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@@ -0,0 +1,504 @@
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+<?php
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+/**
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+ * Prepares a phylogenetic tree for viewing.
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+ *
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+ * @param $phylotree
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+ */
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+function tripal_phylogeny_prepare_tree_viewer($phylotree) {
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+
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+ // Don't prepare for viewing more than once.
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+ if (property_exists($phylotree, 'prepared_to_view') and
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+ $phylotree->prepared_to_view == TRUE) {
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+ return;
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+ }
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+
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+ $module_path = drupal_get_path('module', 'tripal_chado');
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+
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+ drupal_add_js('https://d3js.org/d3.v3.min.js', 'external');
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+
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+ drupal_add_js("$module_path/theme/js/d3.phylogram.js");
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+ drupal_add_js("$module_path/theme/js/tripal_phylogeny.js");
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+ drupal_add_css("$module_path/theme/css/tripal_phylogeny.css");
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+
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+ drupal_add_library('system', 'ui.dialog');
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+
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+ // Don't show tick marks for the taxonomy tree.
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+ $skip_ticks = 0;
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+ if ($phylotree->type_id->name == 'taxonomy') {
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+ $skip_ticks = 1;
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+ }
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+
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+ // Get the tree options as set by the administrator.
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+ $options = json_encode(array(
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+ 'phylogram_width' => variable_get('tripal_phylogeny_default_phylogram_width', 350),
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+ 'root_node_size' => variable_get('tripal_phylogeny_default_root_node_size', 3),
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+ 'interior_node_size' => variable_get('tripal_phylogeny_default_interior_node_size', 0),
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+ 'leaf_node_size' => variable_get('tripal_phylogeny_default_leaf_node_size', 6),
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+ 'skipTicks' => $skip_ticks,
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+ ));
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+
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+ // Get the node colors as set by the administrator.
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+ $colors = array();
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+ $color_defaults = variable_get("tripal_phylogeny_org_colors", array('1' => array('organism' => '', 'color' => '')));
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+ foreach ($color_defaults as $i => $details) {
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+ if ($details['organism']) {
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+ $colors[$details['organism']] = $details['color'];
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+ }
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+ }
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+ $colors = json_encode($colors);
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+
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+ drupal_add_js(array(
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+ 'tripal_chado' => array(
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+ 'phylotree_url' => url('phylotree/' . $phylotree->phylotree_id),
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+ 'phylotree_theme_url' => url($module_path . '/theme'),
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+ 'tree_options' => $options,
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+ 'org_colors' => $colors,
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+ ),
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+ ), 'setting');
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+
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+ if (!property_exists($phylotree, 'has_nodes')) {
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+ // If the nodes haven't loaded then set a value so the template can
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+ // choose not to show the phylogram.
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+ $values = array('phylotree_id' => $phylotree->phylotree_id);
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+ $options = array('limit' => 1, 'offset' => 0, 'has_record' => 1);
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+ $phylotree->has_nodes = chado_select_record('phylonode', array('phylonode_id'), $values, $options);
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+ }
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+ if (!property_exists($phylotree, 'has_features')) {
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+ // If the nodes haven't loaded then set a value so the template can
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+ // choose not to show the circular dendrogram. The chado_select_record()
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+ // API call can't do this query so we have to do it manually.
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+ $sql = "
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+ SELECT count(*) as num_features
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+ FROM {phylonode}
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+ WHERE NOT feature_id IS NULL and phylotree_id = :phylotree_id
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+ LIMIT 1 OFFSET 0
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+ ";
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+ $phylotree->has_features = chado_query($sql, array(':phylotree_id' => $phylotree->phylotree_id))->fetchField();
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+ }
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+
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+ $phylotree->prepared_to_view = TRUE;
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+}
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+
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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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+ // For backwards compatibility with Tripal v2 and the legacy modules of
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+ // Tripal v3 we have two different SQL statements.
