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Improve related stock section on stock details page and add related seedlot info specific to plot and plant details pages ("source of" or "derived from" type) #4755

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merged 10 commits into from
Dec 11, 2023
Merged

Improve related stock section on stock details page and add related seedlot info specific to plot and plant details pages ("source of" or "derived from" type) #4755

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7ead849
moved related stock section
titima15 Dec 4, 2023
854defe
organize different stock types
titima15 Dec 5, 2023
5d81899
removed seedlot from related stocks in trial
titima15 Dec 5, 2023
d0f9b78
seedlot section specific to plot and plant
titima15 Dec 5, 2023
6e8e801
re-organized tissue samples
titima15 Dec 6, 2023
151c2f2
remove tissue sample section from tissue sample details page
titima15 Dec 6, 2023
1f8aaf5
exit loop after blank line
titima15 Dec 6, 2023
f226550
added tissue_samples list_type
titima15 Dec 6, 2023
3005f95
modified test
titima15 Dec 6, 2023
35f5c65
Merge branch 'master' into topic/plot_info
titima15 Dec 6, 2023
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47 changes: 43 additions & 4 deletions lib/CXGN/Stock/RelatedStocks.pm
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Original file line number Diff line number Diff line change
Expand Up @@ -24,26 +24,26 @@ sub get_trial_related_stock {
my $plant_of_type_id = SGN::Model::Cvterm->get_cvterm_row($schema, 'plant_of', 'stock_relationship')->cvterm_id();
my $subplot_of_type_id = SGN::Model::Cvterm->get_cvterm_row($schema, 'subplot_of', 'stock_relationship')->cvterm_id();
my $plant_of_subplot_type_id = SGN::Model::Cvterm->get_cvterm_row($schema, 'plant_of_subplot', 'stock_relationship')->cvterm_id();
my $seed_transaction_type_id = SGN::Model::Cvterm->get_cvterm_row($schema, 'seed transaction', 'stock_relationship')->cvterm_id();
# my $seed_transaction_type_id = SGN::Model::Cvterm->get_cvterm_row($schema, 'seed transaction', 'stock_relationship')->cvterm_id();
my $tissue_sample_of_type_id = SGN::Model::Cvterm->get_cvterm_row($schema, 'tissue_sample_of', 'stock_relationship')->cvterm_id();

my $q = "SELECT stock.stock_id, stock.uniquename, cvterm.name FROM stock_relationship
INNER JOIN stock ON (stock_relationship.subject_id = stock.stock_id)
INNER JOIN cvterm ON (stock.type_id = cvterm.cvterm_id)
WHERE stock_relationship.object_id = ? AND (stock_relationship.type_id = ?
OR stock_relationship.type_id = ? OR stock_relationship.type_id = ? OR stock_relationship.type_id = ? OR stock_relationship.type_id = ? OR stock_relationship.type_id = ?)
OR stock_relationship.type_id = ? OR stock_relationship.type_id = ? OR stock_relationship.type_id = ? OR stock_relationship.type_id = ? )

UNION ALL

SELECT stock.stock_id, stock.uniquename, cvterm.name FROM stock_relationship
INNER JOIN stock ON (stock_relationship.object_id = stock.stock_id)
INNER JOIN cvterm ON (stock.type_id = cvterm.cvterm_id)
WHERE stock_relationship.subject_id = ? AND (stock_relationship.type_id = ?
OR stock_relationship.type_id = ? OR stock_relationship.type_id = ? OR stock_relationship.type_id = ? OR stock_relationship.type_id = ? OR stock_relationship.type_id = ?) ";
OR stock_relationship.type_id = ? OR stock_relationship.type_id = ? OR stock_relationship.type_id = ? OR stock_relationship.type_id = ? ) ";

my $h = $schema->storage->dbh()->prepare($q);

$h->execute($stock_id, $plot_of_type_id, $plant_of_type_id, $subplot_of_type_id, $plant_of_subplot_type_id, $seed_transaction_type_id, $tissue_sample_of_type_id, $stock_id, $plot_of_type_id, $plant_of_type_id, $subplot_of_type_id, $plant_of_subplot_type_id, $seed_transaction_type_id, $tissue_sample_of_type_id);
$h->execute($stock_id, $plot_of_type_id, $plant_of_type_id, $subplot_of_type_id, $plant_of_subplot_type_id, $tissue_sample_of_type_id, $stock_id, $plot_of_type_id, $plant_of_type_id, $subplot_of_type_id, $plant_of_subplot_type_id, $tissue_sample_of_type_id);

my @trial_related_stock =();
while(my($stock_id, $stock_name, $cvterm_name) = $h->fetchrow_array()){
Expand Down Expand Up @@ -175,4 +175,43 @@ sub get_cross_of_progeny {
}


