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KASP and VCF download from project page #4689

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merged 7 commits into from
Oct 11, 2023
Merged

KASP and VCF download from project page #4689

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3f20655
download function for snp data on project page
titima15 Oct 6, 2023
d2627a4
retrieve protocol info for project page
titima15 Oct 6, 2023
51fcb4a
download kasp data on project page
titima15 Oct 9, 2023
577fcdd
test vcf download
titima15 Oct 9, 2023
e9c09c1
test for kasp data download
titima15 Oct 9, 2023
836b885
replace protocol link with project link
titima15 Oct 9, 2023
801e030
fixed syntax
titima15 Oct 9, 2023
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2 changes: 1 addition & 1 deletion js/source/legacy/CXGN/BreedersToolbox/GenotypingTrial.js
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Original file line number Diff line number Diff line change
Expand Up @@ -470,7 +470,7 @@ jQuery(document).ready(function ($) {
return;
}
if (response.success) {
var success_string = "<h4>Go to new <a href='/breeders_toolbox/protocol/"+response.nd_protocol_id+"'>protocol detail page</a></h4>";
var success_string = "<h4>Go to your <a href='/breeders/trial/"+response.project_id+"'>genotyping project page</a></h4>";
console.log(success_string);
jQuery('#upload_genotype_submit_complete').html(success_string);
Workflow.complete('#upload_genotype_submit');
Expand Down
9 changes: 8 additions & 1 deletion lib/CXGN/Genotype/Download/KASPdata.pm
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Expand Up @@ -42,6 +42,11 @@ has 'protocol_id_list' => (
is => 'rw',
);

has 'genotype_data_project_list' => (
isa => 'ArrayRef[Int]|Undef',
is => 'ro',
);

has 'genotypeprop_hash_select' => (
isa => 'ArrayRef[Str]',
is => 'ro',
Expand All @@ -64,13 +69,15 @@ sub download {
my $schema = $self->bcs_schema;
my $people_schema = $self->people_schema;
my $protocol_id_list = $self->protocol_id_list;
my $genotyping_project_list = $self->genotype_data_project_list;
my $genotypeprop_hash_select = ['NT', 'XV', 'YV'];
my $return_only_first_genotypeprop_for_stock = $self->return_only_first_genotypeprop_for_stock;

my $genotypes_search = CXGN::Genotype::Search->new({
bcs_schema=>$schema,
people_schema=>$people_schema,
protocol_id_list=>$protocol_id_list,
genotype_data_project_list=>$genotyping_project_list,
genotypeprop_hash_select=>$genotypeprop_hash_select
});

Expand Down
2 changes: 1 addition & 1 deletion lib/CXGN/Genotype/Search.pm
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Expand Up @@ -773,7 +773,7 @@ sub init_genotype_iterator {
}

#For genotyping_data_project
if ($genotype_data_project_list && scalar($genotype_data_project_list)>0) {
if ($genotype_data_project_list && scalar(@$genotype_data_project_list)>0) {
my $sql = join ("," , @$genotype_data_project_list);
push @where_clause, "project.project_id in ($sql)";
}
Expand Down
34 changes: 29 additions & 5 deletions lib/SGN/Controller/BreedersToolbox/Download.pm
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Expand Up @@ -1057,7 +1057,7 @@ sub download_gbs_action : Path('/breeders/download_gbs_action') {
my $forbid_cache = defined($c->req->param('forbid_cache')) ? $c->req->param('forbid_cache') : 0;
my $dl_token = $c->req->param("gbs_download_token") || "no_token";
my $dl_cookie = "download".$dl_token;

my $genotyping_project_id = $c->req->param("genotyping_project_id");
my (@accession_ids, @accession_list, @accession_genotypes, @unsorted_markers, $accession_data, $id_string, $protocol_id, $trial_id_string, @trial_ids);

$trial_id_string = $c->req->param("trial_ids");
Expand All @@ -1069,11 +1069,12 @@ sub download_gbs_action : Path('/breeders/download_gbs_action') {
$id_string = $c->req->param("ids");
@accession_ids = split(',',$id_string);
$protocol_id = $c->req->param("protocol_id");
if (!$protocol_id){
if ((!defined $protocol_id) && (!defined $genotyping_project_id)){
my $default_genotyping_protocol = $c->config->{default_genotyping_protocol};
$protocol_id = $schema->resultset('NaturalDiversity::NdProtocol')->find({name=>$default_genotyping_protocol})->nd_protocol_id();
}
}

