> my @debug_allopts= $CGI->param( $dataSetName.'_'. $entry->name.'_filter' );
> warn("DEBUG.in2 _filter=$option_name; allopts= @debug_allopts \n") if DEBUG;
> if(@debug_allopts > 1) {
>
> use BioMart::Configuration::BooleanListFilter; # should be in BioMart::Configurator;
> my $att_table = BioMart::AttributeTable->new();
> my $dnames="";
> my $entry1;
>
> foreach my $oname (@debug_allopts){
> my $option = $ct->getOptionByName($oname);
> next if (!$option);
> $dnames .= $option->displayName.", ";
> my $bentry = $option->filter;
> if ($value ne 'Only'){ $bentry->setExcluded; }
> else{ $bentry->setIncluded; }
> $bentry->displayName($option->displayName);
> $att_table->addRow( [ $bentry ] );
> $entry1= $bentry unless($entry1);
> }
>
> ## not working - caller gets only entry1 info; need initialize w/ some of entry info.
> my $blistentry = BioMart::Configuration::BooleanListFilter->new(); #$entry1
> $blistentry->initFromBoolFilter($entry1); # this fixes it
>
> $blistentry->name($entry->name.'_blist'); ## fixme...
> $blistentry->displayName($dnames);
> $blistentry->setTable($att_table);
> if ($value ne 'Only'){ $blistentry->setExcluded; }
> else{ $blistentry->setIncluded; }
> $entry= $blistentry;
> } else { ######
1721a1822
>
1729a1831,1832
> } # dgg
>
1742a1846,1853
>
> ## dgg patch for multilist all values
> if(@debugallvals>1) {
> shift @debugallvals;
> foreach( @debugallvals) { $value .= ','.$_ ; }
> warn "DEBUG.in6: value=$value\n" if DEBUG;
> }
>
1764a1876,1884
>
> ## dgg patch for multilist all values
> my $ismultilist= 0;
> if(@debugallvals>1) {
> shift @debugallvals;
> foreach( @debugallvals) { $value .= ','.$_ ; }
> warn "DEBUG.in7: value=$value\n" if DEBUG; ## this is it
> $ismultilist= 1;
> }
1771,1772c1891,1897
< if ($option && !$nested_option_flag) {
< $value = $option->displayName;# for status panel below
---
>
> if( $ismultilist) { ## dgg
> $value =~ s/,/, /g; #??
> $value = substr($value,0,75)."..." if(length($value)>80);
> }
> if (!$ismultilist && $option && !$nested_option_flag ) {
> $value = $option->displayName;# for status panel below
2502c2627,2629
< my $val = $martview::CGI->param($dataset.'_'.$name);
---
> ## dgg; is below cgi-set wiping out array vals? YES
> my @debugvals= $martview::CGI->param( $dataset.'_'. $name );
> warn("DEBUG.in4 ",$dataset.'_'. $name," vals=",@debugvals,"\n") if DEBUG;
2503a2631,2633
> my $val = $martview::CGI->param($dataset.'_'.$name);
> my $oldval= $val; #dgg
>
2518c2648,2651
< $martview::CGI->param($dataset.'_'.$name, $val);
---
>
> $martview::CGI->param($dataset.'_'.$name, $val)
> unless($oldval eq $val); #dgg; dont wipe out array params !
