pub;
// expand the title
$pub = chado_expand_var($pub, 'field', 'pub.title');
$pub = chado_expand_var($pub, 'field', 'pub.volumetitle');
// get the citation
$values = array(
'pub_id' => $pub->pub_id,
'type_id' => array(
'name' => 'Citation',
),
);
$citation = chado_generate_var('pubprop', $values);
$citation = chado_expand_var($citation, 'field', 'pubprop.value');
// get the abstract
$values = array(
'pub_id' => $pub->pub_id,
'type_id' => array(
'name' => 'Abstract',
),
);
$abstract = chado_generate_var('pubprop', $values);
$abstract = chado_expand_var($abstract, 'field', 'pubprop.value');
$abstract_text = '';
if ($abstract) {
$abstract_text = htmlspecialchars($abstract->value);
}
// get the author list
$values = array(
'pub_id' => $pub->pub_id,
'type_id' => array(
'name' => 'Authors',
),
);
$authors = chado_generate_var('pubprop', $values);
$authors = chado_expand_var($authors, 'field', 'pubprop.value');
$authors_list = 'N/A';
if ($authors) {
$authors_list = $authors->value;
}
// get the first database cross-reference with a url
$options = array('return_array' => 1);
$pub = chado_expand_var($pub, 'table', 'pub_dbxref', $options);
$dbxref = NULL;
if ($pub->pub_dbxref) {
foreach ($pub->pub_dbxref as $index => $pub_dbxref) {
if ($pub_dbxref->dbxref_id->db_id->urlprefix) {
$dbxref = $pub_dbxref->dbxref_id;
}
}
}
// get the URL
// get the author list
$values = array(
'pub_id' => $pub->pub_id,
'type_id' => array(
'name' => 'URL',
),
);
$options = array('return_array' => 1);
$urls = chado_generate_var('pubprop', $values, $options);
$urls = chado_expand_var($urls, 'field', 'pubprop.value');
$url = '';
if (count($urls) > 0) {
$url = $urls[0]->value;
}?>
type_id->name)) . '.inc';
$inc_path = drupal_realpath(drupal_get_path('module', 'tripal_pub') . "/theme/tripal_pub/pub_types/$inc_name");
if (file_exists($inc_path)) {
require_once "pub_types/$inc_name";
}
else {
// ========================================================================
// TO CUSTOMIZE A SPECIFIC PUBLICATION TYPE, CUT-AND-PASTE THE CODE
// BELOW INTO A NEW FILE WITH THE SAME NAME AS THE TYPE (SEE INSTRUCTIONS
// ABOVE), AND EDIT.
// ========================================================================
// 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
// This table for the analysis has a vertical header (down the first column)
// so we do not provide headers here, but specify them in the $rows array below.
$headers = array();
// 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();
// Title row
$title = '';
if ($url) {
$title = l(htmlspecialchars($pub->title), $url, array('attributes' => array('target' => '_blank')));
}
elseif ($dbxref and $dbxref->db_id->urlprefix) {
$title = l(htmlspecialchars($pub->title), $dbxref->db_id->urlprefix . $dbxref->accession, array('attributes' => array('target' => '_blank')));
}
else {
$title = htmlspecialchars($pub->title);
}
$rows[] = array(
array(
'data' => 'Title',
'header' => TRUE,
'width' => '20%',
),
$title,
);
// Authors row
$rows[] = array(
array(
'data' => 'Authors',
'header' => TRUE
),
$authors_list,
);
// Type row
$rows[] = array(
array(
'data' => 'Type',
'header' => TRUE
),
$pub->type_id->name,
);
// Media Title
$rows[] = array(
array(
'data' => 'Media Title',
'header' => TRUE,
'nowrap' => 'nowrap'
),
$pub->series_name,
);
// Volume
$rows[] = array(
array(
'data' => 'Volume',
'header' => TRUE
),
$pub->volume ? $pub->volume : 'N/A',
);
// Issue
$rows[] = array(
array(
'data' => 'Issue',
'header' => TRUE
),
$pub->issue ? $pub->issue : 'N/A'
);
// Year
$rows[] = array(
array(
'data' => 'Year',
'header' => TRUE
),
$pub->pyear
);
// Pages
$rows[] = array(
array(
'data' => 'Page(s)',
'header' => TRUE
),
$pub->pages ? $pub->pages : 'N/A'
);
// Citation row
$rows[] = array(
array(
'data' => 'Citation',
'header' => TRUE
),
htmlspecialchars($citation->value)
);
// allow site admins to see the pub ID
if (user_access('view ids')) {
// Pub ID
$rows[] = array(
array(
'data' => 'Pub ID',
'header' => TRUE,
'class' => 'tripal-site-admin-only-table-row',
),
array(
'data' => $pub->pub_id,
'class' => 'tripal-site-admin-only-table-row',
),
);
}
// Is Obsolete Row
if($pub->is_obsolete == TRUE){
$rows[] = array(
array(
'data' => 'This publication is obsolete
',
'colspan' => 2
),
);
}
// 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' => $rows,
'attributes' => array(
'id' => 'tripal_pub-table-base',
'class' => 'tripal-data-table'
),
'sticky' => FALSE,
'caption' => '',
'colgroups' => array(),
'empty' => '',
);
// once we have our table array structure defined, we call Drupal's theme_table()
// function to generate the table.
print theme_table($table);
if ($abstract_text) { ?>
Abstract