elsif ($format eq 'list_id') { #get accession names from list and tranform them to ids
my $accession_list_id = $c->req->param("genotype_accession_list_list_select");
$protocol_id = $c->req->param("genotyping_protocol_select");
Expand Down Expand Up @@ -1115,6 +1116,16 @@ sub download_gbs_action : Path('/breeders/download_gbs_action') {
}
}

my @protocol_list;
if (defined $protocol_id) {
push @protocol_list, $protocol_id;
}

my @genotyping_project_list;
if (defined $genotyping_project_id) {
push @genotyping_project_list, $genotyping_project_id;
}

my $geno = CXGN::Genotype::DownloadFactory->instantiate(
$download_format, #can be either 'VCF' or 'DosageMatrix'
{
Expand All @@ -1124,7 +1135,7 @@ sub download_gbs_action : Path('/breeders/download_gbs_action') {
accession_list=>\@accession_ids,
#tissue_sample_list=>$tissue_sample_list,
trial_list=>\@trial_ids,
protocol_id_list=>[$protocol_id],
protocol_id_list=>\@protocol_list,
chromosome_list=>$chromosome_numbers,
start_position=>$start_position,
end_position=>$end_position,
Expand All @@ -1133,7 +1144,7 @@ sub download_gbs_action : Path('/breeders/download_gbs_action') {
marker_name_list=>\@marker_name_list,
return_only_first_genotypeprop_for_stock=>$return_only_first_genotypeprop_for_stock,
#markerprofile_id_list=>$markerprofile_id_list,
#genotype_data_project_list=>$genotype_data_project_list,
genotype_data_project_list=>\@genotyping_project_list,
#limit=>$limit,
#offset=>$offset
}
Expand Down Expand Up @@ -1649,6 +1660,18 @@ sub download_kasp_genotyping_data_csv : Path('/breeders/download_kasp_genotyping
my $schema = $c->dbic_schema("Bio::Chado::Schema", "sgn_chado");
my $people_schema = $c->dbic_schema("CXGN::People::Schema");
my $protocol_id = $c->req->param("protocol_id");
my $genotyping_project_id = $c->req->param("genotyping_project_id");

my @protocol_list;
if (defined $protocol_id) {
push @protocol_list, $protocol_id;
}

my @genotyping_project_list;
if (defined $genotyping_project_id) {
push @genotyping_project_list, $genotyping_project_id;
}


my $dir = $c->tempfiles_subdir('download');
my $temp_file_name = $protocol_id . "_" . "KASP_data" . "XXXX";
Expand All @@ -1664,7 +1687,8 @@ sub download_kasp_genotyping_data_csv : Path('/breeders/download_kasp_genotyping
{
bcs_schema=>$schema,
people_schema=>$people_schema,
protocol_id_list=>[$protocol_id],
protocol_id_list=>\@protocol_list,
genotype_data_project_list=>\@genotyping_project_list,
filename => $tempfile,
}
);
Expand Down
75 changes: 63 additions & 12 deletions lib/SGN/Controller/BreedersToolbox/Trial.pm
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Expand Up @@ -31,7 +31,7 @@ sub trial_init : Chained('/') PathPart('breeders/trial') CaptureArgs(1) {
my $trial_id = shift;

$c->stash->{trial_id} = $trial_id;
print STDERR "TRIAL ID = $trial_id\n";
# print STDERR "TRIAL ID = $trial_id\n";

my $schema = $c->dbic_schema("Bio::Chado::Schema");
$c->stash->{schema} = $schema;
Expand Down Expand Up @@ -209,20 +209,71 @@ sub trial_info : Chained('trial_init') PathPart('') Args(0) {
$c->stash->{genotype_data_type} = 'SNP'
}

my $plate_info = CXGN::Genotype::GenotypingProject->new({
my $project_info = CXGN::Genotype::GenotypingProject->new({
bcs_schema => $schema,
project_id => $project_id
});
my ($data, $tc) = $plate_info->get_plate_info();
my ($data, $tc) = $project_info->get_plate_info();
my $has_plate;
if (!$data) {
$has_plate = 'none';
}
$c->stash->{has_plate} = $has_plate;
my @genotyping_project_list = ($project_id);
my $protocol_info = CXGN::Genotype::Protocol::list($schema, undef, undef, undef, undef, undef, \@genotyping_project_list);
if ($protocol_info) {
$c->stash->{marker_names} = $protocol_info->[0]->{marker_names} || [];

my $associated_protocol = $project_info->get_associated_protocol();

