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Merge pull request #205 from teharrison/master
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fixed workbench table bug
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@jaredbischof
jaredbischof committed Dec 18, 2012
2 parents 7c87c95 + 3e772ed commit 3bcb85b
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Showing 2 changed files with 39 additions and 29 deletions.
21 changes: 15 additions & 6 deletions src/MGRAST/lib/Analysis.pm
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Expand Up @@ -672,17 +672,26 @@ sub decode_annotation {
} }


sub type_for_md5s { sub type_for_md5s {
my ($self, $md5s) = @_; my ($self, $md5s, $get_id) = @_;


unless ($md5s && @$md5s) { return {}; } unless ($md5s && @$md5s) { return {}; }
my $data = {}; my $data = {};
my $sql = "SELECT md5, is_protein FROM md5s WHERE _id IN (".join(',', @$md5s).")"; my %umd5 = map {$_, 1} @$md5s;
my $rows = $self->_dbh->selectall_arrayref($sql); my $iter = natatime $self->_chunk, keys %umd5;
if ($rows && @$rows) {
map { $data->{$_->[0]} = $_->[1] ? 'protein' : 'rna' } @$rows; while (my @curr = $iter->()) {
my $sql = "SELECT _id, md5, is_protein FROM md5s WHERE _id IN (".join(',', @curr).")";
my $rows = $self->_dbh->selectall_arrayref($sql);
if ($rows && @$rows) {
if ($get_id) {
map { $data->{$_->[0]} = [ $_->[1], $_->[2] ? 'protein' : 'rna' ] } @$rows;
} else {
map { $data->{$_->[1]} = $_->[2] ? 'protein' : 'rna' } @$rows;
}
}
} }
return $data; return $data;
# md5 => 'protein'|'rna' # md5 => 'protein'|'rna' OR _id => [md5, 'protein'|'rna']
} }


