Get json representation of a phylotree id.

This function is meant to be called via AJAX.

Parameters

int $phylotree_id: the ID of the phylotree node.

Return value

string json

Related topics

File

tripal_phylogeny/tripal_phylogeny.module, line 283

Integrates the Chado Phylotree module with Drupal Nodes & Views

Code

function tripal_phylogeny_ajax_get_tree_json($phylotree_id) {

  $phylotree = chado_generate_var('phylotree', array('phylotree_id' => $phylotree_id));

  // This SQL gets all of the phylonodes for a given tree as well as the
  // features and organisms with which it is assocaited.  Each phylonode
  // can be associated with an orgnaism in one of two ways: 1) via a
  // feature linked by the phylonode.feature_id field or 2) via a
  // a record in the phylonde_organsim table.  Therefore both types of
  // organism records are returned in the query below, but those
  // retrieved via a FK link on features are prefixed with 'fo_'.
  $sql = "
    SELECT
      n.phylonode_id, n.parent_phylonode_id, n.label AS name, n.distance AS length,
      f.feature_id, f.name AS feature_name,
      cvt.name AS cvterm_name,
      o.organism_id, o.common_name, o.abbreviation, o.genus, o.species,
      fo.organism_id AS fo_organism_id, fo.common_name AS fo_common_name,
      fo.abbreviation AS fo_abbreviation, fo.genus as fo_genus, fo.species AS fo_species,
      cf.nid AS feature_node_id,
      fco.nid AS fo_organism_node_id,
      co.nid AS organism_node_id
    FROM {phylonode} n
      LEFT OUTER JOIN {cvterm} cvt              ON n.type_id = cvt.cvterm_id
      LEFT OUTER JOIN {feature} f               ON n.feature_id = f.feature_id
      LEFT OUTER JOIN [chado_feature] cf        ON cf.feature_id = f.feature_id
      LEFT OUTER JOIN {organism} fo             ON f.organism_id = fo.organism_id
      LEFT OUTER JOIN [chado_organism] fco      ON fco.organism_id = fo.organism_id
      LEFT OUTER JOIN {phylonode_organism} po   ON po.phylonode_id = n.phylonode_id
      LEFT OUTER JOIN {organism} o              ON PO.organism_id = o.organism_id
      LEFT OUTER JOIN [chado_organism] co       ON co.organism_id = o.organism_id
    WHERE n.phylotree_id = :phylotree_id
  ";
  $args = array(':phylotree_id' => $phylotree_id);
  $result = chado_query($sql, $args);

  // Fetch all the phylonodes into an assoc array indexed by phylonode_id.
  // Convert from resultset record to array, fixing datatypes. chado_query
  // returns numeric as string and fun stuff like that.
  $phylonodes = array();
  $root_phylonode_ref = null;

  foreach ($result as $r) {
    $phylonode_id = (int) $r->phylonode_id;

    // expect all nodes to have these properties
    $node = array(
      'phylonode_id' => $phylonode_id,
      'parent_phylonode_id' => (int) $r->parent_phylonode_id,
      'length' => (double) $r->length,
      'cvterm_name' => $r->cvterm_name
    );

    // If the nodes are taxonomic then set an equal distance
    if ($phylotree->type_id->name == 'taxonomy') {
      $node['length'] = 0.001;
    }

    // Other props may exist only for leaf nodes
    if ($r->name) {
      $node['name'] = $r->name;
    }
    // If this node is associated with a feature then add in the details
    if ($r->feature_id) {
      $node['feature_id'] = (int) $r->feature_id;
      $node['feature_name'] = $r->feature_name;
      $node['feature_node_id'] = (int) $r->feature_node_id;
    }
    // Add in the organism fields when they are available via the
    // phylonode_organism table.
    if ($r->organism_id) {
      $node['organism_id'] = (int) $r->organism_id;
      $node['common_name'] = $r->common_name;
      $node['abbreviation'] = $r->abbreviation;
      $node['genus'] = $r->genus;
      $node['species'] = $r->species;
      $node['organism_node_id'] = (int) $r->organism_node_id;
      // If the node does not have a name but is linked to an organism
      // then set the name to be that of the genus and species.
      if (!$r->name) {
        $node['name'] = $r->genus . ' ' . $r->species;
      }
    }
    // Add in the organism fields when they are available via the
    // the phylonode.feature_id FK relationship.
    if ($r->fo_organism_id) {
      $node['fo_organism_id'] = (int) $r->fo_organism_id;
      $node['fo_common_name'] = $r->fo_common_name;
      $node['fo_abbreviation'] = $r->fo_abbreviation;
      $node['fo_genus'] = $r->fo_genus;
      $node['fo_species'] = $r->fo_species;
      $node['fo_organism_node_id'] = (int) $r->fo_organism_node_id;
    }

    // Add this node to the list, organized by ID.
    $phylonodes[$phylonode_id] = $node;
  }

  // Populate the children[] arrays for each node.
  foreach ($phylonodes as $key => &$node) {
    if ($node['parent_phylonode_id'] !== 0) {
      $parent_ref = &$phylonodes[$node['parent_phylonode_id']];
      // Append node refernce to children.
      $parent_ref['children'][] = &$node;
    }
    else {
      $root_phylonode_ref = &$node;
    }
  }

  // dump datastructure as json to browser. drupal sets the mime-type correctly.
  drupal_json_output($root_phylonode_ref);
}