mason/ontology/associate_ontology.mas

   1 <%doc>
   2
   3 =head1 NAME
   4
   5 /ontology/associate_ontology.mas - a component for printing a generic 'associate_ontology' javasript form and displaying the ontology annotation
   6
   7 =head1 DESCRIPTION
   8
   9
  10 Parameters:
  11
  12 =over 9
  13
  14 =item object_id
  15
  16 a database id
  17
  18 =item object_name
  19
  20 the type of the object you are annotating
  21
  22 =item cvterm_autocomplete_uri
  23
  24 defaults to /ajax/cvterm/autocomplete
  25
  26 =item cvterm_add_uri
  27
  28 the uri for associating the cvterm with your object
  29
  30 =iterm relationships_uri
  31
  32 populate the relationships drop down menu. defaults to /ajax/cvterm/relationships
  33
  34 =item evidence_uri
  35
  36 populate the evidence code menu. Defaults to /ajax/cvterm/evidence
  37
  38 =item evidence_description_uri
  39
  40 populate the evidence description menu. Defaults to /ajax/cvterm/evidence_description
  41
  42 =iterm show_form
  43
  44 whether the associate form should be printed. Usually only if the user is logged-in
  45
  46 =item ontology_url
  47
  48 the url for displaying the ontology annotation
  49
  50 =back
  51
  52 =head1 AUTHOR
  53
  54 Naama Menda <nm249@cornell.edu>
  55
  56 =cut
  57
  58
  59 </%doc>
  60
  61 <%args>
  62
  63 $object_id
  64 $object_name
  65 $cvterm_autocomplete_uri  => '/ajax/cvterm/autocomplete'
  66 $cvterm_add_uri
  67 $relationships_uri => '/ajax/cvterm/relationships'
  68 $evidence_uri => '/ajax/cvterm/evidence'
  69 $evidence_description_uri => '/ajax/cvterm/evidence_description'
  70 $reference_uri => '/stock/'.$object_id.'/references'
  71 $show_form => 0
  72 $div_id => 'ontology_terms'
  73 $ontology_url
  74
  75 </%args>
  76
  77 <style>
  78   #ontology .evidence {
  79     margin: 1em 0 0 4em;
  80     width: 50%;
  81     border: 1px dotted gray;
  82     padding: 10px;
  83   }
  84   #ontology_show_details {
  85     text-align: right;
  86     margin-bottom: -2em;
  87   }
  88   #ontology_show_details label {
  89     font-weight: bold;
  90   }
  91   .active#ontology_show_details {
  92     background: white;
  93   }
  94 </style>
  95
  96 <& /util/import_javascript.mas, classes=>[qw[ jquery jqueryui popup CXGN.AJAX.Ontology] ]&>
  97
  98   <div id="ontology_show_details" style="display: none">
  99     <form> <input type="checkbox" id="show_details" disabled="true" />
 100       <label for="show_details">Show complete details</label>
 101     </form>
 102   </div>
 103
 104 <div id="ontology" >[loading...] </div>
 105
 106 <script language="javascript">
 107
 108
 109   Ontology.displayOntologies("ontology" , "<% $ontology_url %>");
 110
 111 </script>
 112
 113 % if ($show_form) {
 114 <div id="associate_cvterm_form">
 115   <b>Associate ontology term</b>
 116   <form name="cvterm_form" >
 117     <div id="cvterm_search" >
 118       <input type="text" style="width: 50%" id="term_name" name="term_name" value="Type a term name" onchange="Ontology.updateAutocomplete('<% $cvterm_autocomplete_uri %>')" />
 119       <input type="hidden" id="object_id" name="object_id" value="<% $object_id %>" />
 120
 121       <select id = "db_name" onchange="jQuery('#term_name').val('---Type a term name---')")">
 122         <option value="GO">GO (gene ontology)</option>
 123         <option value="PO">PO (plant ontology)</option>
 124         <option value="SP">SP (Solanaceae phenotypes)</option>
 125       </select><br>
 126
 127       <div style="font-size: 80%; margin-left: 1em; color: #333">type a cvterm name</div>
 128       <div id ="ontology_evidence">
 129         <b>Relationship type:</b>
 130     <select id="relationship_select" style="width: 100%"
 131             onchange="Ontology.populateEvidence('evidence_code_select', '<% $evidence_uri %>' )">
 132     </select>
 133     <b>Evidence code:</b>
 134     <select id="evidence_code_select" style="width: 100%"
 135             onchange="jQuery('#associate_ontology_button').removeAttr('disabled');Ontology.populateEvidence('evidence_description_select', '<% $evidence_description_uri %>' + '?evidence_code_id=' + jQuery('#evidence_code_select').val() );Ontology.getEvidenceWith();Ontology.populateEvidence('reference_select', '<% $reference_uri %>')">
 136     </select>
 137
 138     <b>Evidence description:</b>
 139     <select id="evidence_description_select" style="width: 100%">
 140     </select>
 141
 142     <b>Evidence with:</b>
 143     <select id="evidence_with_select" style="width: 100%">
 144     </select>
 145
 146     <b>Reference:</b>
 147     <select id="reference_select" style="width: 100%">
 148     </select>
 149     <div id="ontology_select_button">
 150       <input type="button"
 151              id="associate_ontology_button"
 152              value="associate term"
 153              disabled="true"
 154              onclick="javascript:Ontology.submitCvtermForm('<% $cvterm_add_uri %>', '<% $ontology_url %>');this.disabled=true"
 155              </div>
 156       </div>
 157
 158     </div>
 159   </form>
 160 </div>
 161
 162 % }