Skip to content

Commit

Permalink
Merge pull request #69 from teharrison/develop
Browse files Browse the repository at this point in the history 
abundance_profile api update
  • Loading branch information
@wilke
wilke committed Jul 24, 2012
2 parents 0143ae9 + b343487 commit 0103395
Show file tree
Hide file tree
Showing 2 changed files with 109 additions and 103 deletions.
48 changes: 30 additions & 18 deletions src/Babel/lib/Babel.pm
View file
Expand Up @@ -212,13 +212,13 @@ sub md5s2organisms_unique {
my ($self, $md5s, $source) = @_;

my $data = {};
my $size = 35000;
my $size = 10000;
my $iter = natatime $size, @$md5s;

while (my @curr = $iter->()) {
my $list = join(",", map {$self->dbh->quote($_)} @curr);
my $statement = "select md5, organism from md5_organism_unique where md5 in ($list) and source = ".$self->dbh->quote($source);
my $rows = $self->dbh->selectall_arrayref($statement);
my $sql = "select md5, organism from md5_organism_unique where md5 in ($list) and source = ".$self->dbh->quote($source);
my $rows = $self->dbh->selectall_arrayref($sql);
if ($rows && (@$rows > 0)) {
map { $data->{$_->[0]} = $_->[1] } @$rows;
}
Expand Down Expand Up @@ -254,27 +254,29 @@ sub md52id4source {
sub md5s2ids4source {
my ($self, $md5s, $source) = @_;

my $srcs = $self->sources;
unless (ref($md5s) && (scalar @$md5s) && $source) {
return [];
}

my $sql = '';
my $srcs = $self->sources;

if ($srcs->{$source} && ($srcs->{$source}{type} =~ /^(protein|rna|ontology)$/)) {
$sql = "select d.id, d.md5 from md5_".$srcs->{$source}{type}." d, sources s where d.source = s._id and s.name = '$source'";
}
else {
unless ($srcs->{$source} && ($srcs->{$source}{type} =~ /^(protein|rna|ontology)$/)) {
return [];
}
if (@$md5s == 1) {
$sql .= " and d.md5 = " . $self->dbh->quote($md5s->[0]);
} else {
$sql .= " and d.md5 in (" . join(",", map {$self->dbh->quote($_)} @$md5s) . ")";

my $sid = $srcs->{$source}{_id};
my $data = [];
my $size = 10000;
my $iter = natatime $size, @$md5s;

while (my @curr = $iter->()) {
my $list = join(",", map {$self->dbh->quote($_)} @curr);
my $sql = "select id, md5 from md5_".$srcs->{$source}{type}." where md5 in ($list) and source = $sid";
my $rows = $self->dbh->selectall_arrayref($sql);
if ($rows && (@$rows > 0)) {
push @$data, @$rows;
}
}

my $rows = $self->dbh->selectall_arrayref($sql);
return ($rows && (@$rows > 0)) ? $rows : [];
return $data;
# [ id, md5 ]
}

sub md5s2sets4source {
Expand Down Expand Up @@ -754,6 +756,16 @@ sub get_organism_tax_id {
return ($rows && (@$rows > 0)) ? $rows->[0] : 0;
}

sub map_organism_tax_id {
my ($self) = @_;
my $data = {};
my $rows = $self->dbh->selectall_arrayref("SELECT name, ncbi_tax_id FROM organisms_ncbi");
if ($rows && (@$rows > 0)) {
%$data = map { $_->[0], $_->[1] } grep { $_->[1] } @$rows;
}
return $data;
}

sub get_taxonomy4level {
my ($self, $level) = @_;

Expand Down
164 changes: 79 additions & 85 deletions src/MGRAST/lib/resources/abundance_profile.pm
View file
Expand Up @@ -16,12 +16,15 @@ sub about {
my $ach = new Babel::lib::Babel;
my $content = { 'description' => "metagenomic abundance profile",
'parameters' => { "id" => "string",
"type" => [ "organism", "function" ],
"source" => { "protein" => [ 'm5nr', map {$_->[0]} @{$ach->get_protein_sources} ],
"type" => [ "organism", "function", "feature" ],
"source" => { "protein" => [ 'M5NR', map {$_->[0]} @{$ach->get_protein_sources} ],
"ontology" => [ map {$_->[0]} @{$ach->get_ontology_sources} ],
"rna" => [ 'm5rna', map {$_->[0]} @{$ach->get_rna_sources} ]
"rna" => [ 'M5RNA', map {$_->[0]} @{$ach->get_rna_sources} ]
}
},
'defaults' => { "source" => "M5NR (organism), or Subsystems (function), or RefSeq (feature)",
"type" => "organism"
},
'return_type' => "application/json" };

