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enable photo traits with brapi #5162

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merged 9 commits into from
Oct 24, 2024
Merged

enable photo traits with brapi #5162

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4bba04a
add photo traits to the BrAPI trait export.
lukasmueller Oct 21, 2024
c605dbe
add is_variable accessor.
lukasmueller Oct 21, 2024
f8d1703
remove deprecated class.
lukasmueller Oct 21, 2024
91ae9bf
if a variable is displayed, show trait properties section, otherwise …
lukasmueller Oct 21, 2024
514093a
fix bizarre request by linter.
lukasmueller Oct 22, 2024
042f72f
change the title of the Trait Properties section to Variable Properties.
lukasmueller Oct 22, 2024
5585831
according to lint, remove undef in return.
lukasmueller Oct 22, 2024
d07bc86
also add multicat while we are at it...
lukasmueller Oct 22, 2024
ad95758
remove variable attribute section for traits.
lukasmueller Oct 23, 2024
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12 changes: 7 additions & 5 deletions lib/CXGN/BrAPI/v2/Scales.pm
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Original file line number Diff line number Diff line change
Expand Up @@ -432,15 +432,17 @@ sub _format_data_type {
if ($value) {
my %formats = (
"categorical" => "Ordinal",
"numeric" => "Numerical",
"qualitative" => "Nominal",
"numerical" => "Numerical",
"nominal" => "Nominal",
"numeric" => "Numerical",
"qualitative" => "Nominal",
"numerical" => "Numerical",
"nominal" => "Nominal",
"code" => "Code",
"date" => "Date" ,
"duration" => "Duration",
"ordinal" => "Ordinal",
"text"=> "Text",
"text" => "Text",
"photo" => "Photo",
"multicat" => "Multicat",
);

$dataType = $formats{lc $value} ? $formats{lc $value} : $dataType;
Expand Down
25 changes: 18 additions & 7 deletions lib/CXGN/Cvterm.pm
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Expand Up @@ -138,7 +138,11 @@ has 'accession' => (
is => 'rw',
);


has 'is_variable' => (
isa => 'Bool',
is => 'rw',
default => sub { return 0; },
);

#########################################

Expand All @@ -149,6 +153,19 @@ sub BUILD {
my $cvterm;
if ($self->cvterm_id){
$cvterm = $self->schema()->resultset("Cv::Cvterm")->find({ cvterm_id => $self->cvterm_id() });

if ($cvterm) {
my $cvterm_rel_rs = $self->schema()->resultset("Cv::CvtermRelationship")->search( { subject_id => $self->cvterm_id });
# require at least one parent to have a variable_of type
#
while (my $row = $cvterm_rel_rs->next()) {
#print STDERR "ROW TYPE: ".$row->type()->name()."\n";
if (uc($row->type()->name) eq uc('variable_of')) {
$self->is_variable(1);
}
}

}
} elsif ($self->accession ) {
my ($db_name, $dbxref_accession) = split "\:", $self->accession;

Expand Down Expand Up @@ -185,12 +202,6 @@ sub BUILD {
return $self;
}







=head2 function get_image_ids

Synopsis: my @images = $self->get_image_ids()
Expand Down
17 changes: 9 additions & 8 deletions lib/SGN/Controller/Cvterm.pm
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Original file line number Diff line number Diff line change
@@ -1,7 +1,7 @@

package SGN::Controller::Cvterm;

use CXGN::Chado::Cvterm; #DEPRECATE this !!
#use CXGN::Chado::Cvterm; #DEPRECATE this !!
use CXGN::Cvterm;

use Moose;
Expand Down Expand Up @@ -35,13 +35,14 @@ sub view_cvterm : Chained('get_cvterm') PathPart('view') Args(0) {
my $cvterm_id = $cvterm ? $cvterm->cvterm_id : undef ;

my $bcs_cvterm = $cvterm->cvterm;


my ($person_id, $user_role, $curator, $submitter, $sequencer);
my $logged_user = $c->user;
my $person_id = $logged_user->get_object->get_sp_person_id if $logged_user;
my $user_role = 1 if $logged_user;
my $curator = $logged_user->check_roles('curator') if $logged_user;
my $submitter = $logged_user->check_roles('submitter') if $logged_user;
my $sequencer = $logged_user->check_roles('sequencer') if $logged_user;
$person_id = $logged_user->get_object->get_sp_person_id if $logged_user;
$user_role = 1 if $logged_user;
$curator = $logged_user->check_roles('curator') if $logged_user;
$submitter = $logged_user->check_roles('submitter') if $logged_user;
$sequencer = $logged_user->check_roles('sequencer') if $logged_user;
my $props = $self->_cvtermprops($cvterm);
my $editable_cvterm_props = "trait_format,trait_default_value,trait_minimum,trait_maximum,trait_details,trait_categories";

Expand Down Expand Up @@ -99,7 +100,7 @@ sub _cvtermprops {
my $properties ;
if ($cvterm) {
my $bcs_cvterm = $cvterm->cvterm;
if (!$bcs_cvterm) { return undef ; }
if (!$bcs_cvterm) { return; }
my $cvtermprops = $bcs_cvterm->search_related("cvtermprops");
while ( my $prop = $cvtermprops->next ) {
push @{ $properties->{$prop->type->name} } , $prop->value ;
Expand Down
12 changes: 9 additions & 3 deletions mason/chado/cvterm.mas
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Original file line number Diff line number Diff line change
Expand Up @@ -47,6 +47,7 @@ my $db_name = $cvterm->db->name;
my $accession = $cvterm->accession;
my $cvterm_name = $cvterm->name;
my $definition = $cvterm->definition;
my $is_variable = $cvterm->is_variable;
my $comment = '' ;#$cvterm->comment;
#$stockref->{props} (hash of arrayrefs of cvtermprops. Keys = prop name, value = prop value)
my $editable_cvterm_props_string = $cvtermref->{editable_cvterm_props};
Expand Down Expand Up @@ -165,7 +166,8 @@ my $edit_privs = $curator ;

% my $props_subtitle = $edit_privs ? "[<a id=\"cvterm_add_props\" href=\"javascript:cvtermprops_addPropDialog()\">Add...</a>]" : "[Add]";

<&| /page/info_section.mas, title => "Trait Properties" , collapsible=> 1, is_subsection => 1, subtitle=>$props_subtitle &>
% if ($is_variable) {
<&| /page/info_section.mas, title => "Variable Properties" , collapsible=> 1, is_subsection => 1, subtitle=>$props_subtitle &>
<& /chado/cvtermprops.mas,
cv_name => 'trait_property',
cvterm_id =>$cvterm_id,
Expand All @@ -176,11 +178,15 @@ my $edit_privs = $curator ;
editable => \@editable_cvterm_props &>
</&>

<h4>Add this term to a list</h4>
% }
% else {


%}

<div id="cvterm_id" style="display:none" ><% $cvterm_name %>|<% $accession %></div>

<&| /page/info_section.mas, title=>"Add to list", collapsible=>1, collapsed=>1 &>
<&| /page/info_section.mas, title=>"Add this term to a list", collapsible=>1, collapsed=>1 &>
<div id="paste_to_list">
LOAD...
</div>
Expand Down