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mmaiers-nmdpmmaiers-nmdp
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perl cleint
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‎client/perl/HFCuS-client.pl‎

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#!/usr/bin/perl
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use strict;
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use warnings;
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use lib 'lib';
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use Getopt::Long;
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use File::Basename;
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# load the API package
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use WWW::SwaggerClient::ApiFactory;
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# load the models used
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use WWW::SwaggerClient::Object::HFCurationResponse;
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use WWW::SwaggerClient::Object::HFCurationRequest;
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use WWW::SwaggerClient::Object::License;
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# for displaying the API response data
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use Data::Dumper;
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#--- options and arguments:
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my $opt_help;
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my $opt_verbose = 0;
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my $action = "";
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my $submission_id;
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my $prg = basename($0);
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if (
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!&GetOptions(
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"help" => \$opt_help,
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"verbose!" => \$opt_verbose, # -verbose, -noverbose
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"action=s" => \$action,
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"sub=s" => \$submission_id,
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)
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)
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{
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print "\n$prg: wrong option\n";
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exit 1;
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}
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if ($opt_help) {
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&help;
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exit 0;
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}
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print "$prg: $action\n" if $opt_verbose;
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if ( $action !~ /(get_sub|get_all|push)/i ) {
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print "\n$prg: wrong action $action\n";
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exit 1;
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}
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if ( $action =~ /get_sub/i && !$submission_id ) {
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print "\n$prg: Submission ID missing for action $action\n";
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exit 1;
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}
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my $base = "http://hfcus.b12x.org:8080";
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my $api_instance = WWW::SwaggerClient::DefaultApi->new();
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$api_instance->{api_client}->{base_url} = $base;
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$api_instance->{api_client}->{ua}->env_proxy;
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print Dumper($api_instance) if $opt_verbose;
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if ( $action eq "get_sub" ) {
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&get_haplotypes( $api_instance, $submission_id );
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}
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elsif ( $action eq "push" ) {
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my $file;
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if ( @ARGV == 1 ) {
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$file = $ARGV[0];
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}
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else {
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print "\n$prg: hfr file missing for action $action\n";
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exit 1;
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}
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&push_haplotypes( $api_instance, $file );
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}
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elsif ( $action eq "get_all" ) {
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&get_all_submissions($api_instance);
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}
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else {
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print "\n$prg: wrong action $action\n";
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exit 1;
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}
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exit 0;
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# end of main
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sub push_haplotypes {
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my ( $api_instance, $file ) = @_;
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my $HFCurReq = WWW::SwaggerClient::Object::HFCurationRequest->new();
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my $HapFreqData =
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WWW::SwaggerClient::Object::HaplotypeFrequencyData->new();
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my $PopData = WWW::SwaggerClient::Object::PopulationData->new();
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my $Lic = WWW::SwaggerClient::Object::License->new();
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my $ResInfo = WWW::SwaggerClient::Object::ResolutionInfo->new();
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print Dumper($HapFreqData) if $opt_verbose;
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# $PopData->{id} = "1";
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$PopData->{name} = "US-CAU";
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$Lic->{type_of_license} = "CC0";
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$ResInfo->{resolution} = "4-Field";
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$HapFreqData->{license} = $Lic;
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$HapFreqData->{resolution_data}->[0] = $ResInfo;
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open( HFR, $file ) || die "$prg: Cannot open file $file: $!";
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my $i = 0;
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while (<HFR>) {
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chomp;
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my ( $hap, $hf ) = split /,/;
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my $HapFreq = WWW::SwaggerClient::Object::HaplotypeFrequency->new();
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$HapFreq->{haplotype_string} = $hap;
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$HapFreq->{frequency} = $hf;
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$HapFreqData->{haplotype_frequency_list}->[$i] = $HapFreq;
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$i++;
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}
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close HFR;
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$HFCurReq->{population_id} = "1";
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# $HFCurReq->{population_data} = $PopData;
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$HFCurReq->{haplotype_frequency_data} = $HapFreqData;
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my $response = $api_instance->hfc_post( hf_curation_request => $HFCurReq );
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print "$0: Submission $response->{submission_id}\n";
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}
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sub get_haplotypes {
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my ( $api_instance, $submission_id ) = @_;
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eval {
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my $haplotypes = $api_instance->hfc_submission_id_haplotypes_get(
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submission_id => $submission_id );
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print Dumper($haplotypes);
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};
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if ($@) {
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warn
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"Exception when calling DefaultApi->hfc_submission_id_haplotypes_get: $@\n";
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}
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} # end sub get_haplotypes
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sub get_all_submissions {
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my ($api_instance) = @_;
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eval {
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my $result = $api_instance->hfc_get();
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print Dumper($result);
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};
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if ($@) {
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warn "Exception when calling DefaultApi->hfc_get: $@\n";
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}
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} # end of get_all_submissions
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#=============================================================================
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sub help {
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#-----------------------------------------------------------------------------
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# Called by: MAIN
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# Purpose: show help
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# Arguments: none
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# Returns: nothing
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# ToDo:
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# Remarks:
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#-----------------------------------------------------------------------------
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my $def_v = $opt_verbose ? "-- verbose" : "-- noverbose";
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print << "__END_OF_HELP__";
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Name
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$prg
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Purpose
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Client for HFCuS
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Syntax
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$prg [--help]
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$prg [--verbose] action=[get|push]
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Options and arguments
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--help show this help
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--[no]verbose set verbose mode; default: $def_v
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--action get_sub: getting HF set by submission ID -sub <submission_id>
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push: push HF set <file>
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get_all: get all submissions
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The action push requires a file with HF data as argument.
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__END_OF_HELP__
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return;
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} # end sub help()
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#=============================================================================
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# end of file
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‎client/perl/README.md‎

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# ```HFCuS-client.pl```
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Haplotype Frequency Curation Service
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Perl Client
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# Requirements
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- Module::Find
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- URI::Query
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- Log::Any
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- Module::Runtime
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- Class::Singleton
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- Date::Parse
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- DateTime
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- Moose::Role

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