if ( defined $associated_protocol && scalar(@$associated_protocol)>0) {
my $protocol_id = $associated_protocol->[0]->[0];
my $protocol_info = CXGN::Genotype::Protocol->new({
bcs_schema => $schema,
nd_protocol_id => $protocol_id
});

my $marker_names = $protocol_info->{marker_names};
my $assay_type = $protocol_info->{assay_type};
$c->stash->{marker_names} = $marker_names;
$c->stash->{assay_type} = $assay_type;

my $marker_info_keys = $protocol_info->marker_info_keys;
my @marker_info_headers = ();
if (defined $marker_info_keys) {
foreach my $info_key (@$marker_info_keys) {
if ($info_key eq 'name') {
push @marker_info_headers, 'Marker Name';
} elsif (($info_key eq 'intertek_name') || ($info_key eq 'facility_name')) {
push @marker_info_headers, 'Facility Marker Name';
} elsif ($info_key eq 'chrom') {
push @marker_info_headers, 'Chromosome';
} elsif ($info_key eq 'pos') {
push @marker_info_headers, 'Position';
} elsif ($info_key eq 'alt') {
if ($assay_type eq 'KASP') {
push @marker_info_headers, 'Y-allele';
} else {
push @marker_info_headers, 'Alternate';
}
} elsif ($info_key eq 'ref') {
if ($assay_type eq 'KASP') {
push @marker_info_headers, 'X-allele';
} else {
push @marker_info_headers, 'Reference';
}
} elsif ($info_key eq 'qual') {
push @marker_info_headers, 'Quality';
} elsif ($info_key eq 'filter') {
push @marker_info_headers, 'Filter';
} elsif ($info_key eq 'info') {
push @marker_info_headers, 'Info';
} elsif ($info_key eq 'format') {
push @marker_info_headers, 'Format';
} elsif ($info_key eq 'sequence') {
push @marker_info_headers, 'Sequence';
}
}
} else {
@marker_info_headers = ('Marker Name','Chromosome','Position','Alternate','Reference','Quality','Filter','Info','Format');
}
$c->stash->{marker_info_headers} = \@marker_info_headers;
}

$c->stash->{template} = '/breeders_toolbox/genotype_data_project.mas';
Expand Down Expand Up @@ -322,8 +373,8 @@ sub trial_download : Chained('trial_init') PathPart('download') Args(1) {
my $self = shift;
my $c = shift;
my $what = shift;
print STDERR "WHAT =".Dumper($what)."\n";
print STDERR Dumper $c->req->params();
# print STDERR "WHAT =".Dumper($what)."\n";
# print STDERR Dumper $c->req->params();
my $schema = $c->dbic_schema('Bio::Chado::Schema', 'sgn_chado');
my $user = $c->user();
if (!$user) {
Expand Down Expand Up @@ -435,7 +486,7 @@ sub trial_download : Chained('trial_init') PathPart('download') Args(1) {
$rel_file = $rel_file . ".$format";
my $tempfile = $c->config->{basepath}."/".$rel_file;

print STDERR "TEMPFILE : $tempfile\n";
# print STDERR "TEMPFILE : $tempfile\n";

my $download = CXGN::Trial::Download->new({
bcs_schema => $schema,
Expand Down Expand Up @@ -474,7 +525,7 @@ sub trial_download : Chained('trial_init') PathPart('download') Args(1) {
sub trials_download_layouts : Path('/breeders/trials/download/layout') Args(0) {
my $self = shift;
my $c = shift;
print STDERR Dumper $c->req->params();
# print STDERR Dumper $c->req->params();
my $schema = $c->dbic_schema('Bio::Chado::Schema', 'sgn_chado');
my $user = $c->user();
if (!$user) {
Expand Down Expand Up @@ -510,7 +561,7 @@ sub trials_download_layouts : Path('/breeders/trials/download/layout') Args(0) {
$rel_file = $rel_file . ".$format";
my $tempfile = $c->config->{basepath}."/".$rel_file;

print STDERR "TEMPFILE : $tempfile\n";
# print STDERR "TEMPFILE : $tempfile\n";

my $trial_download_args = {
bcs_schema => $schema,
Expand Down
12 changes: 8 additions & 4 deletions mason/breeders_toolbox/genotype_data_project.mas
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Expand Up @@ -46,6 +46,8 @@ $genotype_data_type => undef
$trial_owner => undef
$has_plate => undef
$marker_names => undef
$marker_info_headers => undef
$assay_type => undef
</%args>

