bin/find_and_load_longitude_latitude.pl

   1 #!/usr/bin/perl
   2
   3 =head1
   4
   5 find_and_load_longitude_latitude.pl - find long/lat, altitude, country_name, country_code, and program for locations in cxgn databases. optionally can directly update or create the found props in the database
   6
   7 =head1 SYNOPSIS
   8
   9     find_and_load_longitude_latitude.pl -H localhost -D cxgn -O outfile.tsv -s
  10
  11 =head1 COMMAND-LINE OPTIONS
  12   ARGUMENTS
  13   -H localhost
  14   -D database
  15   -O outfile.csv
  16   -s save found props that don't have exisiting values in the database
  17
  18 =head1 DESCRIPTION
  19
  20
  21 =head1 AUTHOR
  22
  23 Nicolas Morales nm529@cornell.edu
  24
  25 =cut
  26
  27 use strict;
  28
  29 use Getopt::Std;
  30 use Data::Dumper;
  31 use Carp qw /croak/ ;
  32 use Pod::Usage;
  33 use Spreadsheet::ParseExcel;
  34 use Bio::Chado::Schema;
  35 use CXGN::DB::InsertDBH;
  36 use CXGN::BreedersToolbox::Projects;
  37 use CXGN::Location;
  38 use LWP::UserAgent;
  39 use Encode       qw( encode );
  40 use JSON;
  41 use SGN::Model::Cvterm;
  42
  43 our ($opt_H, $opt_D, $opt_O, $opt_s);
  44
  45 getopts('H:D:O:s');
  46
  47 if (!$opt_H || !$opt_D || !$opt_O) {
  48     pod2usage(-verbose => 2, -message => "Must provide options -H, -D, and -O \n");
  49 }
  50
  51 my $dbhost = $opt_H;
  52 my $dbname = $opt_D;
  53
  54 my $dbh = CXGN::DB::InsertDBH->new({
  55         dbhost=>$dbhost,
  56         dbname=>$dbname,
  57         dbargs => {AutoCommit => 1, RaiseError => 1}
  58 });
  59
  60 my $schema= Bio::Chado::Schema->connect(  sub { $dbh->get_actual_dbh() } );
  61 $dbh->do('SET search_path TO public,sgn');
  62
  63 open(my $F, ">", $opt_O) || die "Can't open file ".$opt_O;
  64
  65 # print STDERR "LocationName\tLongitudeInDB\tLatitudeInDB\tAltitudeInDB\tCountry\tCountryCode\tProgram\tFoundLongitude\tFoundLatitude\tFoundAltitude\tFoundCountry\tFoundCountryCode\tFoundProgram\n";
  66
  67 print $F "LocationName\tLongitudeInDB\tLatitudeInDB\tAltitudeInDB\tCountry\tCountryCode\tProgram\tFoundLongitude\tFoundLatitude\tFoundAltitude\tFoundCountry\tFoundCountryCode\tFoundProgram\n";
  68
  69 my $program_trial_relationship_id = SGN::Model::Cvterm->get_cvterm_row($schema, "breeding_program_trial_relationship", "project_relationship")->cvterm_id();
  70 my $project_location_cvterm_id = SGN::Model::Cvterm->get_cvterm_row($schema, "project location", "project_property")->cvterm_id();
  71
  72 my $project_object = CXGN::BreedersToolbox::Projects->new( { schema => $schema });
  73 my $all_locations = decode_json $project_object->get_location_geojson();
  74
  75 foreach my $location_hash (@$all_locations) {
  76
  77     my $location = $location_hash->{'properties'};
  78     my $name = $location->{'Name'};
  79     my $id = $location->{'Id'};
  80     my ($longitude, $latitude, $altitude, $country_name, $country_code, $program);
  81     my ($found_latitude, $found_longitude, $found_altitude, $found_country_name, $found_country_code, $found_program);
  82
  83     #retrieve coordinates from name
  84     $name =~ s/\s/+/g;
  85     my $server_endpoint1 = "http://maps.googleapis.com/maps/api/geocode/json?address=$name";
  86     my $req = HTTP::Request->new(GET => $server_endpoint1);
  87     $req->header('content-type' => 'application/json');
  88     my $ua = LWP::UserAgent->new;
  89     my $resp = $ua->request($req);
  90     if ($resp->is_success) {
  91         my $message = $resp->decoded_content;
  92         my $json_utf8 = encode('UTF-8', $message);
  93         my $message_hash = decode_json $json_utf8;
  94         my $location = $message_hash->{'results'}->[0]->{'geometry'}->{'location'};
  95         $found_latitude = $location->{'lat'};
  96         $found_longitude = $location->{'lng'};
  97         $latitude = $location_hash->{'properties'}->{'Latitude'} || $found_latitude;
  98         $longitude = $location_hash->{'properties'}->{'Longitude'} || $found_longitude;
  99     }
 100
 101     #retrieve altitude from coordinates
 102     my $server_endpoint2 = "http://www.datasciencetoolkit.org/coordinates2statistics/$latitude%2c$longitude?statistics=elevation";
 103     $req = HTTP::Request->new(GET => $server_endpoint2);
