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Anthony Bretaudeau authored4cd4c20c
tripal_feature_relationships.tpl.php 9.09 KiB
<?php
/* Typically in a Tripal template, the data needed is retrieved using a call to
* chado_expand_var function. For example, to retrieve all
* of the feature relationships for this node, the following function call would
* be made:
*
* $feature = chado_expand_var($feature,'table','feature_relationship');
*
* However, this function call can be extremely slow when there are numerous
* relationships. This is because the chado_expand_var function is recursive
* and expands all data following the foreign key relationships tree.
* Therefore, to speed retrieval of data, a special variable is provided to
* this template:
*
* $feature->all_relationships;
*
* This variable is an array with two sub arrays with the keys 'object' and
* 'subject'. The array with key 'object' contains relationships where the
* feature is the object, and the array with the key 'subject' contains
* relationships where the feature is the subject
*/
$feature = $variables['node']->feature;
$all_relationships = $feature->all_relationships;
$object_rels = $all_relationships['object'];
$subject_rels = $all_relationships['subject'];
if (count($object_rels) > 0 or count($subject_rels) > 0) { ?>
<div class="tripal_feature-data-block-desc tripal-data-block-desc"></div> <?php
// first add in the subject relationships.
foreach ($subject_rels as $rel_type => $rels){
foreach ($rels as $obj_type => $objects){
// Make the verb in the sentence make sense in English.
switch ($rel_type) {
case 'integral part of':
case 'instance of':
$verb = 'is an';
break;
case 'proper part of':
case 'transformation of':
case 'genome of':
case 'part of':
case 'position of':
case 'sequence of':
case 'variant of':
$verb = 'is a';
break;
case 'derives from':
case 'connects on':
case 'contains':
case 'finishes':
case 'guides':
case 'has origin':
case 'has part':
case 'has quality':
case 'is consecutive sequence of':
case 'maximally overlaps':
case 'overlaps':
case 'starts':
$verb = '';
break;
default:
$verb = 'is';
} ?>
<p>This <?php print $feature->type_id->name;?> <?php print $verb ?> <?php print $rel_type ?> the following <b><?php print $obj_type ?></b> feature(s): <?php
// the $headers array is an array of fields to use as the colum headers. // additional documentation can be found here
// https://api.drupal.org/api/drupal/includes%21theme.inc/function/theme_table/7
$headers = array('Feature Name' ,'Unique Name', 'Species', 'Type', 'Position');
// the $rows array contains an array of rows where each row is an array
// of values for each column of the table in that row. Additional documentation
// can be found here:
// https://api.drupal.org/api/drupal/includes%21theme.inc/function/theme_table/7
$rows = array();
foreach ($objects as $object){
// link the feature to it's node
$feature_name = $object->record->object_id->name;
if (property_exists($object->record, 'nid')) {
$feature_name = l($feature_name, "node/" . $object->record->nid, array('attributes' => array('target' => "_blank")));
}
// link the organism to it's node
$organism = $object->record->object_id->organism_id;
$organism_name = $organism->genus ." " . $organism->species;
if (property_exists($organism, 'nid')) {
$organism_name = l("<i>" . $organism->genus . " " . $organism->species . "</i>", "node/" . $organism->nid, array('html' => TRUE));
}
$location = '?';
if (isset($object->parent_featurelocs[0])) {
$loc = $object->parent_featurelocs[0];
$location = $loc->srcfeature_name.' '. ($loc->fmin + 1) . ".." . $loc->fmax . " " . ($loc->strand == -1 ? '-' : '+');
}
$rows[] = array(
array('data' => $feature_name, 'width' => '28%'),
array('data' => $object->record->object_id->uniquename, 'width' => '25%'),
array('data' => $organism_name, 'width' => '25%'),
array('data' => $object->record->object_id->type_id->name, 'width' => '12%'),
array('data' => $location, 'width' => '12%'),
);
}
// the $table array contains the headers and rows array as well as other
// options for controlling the display of the table. Additional
// documentation can be found here:
// https://api.drupal.org/api/drupal/includes%21theme.inc/function/theme_table/7
$table = array(
'header' => $headers,
'rows' => $rows,
'attributes' => array(
'id' => 'tripal_feature-table-relationship-object',
'class' => 'tripal-data-table'
),
'sticky' => FALSE,
'caption' => '',
'colgroups' => array(),
'empty' => '',
);
// once we have our table array structure defined, we call Drupal's theme_table()
// function to generate the table.
