Merge pull request #5304 from solgenomics/topic/germplasm_acquisition…

…_date BrAPI: set default germplasm acquisitionDate and use in filtering
solgenomics · Feb 10, 2025 · 5b768e4 · 5b768e4
2 parents 597e8d8 + ee1e740
commit 5b768e4
Show file tree

Hide file tree

Showing 4 changed files with 102 additions and 23 deletions.
diff --git a/lib/CXGN/BrAPI/v1/Germplasm.pm b/lib/CXGN/BrAPI/v1/Germplasm.pm
@@ -31,6 +31,9 @@ sub search {
     my $synonyms_arrayref = $params->{synonym} || ($params->{synonyms} || ());
     my $subtaxa = $params->{germplasmSubTaxa}->[0];
     my $match_method = $params->{matchMethod}->[0] || 'exact';
+    my $acquisitionDate = ref $params->{acquisitionDate} eq 'ARRAY' ? $params->{acquisitionDate}->[0] : $params->{acquisitionDate};
+    my $minAcquisitionDate = ref $params->{minAcquisitionDate} eq 'ARRAY' ? $params->{minAcquisitionDate}->[0] : $params->{minAcquisitionDate};
+    my $maxAcquisitionDate = ref $params->{maxAcquisitionDate} eq 'ARRAY' ? $params->{maxAcquisitionDate}->[0] : $params->{maxAcquisitionDate};
 
     if ($match_method ne 'exact' && $match_method ne 'wildcard') {
         push @$status, { 'error' => "matchMethod '$match_method' not recognized. Allowed matchMethods: wildcard, exact. Wildcard allows % or * for multiple characters and ? for single characters." };
@@ -89,7 +92,10 @@ sub search {
         stockprop_columns_view=>{'accession number'=>1, 'PUI'=>1, 'seed source'=>1, 'institute code'=>1, 'institute name'=>1, 'biological status of accession code'=>1, 'country of origin'=>1, 'type of germplasm storage code'=>1, 'acquisition date'=>1, 'ncbi_taxonomy_id'=>1},
         limit=>$limit,
         offset=>$offset,
-        display_pedigree=>1
+        display_pedigree=>1,
+        acquisition_date=>$acquisitionDate,
+        min_acquisition_date=>$minAcquisitionDate,
+        max_acquisition_date=>$maxAcquisitionDate
     });
     my ($result, $total_count) = $stock_search->search();
 
@@ -126,7 +132,7 @@ sub search {
             subtaxa=>$_->{subtaxa},
             subtaxaAuthority=>$_->{subtaxaAuthority},
             donors=>$_->{donors},
-            acquisitionDate=>$_->{'acquisition date'},
+            acquisitionDate=>$_->{'acquisition date'} eq '' ? $_->{'create_date'} : $_->{'acquisition date'},
             breedingMethodDbId=>undef,
             documentationURL=>undef,
             germplasmGenus=>$_->{genus},
@@ -198,7 +204,7 @@ sub germplasm_detail {
         subtaxa=>$result->[0]->{subtaxa},
         subtaxaAuthority=>$result->[0]->{subtaxaAuthority},
         donors=>$result->[0]->{donors},
-        acquisitionDate=>$result->[0]->{'acquisition date'},
+        acquisitionDate=>$result->[0]->{'acquisition date'} eq '' ? $result->[0]->{'create_date'} : $result->[0]->{'acquisition date'}
     );
     my $pagination = CXGN::BrAPI::Pagination->pagination_response($total_count,1,0);
     return CXGN::BrAPI::JSONResponse->return_success(\%result, $pagination, \@data_files, $status, 'Germplasm detail result constructed');

diff --git a/lib/CXGN/BrAPI/v2/Germplasm.pm b/lib/CXGN/BrAPI/v2/Germplasm.pm
@@ -43,6 +43,9 @@ sub search {
     my $progeny_db_id = $params->{progenyDbId} || ($params->{progenyDbIds} || ());
     my $external_reference_id_arrayref = $params->{externalReferenceID} || ($params->{externalReferenceIDs} || ());
     my $external_reference_source_arrayref = $params->{externalReferenceSource} || ($params->{externalReferenceSources} || ());
+    my $acquisitionDate = ref $params->{acquisitionDate} eq 'ARRAY' ? $params->{acquisitionDate}->[0] : $params->{acquisitionDate};
+    my $minAcquisitionDate = ref $params->{minAcquisitionDate} eq 'ARRAY' ? $params->{minAcquisitionDate}->[0] : $params->{minAcquisitionDate};
+    my $maxAcquisitionDate = ref $params->{maxAcquisitionDate} eq 'ARRAY' ? $params->{maxAcquisitionDate}->[0] : $params->{maxAcquisitionDate};
 
