tripal_stock_nd_phenotypes.tpl.php
- 2.x tripal_natural_diversity/theme/templates/tripal_stock_nd_phenotypes.tpl.php
- 3.x legacy/tripal_natural_diversity/theme/templates/tripal_stock_nd_phenotypes.tpl.php
1 theme call to tripal_stock_nd_phenotypes.tpl.php
- tripal_natural_diversity_node_view in tripal_natural_diversity/
tripal_natural_diversity.module - Implements hook_node_view(). Acts on all content types.
File
tripal_natural_diversity/theme/templates/tripal_stock_nd_phenotypes.tpl.phpView source
- <?php
- /*
- * Phenotype relationships with stocks are stored in the natural diversity tables.
- * If a stock has phenotypes associated then you can find the data by traversing
- * the foreign key (FK) relationships in this manner:
- *
- * stock => nd_experiment_stock => nd_experiment => nd_experiment_phenotype => phenotype.
- *
- * You can find ancillary information about data associated with a phenotype such as
- * a contact, pub, protocol, project, phenotype, dbxref by using the
- * nd_experiment.nd_experiment_id value and traversing the other FK relationships
- *
- * stock => nd_experiment_stock => nd_experiment => nd_experiment_phenotype => phenotype
- * => nd_experiment_phenotype => phenotype
- * => nd_experiment_project => project
- * => nd_experiment_pub => pub
- * => nd_experiment_contact => contact
- * => nd_experiment_dbxref => dbxref
- * => nd_experiment_protocol => protocol
- * => nd_experiment_stockprop
- * => nd_experiment_stock_dbxref
- *
- * In the FK relationships shown above, the nd_experiment_id value represents a single
- * experimental value that may have all of the ancilliary data associated with it.
- * If the phenotype record shares an nd_experiment_id with a phenotype, pub, contact,
- * protocol, etc then all of that data is associated with the phenotype and vice-versa.
- *
- * Techincally, we can skip including the 'nd_experiment' table when traversing the FK's
- * because we have the nd_experiment_id value when we get the nd_experiment_stock record.
- *
- * When lots of phenotypes are associated with a stock (e.g. thousands) then traversing
- * the FK relationships as described above can be very slow. Ideally, we only need to
- * show a small subset with a pager. Therefore, a list of nd_experiment_phenotype_id's
- * are provided to this template automatically within the stock object.
- *
- */
-
- // get the current stock
- $stock = $variables['node']->stock;
-
- // specify the number of phenotypes to show by default and the unique pager ID
- $num_results_per_page = 25;
- $stock_pager_id = 10;
-
-
- // the nd_experiment_phenotype IDs get passed into this template, so we use
- // those to iterate and show a subset via a pager. This is faster than trying
- // to traverse all of the FK relationship, especially when thousands of
- // associations may be present. Because the nd_experiment_id in Chado
- // can be associated with other data types it becomes slow to use the
- // chado_expand_var functions that we would normal use.
- $nd_experiment_phenotype_ids = $stock->nd_experiment_phenotype_ids;
- $total_records = count($nd_experiment_phenotype_ids);
-
- // initialize the Drupal pager
- $current_page_num = pager_default_initialize($total_records, $num_results_per_page, $stock_pager_id);
- $offset = $num_results_per_page * $current_page_num;
-
-
- $phenotypes = array();
- if ($total_records > 0) {
-
- // iterate through the nd_experiment_phenotype_ids and get the phenotype record
- for ($i = $offset ; $i < $offset + $num_results_per_page; $i++) {
- // expand the nd_experiment record to include the nd_experiment_phenotype table
- // there many be many phenotypes for a stock so we want to use a pager to limit
- // the results returned
- $options = array(
- 'return_array' => 1,
- 'include_fk' => array(
- 'phenotype_id' => array(
- 'type_id' => 1,
- )
- ),
- );
- $values = array('nd_experiment_phenotype_id' => $nd_experiment_phenotype_id);
- $nd_experiment_phenotype = chado_generate_var('nd_experiment_phenotype', $values);
- $phenotype = $nd_experiment_phenotype->phenotype_id;
- $phenotypes[$phenotype->phenotype_id]['phenotype'] = $phenotype;
- $phenotypes[$phenotype->phenotype_id]['nd_experiment_id'] = $nd_experiment_phenotype->nd_experiment_id->nd_experiment_id;
- }
- }
-
- if (count($phenotypes) > 0) {?>
- <div class="tripal_stock-data-block-desc tripal-data-block-desc">
- The following <?php print number_format($total_records) ?> phenotypes(s) have been recorded.