 104     $req->header('content-type' => 'application/json');
 105     $ua = LWP::UserAgent->new;
 106     $resp = $ua->request($req);
 107     if ($resp->is_success) {
 108         my $message = $resp->decoded_content;
 109         my $json_utf8 = encode('UTF-8', $message);
 110         my $message_hash = decode_json $json_utf8;
 111         $found_altitude = $message_hash->[0]->{'statistics'}->{'elevation'}->{'value'};
 112         $altitude = $location->{'Altitude'} || $found_altitude;
 113     }
 114
 115     #retrieve country code and name from coordinates
 116     my $server_endpoint3 = "http://www.datasciencetoolkit.org/coordinates2politics/$latitude%2c$longitude?";
 117     $req = HTTP::Request->new(GET => $server_endpoint3);
 118     $req->header('content-type' => 'application/json');
 119     $ua = LWP::UserAgent->new;
 120     $resp = $ua->request($req);
 121     if ($resp->is_success) {
 122         my $message = $resp->decoded_content;
 123         my $json_utf8 = encode('UTF-8', $message);
 124         my $message_hash = decode_json $json_utf8;
 125         $found_country_name = $message_hash->[0]->{'politics'}->[0]->{'name'};
 126         $found_country_code = uc($message_hash->[0]->{'politics'}->[0]->{'code'});
 127         $country_name = $location->{'Country'} || $found_country_name;
 128         $country_code = $location->{'Code'} || $found_country_code;
 129
 130     }
 131
 132     #retrieve breeding program from associated trials
 133     my $program_query = "SELECT geo.nd_geolocation_id,
 134         breeding_program.name,
 135         count(distinct(projectprop.project_id))
 136         FROM nd_geolocation AS geo
 137         LEFT JOIN projectprop ON (projectprop.value::INT = geo.nd_geolocation_id AND projectprop.type_id=?)
 138         LEFT JOIN project AS trial ON (trial.project_id=projectprop.project_id)
 139         LEFT JOIN project_relationship ON (subject_project_id=trial.project_id AND project_relationship.type_id =?)
 140         LEFT JOIN project breeding_program ON (breeding_program.project_id=object_project_id)
 141         WHERE nd_geolocation_id =?
 142         GROUP BY 1,2
 143         ORDER BY 3
 144         LIMIT 1";
 145     my $prepared_query=$dbh->prepare($program_query);
 146     $prepared_query->execute($project_location_cvterm_id, $program_trial_relationship_id, $id);
 147     my ($geo_id, $found_program, $count) = $prepared_query->fetchrow_array();
 148     $program = $location->{'Program'} || $found_program;
 149
 150
 151     # print STDERR "$name saved props:\t".$location->{'Longitude'}."\t".$location->{'Latitude'}."\t".$location->{'Altitude'}."\t".$location->{'Country'}."\t".$location->{'Code'}."\t".$location->{'Program'}."\n$name found props:\t".$found_longitude."\t".$found_latitude."\t".$found_altitude."\t".$found_country_name."\t".$found_country_code."\t".$found_program."\n";
 152
 153     print $F $name."\t".$location->{'Longitude'}."\t".$location->{'Latitude'}."\t".$location->{'Altitude'}."\t".$location->{'Country'}."\t".$location->{'Code'}."\t".$location->{'Program'}."\t".$found_longitude."\t".$found_latitude."\t".$found_altitude."\t".$found_country_name."\t".$found_country_code."\t".$found_program."\n";
 154
 155     if ($opt_s){
 156
 157         print STDERR "Updating $name with properties:
 158         country_name => $country_name,
 159         country_code => $country_code,
 160         breeding_program => $program,
 161         latitude => $latitude,
 162         longitude => $longitude,
 163         altitude => $altitude \n";
 164
 165         my $updated_location = CXGN::Location->new( {
 166             bcs_schema => $schema,
 167             nd_geolocation_id => $id,
 168             country_name => $country_name,
 169             country_code => $country_code,
 170             breeding_program => $program,
 171             latitude => $latitude,
 172             longitude => $longitude,
 173             altitude => $altitude,
 174         });
 175
 176         my $store = $updated_location->store_location();
 177
 178         if ($store->{'error'}) {
 179             print STDERR $store->{'error'}."\n";
 180         }
 181
 182     }
 183 }
 184
 185 close($F);