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@@ -114,23 +114,7 @@ function tripal_phylogeny_menu() {
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'access arguments' => array('administer tripal phylotree'),
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'type' => MENU_CALLBACK,
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);
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-
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- $items['chado_phylotree/%'] = array(
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- 'page callback' => 'phylotree_by_name',
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- 'page arguments' => array(1),
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- // allow all anonymous http clients
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- 'access callback' => TRUE
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- );
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-
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- // create a route for viewing json of all phylonodes having this phylotree_id
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- $items['chado_phylotree/%/json'] = array(
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- 'page callback' => 'phylotree_json',
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- 'page arguments' => array(1),
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- // allow all anonymous http clients
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- 'access callback' => TRUE
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- );
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-
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- // Data Loaders
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+ // Data Loaders
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$items['admin/tripal/loaders/newic_phylotree_loader'] = array(
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'title' => 'Phylogenetic Trees (Newic format)',
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'description' => 'Loads phylogenetic trees in Newic format. (Redirects to create a phylogenetic tree content type)',
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@@ -151,15 +135,22 @@ function tripal_phylogeny_menu() {
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);
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$items['taxonomy_view'] = array(
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- 'title' => 'Site Taxonomy',
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- 'description' => 'A taxonomy viewer for the species on this site.',
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- 'page callback' => 'drupal_get_form',
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- 'page arguments' => array('tripal_phylogeny_taxonomy_viewer'),
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+ 'title' => 'Taxonomy',
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+ 'description' => 'Taxonomic view of the species available on this site.',
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+ 'page callback' => 'tripal_phylogeny_taxonomy_view',
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'access arguments' => array('access taxonomy content'),
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'file' => '/includes/tripal_phylogeny.taxonomy.inc',
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'type' => MENU_NORMAL_ITEM,
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);
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+ // create a route for viewing json of all phylonodes having this phylotree_id
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+ $items['ajax/chado_phylotree/%/json'] = array(
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+ 'page callback' => 'tripal_phylogeny_ajax_get_tree_json',
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+ 'page arguments' => array(2),
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+ // allow all anonymous http clients
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+ 'access callback' => TRUE
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+ );
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+
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return $items;
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}
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@@ -277,7 +268,131 @@ function tripal_phylogeny_help ($path, $arg) {
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}
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}
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-// hack to suppress the 'Submitted by...' info drupal adds to nodes
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-$variables['display_submitted'] = FALSE;
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+/**
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+ * Get json representation of a phylotree id.
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+ *
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+ * This function is meant to be called via AJAX.
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+ *
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+ * @param int $phylotree_id
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+ * the ID of the phylotree node.
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+ *
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+ * @return string json
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+ *
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+ * @ingroup tripal_phylogeny
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+ */
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+function tripal_phylogeny_ajax_get_tree_json($phylotree_id) {
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+
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+ $phylotree = chado_generate_var('phylotree', array('phylotree_id' => $phylotree_id));
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+
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+ // This SQL gets all of the phylonodes for a given tree as well as the
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+ // features and organisms with which it is assocaited. Each phylonode
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+ // can be associated with an orgnaism in one of two ways: 1) via a
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+ // feature linked by the phylonode.feature_id field or 2) via a
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+ // a record in the phylonde_organsim table. Therefore both types of
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+ // organism records are returned in the query below, but those
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+ // retrieved via a FK link on features are prefixed with 'fo_'.