- </div><?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('Phenotypes', 'Project');
-
- // 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
- $rows = array();
-
- // iterate through the nd_experiment_stock records and get
- // each experiment and the associated phenotypes
- foreach ($phenotypes as $info){
- $phenotype = $info['phenotype'];
- $nd_experiment_id = $info['nd_experiment_id'];
-
- // get the nd_experiment record
- $nd_experiment = chado_generate_var('nd_experiment', array('nd_experiment_id' => $nd_experiment_id));
-
- $details = '';
-
- if ($phenotype->name) {
- $details .= "Name: $phenotype->name<br>";
- }
-
- // add in the attribute type pheonotypes values are stored qualitatively or quantitatively.
- // If qualitatively the cvalue_id will link to a type. If quantitative we
- // use the value column
- $details .= ucwords(preg_replace('/_/', ' ', $phenotype->attr_id->name)) . ': ';
- if ($phenotype->cvalue_id) {
- $details .= ucwords(preg_replace('/_/', ' ', $phenotype->cvalue_id->name)) . '<br>';
- }
- else {
- $details .= $phenotype->value . '<br>';
- }
-
- // get the observable unit and add it to the details
- if ($phenotype->observable_id) {
- $details .= "Observable Unit: " . ucwords(preg_replace('/_/', ' ', $phenotype->observable_id->name)) . '<br>';
- }
-
- // get the evidence unit and add it to the details
- if ($phenotype->assay_id) {
- $details .= "Evidence: " . ucwords(preg_replace('/_/', ' ', $phenotype->assay_id->name)) . '<br>';
- }
-
- // Get the project for this experiment. For each nd_experiment_id there should only be one project
- // but the database does not constrain that there only be one project so just in case we get them all
- $projects = array();
- $values = array('nd_experiment_id' => $nd_experiment_stock->nd_experiment_id->nd_experiment_id);
- $nd_experiment_project = chado_generate_var('nd_experiment_project', $values, $options);
- $nd_experiment_projects = $nd_experiment_project;
- foreach ($nd_experiment_projects as $nd_experiment_project) {
- // we do have a project record, so add it to our $phenotypes array for display below
- $projects = $nd_experiment_project->project_id;
- }
- $pnames = 'N/A';
- foreach ($projects as $project) {
- $project = $project->project_id;
- $name = $project->name;
- if (property_exists($project, 'nid')) {
- $name = l($name, "node/" . $project->nid, array('attributes' => array('target' => '_blank')));
- }
- $pnames .= $name . '<br>';
- }
- $pnames = substr($pnames, 0, -4); // remove trailing <br>
-
- $rows[] = array(
- $details,
- $pnames,
- );
- }
- // 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' => $rows,
- 'attributes' => array(
- 'id' => 'tripal_natural_diversity-table-phenotypes',
- 'class' => 'tripal-data-table'
- ),
- 'sticky' => FALSE,
- 'caption' => '',
- 'colgroups' => array(),
- 'empty' => '',
- );
- // once we have our table array structure defined, we call Drupal's theme_table()
- // function to generate the table.
- print theme_table($table);
-
- // the $pager array values that control the behavior of the pager. For
- // documentation on the values allows in this array see:
- // https://api.drupal.org/api/drupal/includes!pager.inc/function/theme_pager/7
- // here we add the paramter 'block' => 'features'. This is because
- // the pager is not on the default block that appears. When the user clicks a
- // page number we want the browser to re-appear with the page is loaded.
- // We remove the 'pane' parameter from the original query parameters because
- // Drupal won't reset the parameter if it already exists.
- $get = $_GET;
- unset($_GET['pane']);
- $pager = array(
- 'tags' => array(),
- 'element' => $stock_pager_id,
- 'parameters' => array(
- 'pane' => 'genotypes'
- ),
- 'quantity' => $num_results_per_page,
- );
- print theme_pager($pager);
- $_GET = $get;
- }