Design Specs: Evidence Handling

API

the base function

by calling the _get_evidence($node,$type) subroutine in lib/API/Object.pm

argument $type is optional. If specified, only this type of evidence is retrieved.

returns a hash reference containing all the types of evidences to the right of the node

 code snippet: 
 sub _get_evidence {
 ...
 ...
 $data{$type}{$evidence}{id} = "$evidence"; 
 $data{$type}{$evidence}{label} = "$label"; 
 $data{$type}{$evidence}{class} = lc($class) if(defined $class);
 ...
 ...
 return %data ? \%data :undef;
 }

use it in each class module

e.g. in lib/API/Object/Gene.pm

 sub gene_ontology {
  ...
  push @{ $data{$facet} }, {
               method        => $1,
               evidence_code => {text=>"$evidence_code",evidence=>$self->_get_evidence($evidence_code)},
               term          => $self->_pack_obj($go_term),
           };
  ...
 }

Template

generic evidence macro

in root/templates/shared/page_elements.tt2 we defined the evidence macro

  [% MACRO evidence(data, id) BLOCK %]

data is the returned hash reference and id sets the div id number/label in case there are multiple evidence display on same page

• e.g. root/templates/classes/gene/overview.tt2

  
    FOREACH sd IN fields.structured_description.data.keys;
          WRAPPER $field_block title=String.capital;
               FOREACH obj IN fields.structured_description.data.$sd;
                   '<div class="text-width" style="margin:0.5em">';
                      markup(obj.text);
                      evidence(obj.evidence,sd);
                   '</div>';
               END;
           END;
    END;
   

DataTable

in the jquery_data_table_html macro we also added evidence handling

if a cell in the table contains evidence information, it will be shown up automatically.

• the data structure returned from API for the cell element should be like:

 { text=>...,
   evidence=>...
 }

eg. gene ontology widget on the gene page