sub organisms_for_taxids { sub organisms_for_taxids {
Expand Down
47 changes: 24 additions & 23 deletions src/MGRAST/lib/WebPage/Analysis.pm
View file
Expand Up @@ -1574,7 +1574,7 @@ sub workbench_hits_table {
my $analysis_data = $self->{mgdb}->get_md5_data(\@md5s); my $analysis_data = $self->{mgdb}->get_md5_data(\@md5s);
my $source_info = $self->{mgdb}->_sources; my $source_info = $self->{mgdb}->_sources;
my $ss_map = $has_ss ? $self->{mgdb}->get_hierarchy('ontology', 'Subsystems') : {}; my $ss_map = $has_ss ? $self->{mgdb}->get_hierarchy('ontology', 'Subsystems') : {};
my $md5_type = $has_m5nr ? $self->{mgdb}->type_for_md5s(\@md5s) : {}; my $md5_type = $self->{mgdb}->type_for_md5s(\@md5s, 1); # id => [md5, type]
my $source_data = {}; # md5 => [ source, id, function ] my $source_data = {}; # md5 => [ source, id, function ]
if (@ach_srcs > 0) { if (@ach_srcs > 0) {
map { $source_data->{$_->[1]} = [ @$_[4,0,2] ] } grep { $_->[2] } @{$self->{mgdb}->annotation_for_md5s(\@md5s, \@ach_srcs)}; map { $source_data->{$_->[1]} = [ @$_[4,0,2] ] } grep { $_->[2] } @{$self->{mgdb}->annotation_for_md5s(\@md5s, \@ach_srcs)};
Expand Down Expand Up @@ -1608,26 +1608,27 @@ sub workbench_hits_table {
my @table_data = (); my @table_data = ();
foreach my $row ( @$analysis_data ) { foreach my $row ( @$analysis_data ) {
my ($mg, $md5, $num, $seek, $len) = @$row[0,1,2,9,10]; my ($mg, $md5, $num, $seek, $len) = @$row[0,1,2,9,10];
if (exists $source_data->{$md5}) { my $md5sum = $md5_type->{$md5}[0];
foreach my $set ( sort {($a->[0] cmp $b->[0]) || ($a->[1] cmp $b->[1])} @{$source_data->{$md5}} ) { if (exists $source_data->{$md5sum}) {
if (exists $source_info->{$set->[0]}) { foreach my $set ( sort {($a->[0] cmp $b->[0]) || ($a->[1] cmp $b->[1])} @{$source_data->{$md5sum}} ) {
my $id = exists($ss_map->{$set->[1]}) ? $ss_map->{$set->[1]}[2] : $set->[1]; if (exists $source_info->{$set->[0]}) {
my $type = $source_info->{$set->[0]}{type}; my $id = exists($ss_map->{$set->[1]}) ? $ss_map->{$set->[1]}[2] : $set->[1];
my $idl = $source_info->{$set->[0]}{link} ? "<a target=_blank href='".$source_info->{$set->[0]}{link}.$id."'>".$id."</a>" : $set->[1]; my $type = $source_info->{$set->[0]}{type};
my $readl = $num; my $idl = $source_info->{$set->[0]}{link} ? "<a target=_blank href='".$source_info->{$set->[0]}{link}.$id."'>".$id."</a>" : $set->[1];
if ($type eq 'rna') { my $readl = $num;
$readl = qq~<a style='cursor:pointer' onclick='execute_ajax("get_reads_table", "read_div", "metagenome=$mg&md5=$md5&seek=$seek&length=$len&type=$type");'>$num</a>~; if ($type eq 'rna') {
} else { $readl = qq~<a style='cursor:pointer' onclick='execute_ajax("get_reads_table", "read_div", "metagenome=$mg&md5=$md5sum&seek=$seek&length=$len&type=$type");'>$num</a>~;
$readl = qq~<a style='cursor:pointer' onclick='execute_ajax("get_read_align", "read_div", "metagenome=$mg&md5=$md5&seek=$seek&length=$len&type=$type");'>$num</a>~; } else {
} $readl = qq~<a style='cursor:pointer' onclick='execute_ajax("get_read_align", "read_div", "metagenome=$mg&md5=$md5&seek=$seek&length=$len&type=$type");'>$num</a>~;
push @table_data, [ $mg, $set->[0], $idl, $set->[2], $readl, @$row[3..8], $md5 ]; }
} push @table_data, [ $mg, $set->[0], $idl, $set->[2], $readl, @$row[3..8], $md5sum ];
}
} }
} }
if ($has_m5nr && exists($md5_type->{$md5}) && ($md5_type->{$md5} eq 'protein')) { if ($has_m5nr && ($md5_type->{$md5}[1] eq 'protein')) {
my $md5l = "<a target=_blank href='http://tools.metagenomics.anl.gov/m5nr/?page=SearchResults&search_type=md5&query=$md5'>$md5</a>"; my $md5l = "<a target=_blank href='http://tools.metagenomics.anl.gov/m5nr/?page=SearchResults&search_type=md5&query=$md5sum'>$md5sum</a>";
my $readl = qq~<a style='cursor:pointer' onclick='execute_ajax("get_read_align", "read_div", "metagenome=$mg&md5=$md5&seek=$seek&length=$len&type=protein");'>$num</a>~; my $readl = qq~<a style='cursor:pointer' onclick='execute_ajax("get_read_align", "read_div", "metagenome=$mg&md5=$md5&seek=$seek&length=$len&type=protein");'>$num</a>~;
push @table_data, [ $mg, 'M5NR', $md5l, '', $readl, @$row[3..8], $md5 ]; push @table_data, [ $mg, 'M5NR', $md5l, '', $readl, @$row[3..8], $md5sum ];
} }
} }


Expand Down Expand Up @@ -1748,18 +1749,18 @@ sub get_reads_table {
## ##


if ( @{$sims->{$md5}} > 25 ) { if ( @{$sims->{$md5}} > 25 ) {
$table->show_top_browse(1); $table->show_top_browse(1);
$table->show_bottom_browse(1); $table->show_bottom_browse(1);
$table->items_per_page(25); $table->items_per_page(25);
$table->show_select_items_per_page(1); $table->show_select_items_per_page(1);
} }
$table->show_column_select(1); $table->show_column_select(1);
$table->columns($columns); $table->columns($columns);
$table->data(\@data); $table->data(\@data);
my $reads = scalar( @{$sims->{$md5}} ); my $reads = scalar( @{$sims->{$md5}} );
my $html = "<p>Hit table for $reads read" . (($reads > 1) ? "s" : "") . " within metagenome " . $job->name() . " ($mgid)"; my $html = "<p>Hit table for $reads read" . (($reads > 1) ? "s" : "") . " within metagenome " . $job->name() . " ($mgid)";
if ($type ne 'rna') { if ($type ne 'rna') {
$html .= " against sequence <a target=_blank href='http://tools.metagenomics.anl.gov/m5nr/?page=SearchResults&search_type=md5&query=$md5'>$md5</a>"; $html .= " against sequence <a target=_blank href='http://tools.metagenomics.anl.gov/m5nr/?page=SearchResults&search_type=md5&query=$md5'>$md5</a>";
} }
$html .= "</p>" . $table->output(); $html .= "</p>" . $table->output();


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