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| <?php | ||
|
|
||
| /** | ||
| * Provides a search for SO:sequence_variant chado feature-based Tripal Content. | ||
| * | ||
| */ | ||
| class SequenceVariantSearch extends KPSEARCH { | ||
|
|
||
| /** | ||
| * The human readable title of this search. This will be used in listings | ||
| * and shown on the search page as the title. | ||
| */ | ||
| public static $title = 'Sequence Variant Search'; | ||
|
|
||
| /** | ||
| * The machine name of the module providing this search. | ||
| */ | ||
| public static $module = 'kp_searches'; | ||
|
|
||
| /** | ||
| * A description of this search. This is shown at the top of the search page | ||
| * and used for the menu item. | ||
| */ | ||
| public static $description = 'While the term variant refers to a position in the genome with variation, genetic marker refers specifically to an assay which samples that variation.'; | ||
|
|
||
| /** | ||
| * The machine names of the permissions with access to this search. This is | ||
| * used to map your search to existing permissions. It must be an array and | ||
| * is used in hook_menu(). Some examples include 'access content' | ||
| * and 'administer tripal'. | ||
| */ | ||
| public static $permissions = ['access content']; | ||
|
|
||
| /** | ||
| * If TRUE, this search will require the submit button to be clicked before | ||
| * executing the query; whereas, if FALSE it will be executed on the | ||
| * first page load without parameters. | ||
| * | ||
| * NOTE: to control the results without parameters check $this->submitted | ||
| * in getQuery() and if FALSE return your pre-submit query. | ||
| */ | ||
| public static $require_submit = TRUE; | ||
|
|
||
| /** | ||
| * Add a pager to search results | ||
| * with $num_items_per_page results on a single page. | ||
| * NOTE: Your query has to handle paging. | ||
| */ | ||
| public static $pager = TRUE; | ||
| public static $num_items_per_page = 50; | ||
|
|
||
| /** | ||
| * This defined the hook_menu definition for this search. At a minimum the | ||
| * path is required. | ||
| */ | ||
| public static $menu = [ | ||
| 'path' => 'search/variants', | ||
| // @todo support menu items. | ||
| ]; | ||
|
|
||
| /** | ||
| * Add CSS/JS to the form/results page. | ||
| * NOTE: paths supplied should be relative to $module. | ||
| */ | ||
| public static $attached = [ | ||
| 'css' => [ | ||
| 'css/all_kp_searches.css', | ||
| ], | ||
| 'js' => [], | ||
| ]; | ||
|
|
||
| /** | ||
| * Information regarding the fields and filters for this search. | ||
| */ | ||
| public static $info = [ | ||
| // Lists the columns in your results table. | ||
| 'fields' => [ | ||
| 'name' => [ | ||
| 'title' => 'Name', | ||
| 'entity_link' => [ | ||
| 'chado_table' => 'feature', | ||
| 'id_column' => 'feature_id' | ||
| ], | ||
| ], | ||
| 'type' => [ | ||
| 'title' => 'Variant Type', | ||
| ], | ||
| 'species' => [ | ||
| 'title' => 'Source Species', | ||
| 'entity_link' => [ | ||
| 'chado_table' => 'organism', | ||
| 'id_column' => 'organism_id' | ||
| ], | ||
| ], | ||
| ], | ||
| // The filter criteria available to the user. | ||
| // This is used to generate a search form which can be altered. | ||
| 'filters' => [ | ||
| 'genus' => [ | ||
| 'title' => 'Genus', | ||
| 'help' => 'The legume species the Sequence Variant was designed for (e.g. Lens culinaris).', | ||
| ], | ||
| 'species' => [ | ||
| 'title' => 'Species', | ||
| 'help' => '', | ||
| ], | ||
| 'type' => [ | ||
| 'title' => 'Variant Type', | ||
| 'help' => 'The type of variant you are interested in (e.g. SNP).', | ||
| //'default' => 'Exome Capture', | ||
| ], | ||
| 'project' => [ | ||
| 'title' => 'Experiment', | ||
| 'help' => 'The experiment you are interested in (e.g. AGILE; partial names are accepted).', | ||