>
2719c2852
< #warn("UPDATE SELECTION 4 $$");
---
> warn("UPDATE SELECTION 4 $$");
2721c2854
< #warn("UPDATE SELECTION 5 $$");
---
> warn("UPDATE SELECTION 5 $$");
2723c2856
< #warn("UPDATE SELECTION FINISHED $$ \n");
---
> warn("UPDATE SELECTION FINISHED $$ \n");
2808a2942,2947
> ## dgg; patch for flaky mod_perl print
> # local(*TMPOUT);
> # my $tmp_file = $SiteDefs::ENSEMBL_TMP_DIR ."/results.$$";
> # open( TMPOUT, ">$tmp_file" );
> # $fmt_printer_args{-filehandle}= *TMPOUT;
>
2818d2956
<
2827c2965
< print($error);
---
> martview::print($error);
2861a3000,3007
>
> ## dgg patch
> # close(TMPOUT);
> # open( TMPOUT, "$tmp_file" );
> # my $r = Apache->request;
> # $r->send_fd( *TMPOUT);
> # close(TMPOUT); unlink $tmp_file;
>
2879c3025
< print "SQL FAILED - LIKELY XML MISCONFIGURATION ERROR";
---
> martview::print "SQL FAILED - LIKELY XML MISCONFIGURATION ERROR";
3008c3154
< print "SQL FAILED - LIKELY XML MISCONFIGURATION ERROR";
---
> martview::print "SQL FAILED - LIKELY XML MISCONFIGURATION ERROR";
3052c3198
< print "SQL FAILED - LIKELY XML MISCONFIGURATION ERROR";
---
> martview::print "SQL FAILED - LIKELY XML MISCONFIGURATION ERROR";
3113c3259
< print "SQL FAILED - LIKELY XML MISCONFIGURATION ERROR";
---
> martview::print "SQL FAILED - LIKELY XML MISCONFIGURATION ERROR";
3131c3277,3284
< my $header = '>'.join('|',@$row);
---
> my $header = '>'.join('|',@$row);
> ## dgg; this is yucky; want field keys
> ## >ID key=val; key=val; ... from here? or $fields_ref
> # foreach my $field( @$display_ref ){
> # push( @headers, $field."\t" );
> # }
>
>
3331a3485,3491
>
> my @debugallvals= @values;
> # my @debugfilt= $CGI->param( $dataSetName.'_'. $entry->name.'_filter' );
> # my @debuglist= $CGI->param( $dataSetName.'_'. $name.'_list' ); #NOTE $name not entry.name
> warn("DEBUG.in3 ",$dataSetName,'_',$entry->name," vals=@values\n") if DEBUG;
> # warn("DEBUG.in3 _list ",@debuglist," \n");
> # warn("DEBUG.in3 _filters ",@debugfilt," \n");
3371a3532,3541
>
> ## dgg again; all values
> my $ismultilist= 0;
> if(@debugallvals>1) {
> shift @debugallvals;
> foreach( @debugallvals) { $value .= ','.$_ ; }
> warn "DEBUG.in8: value=$value\n" if DEBUG;
> $ismultilist= 1;
> }
>
3391a3562,3596
>
> ## dgg; fixme again same as above
> ## dgg; need patch here? YES for multiselect list
> ## but boolfilter doesnt support multi-list; how to do?
> ## need to query->addFilter( join( ' OR ', @ entries ) );
> my @debug_allopts= $CGI->param( $dataSetName.'_'. $entry->name.'_filter' );
> if(@debug_allopts > 1) {
> ## use BioMart::Configuration::BooleanListFilter; # should be in BioMart::Configurator;
> my $att_table = BioMart::AttributeTable->new();
> my $dnames="";
> my $entry1;
>
> foreach my $oname (@debug_allopts){
> my $option = $ct->getOptionByName($oname);
> next if (!$option);
> $dnames .= $option->displayName.", ";
> my $bentry = $option->filter;
> if ($value ne 'Only'){ $bentry->setExcluded; }
> else{ $bentry->setIncluded; }
> $bentry->displayName($option->displayName);
> $att_table->addRow( [ $bentry ] );
> $entry1= $bentry unless($entry1);
> }
>
> my $blistentry = BioMart::Configuration::BooleanListFilter->new(); #$entry1
> $blistentry->initFromBoolFilter($entry1); # this fixes it
>
> $blistentry->name($entry->name.'_blist'); ## fixme...
> $blistentry->displayName($dnames);
> $blistentry->setTable($att_table);
> if ($value ne 'Only'){ $blistentry->setExcluded; }
> else{ $blistentry->setIncluded; }
> $entry= $blistentry;
> } else { ######
>
3393a3599
>
3396a3603,3610
>
> my $ismultilist= 0;
> if(@debugallvals>1) {
> shift @debugallvals;
> foreach( @debugallvals) { $value .= ','.$_ ; }
> warn "DEBUG.in9: value=$value\n" if DEBUG;
> $ismultilist= 1;
> }
3413a3628
> } ###### end dgg
3450a3666,3673
>
> my $ismultilist= 0;
> if(@debugallvals>1) {
> shift @debugallvals;
> foreach( @debugallvals) { $value .= ','.$_ ; }
> warn "DEBUG.in10: value=$value\n" if DEBUG; ## this is it
> $ismultilist= 1;
> }