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- <?php
- /**
- * @file
- * Provides API functions specificially for managing feature
- * records in Chado.
- */
- /**
- * @defgroup tripal_organism_api Chado Organism
- * @ingroup tripal_chado_api
- * @{
- * Provides API functions specificially for managing organism
- * records in Chado.
- * @}
- */
- /**
- * Retrieves a chado organism variable.
- *
- * @param $identifier
- * An array with the key stating what the identifier is. Supported keys (only
- * on of the following unique keys is required):
- * - organism_id: the chado organism.organism_id primary key.
- * - genus & species: the chado organism.genus field & organism.species
- * field. There are also some specially handled keys. They are:
- * - property: An array/object describing the property to select records
- * for.
- * It should at least have either a type_name (if unique across cvs) or
- * type_id. Other supported keys include: cv_id/cv_name (of the type),
- * value and rank.
- * @param $options
- * An array of options. Supported keys include:
- * - Any keys supported by chado_generate_var(). See that function
- * definition for additional details.
- *
- * NOTE: the $identifier parameter can really be any array similar to $values
- * passed into chado_select_record(). It should fully specify the organism
- * record to be returned.
- *
- * @return
- * If unique values were passed in as an identifier then an object describing
- * the organism will be returned (will be a chado variable from
- * chado_generate_var()). Otherwise, NULL will be returned.
- *
- * @ingroup tripal_organism_api
- */
- function chado_get_organism($identifiers, $options = []) {
- // Set Defaults.
- if (!isset($options['include_fk'])) {
- // Tells chado_generate_var not to follow any foreign keys.
- $options['include_fk'] = [];
- }
- // Error Checking of parameters.
- if (!is_array($identifiers)) {
- tripal_report_error(
- 'tripal_organism_api',
- TRIPAL_ERROR,
- "chado_get_organism: The identifier passed in is expected to be an array with the key
- matching a column name in the organism table (ie: organism_id or name). You passed in %identifier.",
- [
- '%identifier' => print_r($identifiers, TRUE),
- ]
- );
- }
- elseif (empty($identifiers)) {
- tripal_report_error(
- 'tripal_organism_api',
- TRIPAL_ERROR,
- "chado_get_organism: You did not pass in anything to identify the organism you want. The identifier
- is expected to be an array with the key matching a column name in the organism table
- (ie: organism_id or name). You passed in %identifier.",
- [
- '%identifier' => print_r($identifiers, TRUE),
- ]
- );
- }
- // If one of the identifiers is property then use chado_get_record_with_property().
- if (isset($identifiers['property'])) {
- $property = $identifiers['property'];
- unset($identifiers['property']);
- $organism = chado_get_record_with_property(
- ['table' => 'organism', 'base_records' => $identifiers],
- ['type_name' => $property],
- $options
- );
- }
- // Else we have a simple case and we can just use chado_generate_var to get
- // the analysis.
- else {
- // Try to get the organism
- $organism = chado_generate_var(
- 'organism',
- $identifiers,
- $options
- );
- }
- // Ensure the organism is singular. If it's an array then it is not singular.
- if (is_array($organism)) {
- tripal_report_error(
- 'tripal_organism_api',
- TRIPAL_ERROR,
- "chado_get_organism: The identifiers you passed in were not unique. You passed in %identifier.",
- [
- '%identifier' => print_r($identifiers, TRUE),
- ]
- );
- }
- // Report an error if $organism is FALSE since then chado_generate_var has
- // failed.
- elseif ($organism === FALSE) {
- tripal_report_error(
- 'tripal_organism_api',
- TRIPAL_ERROR,
- "chado_get_organism: chado_generate_var() failed to return a organism based on the identifiers
- you passed in. You should check that your identifiers are correct, as well as, look
- for a chado_generate_var error for additional clues. You passed in %identifier.",
- [
- '%identifier' => print_r($identifiers, TRUE),
- ]
- );
- }
- // Else, as far we know, everything is fine so give them their organism :)
- else {
- return $organism;
- }
- }
- /**
- * Returns the full scientific name of an organism.
- *
- * @param $organism
- * An organism object.
- *
- * @return
- * The full scientific name of the organism.
- *
- * @ingroup tripal_organism_api
- */
- function chado_get_organism_scientific_name($organism) {
- $name = $organism->genus . ' ' . $organism->species;
- // For Chado v1.3 we have a type_id and infraspecific name.
- if (property_exists($organism, 'type_id')) {
- $rank = '';
- // For organism objects crated using chado_generate_var.
- if (is_object($organism->type_id)) {
- if ($organism->type_id) {
- $rank = $organism->type_id->name;
- }
- }
- else {
- $rank_term = chado_get_cvterm(['cvterm_id' => $organism->type_id]);
- if ($rank_term) {
- $rank = $rank_term->name;
- }
- }
- if ($rank) {
- $rank = chado_abbreviate_infraspecific_rank($rank);
- $name .= ' ' . $rank . ' ' . $organism->infraspecific_name;
- }
- else {
- if ($organism->infraspecific_name) {
- $name .= ' ' . $organism->infraspecific_name;
- }
- }
- }
- return $name;
- }
- /**
- * Returns a list of organisms that are currently synced with Drupal to use in
- * select lists.