| ], | ||
| 'start-backbone' => [ | ||
| 'title' => 'Start: Backbone', | ||
| 'help' => 'The name of the sequence the variants are located on.' | ||
| ], | ||
| 'start-pos' => [ | ||
| 'title' => 'Start: Position', | ||
| 'help' => 'The numeric start position of the range you are interested in.' | ||
| ], | ||
| 'end-pos' => [ | ||
| 'title' => 'End: Position', | ||
| 'help' => 'The numeric end position of the range you are interested in.' | ||
| ], | ||
| 'name' => [ | ||
| 'title' => 'Name', | ||
| 'help' => 'The name or accession of the variant (e.g. LcC00002p390; partial names are accepted).', | ||
| ], | ||
| ], | ||
| ]; | ||
|
|
||
| /** | ||
| * Text that should appear on the button at the bottom of the importer | ||
| * form. | ||
| */ | ||
| public static $button_text = 'Search'; | ||
|
|
||
| /** | ||
| * Generate the filter form. | ||
| * | ||
| * The base class will generate textfields for each filter defined in $info, | ||
| * set defaults, labels and descriptions, as well as, create the search | ||
| * button. | ||
| * | ||
| * Extend this method to alter the filter form. | ||
| */ | ||
| public function form($form, $form_state) { | ||
| $form = parent::form($form, $form_state); | ||
|
|
||
| // Add a crop selector. | ||
| $this->addCropFormElement($form, $form_state); | ||
|
|
||
| // Add a Scientific name selector. | ||
| $this->addSpeciesFormElement($form, $form_state); | ||
|
|
||
| // Make the variant type a drop-down. | ||
| $options = unserialize(variable_get('kp_searches_variant_types', 'a:0{}')); | ||
| $form['type']['#type'] = 'select'; | ||
| $form['type']['#options'] = $options; | ||
| $form['type']['#empty_option'] = ' - Select -'; | ||
|
|
||
| // Make the project an autocomplete. | ||
| // DEPENDENCY: nd_genotypes. | ||
| $form['project']['#autocomplete_path'] = 'tripal_ajax/nd_genotypes/project/name'; | ||
|
|
||
| // Add a sequence range element. | ||
| $description = 'The range of the genome you would like to display variants from.'; | ||
| $form['seq_range'] = array( | ||
| '#type' => 'markup', | ||
| '#prefix' => '<div class="seq-range-element form-item"><label>Genome Range</label>', | ||
| '#suffix' => '<div class="description">' . $description . '</div></div>', | ||
| ); | ||
| // Group the sequence range elements. | ||
| $form['seq_range']['start-label'] = [ | ||
| '#type' => 'item', | ||
| '#markup' => 'From', | ||
| ]; | ||
| $form['seq_range']['start-backbone'] = $form['start-backbone']; | ||
| $form['seq_range']['start-backbone']['#attributes']['placeholder'] = 'Sequence Name'; | ||
| unset($form['start-backbone']); | ||
| $form['seq_range']['start-pos'] = $form['start-pos']; | ||
| $form['seq_range']['start-pos']['#attributes']['placeholder'] = 'Start Position'; | ||
| unset($form['start-pos']); | ||
| $form['seq_range']['end-label'] = [ | ||
| '#type' => 'item', | ||
| '#markup' => 'to', | ||
| ]; | ||
| $form['seq_range']['end-pos'] = $form['end-pos']; | ||
| $form['seq_range']['end-pos']['#attributes']['placeholder'] = 'End Position'; | ||
| unset($form['end-pos']); | ||
|
|
||
| return $form; | ||
| } | ||
|
|
||
| /** | ||
| * Allows custom searches to validate the form results. | ||
| * Use form_set_error() to signal invalid values. | ||
| */ | ||
| public function validateForm($form, $form_state) { | ||
| $values = $form_state['values']; | ||
|
|
||
| // If any of the range elements are filled out... | ||
| if ($values['start-backbone'] != '' | ||
| OR $values['start-pos'] != '' | ||
| OR $values['end-pos'] != '') { | ||
|
|
||
| // Then they all need to be! | ||
| if ($values['start-backbone'] == '') { | ||
| form_set_error('start-backbone', | ||
| 'Genome Range: The sequence name is required.'); | ||
| } | ||
| if ($values['start-pos'] == '') { | ||
| form_set_error('start-pos', | ||
