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fix bad api m5nr return structure #305

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merged 1 commit into from
May 3, 2013
Merged

fix bad api m5nr return structure #305

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22 changes: 14 additions & 8 deletions src/MGRAST/lib/resources2/m5nr.pm
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Original file line number Diff line number Diff line change
Expand Up @@ -29,16 +29,13 @@ sub new {
['level2', 'ontology level' ],
['level1', 'top ontology level'] ]
};
$self->{attributes} = { taxonomy => { id => [ 'string', 'unique object identifier' ],
data => [ 'list', ['list', 'requested taxonomy levels, from highest to lowest'] ],
$self->{attributes} = { taxonomy => { data => [ 'list', ['list', 'requested taxonomy levels, from highest to lowest'] ],
version => [ 'integer', 'version of the object' ],
url => [ 'uri', 'resource location of this object instance' ] },
ontology => { id => [ 'string', 'unique object identifier' ],
data => [ 'list', ['list', 'requested ontology levels, from highest to lowest'] ],
ontology => { data => [ 'list', ['list', 'requested ontology levels, from highest to lowest'] ],
version => [ 'integer', 'version of the object' ],
url => [ 'uri', 'resource location of this object instance' ] },
sources => { id => [ 'string', 'unique object identifier' ],
data => [ 'hash', [{'key' => ['string', 'source name'],
sources => { data => [ 'hash', [{'key' => ['string', 'source name'],
'value' => ['object', 'source object']}, 'source object hash'] ],
version => [ 'integer', 'version of the object' ],
url => [ 'uri', 'resource location of this object instance' ] }
Expand Down Expand Up @@ -89,7 +86,7 @@ sub info {
'method' => "GET",
'type' => "synchronous",
'attributes' => $self->{attributes}{taxonomy},
'parameters' => { 'options' => { 'min_level' => ['cv', $self->{hierarchy}{taxonomy}],
'parameters' => { 'options' => {
'id_map' => ['boolean', 'if true overrides other options and returns a map { NCBI tax ID: [taxonomy levels] }'],
'min_level' => ['cv', $self->{hierarchy}{taxonomy}],
'parent_name' => ['string', 'name of taxanomy group to retrieve children of']
Expand Down Expand Up @@ -134,13 +131,15 @@ sub static {
unless (ref($mgdb)) {
$self->return_data({"ERROR" => "could not connect to analysis database"}, 500);
}
my $data = [];
my $url = $self->cgi->url.'/m5nr/'.$type;
my $data = [];
my $pname = $self->cgi->param('parent_name') || '';

if ($type eq 'ontology') {
my @ont_hier = map { $_->[0] } @{$self->{hierarchy}{ontology}};
my $source = $self->cgi->param('source') || 'Subsystems';
my $min_lvl = $self->cgi->param('min_level') || 'function';
$url .= '?source='.$source.'&min_level='.$min_lvl;
if ( grep(/^$min_lvl$/, @ont_hier) ) {
if ($min_lvl eq 'function') {
$min_lvl = ($source =~ /^[NC]OG$/) ? 'level3' : 'level4';
Expand All @@ -149,6 +148,7 @@ sub static {
$self->return_data({"ERROR" => "invalid min_level for m5nr/ontology: ".$min_lvl." - valid types are [".join(", ", @ont_hier)."]"}, 500);
}
if ( $self->cgi->param('id_map') ) {
$url .= '&id_map=1';
$data = $mgdb->get_hierarchy('ontology', $source);
} elsif ($pname && ($min_lvl ne 'level1')) {
$data = $mgdb->get_hierarchy_slice('ontology', $source, $pname, $min_lvl);
Expand All @@ -158,12 +158,14 @@ sub static {
} elsif ($type eq 'taxonomy') {
my @tax_hier = map { $_->[0] } @{$self->{hierarchy}{taxonomy}};
my $min_lvl = $self->cgi->param('min_level') || 'species';
$url .= '?min_level='.$min_lvl;
if ( grep(/^$min_lvl$/, @tax_hier) ) {
$min_lvl = 'tax_'.$min_lvl;
} else {
$self->return_data({"ERROR" => "invalid min_level for m5nr/taxonomy: ".$min_lvl." - valid types are [".join(", ", @tax_hier)."]"}, 500);
}
if ( $self->cgi->param('id_map') ) {
$url .= '&id_map=1';
$data = $mgdb->get_hierarchy('organism', undef, 1);
} elsif ($pname && ($min_lvl ne 'tax_domain')) {
$data = $mgdb->get_hierarchy_slice('organism', undef, $pname, $min_lvl);
Expand All @@ -175,6 +177,10 @@ sub static {
delete $data->{GO};
}

my $obj = { data => $data,
version => 1,
url => $url };

# return cached if exists
$self->return_cached();
# cache this!
Expand Down