print theme_table($table); ?>
</p>
<br><?php
}
}
// second add in the object relationships.
foreach ($object_rels as $rel_type => $rels){
foreach ($rels as $subject_type => $subjects){
// Make the verb in the sentence make sense in English.
switch ($rel_type) {
case 'integral part of':
case 'instance of':
$verb = 'are an'; break;
case 'proper part of':
case 'transformation of':
case 'genome of':
case 'part of':
case 'position of':
case 'sequence of':
case 'variant of':
$verb = 'are a';
break;
case 'derives from':
case 'connects on':
case 'contains':
case 'finishes':
case 'guides':
case 'has origin':
case 'has part':
case 'has quality':
case 'is consecutive sequence of':
case 'maximally overlaps':
case 'overlaps':
case 'starts':
$verb = '';
break;
default:
$verb = 'are';
} ?>
<p>The following <b><?php print $subjects[0]->record->subject_id->type_id->name ?></b> feature(s) <?php print $verb ?> <?php print $rel_type ?> this <?php print $feature->type_id->name;?>: <?php
// the $headers array is an array of fields to use as the colum headers.
// additional documentation can be found here
// https://api.drupal.org/api/drupal/includes%21theme.inc/function/theme_table/7
$headers = array('Feature Name' ,'Unique Name', 'Species', 'Type', 'Position');
// the $rows array contains an array of rows where each row is an array
// of values for each column of the table in that row. Additional documentation
// can be found here:
// https://api.drupal.org/api/drupal/includes%21theme.inc/function/theme_table/7
$rows = array();
foreach ($subjects as $subject){
// link the feature to it's node
$feature_name = $subject->record->subject_id->name;
if (property_exists($subject->record, 'nid')) {
$feature_name = l($feature_name, "node/" . $subject->record->nid, array('attributes' => array('target' => "_blank")));
}
// link the organism to it's node
$organism = $subject->record->subject_id->organism_id;
$organism_name = $organism->genus ." " . $organism->species;
if (property_exists($organism, 'nid')) {
$organism_name = l("<i>" . $organism->genus . " " . $organism->species . "</i>", "node/" . $organism->nid, array('html' => TRUE));
}
$location = '?';
if (isset($subject->child_featurelocs[0])) {
$loc = $subject->child_featurelocs[0];
$location = $loc->srcfeature_name.' '. ($loc->fmin + 1) . ".." . $loc->fmax . " " . ($loc->strand == -1 ? '-' : '+');
}
$rows[] = array(
array('data' => $feature_name, 'width' => '28%'),
array('data' =>$subject->record->subject_id->uniquename, 'width' => '25%'),
array('data' =>$organism_name, 'width' => '25%'),
array('data' =>$subject->record->subject_id->type_id->name, 'width' => '12%'),
array('data' => $location, 'width' => '12%'),
);
}
// the $table array contains the headers and rows array as well as other
// options for controlling the display of the table. Additional
// documentation can be found here:
// https://api.drupal.org/api/drupal/includes%21theme.inc/function/theme_table/7
$table = array( 'header' => $headers,
'rows' => $rows,
'attributes' => array(
'id' => 'tripal_feature-table-relationship-subject',
'class' => 'tripal-data-table'
),
'sticky' => FALSE,
'caption' => '',
'colgroups' => array(),
'empty' => '',
);
// once we have our table array structure defined, we call Drupal's theme_table()
// function to generate the table.
print theme_table($table); ?>
</p>
<br><?php
}
}
}