Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

hotfix back to develop #215

Merged
merged 4 commits into from Dec 20, 2012
Merged

hotfix back to develop #215

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
4 commits
Select commit Hold shift + click to select a range
556d32e
fixed bug in job_delete
Dec 19, 2012
156623a
Merge pull request #213 from teharrison/master
teharrison Dec 20, 2012
c3d9b79
fixed bug in workbench display table
Dec 20, 2012
18ed6d5
Merge pull request #214 from teharrison/master
jaredbischof Dec 20, 2012
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Jump to
Jump to file
Failed to load files.
Diff view
Diff view
28 changes: 18 additions & 10 deletions src/MGRAST/lib/Analysis.pm
View file
Open in desktop
Expand Up @@ -729,7 +729,7 @@ sub delete_job {
my $all = $self->_dbh->selectcol_arrayref("SELECT DISTINCT version FROM job_info WHERE job = ".$job);
eval {
$self->_dbh->do("DELETE FROM job_info WHERE job = ".$job);
foreach my $tbl (keys %{$self->_jtbl}) {
foreach my $tbl (values %{$self->_jtbl}) {
$self->_dbh->do("DELETE FROM $tbl WHERE version IN (".join(",", @$all).") AND job = ".$job);
}
};
Expand Down Expand Up @@ -1599,10 +1599,14 @@ sub get_md5_data {

my $data = {};
my $jobs = [];
while ( my ($mg, $j) = each %{$self->_job_map} ) {
my $c = $self->_memd->get($mg.$cache_key);
if ($c) { $data->{$mg} = $c; }
else { push @$jobs, $j; }
if ($md5s && (@$md5s > 0)) {
$jobs = $self->_jobs;
} else {
while ( my ($mg, $j) = each %{$self->_job_map} ) {
my $c = $self->_memd->get($mg.$cache_key);
if ($c) { $data->{$mg} = $c; }
else { push @$jobs, $j; }
}
}
unless (@$jobs) { return [ map { @$_ } values %$data ]; }

Expand All @@ -1611,7 +1615,7 @@ sub get_md5_data {
$alen = (defined($alen) && ($alen =~ /^\d+$/)) ? "j.len_avg >= $alen" : "";

my %umd5s = ($md5s && (@$md5s > 0)) ? map {$_, 1} @$md5s : {};
my $qmd5s = ($md5s && (@$md5s > 0)) ? "j.md5 IN (" . join(",", map {"'$_'"} keys %umd5s) . ")" : "";
my $qmd5s = ($md5s && (@$md5s > 0)) ? "j.md5 IN (" . join(",", keys %umd5s) . ")" : "";
my $qseek = $ignore_sk ? "" : "j.seek IS NOT NULL AND j.length IS NOT NULL";
my $qrep = $rep_org_src ? "j.md5=r.md5 AND r.source=".$self->_src_id->{$rep_org_src} : "";
my $where = $self->_get_where_str(['j.'.$self->_qver, "j.job IN (".join(",", @$jobs).")", $qrep, $qmd5s, $eval, $ident, $alen, $qseek]);
Expand Down Expand Up @@ -1643,10 +1647,14 @@ sub get_md5_abundance {

my $data = {};
my $jobs = [];
while ( my ($mg, $j) = each %{$self->_job_map} ) {
my $c = $self->_memd->get($mg.$cache_key);
if ($c) { $data->{$mg} = $c; }
else { push @$jobs, $j; }
if ($md5s && (@$md5s > 0)) {
$jobs = $self->_jobs;
} else {
while ( my ($mg, $j) = each %{$self->_job_map} ) {
my $c = $self->_memd->get($mg.$cache_key);
if ($c) { $data->{$mg} = $c; }
else { push @$jobs, $j; }
}
}
unless (@$jobs) { return $data; }

Expand Down
4 changes: 2 additions & 2 deletions src/MGRAST/lib/WebPage/Analysis.pm
View file
Open in desktop
Expand Up @@ -1577,7 +1577,7 @@ sub workbench_hits_table {
my $md5_type = $self->{mgdb}->type_for_md5s(\@md5s, 1); # id => [md5, type]
my $source_data = {}; # md5 => [ source, id, function ]
if (@ach_srcs > 0) {
map { $source_data->{$_->[1]} = [ @$_[4,0,2] ] } grep { $_->[2] } @{$self->{mgdb}->annotation_for_md5s(\@md5s, \@ach_srcs)};
map { push @{$source_data->{$_->[1]}}, [ @$_[4,0,2] ] } grep { $_->[2] } @{$self->{mgdb}->annotation_for_md5s(\@md5s, \@ach_srcs)};
}

my $html = "<p>Hits for " . scalar(@md5s) . " unique sequences within ";
Expand All @@ -1604,7 +1604,7 @@ sub workbench_hits_table {
$html .= "source ".$srcs[0];
}
$html .= "</p>";

my @table_data = ();
foreach my $row ( @$analysis_data ) {
my ($mg, $md5, $num, $seek, $len) = @$row[0,1,2,9,10];
Expand Down