Merge pull request #3496 from solgenomics/topic/fix_pagination

fix brapi search pagination
solgenomics · Apr 23, 2021 · 235d5f8 · 235d5f8
2 parents 1dadadd + 1d85a3b
commit 235d5f8
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Showing 5 changed files with 35 additions and 25 deletions.
diff --git a/lib/CXGN/BrAPI/v2/BreedingMethods.pm b/lib/CXGN/BrAPI/v2/BreedingMethods.pm
@@ -32,9 +32,12 @@ sub search {
 	}
 
     foreach (@crosstypes){
+    	my $id = $_;
+    	$id =~ s/ /_/g;
+
         push @data, {
             abbreviation=>$_,
-            breedingMethodDbId=>$_ =~ s/ /_/g,
+            breedingMethodDbId=>$id,
             breedingMethodName=>$_,
             description=>$_,
         };

diff --git a/lib/CXGN/BrAPI/v2/Results.pm b/lib/CXGN/BrAPI/v2/Results.pm
@@ -38,7 +38,8 @@ sub save_results {
 
     my $search_id = substr($tempfile, -16);
     my %result = ( searchResultDbId => $search_id );
-    my $pagination = CXGN::BrAPI::Pagination->pagination_response(0,$page_size,$page);
+    #Pagination should be present in BrAPI only if data available in the result 
+    my $pagination = {}; #CXGN::BrAPI::Pagination->pagination_response(0,$page_size,$page); 
     return CXGN::BrAPI::JSONResponse->return_success(\%result, $pagination, \@data_files, $status, "search $search_type result constructed");
 
 }

diff --git a/lib/SGN/Controller/AJAX/BrAPI.pm b/lib/SGN/Controller/AJAX/BrAPI.pm
@@ -725,7 +725,7 @@ sub germplasm_search_old_GET {
 sub germplasm_search_old_POST {
     my $self = shift;
     my $c = shift;
-    my ($auth) = _authenticate_user($c);
+    # my ($auth) = _authenticate_user($c);
     my $clean_inputs = $c->stash->{clean_inputs};
     my $brapi = $self->brapi_module;
     my $brapi_module = $brapi->brapi_wrapper('Germplasm');
@@ -1537,7 +1537,7 @@ sub allelematrix_GET {
 sub allelematrix_search_process {
     my $self = shift;
     my $c = shift;
-    my ($auth) = _authenticate_user($c);
+    # my ($auth) = _authenticate_user($c);
 
     my $clean_inputs = $c->stash->{clean_inputs};
     my $format = $clean_inputs->{format}->[0];
@@ -1899,7 +1899,7 @@ sub studies_search  : Chained('brapi') PathPart('studies-search') Args(0) : Acti
 sub studies_search_POST {
     my $self = shift;
     my $c = shift;
-    my ($auth) = _authenticate_user($c);
+    # my ($auth) = _authenticate_user($c);
     my $clean_inputs = $c->stash->{clean_inputs};
     my $brapi = $self->brapi_module;
     my $brapi_module = $brapi->brapi_wrapper('Studies');
@@ -2497,7 +2497,7 @@ sub phenotypes_search : Chained('brapi') PathPart('phenotypes-search') Args(0) :
 sub phenotypes_search_POST {
     my $self = shift;
     my $c = shift;
-    my ($auth) = _authenticate_user($c);
+    # my ($auth) = _authenticate_user($c);
     my $clean_inputs = $c->stash->{clean_inputs};
     my $brapi = $self->brapi_module;
     my $brapi_module = $brapi->brapi_wrapper('ObservationUnits');
@@ -2652,7 +2652,7 @@ sub phenotypes_search_table_GET {
 sub process_phenotypes_search_table {
 	my $self = shift;
 	my $c = shift;
-	my ($auth) = _authenticate_user($c);
+	# my ($auth) = _authenticate_user($c);
 	my $clean_inputs = $c->stash->{clean_inputs};
 	my $brapi = $self->brapi_module;
 	my $brapi_module = $brapi->brapi_wrapper('ObservationTables');
@@ -2692,7 +2692,7 @@ sub phenotypes_search_csv_GET {
 sub process_phenotypes_search_csv {
 	my $self = shift;
 	my $c = shift;
-	my ($auth) = _authenticate_user($c);
+	# my ($auth) = _authenticate_user($c);
 	my $clean_inputs = $c->stash->{clean_inputs};
 	my $dir = $c->tempfiles_subdir('download');
 	my $time_stamp = strftime "%Y-%m-%dT%H%M%S", localtime();
@@ -2735,7 +2735,7 @@ sub phenotypes_search_tsv_GET {
 sub process_phenotypes_search_tsv {
 	my $self = shift;
 	my $c = shift;
-	my ($auth) = _authenticate_user($c);
+	# my ($auth) = _authenticate_user($c);
 	my $clean_inputs = $c->stash->{clean_inputs};
 	my $dir = $c->tempfiles_subdir('download');
 	my $time_stamp = strftime "%Y-%m-%dT%H%M%S", localtime();
@@ -3238,7 +3238,7 @@ sub observationvariable_search_GET {
 sub _observationvariable_search_process {
 	my $self = shift;
 	my $c = shift;
-    my ($auth) = _authenticate_user($c);
+    # my ($auth) = _authenticate_user($c);
 
 	my $clean_inputs = $c->stash->{clean_inputs};
 	my $brapi = $self->brapi_module;
@@ -3327,7 +3327,7 @@ sub samples_list_GET {
 sub _sample_search_process {
     my $self = shift;
     my $c = shift;
-    my ($auth) = _authenticate_user($c);
+    # my ($auth) = _authenticate_user($c);
     my $clean_inputs = $c->stash->{clean_inputs};
     my $brapi = $self->brapi_module;
     my $brapi_module = $brapi->brapi_wrapper('Samples');
@@ -4009,7 +4009,7 @@ sub observations_search_GET {
 sub observations_search_process {
 	my $self = shift;
 	my $c = shift;
-	my ($auth) = _authenticate_user($c);
+	# my ($auth) = _authenticate_user($c);
 	my $clean_inputs = $c->stash->{clean_inputs};
 	my $brapi = $self->brapi_module;
 	my $brapi_module = $brapi->brapi_wrapper('Observations');
@@ -5084,6 +5084,12 @@ sub save_results {
 
     my $brapi = $self->brapi_module;
     my $brapi_module = $brapi->brapi_wrapper($search_type);
+
+    #set default value to 100000 to get as much as possible records when page size is not a parameter
+    if(!$search_params->{pageSize}) {
+    	$brapi_module->{page_size} = 100000;
+	}
+
     my $search_result = $brapi_module->search($search_params,$c);
 
     my $dir = $c->tempfiles_subdir('/brapi_searches');