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+ if (module_exists('tripal_phylogeny')) {
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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 associated. Each phylonode
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+ // can be associated with an organism 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_nid,
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+ fco.nid AS fo_organism_nid,
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+ co.nid AS organism_nid
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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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+ }
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+ else {
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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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+ 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 {organism} fo ON f.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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+ WHERE n.phylotree_id = :phylotree_id
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+ ";
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+ }
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+ $args = array(':phylotree_id' => $phylotree_id);
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+ $results = chado_query($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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+ $root_phylonode_ref = null;
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+
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+ if ($results) {
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+ while($r = $results->fetchObject()) {
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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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+ if (module_exists('tripal_phylogeny')) {
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+ $node['feature_nid'] = (int) $r->feature_nid;
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+ }
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+ }
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+ // Add in the organism fields when they are available via the
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+ // phylonode_organism table.
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+ if ($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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+ if (module_exists('tripal_phylogeny')) {
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+ $node['organism_nid'] = (int) $r->organism_nid;
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+ }
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+ // If the node does not have a name but is linked to an organism
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+ // then set the name to be that of the genus and species.
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+ if (!$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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+ if (module_exists('tripal_phylogeny')) {
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+ $node['fo_organism_nid'] = (int) $r->fo_organism_nid;
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+ }
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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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+
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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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+
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+/**
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+ * @file
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+ * This file contains the functions used for administration of the module
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+ *
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+ */
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+
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+function tripal_phylogeny_admin_phylotrees_listing() {
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+ $output = '';
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+
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+ // set the breadcrumb
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+ $breadcrumb = array();
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+ $breadcrumb[] = l('Home', '<front>');
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+ $breadcrumb[] = l('Administration', 'admin');
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+ $breadcrumb[] = l('Tripal', 'admin/tripal');
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+ $breadcrumb[] = l('Data Storage', 'admin/tripal/storage');
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+ $breadcrumb[] = l('Chado', 'admin/tripal/storage/chado');
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+ drupal_set_breadcrumb($breadcrumb);
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+
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+ // Add the view
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+ $view = views_embed_view('tripal_phylogeny_admin_phylotree','default');
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+ if (isset($view)) {
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+ $output .= $view;
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+ }
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+ else {
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+ $output .= '<p>The Phylotree module uses primarily views to provide an '
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+ . 'administrative interface. Currently one or more views needed for this '
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+ . 'administrative interface are disabled. <strong>Click each of the following links to '
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+ . 'enable the pertinent views</strong>:</p>';
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+ $output .= '<ul>';
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+ $output .= '<li>'.l('Phylotree View', 'admin/tripal/extension/tripal_phylogeny/views/phylotree/enable').'</li>';
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+ $output .= '</ul>';
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+ }
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+ return $output;
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+}
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+
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+
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+/**
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+ *
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+ * @param unknown $form
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+ * @param unknown $form_state
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+ */
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+function tripal_phylogeny_default_plots_form($form, &$form_state) {
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+ $form = array();
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+
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+ $form['plot_settings'] = array(
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+ '#type' => 'fieldset',
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+ '#title' => t('Plot Settings'),
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+ '#description' => t('You can customize settings for each plot'),
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+ '#collapsible' => TRUE,
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+ '#collapsed' => FALSE
