lib/CXGN/NOAANCDC.pm

   1
   2 =head1 NAME
   3
   4 CXGN::NOAANCDC - helper class for getting weather data from NOAA NCDC weather stations
   5
   6 =head1 SYNOPSYS
   7
   8 my $noaa = CXGN::NOAANCDC->new({
   9     bcs_schema => $schema,
  10     data_types => ['TMIN', 'TMAX', 'PRCP'],
  11     start_date => "2019-01-13", #YYYY-MM-DD
  12     end_date => "2019-12-19", #YYYY-MM-DD
  13     noaa_station_id => "GHCND:US1NCBC0005",
  14     noaa_ncdc_access_token => $noaa_ncdc_access_token
  15 });
  16 my $temperature_averaged_growing_degree_days = $noaa->get_temperature_averaged_gdd($gdd_base_temperature);
  17
  18 # Musgrave stationid = GHCND:USC00300331
  19
  20 # Datatypes:
  21 # PRCP Total Precipitation (+Musgrave)
  22 # F2MN Faster 2 minute wind speed (-Musgrave)
  23 # TMAX Maximum Temperature (+Musgrave)
  24 # TMIN Minimum Temperature (+Musgrave)
  25 # TOBS Temperatue at observation time (+Musgrave)
  26 # TAVG Average Temperature (-Musgrave)
  27 # F5SC Fastest 5 second wind speed (-Musgrave)
  28 # AWND Average Wind Speed (-Musgrave)
  29 # FSMI Fastest Mile (ddfff) (-Musgrave)
  30 # FSMN Fastest One-minute Wind (ddfff) (-Musgrave)
  31 # PRES Station Pressure (-Musgrave)
  32 # RWND Resultant Wind Speed (-Musgrave)
  33 # SLVP Sea Level Pressure (-Musgrave)
  34 # TMPW Wet Bulb Temperature (-Musgrave)
  35 # FSIN Fastest Instantaneous Wind (ddfff) (-Musgrave)
  36 # WDMV 24_hour Wind Movement (-Musgrave)
  37 # MNTP Average Temperature (-Musgrave)
  38 # DPTP Dew Point Temperature (-Musgrave)
  39
  40 =head1 AUTHOR
  41
  42 Nicolas Morales <nm529@cornell.edu>
  43
  44 =head1 METHODS
  45
  46 =cut
  47
  48 package CXGN::NOAANCDC;
  49
  50 use Moose;
  51 use Data::Dumper;
  52 use Try::Tiny;
  53 use SGN::Model::Cvterm;
  54 use LWP::UserAgent;
  55 use JSON;
  56 use Math::Round;
  57
  58 has 'bcs_schema' => (
  59     isa => 'Bio::Chado::Schema',
  60     is => 'rw',
  61     required => 1
  62 );
  63
  64 has 'data_types' => (
  65     isa => 'ArrayRef',
  66     is => 'rw',
  67 );
  68
  69 has 'start_date' => (
  70     isa => 'Str',
  71     is => 'rw',
  72     required => 1
  73 );
  74
  75 has 'end_date' => (
  76         isa => 'Str',
  77         is => 'rw',
  78     required => 1
  79 );
  80
  81 has 'noaa_station_id' => (
  82     isa => 'Str',
  83         is => 'rw',
  84     required => 1
  85 );
  86
  87 has 'noaa_ncdc_access_token' => (
  88     isa => 'Str',
  89         is => 'rw',
  90     required => 1
  91 );
  92
  93 sub get_noaa_data {
  94     my $self = shift;
  95
  96     my $data_types_string = '&datatypeid=';
  97     $data_types_string .= join '&datatypeid=', @{$self->data_types};
  98
  99     my $ua = LWP::UserAgent->new(
 100         ssl_opts => { verify_hostname => 0 }
 101     );
 102     my $server_endpoint = "https://www.ncdc.noaa.gov/cdo-web/api/v2/data?stationid=".$self->noaa_station_id."&limit=1000&datasetid=GHCND".$data_types_string."&startdate=".$self->start_date."&enddate=".$self->end_date;
 103
 104     print STDERR $server_endpoint."\n";
 105     my $resp = $ua->get($server_endpoint, "token"=>$self->noaa_ncdc_access_token);
 106
 107     my $message_hash = {};
 108     if ($resp->is_success) {
 109         my $message = $resp->decoded_content;
 110         $message_hash = decode_json $message;
 111         # print STDERR Dumper $message_hash;
 112     }
 113     else {
 114         print STDERR Dumper $resp;
 115     }
 116     return $message_hash;
 117 }
 118
 119 sub get_temperature_averaged_gdd {
 120     my $self = shift;
 121     my $gdd_base_temperature = shift || '50'; #For Maize use 50
 122     my $result = 0;
 123
 124     $self->data_types(['TMIN','TMAX']);
 125
 126     my $message_hash = $self->get_noaa_data();
 127
 128     my %weather_hash;
 129     foreach (@{$message_hash->{results}}) {
 130         $weather_hash{$_->{date}}->{$_->{datatype}} = $_->{value};
 131     }
 132     foreach (values %weather_hash) {
 133         if (defined($_->{TMIN}) & defined($_->{TMAX})) {
 134             #TMAX and TMIN are in tenths of C
 135             my $tmax_f = (9/5)*($_->{TMAX}/10) + 32;
 136             my $tmin_f = (9/5)*($_->{TMIN}/10) + 32;
 137             my $gdd_accumulation = (($tmax_f + $tmin_f)/2) - $gdd_base_temperature;
 138             if ($gdd_accumulation > 0) {
 139                 $result = $result + $gdd_accumulation;
 140             }
 141         }
 142     }
 143
 144     return round($result);
 145 }
 146
 147 sub get_averaged_precipitation {
 148     my $self = shift;
 149     my $result = 0;
 150
 151     $self->data_types(['PRCP']);
 152
 153     my $message_hash = $self->get_noaa_data();
 154
 155     my %weather_hash;
 156     foreach (@{$message_hash->{results}}) {
 157         $weather_hash{$_->{date}}->{$_->{datatype}} = $_->{value};
 158     }
 159     foreach (values %weather_hash) {
 160         if (defined($_->{PRCP})) {
 161             $result = $result + $_->{PRCP};
 162         }
 163     }
 164
 165     return $result;
 166 }
 167
 168 1;
 169