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fixes / updates to api2 #123

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merged 3 commits into from Oct 4, 2012
Merged

fixes / updates to api2 #123

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4e5976c
fixed typos
Oct 4, 2012
dbc9414
fixed typos in links, added project as id / url tuple
Oct 4, 2012
513f41d
make return data consistant with attributes in info
Oct 4, 2012
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2 changes: 1 addition & 1 deletion src/MGRAST/lib/resources2/library.pm
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Expand Up @@ -248,7 +248,7 @@ sub check_pagination {
next if ($param eq 'offset');
$additional_params .= $param."=".$cgi->param($param)."&";
}
if (length($additional_params) {
if (length($additional_params)) {
chop $additional_params;
}
my $prev_offset = $offset - $limit;
Expand Down
39 changes: 13 additions & 26 deletions src/MGRAST/lib/resources2/metagenome.pm
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Expand Up @@ -108,10 +108,9 @@ sub attributes {
return { "id" => [ 'string', 'unique object identifier' ],
"name" => [ 'string', 'human readable identifier' ],
"sequence_type" => [ 'string', 'sequencing type' ],
"file_size" => [ 'integer', 'sequence file size in bytes' ],
"library" => [ 'reference library', 'reference to the related library object' ],
"sample" => [ 'reference sample', 'reference to the related sample object' ],
"primary_project" => [ 'reference project', 'reference to the primary project object' ],
"project" => [ 'reference project', 'reference to the project object' ],
"metadata" => [ 'hash', 'key value pairs describing metadata' ],
"created" => [ 'date', 'time the object was first created' ],
"version" => [ 'integer', 'version of the object' ],
Expand Down Expand Up @@ -194,37 +193,25 @@ sub prepare_data {
my $objects = [];
foreach my $job (@$data) {
my $obj = {};
$obj->{id} = "mgm".$job->{metagenome_id};
$obj->{name} = $job->{name};
$obj->{url} = $cgi->url.'/metagenome/'.$obj->{id};
$obj->{created} = $job->{created_on};
$obj->{id} = "mgm".$job->{metagenome_id};
$obj->{name} = $job->{name};
$obj->{url} = $cgi->url.'/metagenome/'.$obj->{id};
$obj->{created} = $job->{created_on};

if ($cgi->param('verbosity')) {
if ($cgi->param('verbosity') eq 'full') {
$obj->{metadata} = $jobdata->{$job->{metagenome_id}};
$obj->{metadata} = $jobdata->{$job->{metagenome_id}};
}
if ($cgi->param('verbosity') eq 'verbose' || $cgi->param('verbosity') eq 'full') {
if ($jobdata->{$job->{metagenome_id}}) {
if ($jobdata->{$job->{metagenome_id}}->{project}) {
$obj->{project_name} = $jobdata->{$job->{metagenome_id}}->{project}->{name} || "";
if ($jobdata->{$job->{metagenome_id}}->{project}->{data}) {

$obj->{PI} = ($jobdata->{$job->{metagenome_id}}->{project}->{data}->{PI_firstname} || "")." ".($jobdata->{$job->{metagenome_id}}->{project}->{data}->{PI_lastname} || "");
}
}
if ($jobdata->{$job->{metagenome_id}}->{sample} && $jobdata->{$job->{metagenome_id}}->{sample}->{data}) {
$obj->{country} = $jobdata->{$job->{metagenome_id}}->{sample}->{data}->{country} || "";
$obj->{biome} = $jobdata->{$job->{metagenome_id}}->{sample}->{data}->{biome} || "";
$obj->{location} = $jobdata->{$job->{metagenome_id}}->{sample}->{data}->{location} || "";
}
}
$obj->{sample} = $job->{sample} ? [ "mgs".$job->sample->ID, $cgi->url."sample/mgs".$job->sample->ID ] : undef;
$obj->{library} = $job->{library} ? [ "mgl".$job->library->ID, $cgi->url."/library/mgl".$job->library->ID ] : undef;
$obj->{version} = 1;
$obj->{sequence_type} = $job->{sequence_type};
$obj->{project} = $job->{primary_project} ? [ "mgp".$job->primary_project->id, $cgi->url."/project/mgp".$job->primary_project->id ] : undef;
$obj->{sample} = $job->{sample} ? [ "mgs".$job->sample->ID, $cgi->url."/sample/mgs".$job->sample->ID ] : undef;
$obj->{library} = $job->{library} ? [ "mgl".$job->library->ID, $cgi->url."/library/mgl".$job->library->ID ] : undef;
} elsif ($cgi->param('verbosity') ne 'minimal') {
return_data({ "ERROR" => "invalid value for option verbosity", 400);
return_data({ "ERROR" => "invalid value for option verbosity" }, 400);
}
}

push(@$objects, $obj);
}

Expand Down Expand Up @@ -262,7 +249,7 @@ sub check_pagination {
next if ($param eq 'offset');
$additional_params .= $param."=".$cgi->param($param)."&";
}
if (length($additional_params) {
if (length($additional_params)) {
chop $additional_params;
}
my $prev_offset = $offset - $limit;
Expand Down
2 changes: 1 addition & 1 deletion src/MGRAST/lib/resources2/project.pm
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Expand Up @@ -251,7 +251,7 @@ sub check_pagination {
next if ($param eq 'offset');
$additional_params .= $param."=".$cgi->param($param)."&";
}
if (length($additional_params) {
if (length($additional_params)) {
chop $additional_params;
}
my $prev_offset = $offset - $limit;
Expand Down
2 changes: 1 addition & 1 deletion src/MGRAST/lib/resources2/sample.pm
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Expand Up @@ -250,7 +250,7 @@ sub check_pagination {
next if ($param eq 'offset');
$additional_params .= $param."=".$cgi->param($param)."&";
}
if (length($additional_params) {
if (length($additional_params)) {
chop $additional_params;
}
my $prev_offset = $offset - $limit;
Expand Down
2 changes: 1 addition & 1 deletion src/MGRAST/lib/resources2/sequences.pm
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Expand Up @@ -230,7 +230,7 @@ sub check_pagination {
next if ($param eq 'offset');
$additional_params .= $param."=".$cgi->param($param)."&";
}
if (length($additional_params) {
if (length($additional_params)) {
chop $additional_params;
}
my $prev_offset = $offset - $limit;
Expand Down
2 changes: 1 addition & 1 deletion src/MGRAST/lib/resources2/sequenceset.pm
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Expand Up @@ -259,7 +259,7 @@ sub check_pagination {
next if ($param eq 'offset');
$additional_params .= $param."=".$cgi->param($param)."&";
}
if (length($additional_params) {
if (length($additional_params)) {
chop $additional_params;
}
my $prev_offset = $offset - $limit;
Expand Down