sub get_plot_plant_related_seedlots {
my $self = shift;
my $stock_id = $self->stock_id;
my $schema = $self->dbic_schema();
my $seed_transaction_type_id = SGN::Model::Cvterm->get_cvterm_row($schema, 'seed transaction', 'stock_relationship')->cvterm_id();

my @related_seedlots;

my $q1 = "SELECT distinct(stock.stock_id), stock.uniquename, cvterm.name FROM stock_relationship
INNER JOIN stock ON (stock_relationship.subject_id = stock.stock_id)
INNER JOIN cvterm ON (stock.type_id = cvterm.cvterm_id)
WHERE stock_relationship.object_id = ? AND stock_relationship.type_id = ? ";

my $h1 = $schema->storage->dbh()->prepare($q1);

$h1->execute($stock_id, $seed_transaction_type_id);

while(my($stock_id, $stock_name, $stock_type) = $h1->fetchrow_array()){
push @related_seedlots, ['source of', $stock_type, $stock_id, $stock_name]
}

my $q2 = "SELECT distinct(stock.stock_id), stock.uniquename, cvterm.name FROM stock_relationship
INNER JOIN stock ON (stock_relationship.object_id = stock.stock_id)
INNER JOIN cvterm ON (stock.type_id = cvterm.cvterm_id)
WHERE stock_relationship.subject_id = ? AND stock_relationship.type_id = ? ";

my $h2 = $schema->storage->dbh()->prepare($q2);

$h2->execute($stock_id, $seed_transaction_type_id);

while(my($stock_id, $stock_name, $stock_type) = $h2->fetchrow_array()){
push @related_seedlots, ['derived from', $stock_type, $stock_id, $stock_name]
}

return\@related_seedlots;

}


1;
14 changes: 11 additions & 3 deletions lib/CXGN/Stock/Seedlot/ParseUpload/Plugin/SeedlotHarvestedXLS.pm
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Original file line number Diff line number Diff line change
Expand Up @@ -148,6 +148,10 @@ sub _validate_with_plugin {
$box_name = $worksheet->get_cell($row,6)->value();
}

if (!defined $seedlot_name && !defined $cross_name) {
last;
}

if (!$seedlot_name || $seedlot_name eq '' ) {
push @error_messages, "Cell A$row_name: seedlot_name missing.";
}
Expand Down Expand Up @@ -263,6 +267,11 @@ sub _parse_with_plugin {
$cross_name =~ s/^\s+|\s+$//g;
$seen_cross_names{$cross_name}++;
}

if (!defined $seedlot_name && !defined $cross_name) {
last;
}

}
my $cross_cvterm_id = SGN::Model::Cvterm->get_cvterm_row($schema, 'cross', 'stock_type')->cvterm_id();
my $seedlot_cvterm_id = SGN::Model::Cvterm->get_cvterm_row($schema, 'seedlot', 'stock_type')->cvterm_id();
Expand Down Expand Up @@ -325,9 +334,8 @@ sub _parse_with_plugin {
$box_name =~ s/^\s+|\s+$//g;
}

#skip blank lines
if (!$seedlot_name && !$cross_name && !$description) {
next;
if (!defined $seedlot_name && !defined $cross_name) {
last;
}


Expand Down
20 changes: 15 additions & 5 deletions lib/CXGN/Stock/Seedlot/ParseUpload/Plugin/SeedlotXLS.pm
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Original file line number Diff line number Diff line change
Expand Up @@ -168,6 +168,11 @@ sub _validate_with_plugin {
$source = $worksheet->get_cell($row, 8)->value();
$source =~ s/^\s+|\s+$//g;
}

if (!defined $seedlot_name && !defined $accession_name) {
last;
}

if (!$seedlot_name || $seedlot_name eq '' ) {
push @error_messages, "Cell A$row_name: seedlot_name missing.";
}
Expand Down Expand Up @@ -304,7 +309,13 @@ sub _parse_with_plugin {
$accession_name =~ s/^\s+|\s+$//g; #trim whitespace from front and end...
$seen_accession_names{$accession_name}++;
}

if (!defined $seedlot_name && !defined $accession_name) {
last;
}

}

my $accession_cvterm_id = SGN::Model::Cvterm->get_cvterm_row($schema, 'accession', 'stock_type')->cvterm_id();
my $seedlot_cvterm_id = SGN::Model::Cvterm->get_cvterm_row($schema, 'seedlot', 'stock_type')->cvterm_id();
my $synonym_cvterm_id = SGN::Model::Cvterm->get_cvterm_row($schema, 'stock_synonym', 'stock_property')->cvterm_id();
Expand Down Expand Up @@ -379,15 +390,14 @@ sub _parse_with_plugin {
$source = $worksheet->get_cell($row, 8)->value();
}

if (!defined $seedlot_name && !defined $accession_name) {
last;
}

$seedlot_name =~ s/^\s+|\s+$//g; #trim whitespace from front and end...
$accession_name =~ s/^\s+|\s+$//g; #trim whitespace from front and end...
$source =~ s/^\s+|\s+$//g; # also trim