print $cgi->header(-type => 'application/json',
Expand All @@ -42,6 +45,14 @@ sub request {
exit 0;
}

if (scalar(@$rest) && $rest->[0] eq 'available_sources') {
print $cgi->header(-type => 'application/json',
-status => 200,
-Access_Control_Allow_Origin => '*' );
print $json->encode($mgdb->get_sources);
exit 0;
}

if ($error) {
print $cgi->header(-type => 'text/plain',
-status => 500,
Expand Down Expand Up @@ -92,16 +103,9 @@ sub request {
$params->{$key} = $value;
}

my $source = 'M5NR';
if ($params->{source}) {
$source = $params->{source};
} elsif ($cgi->param('source')) {
$source = $cgi->param('source');
}

if ($cgi->param('type')) {
$params->{type} = $cgi->param('type');
}
$params->{type} = $cgi->param('type') ? $cgi->param('type') : 'organism';
$params->{source} = $cgi->param('source') ? $cgi->param('source') :
(($params->{type} eq 'organism') ? 'M5NR' : (($params->{type} eq 'function') ? 'Subsystems': 'RefSeq'));

my $mgdb = MGRAST::Analysis->new( $master->db_handle );
unless (ref($mgdb)) {
Expand All @@ -113,97 +117,82 @@ sub request {
}
$mgdb->set_jobs([$id]);

my $ach = new Babel::lib::Babel;
unless (ref($ach)) {
my $all_srcs = $mgdb->ach->sources();
unless (exists $all_srcs->{ $params->{source} }) {
print $cgi->header(-type => 'text/plain',
-status => 500,
-Access_Control_Allow_Origin => '*' );
print "ERROR: Could not access ontology database";
exit 0;
}
if (scalar(@$rest) && $rest->[0] eq 'available_sources') {
print $cgi->header(-type => 'application/json',
-status => 200,
-status => 400,
-Access_Control_Allow_Origin => '*' );
print $json->encode($mgdb->get_sources);
print "ERROR: Invalid source for profile call: ".$params->{source}." - valid types are [".join(",", keys %$all_srcs)."]";
exit 0;
}

my $data;
if (! $params->{type} || ($params->{type} && $params->{type} eq 'organism')) {
my $strain2tax = {};
my $dbh = $ach->dbh;
my $rows = $dbh->selectall_arrayref("select name, ncbi_tax_id from organisms_ncbi");
%$strain2tax = map { $_->[0] => $_->[1] } @$rows;

my ($md5_abund, $result) = $mgdb->get_organisms_for_sources([$source]);
my $values = [];
my $rows = [];
my $ttype = '';
my $columns = [ { id => 'abundance', metadata => { metagenome => 'mgm'.$id } },
{ id => 'e-value', metadata => { metagenome => 'mgm'.$id } },
{ id => 'percent identity', metadata => { metagenome => 'mgm'.$id } },
{ id => 'alignment length', metadata => { metagenome => 'mgm'.$id } }
];

if ($params->{type} eq 'organism') {
$ttype = 'Taxon';
my $strain2tax = $mgdb->ach->map_organism_tax_id();
my ($md5_abund, $result) = $mgdb->get_organisms_for_sources([$params->{source}]);
# mgid, source, tax_domain, tax_phylum, tax_class, tax_order, tax_family, tax_genus, tax_species, name, abundance, sub_abundance, exp_avg, exp_stdv, ident_avg, ident_stdv, len_avg, len_stdv, md5s

my ($sec,$min,$hour,$mday,$mon,$year,$wday,$yday,$isdst) = localtime(time);

my $values = [];
my $tax = [];
foreach my $row (@$result) {
if (! $strain2tax->{$row->[9]}) {
next;
}
next unless (exists $strain2tax->{$row->[9]});
my $tax_str = [ "k__".$row->[2], "p__".$row->[3], "c__".$row->[4], "o__".$row->[5], "f__".$row->[6], "g__".$row->[7], "s__".$row->[9] ];
push(@$tax, { "id" => $strain2tax->{$row->[9]}, "metadata" => { "taxonomy" => $tax_str } });
push(@$values, [ int($row->[10]) ]);
push(@$rows, { "id" => $strain2tax->{$row->[9]}, "metadata" => { "taxonomy" => $tax_str } });
push(@$values, [ toFloat($row->[10]), toFloat($row->[12]), toFloat($row->[14]), toFloat($row->[16]) ]);
}