| 'Genome Range: The range start position is required.'); | ||
| } | ||
| if ($values['end-pos'] == '') { | ||
| form_set_error('end-pos', | ||
| 'Genome Range: The range end position is required.'); | ||
| } | ||
| } | ||
| } | ||
|
|
||
| /** | ||
| * Determine the query for the Sequence Variant search. | ||
| * | ||
| * @param string $query | ||
| * The full SQL query to execute. This will be executed using chado_query() | ||
| * so use curly brackets appropriately. Use :placeholders for any values. | ||
| * @param array $args | ||
| * An array of arguments to pass to chado_query(). Keys must be the | ||
| * placeholders in the query and values should be what you want them set to. | ||
| */ | ||
| public function getQuery(&$query, &$args, $offset) { | ||
|
|
||
| // Retrieve the filter results already set. | ||
| $filter_results = $this->values; | ||
| // @debug dpm($filter_results, '$filter_results'); | ||
|
|
||
| $query = " | ||
| SELECT variant.feature_id, variant.name as name, type.value as type, o.organism_id, o.genus||' '||o.species as species | ||
| FROM {feature} variant | ||
| LEFT JOIN {organism} o ON o.organism_id=variant.organism_id | ||
| LEFT JOIN {featureprop} type ON type.feature_id = variant.feature_id | ||
| AND type.type_id IN | ||
| (SELECT cvterm_id FROM chado.cvterm WHERE name='additionalType') "; | ||
|
|
||
| $where = ["variant.type_id IN (SELECT cvterm_id FROM {cvterm} WHERE name='sequence_variant')"]; | ||
| $joins = []; | ||
|
|
||
| // -- Genus. | ||
| if ($filter_results['genus'] != '') { | ||
| $where[] = "o.genus ~* :genus"; | ||
| $args[':genus'] = $filter_results['genus']; | ||
| } | ||
|
|
||
| // -- Species. | ||
| if ($filter_results['species'] != '') { | ||
| $where[] = "o.species ~* :species"; | ||
| $args[':species'] = $filter_results['species']; | ||
| } | ||
|
|
||
| // -- Type. | ||
| if ($filter_results['type'] != '') { | ||
| $where[] = "type.value ~ :type"; | ||
| $args[':type'] = $filter_results['type']; | ||
| } | ||
|
|
||
| // -- Project. | ||
| if ($filter_results['project'] != '') { | ||
| $where[] = "project.name ~ :project"; | ||
| $args[':project'] = $filter_results['project']; | ||
| $joins[] = 'LEFT JOIN {project_feature} pf ON pf.feature_id=variant.feature_id'; | ||
| $joins[] = 'LEFT JOIN {project} project ON project.project_id=pf.project_id'; | ||
| } | ||
|
|
||
| // -- Name. | ||
| if ($filter_results['name'] != '') { | ||
| $where[] = "(variant.name ~ :name OR variant.uniquename = :name)"; | ||
| $args[':name'] = $filter_results['name']; | ||
| } | ||
|
|
||
| // -- Genome Range. | ||
| if ($filter_results['start-pos'] != '' | ||
| AND $filter_results['end-pos'] != '') { | ||
|
|
||
| $joins[] = 'LEFT JOIN {featureloc} loc | ||
| ON loc.feature_id=variant.feature_id'; | ||
| $where[] = 'loc.fmin BETWEEN :start AND :end'; | ||
| $args[':start'] = $filter_results['start-pos']; | ||
| $args[':end'] = $filter_results['end-pos']; | ||
| $where[] = 'loc.srcfeature_id IN | ||
| (SELECT feature_id FROM {feature} | ||
| WHERE name=:backbone OR uniquename=:backbone)'; | ||
| $args[':backbone'] = $filter_results['start-backbone']; | ||
| } | ||
|
|
||
| // Finally, add it to the query. | ||
| if (!empty($joins)) { | ||
| $query .= implode("\n",$joins); | ||
| } | ||
| if (!empty($where)) { | ||
| $query .= "\n" . ' WHERE ' . implode(' AND ',$where); | ||
| } | ||
|
|
||
| // Sort even though it is SLOW b/c ppl expect it. | ||
| $query .= "\n" . ' ORDER BY variant.name ASC'; | ||
|
|
||
| // Handle paging. | ||
| $limit = $this::$num_items_per_page + 1; | ||
| $query .= "\n" . ' LIMIT ' . $limit . ' OFFSET ' . $offset; | ||
|
|
||
| // @debug dpm(strtr(str_replace(['{','}'], ['chado.', ''], $query), $args), 'query'); | ||
| } | ||
| } |
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