#skip blank lines
if (!$seedlot_name && !$accession_name && !$description) {
next;
}

my $accession_stock_id;
if ($acc_synonyms_lookup{$accession_name}){
my @accession_names = keys %{$acc_synonyms_lookup{$accession_name}};
Expand Down
9 changes: 6 additions & 3 deletions lib/CXGN/Stock/Seedlot/ParseUpload/Plugin/SeedlotsToNewSeedlots.pm
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Original file line number Diff line number Diff line change
Expand Up @@ -164,6 +164,10 @@ sub _validate_with_plugin {
$new_seedlot_box_name = $worksheet->get_cell($row,6)->value();
}

if (!defined $from_seedlot_name && !defined $to_new_seedlot_name) {
last;
}

if (!$from_seedlot_name || $from_seedlot_name eq '' ) {
push @error_messages, "Cell A$row_name: from_seedlot_name missing.";
} else {
Expand Down Expand Up @@ -335,9 +339,8 @@ sub _parse_with_plugin {
$new_seedlot_quality = $worksheet->get_cell($row,8)->value();
}

#skip blank lines
if (!$to_new_seedlot_name && !$from_seedlot_name) {
next;
if (!defined $to_new_seedlot_name && !defined $from_seedlot_name) {
last;
}

my $from_seedlot_rs = $schema->resultset("Stock::Stock")->find({
Expand Down
9 changes: 6 additions & 3 deletions lib/CXGN/Stock/Seedlot/ParseUpload/Plugin/SeedlotsToPlots.pm
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Original file line number Diff line number Diff line change
Expand Up @@ -137,6 +137,10 @@ sub _validate_with_plugin {
$transaction_description = $worksheet->get_cell($row,5)->value();
}

if (!defined $from_seedlot_name && !defined $to_plot_name) {
last;
}

if (!$from_seedlot_name || $from_seedlot_name eq '' ) {
push @error_messages, "Cell A$row_name: from_seedlot_name missing.";
} else {
Expand Down Expand Up @@ -280,9 +284,8 @@ sub _parse_with_plugin {
$transaction_description = $worksheet->get_cell($row,5)->value();
}

#skip blank lines
if (!$to_plot_name && !$from_seedlot_name) {
next;
if (!defined $from_seedlot_name && !defined $to_plot_name) {
last;
}

my $from_seedlot_rs = $schema->resultset("Stock::Stock")->find({
Expand Down
9 changes: 6 additions & 3 deletions lib/CXGN/Stock/Seedlot/ParseUpload/Plugin/SeedlotsToSeedlots.pm
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Original file line number Diff line number Diff line change
Expand Up @@ -136,6 +136,10 @@ sub _validate_with_plugin {
$transaction_description = $worksheet->get_cell($row,5)->value();
}

if (!defined $from_seedlot_name && !defined $to_seedlot_name) {
last;
}

if (!$from_seedlot_name || $from_seedlot_name eq '' ) {
push @error_messages, "Cell A$row_name: from_seedlot_name missing.";
} else {
Expand Down Expand Up @@ -270,9 +274,8 @@ sub _parse_with_plugin {
$transaction_description = $worksheet->get_cell($row,5)->value();
}

#skip blank lines
if (!$to_seedlot_name && !$from_seedlot_name) {
next;
if (!defined $from_seedlot_name && !defined $to_seedlot_name) {
last;
}

my $from_seedlot_rs = $schema->resultset("Stock::Stock")->find({
Expand Down
95 changes: 82 additions & 13 deletions lib/SGN/Controller/AJAX/Stock.pm
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Expand Up @@ -1924,15 +1924,65 @@ sub get_trial_related_stock:Chained('/stock/get_stock') PathPart('datatables/tri
my $trial_related_stock = CXGN::Stock::RelatedStocks->new({dbic_schema => $schema, stock_id =>$stock_id});
my $result = $trial_related_stock->get_trial_related_stock();
my @stocks;
my @accessions;
my @crosses;
my @family_names;
my @plots;
my @subplots;
my @plants;
my @tissue_samples;
my @seedlots;
my @others;
foreach my $r (@$result){
my ($stock_id, $stock_name, $cvterm_name) = @$r;
my $url;
if ($cvterm_name eq 'seedlot'){
$url = qq{<a href = "/breeders/seedlot/$stock_id">$stock_name</a>};
} else {
$url = qq{<a href = "/stock/$stock_id/view">$stock_name</a>};
}
push @stocks, [$url, $cvterm_name, $stock_name];
my ($stock_id, $stock_name, $cvterm_name) = @$r;
my $url;