$data = { "id" => "mgm".$id,
"format" => "Biological Observation Matrix 0.9.1",
"format_url" => "http://biom-format.org",
"type" => "Taxon table",
"generated_by" => "MG-RAST revision ".$Conf::server_version,
"date" => strftime("%Y-%m-%dT%H:%M:%S", localtime),
"matrix_type" => "dense",
"matrix_element_type" => "int",
"shape" => [ scalar(@$values), 1 ],
"rows" => $tax,
"columns" => [ { "id" => $id, "metadata" => undef } ],
"data" => $values };

} elsif ($params->{type} && $params->{type} eq 'function') {

my $function2ont = $ach->get_all_ontology4source_hash($source);
my ($md5_abund, $result) = $mgdb->get_ontology_for_source($source);
}
elsif ($params->{type} eq 'function') {
$ttype = 'Function';
my $function2ont = $mgdb->ach->get_all_ontology4source_hash($params->{source});
my ($md5_abund, $result) = $mgdb->get_ontology_for_source($params->{source});
# mgid, id, annotation, abundance, sub_abundance, exp_avg, exp_stdv, ident_avg, ident_stdv, len_avg, len_stdv, md5s

my ($sec,$min,$hour,$mday,$mon,$year,$wday,$yday,$isdst) = localtime(time);

my $values = [];
my $numrows = scalar(@$result);
my $ont = [];
foreach my $row (@$result) {
next unless ($function2ont->{$row->[1]});
next unless (exists $function2ont->{$row->[1]});
my $ont_str = [ map { defined($_) ? $_ : '-' } @{$function2ont->{$row->[1]}} ];
push(@$ont, { "id" => $row->[1], "metadata" => { "ontology" => $ont_str } });
push(@$values, [ int($row->[3]) ]);
push(@$rows, { "id" => $row->[1], "metadata" => { "ontology" => $ont_str } });
push(@$values, [ toFloat($row->[3]), toFloat($row->[5]), toFloat($row->[7]), toFloat($row->[9]) ]);
}
$data = { "id" => "mgm".$id,
"format" => "Biological Observation Matrix 0.9.1",
"format_url" => "http://biom-format.org",
"type" => "Function table",
"generated_by" => "MG-RAST revision ".$Conf::server_version,
"date" => strftime("%Y-%m-%dT%H:%M:%S", localtime),
"matrix_type" => "dense",
"matrix_element_type" => "int",
"shape" => [ scalar(@$values), 1 ],
"rows" => $ont,
"columns" => [ { "id" => $id, "metadata" => undef } ],
"data" => $values };

} else {
}
elsif ($params->{type} eq 'feature') {
$ttype = 'Gene';
my $md52id = {};
my $result = $mgdb->get_md5_data(undef, undef, undef, undef, 1);
# mgid, md5, abundance, exp_avg, exp_stdv, ident_avg, ident_stdv, len_avg, len_stdv, seek, length
my @md5s = map { $_->[1] } @$result;
map { push @{$md52id->{$_->[1]}}, $_->[0] } @{ $mgdb->ach->md5s2ids4source(\@md5s, $params->{source}) };
foreach my $row (@$result) {
next unless (exists $md52id->{$row->[1]});
push(@$rows, { "id" => $row->[1], "metadata" => { $params->{source}." ID" => $md52id->{$row->[1]} } });
push(@$values, [ toFloat($row->[2]), toFloat($row->[3]), toFloat($row->[5]), toFloat($row->[7]) ]);
}
}
else {
print $cgi->header(-type => 'text/plain',
-status => 400,
-Access_Control_Allow_Origin => '*' );
print "ERROR: Invalid type for profile call: ".$params->{type}." - valid types are [ 'organism', 'function' ]";
print "ERROR: Invalid type for profile call: ".$params->{type}." - valid types are [ 'organism', 'function', 'feature' ]";
exit 0;
}

my $data = { "id" => "mgm".$id,
"format" => "Biological Observation Matrix 1.0",
"format_url" => "http://biom-format.org",
"type" => $ttype." table",
"generated_by" => "MG-RAST revision ".$Conf::server_version,
"date" => strftime("%Y-%m-%dT%H:%M:%S", localtime),
"matrix_type" => "dense",
"matrix_element_type" => "float",
"shape" => [ scalar(@$values), 4 ],
"rows" => $rows,
"columns" => $columns,
"data" => $values };

print $cgi->header(-type => 'application/json',
-status => 200,
-Access_Control_Allow_Origin => '*' );
Expand All @@ -212,6 +201,11 @@ sub request {

}

sub toFloat {
my ($x) = @_;
return $x * 1.0;
}

sub TO_JSON { return { %{ shift() } }; }

1;

0 comments on commit 0103395

Please sign in to comment.