<& /util/import_javascript.mas, classes => [ 'jquery.iframe-post-form', 'CXGN.Trial' , 'jstree/dist/jstree', 'CXGN.BreedersToolbox.HTMLSelect', 'moment_min', 'daterangepicker' ] &>
Expand All @@ -60,10 +62,12 @@ $marker_names => undef

<& /page/detail_page_2_col_section.mas, trial_id => $trial_id, info_section_title => "<h4 style='display:inline'>Genotyping Protocols</h4>", info_section_subtitle => 'View basic information about the genotyping protocols used in this genotyping project.', icon_class => "glyphicon glyphicon-cog", info_section_id => "genotyping_data_project_protocols" &>

% if ($genotype_data_type ne 'SSR') {
<& /page/detail_page_2_col_section.mas, trial_id => $trial_id, info_section_title => "<h4 style='display:inline'>Genotyping Data</h4>", info_section_subtitle => 'View and download genotyping data.', icon_class => "glyphicon glyphicon-map-marker", info_section_id => "genotyping_data_project_data" &>
% } elsif ($genotype_data_type eq 'SSR') {
<& /page/detail_page_2_col_section.mas, trial_id => $trial_id, marker_names => $marker_names, info_section_title => "<h4 style='display:inline'>Genotype Data</h4>", info_section_subtitle => 'View and download genotyping data from this project.',buttons_html => '<button class="btn btn-sm btn-primary" style="margin:3px" id="download_project_ssr_data_link">Download SSR Data</button>', icon_class => "glyphicon glyphicon-save-file", info_section_id => "project_pcr_genotype_data" &>
% if ($genotype_data_type eq 'SSR') {
<& /page/detail_page_2_col_section.mas, trial_id => $trial_id, marker_names => $marker_names, info_section_title => "<h4 style='display:inline'>Genotype Data</h4>", info_section_subtitle => 'View and download genotyping data from this project.',buttons_html => '<button class="btn btn-sm btn-primary" style="margin:3px" id="download_project_ssr_data_link">Download SSR Data</button>', icon_class => "glyphicon glyphicon-save-file", info_section_id => "project_pcr_genotype_data" &>
% } elsif ($assay_type eq 'KASP') {
<& /page/detail_page_2_col_section.mas, trial_id => $trial_id, info_section_title => "<h4 style='display:inline'>Genotyping Data</h4>", info_section_subtitle => 'View and download genotyping data.', icon_class => "glyphicon glyphicon-map-marker", buttons_html => '<button class="btn btn-primary" style="margin:3px" id="project_genotype_data_download_all_vcf">Download All Genotype Data VCF</button><button class="btn btn-primary" style="margin:3px" id="project_genotype_data_download_all_dosagematrix">Download All Genotype Data Dosage Matrix</button><button class="btn btn-default" style="margin:3px" id="kasp_project_genotype_data_download_all_csv">Download All Genotype Data (CSV)</button>', info_section_id => "genotyping_data_project_data" &>
% } else {
<& /page/detail_page_2_col_section.mas, trial_id => $trial_id, info_section_title => "<h4 style='display:inline'>Genotyping Data</h4>", info_section_subtitle => 'View and download genotyping data.', icon_class => "glyphicon glyphicon-map-marker", buttons_html => '<button class="btn btn-primary" style="margin:3px" id="project_genotype_data_download_all_vcf">Download All Genotype Data VCF</button><button class="btn btn-primary" style="margin:3px" id="project_genotype_data_download_all_dosagematrix">Download All Genotype Data Dosage Matrix</button>', info_section_id => "genotyping_data_project_data" &>
% }

% my $data_agreement_link = '<button class="btn btn-sm btn-primary" disabled style="margin:3px">Add/edit data agreement</button>';
Expand Down
22 changes: 22 additions & 0 deletions mason/breeders_toolbox/genotyping_data_project/genotype_data.mas
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Expand Up @@ -36,8 +36,10 @@ jQuery(document).ready(function () {
'ajax': '/ajax/genotyping_data/search?genotyping_data_project_id_list=<% $trial_id %>',
});

var refresh_results;
jQuery("#project_genotype_data_forbid_cache").change(function(){
if (jQuery(this).is(":checked")) {
refresh_results = '1';
var project_genotypes_data_table = jQuery('#genotyping_data_project_genotype_data').DataTable({
'destroy' : true,
'searching' : false,
Expand All @@ -50,6 +52,26 @@ jQuery(document).ready(function () {
}
});