     if ( $collection || $progeny_db_id || $parent_db_id ){
         push @$status, { 'error' => 'The following search parameters are not implemented: collection, parentDbId, progenyDbId' };
@@ -148,7 +151,10 @@ sub search {
         external_ref_source_list=>$external_reference_source_arrayref,
         limit=>$limit,
         offset=>$offset,
-        display_pedigree=>1
+        display_pedigree=>1,
+        acquisition_date=>$acquisitionDate,
+        min_acquisition_date=>$minAcquisitionDate,
+        max_acquisition_date=>$maxAcquisitionDate
     });
     my ($result, $total_count) = $stock_search->search();
 
@@ -228,7 +234,7 @@ sub search {
         #Populating data
         push @data, {
             accessionNumber=>$_->{'accession number'},
-            acquisitionDate=>$_->{'acquisition date'} eq '' ? undef : $_->{'acquisition date'},
+            acquisitionDate=>$_->{'acquisition date'} eq '' ? $_->{'create_date'} : $_->{'acquisition date'},
             additionalInfo=>$additional_info,
             biologicalStatusOfAccessionCode=>$_->{'biological status of accession code'} || 0,
             biologicalStatusOfAccessionDescription=>undef,
@@ -606,7 +612,7 @@ sub germplasm_mcpd {
             subtaxon=>$_->{subtaxa},
             subtaxonAuthority=>$_->{subtaxaAuthority},
             donorInfo=>\@donors,
-            acquisitionDate=>$_->{'acquisition date'} eq '' ? undef : $_->{'acquisition date'}
+            acquisitionDate=>$_->{'acquisition date'} eq '' ? $_->{'create_date'} : $_->{'acquisition date'}
         );
     }
     my $total_count = (%result) ? 1 : 0;
@@ -1202,7 +1208,7 @@ sub _simple_search {
 
         push @data, {
             accessionNumber=>$_->{'accession number'},
-            acquisitionDate=>$_->{'acquisition date'} eq '' ? undef : $_->{'acquisition date'},
+            acquisitionDate=>$_->{'acquisition date'} eq '' ? $_->{'create_date'} : $_->{'acquisition date'},
             additionalInfo=> $additional_info,
             biologicalStatusOfAccessionCode=>$_->{'biological status of accession code'} || 0,
             biologicalStatusOfAccessionDescription=>undef,

diff --git a/lib/CXGN/Stock/Search.pm b/lib/CXGN/Stock/Search.pm
@@ -251,6 +251,21 @@ has 'external_ref_source_list' => (
     is => 'rw',
 );
 
+has 'acquisition_date' => (
+    isa => 'Str|Int|Undef',
+    is => 'rw'
+);
+
+has 'min_acquisition_date' => (
+    isa => 'Str|Int|Undef',
+    is => 'rw'
+);
+
+has 'max_acquisition_date' => (
+    isa => 'Str|Int|Undef',
+    is => 'rw'
+);
+
 sub search {
     my $self = shift;
     print STDERR "CXGN::Stock::Search search start\n";
@@ -281,6 +296,9 @@ sub search {
     my @external_ref_source_array = $self->external_ref_source_list ? @{$self->external_ref_source_list} : ();
     my $limit = $self->limit;
     my $offset = $self->offset;
+    my $acquisition_date = $self->acquisition_date;
+    my $min_acquisition_date = $self->min_acquisition_date;
+    my $max_acquisition_date = $self->max_acquisition_date;
 
     my $advanced_search = 0; #this is for joining nd_experiment and its related tables
 
@@ -490,11 +508,57 @@ sub search {
     }
     if ( !$and_conditions) {  $and_conditions = [ { 'me.type_id' => { '!=' => undef } } ] };
 