if ($cvterm_name eq 'cross') {
$url = qq{<a href = "/cross/$stock_id">$stock_name</a>};
} elsif ($cvterm_name eq 'family_name') {
$url = qq{<a href = "/family/$stock_id/">$stock_name</a>};
} else {
$url = qq{<a href = "/stock/$stock_id/view">$stock_name</a>};
}

if ($cvterm_name eq 'accession') {
push @accessions, [$cvterm_name, $url, $stock_name];
} elsif ($cvterm_name eq 'cross') {
push @crosses, [$cvterm_name, $url, $stock_name];
} elsif ($cvterm_name eq 'family_name') {
push @family_names, [$cvterm_name, $url, $stock_name];
} elsif ($cvterm_name eq 'plot') {
push @plots, [$cvterm_name, $url, $stock_name];
} elsif ($cvterm_name eq 'subplot') {
push @subplots, [$cvterm_name, $url, $stock_name];
} elsif ($cvterm_name eq 'plant') {
push @plants, [$cvterm_name, $url, $stock_name];
}
}

if (scalar(@accessions) > 0) {
push @stocks, @accessions;
}
if (scalar(@crosses) > 0) {
push @stocks, @crosses;
}
if (scalar(@family_names) > 0) {
push @stocks, @family_names;
}
if (scalar(@plots) > 0) {
push @stocks, @plots;
}
if (scalar(@subplots) > 0) {
push @stocks, @subplots;
}
if (scalar(@plants) > 0) {
push @stocks, @plants;
}
if (scalar(@seedlots) > 0) {
push @stocks, @seedlots;
}
if (scalar(@others) > 0) {
push @stocks, @others;
}

$c->stash->{rest}={data=>\@stocks};
Expand Down Expand Up @@ -2019,13 +2069,32 @@ sub get_stock_for_tissue:Chained('/stock/get_stock') PathPart('datatables/stock_

my ($stock_id, $stock_name, $cvterm_name) = @$r;

push @stocks, [qq{<a href = "/stock/$stock_id/view">$stock_name</a>}, $cvterm_name, $stock_name];
push @stocks, [$cvterm_name, qq{<a href = "/stock/$stock_id/view">$stock_name</a>}, $stock_name];
}

$c->stash->{rest}={data=>\@stocks};

}


sub get_plot_plant_related_seedlots:Chained('/stock/get_stock') PathPart('datatables/plot_plant_related_seedlots') Args(0){
my $self = shift;
my $c = shift;
my $stock_id = $c->stash->{stock_row}->stock_id();

my $schema = $c->dbic_schema("Bio::Chado::Schema", 'sgn_chado');
my $progenies = CXGN::Stock::RelatedStocks->new({dbic_schema => $schema, stock_id =>$stock_id});
my $result = $progenies->get_plot_plant_related_seedlots();
my @stocks;
foreach my $r (@$result){
my ($transaction_type, $stock_type, $stock_id, $stock_name) = @$r;
push @stocks, [$transaction_type, $stock_type, qq{<a href = "/breeders/seedlot/$stock_id">$stock_name</a>}, $stock_name];
}

$c->stash->{rest}={data=>\@stocks};
}


sub get_stock_datatables_genotype_data : Chained('/stock/get_stock') :PathPart('datatables/genotype_data') : ActionClass('REST') { }

sub get_stock_datatables_genotype_data_GET {
Expand Down Expand Up @@ -2277,7 +2346,7 @@ sub stock_additional_file_upload :Chained('/stock/get_stock') PathPart('upload_a
$c->stash->{rest} = {error=>$result->{error}};
$c->detach();
}

$c->stash->{rest} = { success => 1, file_id => $result->{file_id} };
}

Expand All @@ -2294,11 +2363,11 @@ sub get_accession_additional_file_uploaded :Chained('/stock/get_stock') PathPart
my @file_array;
my %file_info;

my $q = "SELECT file_id, m.create_date, p.sp_person_id, p.username, basename, dirname, filetype
my $q = "SELECT file_id, m.create_date, p.sp_person_id, p.username, basename, dirname, filetype
FROM phenome.stock_file
JOIN metadata.md_files using(file_id)
JOIN metadata.md_files using(file_id)
LEFT JOIN metadata.md_metadata as m using(metadata_id)
LEFT JOIN sgn_people.sp_person as p ON (p.sp_person_id=m.create_person_id)
LEFT JOIN sgn_people.sp_person as p ON (p.sp_person_id=m.create_person_id)
WHERE stock_id=? and m.obsolete = 0 and metadata.md_files.filetype='accession_additional_file_upload' ORDER BY file_id ASC";

my $h = $c->dbc->dbh()->prepare($q);
Expand Down
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