jQuery('#project_genotype_data_download_all_vcf').click(function(){
if (refresh_results) {
window.location.replace("/breeders/download_gbs_action/?genotyping_project_id=<% $trial_id %>&download_format=VCF&format=accession_ids&forbid_cache=1");
} else {
window.location.replace("/breeders/download_gbs_action/?genotyping_project_id=<% $trial_id %>&download_format=VCF&format=accession_ids");
}
});

jQuery('#project_genotype_data_download_all_dosagematrix').click(function(){
if (refresh_results) {
window.location.replace("/breeders/download_gbs_action/?genotyping_project_id=<% $trial_id %>&download_format=DosageMatrix&format=accession_ids&forbid_cache=1");
} else {
window.location.replace("/breeders/download_gbs_action/?genotyping_project_id=<% $trial_id %>&download_format=DosageMatrix&format=accession_ids");
}
});

jQuery('#kasp_project_genotype_data_download_all_csv').click(function(){
window.location.replace("/breeders/download_kasp_genotyping_data_csv/?genotyping_project_id=<% $trial_id %>");
});


});

Expand Down
35 changes: 35 additions & 0 deletions t/unit_fixture/CXGN/Uploading/KASPGenotypes.t
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Expand Up @@ -134,6 +134,41 @@ my $genotypes_search_1 = CXGN::Genotype::Search->new({
my ($total_count_1, $data_1) = $genotypes_search_1->get_genotype_info();
is($total_count_1, 5);

#test KASP data download from project page

my $kasp_project_response = $ua->get("http://localhost:3010/breeders/download_kasp_genotyping_data_csv/?genotyping_project_id=$genotyping_project_id_1");
my $kasp_project_message = $kasp_project_response->decoded_content;

my $kasp_data = '"MARKER NAME","SAMPLE NAME","SNP CALL (X,Y)","X VALUE","Y VALUE"
"S01_0001","new_accession_1","T,T","1.36",".58"
"S01_0001","new_accession_2","T,T","1.25",".49"
"S01_0001","new_accession_3","T,G","1.57","1.38"
"S01_0001","new_accession_4","T,G","1.24","1.56"
"S01_0001","new_accession_5","./.",".65",".58"
"S01_0002","new_accession_1","A,A","1.43",".59"
"S01_0002","new_accession_2","A,G","1.25","1.43"
"S01_0002","new_accession_3","A,G","1.22","1.41"
"S01_0002","new_accession_4","A,G","1.11","1.27"
"S01_0002","new_accession_5","A,A","1.65",".62"
"S02_0001","new_accession_1","T,T","1.75",".75"
"S02_0001","new_accession_2","T,T","1.21",".61"
"S02_0001","new_accession_3","T,T","1.17",".46"
"S02_0001","new_accession_4","T,C","1.59","1.46"
"S02_0001","new_accession_5","T,C","1.26","1.31"
"S02_0002","new_accession_1","A,A","1.75",".32"
"S02_0002","new_accession_2","A,A","1.38",".59"
"S02_0002","new_accession_3","A,C","1.36","1.47"
"S02_0002","new_accession_4","A,A","1.75",".74"
"S02_0002","new_accession_5","A,C","1.32","1.46"
"S03_0001","new_accession_1","C,C","1.76",".38"
"S03_0001","new_accession_2","C,C","1.47",".24"
"S03_0001","new_accession_3","C,T","1.86","1.48"
"S03_0001","new_accession_4","C,T","1.23","1.49"
"S03_0001","new_accession_5","C,T","1.11","1.23"
';

is($kasp_project_message, $kasp_data);

#test upload kasp data using facility names
#store facility sample Names
my $plate_file = $f->config->{basepath} . "/t/data/genotype_trial_upload/plate_with_identifier_upload.xls";
Expand Down
4 changes: 4 additions & 0 deletions t/unit_fixture/CXGN/Uploading/VCFGenotypes.t
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Expand Up @@ -495,6 +495,10 @@ $message = $response->decoded_content;
#print STDERR Dumper $message;
is($message, $dosage_matrix_string);

#testing genotype data download from project page
my $project_response = $ua->get("http://localhost:3010/breeders/download_gbs_action/?genotyping_project_id=$project_id&download_format=VCF&format=accession_ids&forbid_cache=1");
my $project_message = $project_response->decoded_content;
is($project_message, $dosage_matrix_string);

#Testing genotype search with marker names filter from marker set list object
my $marker_names_filtered = ["S1_21594", "S1_21597", "S1_75465"];
Expand Down