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+ $sql = "
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+ SELECT
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+ n.phylonode_id, n.parent_phylonode_id, n.label AS name, n.distance AS length,
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+ f.feature_id, f.name AS feature_name,
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+ cvt.name AS cvterm_name,
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+ o.organism_id, o.common_name, o.abbreviation, o.genus, o.species,
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+ fo.organism_id AS fo_organism_id, fo.common_name AS fo_common_name,
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+ fo.abbreviation AS fo_abbreviation, fo.genus as fo_genus, fo.species AS fo_species,
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+ cf.nid AS feature_node_id,
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+ fco.nid AS fo_organism_node_id,
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+ co.nid AS organism_node_id
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+ FROM {phylonode} n
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+ LEFT OUTER JOIN {cvterm} cvt ON n.type_id = cvt.cvterm_id
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+ LEFT OUTER JOIN {feature} f ON n.feature_id = f.feature_id
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+ LEFT OUTER JOIN [chado_feature] cf ON cf.feature_id = f.feature_id
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+ LEFT OUTER JOIN {organism} fo ON f.organism_id = fo.organism_id
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+ LEFT OUTER JOIN [chado_organism] fco ON fco.organism_id = fo.organism_id
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+ LEFT OUTER JOIN {phylonode_organism} po ON po.phylonode_id = n.phylonode_id
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+ LEFT OUTER JOIN {organism} o ON PO.organism_id = o.organism_id
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+ LEFT OUTER JOIN [chado_organism] co ON co.organism_id = o.organism_id
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+ WHERE n.phylotree_id = :phylotree_id
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+ ";
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+ $args = array(':phylotree_id' => $phylotree_id);
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+ $result = chado_query($sql, $args);
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+
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+ // Fetch all the phylonodes into an assoc array indexed by phylonode_id.
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+ // Convert from resultset record to array, fixing datatypes. chado_query
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+ // returns numeric as string and fun stuff like that.
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+ $phylonodes = array();
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+ $root_phylonode_ref = null;
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+
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+ foreach ($result as $r) {
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+ $phylonode_id = (int) $r->phylonode_id;
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+
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+ // expect all nodes to have these properties
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+ $node = array(
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+ 'phylonode_id' => $phylonode_id,
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+ 'parent_phylonode_id' => (int) $r->parent_phylonode_id,
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+ 'length' => (double) $r->length,
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+ 'cvterm_name' => $r->cvterm_name
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+ );
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+
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+ // If the nodes are taxonomic then set an equal distance
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+ if ($phylotree->type_id->name == 'taxonomy') {
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+ $node['length'] = 0.001;
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+ }
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+
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+ // Other props may exist only for leaf nodes
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+ if ($r->name) {
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+ $node['name'] = $r->name;
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+ }
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+ // If this node is associated with a feature then add in the details
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+ if ($r->feature_id) {
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+ $node['feature_id'] = (int) $r->feature_id;
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+ $node['feature_name'] = $r->feature_name;
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+ $node['feature_node_id'] = (int) $r->feature_node_id;
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+ }
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+ // Add in the organism fields when they are available via the
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+ // phylonode_organism table.
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+ if ($r->organism_id) {
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+ $node['organism_id'] = (int) $r->organism_id;
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+ $node['common_name'] = $r->common_name;
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+ $node['abbreviation'] = $r->abbreviation;
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+ $node['genus'] = $r->genus;
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+ $node['species'] = $r->species;
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+ $node['organism_node_id'] = (int) $r->organism_node_id;
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+ // If the node does not have a name but is linked to an organism
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+ // then set the name to be that of the genus and species.
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+ if (!$r->name) {
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+ $node['name'] = $r->genus . ' ' . $r->species;
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+ }
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+ }
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+ // Add in the organism fields when they are available via the
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+ // the phylonode.feature_id FK relationship.
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+ if ($r->fo_organism_id) {
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+ $node['fo_organism_id'] = (int) $r->fo_organism_id;
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+ $node['fo_common_name'] = $r->fo_common_name;
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+ $node['fo_abbreviation'] = $r->fo_abbreviation;
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+ $node['fo_genus'] = $r->fo_genus;
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+ $node['fo_species'] = $r->fo_species;
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+ $node['fo_organism_node_id'] = (int) $r->fo_organism_node_id;
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+ }
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+
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+ // Add this node to the list, organized by ID.
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+ $phylonodes[$phylonode_id] = $node;
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+ }
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+
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+ // Populate the children[] arrays for each node.
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+ foreach ($phylonodes as $key => &$node) {
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+ if ($node['parent_phylonode_id'] !== 0) {
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+ $parent_ref = &$phylonodes[ $node['parent_phylonode_id']];
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+ // Append node refernce to children.
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+ $parent_ref['children'][] = &$node;
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+ }
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+ else {
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+ $root_phylonode_ref = &$node;
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+ }
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+ }
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+
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+ // dump datastructure as json to browser. drupal sets the mime-type correctly.
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+ drupal_json_output($root_phylonode_ref);
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+}
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+
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Stephen Ficklin