- *
- * @param $syncd_only
- * Whether or not to return all chado organisms or just those sync'd with
- * drupal. Defaults to TRUE (only sync'd organisms).
- *
- * @return
- * An array of organisms sync'd with Drupal where each value is the organism
- * scientific name and the keys are organism_id's.
- *
- * @ingroup tripal_organism_api
- */
- function chado_get_organism_select_options($syncd_only = TRUE) {
- $org_list = [];
- $org_list[] = 'Select an organism';
- if ($syncd_only) {
- $sql = "
- SELECT *
- FROM [chado_organism] CO
- INNER JOIN {organism} O ON O.organism_id = CO.organism_id
- ORDER BY O.genus, O.species
- ";
- $orgs = chado_query($sql);
- // Iterate through the organisms and build an array of those that are synced.
- foreach ($orgs as $org) {
- $org_list[$org->organism_id] = $org->genus . ' ' . $org->species;
- }
- }
- else {
- // use this SQL statement for getting the organisms
- $csql = "SELECT * FROM {organism} ORDER BY genus, species";
- $orgs = chado_query($csql);
- // Iterate through the organisms and build an array of those that are synced.
- foreach ($orgs as $org) {
- $org_list[$org->organism_id] = $org->genus . ' ' . $org->species;
- }
- }
- return $org_list;
- }
- /**
- * Return the path for the organism image.
- *
- * @param $organism
- * An organism table record.
- *
- * @return
- * If the type parameter is 'url' (the default) then the fully qualified
- * url to the image is returend. If no image is present then NULL is returned.
- *
- * @ingroup tripal_organism_api
- */
- function chado_get_organism_image_url($organism) {
- $url = '';
- if (!is_object($organism)) {
- return NULL;
- }
- // Get the organism's node.
- $nid = chado_get_nid_from_id('organism', $organism->organism_id);
- // Look in the file_usage table of Drupal for the image file. This
- // is the current way for handling uploaded images. It allows the file to
- // keep it's proper name and extension.
- $fid = db_select('file_usage', 'fu')
- ->fields('fu', ['fid'])
- ->condition('module', 'tripal_organism')
- ->condition('type', 'organism_image')
- ->condition('id', $nid)
- ->execute()
- ->fetchField();
- if ($fid) {
- $file = file_load($fid);
- return file_create_url($file->uri);
- }
- // First look for an image with the genus/species name. This is old-style
- // tripal and we keep it for backwards compatibility.
- $base_path = realpath('.');
- $image_dir = tripal_get_files_dir('tripal_organism') . "/images";
- $image_name = $organism->genus . "_" . $organism->species . ".jpg";
- $image_path = "$base_path/$image_dir/$image_name";
- if (file_exists($image_path)) {
- $url = file_create_url("$image_dir/$image_name");
- return $url;
- }
- // If we don't find the file using the genus ans species then look for the
- // image with the node ID in the name. This method was used for Tripal 1.1
- // and 2.x-alpha version.
- $image_name = $nid . ".jpg";
- $image_path = "$base_path/$image_dir/$image_name";
- if (file_exists($image_path)) {
- $url = file_create_url("$image_dir/$image_name");
- return $url;
- }
- return NULL;
- }
- /**
- * This function is intended to be used in autocomplete forms
- * for searching for organisms that begin with the provided string.
- *
- * @param $text
- * The string to search for.
- *
- * @return
- * A json array of terms that begin with the provided string.
- *
- * @ingroup tripal_organism_api
- */
- function chado_autocomplete_organism($text) {
- $matches = [];
- $genus = $text;
- $species = '';
- if (preg_match('/^(.*?)\s+(.*)$/', $text, $matches)) {
- $genus = $matches[1];
- $species = $matches[2];
- }
- $sql = "SELECT * FROM {organism} WHERE lower(genus) like lower(:genus) ";
- $args = [];
- $args[':genus'] = $genus . '%';
- if ($species) {
- $sql .= "AND lower(species) like lower(:species) ";
- $args[':species'] = $species . '%';
- }
- $sql .= "ORDER BY genus, species ";
- $sql .= "LIMIT 25 OFFSET 0 ";
- $results = chado_query($sql, $args);
- $items = [['args' => [$sql => $args]]];
- foreach ($results as $organism) {
- $name = chado_get_organism_scientific_name($organism);
- $items["$name [id: $organism->organism_id]"] = $name;
- }
- drupal_json_output($items);
- }
- /**
- * A handy function to abbreviate the infraspecific rank.
- *
- * @param $rank
- * The rank below species.
- *
- * @return
- * The proper abbreviation for the rank.
- *
- * @ingroup tripal_organism_api
- */
- function chado_abbreviate_infraspecific_rank($rank) {
- $abb = '';
- switch ($rank) {
- case 'no_rank':
- $abb = '';
- break;
- case 'subspecies':
- $abb = 'subsp.';
- break;
- case 'varietas':
- $abb = 'var.';
- break;
- case 'variety':
- $abb = 'var.';
- break;
- case 'subvarietas':
- $abb = 'subvar.';
- break;
- case 'subvariety':
- $abb = 'subvar.';
- break;
- case 'forma':
- $abb = 'f.';
- break;
- case 'subforma':
- $abb = 'subf.';
- break;
- default:
- $abb = $rank;
- }
- return $abb;
- }
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