+    my $acq_date_join = $acquisition_date || $min_acquisition_date || $max_acquisition_date ? 'stockprops' : '';
+    my $acq_date_conditions = $acquisition_date || $min_acquisition_date || $max_acquisition_date ? { "-and" => [] } : {};
+    if ( $acquisition_date ) {
+        my $f = {
+            "-or" => [
+                {
+                    "to_char(me.create_date, 'YYYYMMDD')" => $acquisition_date
+                },
+                {
+                    'stockprops_2.type_id' => SGN::Model::Cvterm->get_cvterm_row($schema, 'acquisition date', 'stock_property')->cvterm_id(),
+                    'stockprops_2.value' => $acquisition_date
+                }
+            ]
+        };
+        push(@{$acq_date_conditions->{'-and'}}, $f)
+    }
+    if ( $min_acquisition_date ) {
+        my $f = {
+            "-or" => [
+                {
+                    "to_char(me.create_date, 'YYYYMMDD')" => { '>=', $min_acquisition_date }
+                },
+                {
+                    'stockprops_2.type_id' => SGN::Model::Cvterm->get_cvterm_row($schema, 'acquisition date', 'stock_property')->cvterm_id(),
+                    'stockprops_2.value' => { '>=', $min_acquisition_date }
+                }
+            ]
+        };
+        push(@{$acq_date_conditions->{'-and'}}, $f)
+    }
+    if ( $max_acquisition_date ) {
+        my $f = {
+            "-or" => [
+                {
+                    "to_char(me.create_date, 'YYYYMMDD')" => { '<=', $max_acquisition_date }
+                },
+                {
+                    'stockprops_2.type_id' => SGN::Model::Cvterm->get_cvterm_row($schema, 'acquisition date', 'stock_property')->cvterm_id(),
+                    'stockprops_2.value' => { '<=', $max_acquisition_date }
+                }
+            ]
+        };
+        push(@{$acq_date_conditions->{'-and'}}, $f)
+    }
+
     #$schema->storage->debug(1);
     my $search_query = {
         -and => [
             $or_conditions,
             $and_conditions,
+            $acq_date_conditions
         ],
     };
     if (!$self->include_obsolete) {
@@ -528,14 +592,15 @@ sub search {
     print STDERR "**stock search q " . Dumper($search_query)  ."\n";
     print STDERR "***stock_join= " . Dumper($stock_join) ." \n\n";
     my $rs = $schema->resultset("Stock::Stock")->search(
-    $search_query,
-    {
-        join => ['type', 'organism', 'stockprops', $stock_join],
-        '+select' => [ 'type.name' , 'organism.species' , 'organism.common_name', 'organism.genus'],
-        '+as'     => [ 'cvterm_name' , 'species', 'common_name', 'genus'],
-        order_by  => 'me.name',
-        distinct=>1
-    });
+        $search_query,
+        {
+            join => ['type', 'organism', 'stockprops', $stock_join, $acq_date_join],
+            '+select' => [ 'type.name' , 'organism.species' , 'organism.common_name', 'organism.genus'],
+            '+as'     => [ 'cvterm_name' , 'species', 'common_name', 'genus'],
+            order_by  => 'me.name',
+            distinct=>1
+        }
+    );
 
     my $records_total = $rs->count();
     print STDERR "total records: ".$records_total;
@@ -625,7 +690,7 @@ ORDER BY organism_id ASC;";
     # Get additional stock properties (pedigree, synonyms, donor info)
     my $stock_query = "SELECT stock.stock_id, stock.uniquename, stock.organism_id,
                mother.uniquename AS female_parent, father.uniquename AS male_parent, m_rel.value AS cross_type,
-               props.stock_synonym, props.donor, props.\"donor institute\", props.\"donor PUI\", family.uniquename AS family_name
+               props.stock_synonym, props.donor, props.\"donor institute\", props.\"donor PUI\", family.uniquename AS family_name, to_char(stock.create_date, 'YYYYMMDD')
         FROM stock
         LEFT JOIN stock_relationship m_rel ON (stock.stock_id = m_rel.object_id AND m_rel.type_id = (SELECT cvterm_id FROM cvterm WHERE name = 'female_parent'))
         LEFT JOIN stock mother ON (m_rel.subject_id = mother.stock_id)
@@ -653,6 +718,7 @@ ORDER BY organism_id ASC;";
         my @donor_institutes = keys %{$donor_inst_json};
         my @donor_puis = keys %{$donor_pui_json};
         my $population_name = $r[10] || undef;
+        my $create_date = $r[11];
 
         # add stock props to the result hash
         $result_hash{$stock_id}{pedigree} = $self->display_pedigree ? $mother . '/' . $father : 'DISABLED';
@@ -676,6 +742,7 @@ ORDER BY organism_id ASC;";
         $result_hash{$stock_id}{subtaxaAuthority} = defined($organism_props{$organism_id}) ? $organism_props{$organism_id}->{'subtaxa authority'} : undef;
 
         $result_hash{$stock_id}{population_name} = $population_name;
+        $result_hash{$stock_id}{create_date} = $create_date;
     }
 
     if ($self->stockprop_columns_view && scalar(keys %{$self->stockprop_columns_view})>0 && scalar(@result_stock_ids)>0){