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+ );
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+
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+ $form['plot_settings']['phylogram_width'] = array(
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+ '#type' => 'textfield',
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+ '#title' => 'Tree Width',
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+ '#description' => 'Please specify the width in pixels for the phylogram',
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+ '#default_value' => variable_get('tripal_phylogeny_default_phylogram_width', 350),
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+ '#element_validate' => array(
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+ 'element_validate_integer_positive'
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+ ),
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+ '#size' => 5,
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+ );
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+
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+ $form['node_settings'] = array(
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+ '#type' => 'fieldset',
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+ '#title' => t('Node Settings'),
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+ '#description' => t('You can customize settings for the nodes on the trees.'),
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+ '#collapsible' => TRUE,
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+ '#collapsed' => FALSE
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+ );
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+ $form['node_settings']['root_node_size'] = array(
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+ '#type' => 'textfield',
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+ '#title' => 'Root Node Size',
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+ '#description' => 'Please specify a size for the root node size. If set to zero, the node will not appear.',
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+ '#default_value' => variable_get('tripal_phylogeny_default_root_node_size', 3),
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+ '#element_validate' => array(
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+ 'element_validate_integer'
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+ ),
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+ '#size' => 3,
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+ );
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+ $form['node_settings']['interior_node_size'] = array(
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+ '#type' => 'textfield',
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+ '#title' => 'Interor Node Size',
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+ '#description' => 'Please specify a size for the interior node size. If set to zero, the node will not appear.',
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+ '#default_value' => variable_get('tripal_phylogeny_default_interior_node_size', 0),
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+ '#element_validate' => array(
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+ 'element_validate_integer'
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+ ),
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+ '#size' => 3,
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+ );
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+ $form['node_settings']['leaf_node_size'] = array(
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+ '#type' => 'textfield',
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+ '#title' => 'Leaf Node Size',
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+ '#description' => 'Please specify a size for the leaf node size. If set to zero, the node will not appear.',
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+ '#default_value' => variable_get('tripal_phylogeny_default_leaf_node_size', 6),
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+ '#element_validate' => array(
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+ 'element_validate_integer'
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+ ),
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+ '#size' => 3,
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+ );
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+
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+ // Get the number of organism colors that already exist. If the site admin
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+ // has set colors then those settings will be in a Drupal variable which we
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+ // will retrieve. Otherwise the num_orgs defaults to 1 and a single
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+ // set of fields is provided.
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+ $num_orgs = variable_get("tripal_phylogeny_num_orgs", 1);
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+ if (array_key_exists('values', $form_state) and array_key_exists('num_orgs', $form_state['values'])) {
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+ $num_orgs = $form_state['values']['num_orgs'];
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+ }
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+ // The default values for each organism color are provided in a d
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+ // Drupal variable that gets set when the form is set.
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+ $color_defaults = variable_get("tripal_phylogeny_org_colors", array('1' => array('organism' => '', 'color' => '')));
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+
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+ $form['node_settings']['desc'] = array(
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+ '#type' => 'item',
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+ '#title' => t('Node Colors by Organism'),
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+ '#markup' => t('If the trees are associated with features (e.g. proteins)
|
|
|
+ then the nodes can be color-coded by their organism. This helps the user
|
|
|
+ visualize which nodes belong to each organism. Please enter the
|
|
|
+ name of the organism and it\'s corresponding color in HEX code (e.g. #FF0000 == red).
|
|
|
+ Organisms that are not given a color will be gray.'),
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|
|
+ );
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|
|
+ $form['node_settings']['org_table']['num_orgs'] = array(
|
|
|
+ '#type' => 'value',
|
|
|
+ '#value' => $num_orgs,
|
|
|
+ );
|
|
|
+
|
|
|
+ // Iterate through the number of organism colors and add a field for each one.
|
|
|
+ for ($i = 0; $i < $num_orgs; $i++) {
|
|
|
+ $form['node_settings']['org_table']['organism_' . $i] = array(
|
|
|
+ '#type' => 'textfield',
|
|
|
+ '#default_value' => array_key_exists($i, $color_defaults) ? $color_defaults[$i]['organism'] : '',
|
|
|
+ '#autocomplete_path' => "admin/tripal/legacy/tripal_organism/organism/auto_name",
|
|
|
+ '#description' => t('Please enter the name of the organism.'),
|
|
|
+ '#size' => 30,
|
|
|
+ );
|
|
|
+ $form['node_settings']['org_table']['color_' . $i] = array(
|
|
|
+ '#type' => 'textfield',
|
|
|
+ '#description' => t('Please provide a color in Hex format (e.g. #FF0000).'),
|
|
|
+ '#default_value' => array_key_exists($i, $color_defaults) ? $color_defaults[$i]['color'] : '',
|
|
|
+ '#suffix' => "<div id=\"color-box-$i\" style=\"width: 30px;\"></div>",
|
|
|
+ '#size' => 10,
|
|
|
+ );
|
|
|
+ }
|
|
|
+ $form['node_settings']['org_table']['add'] = array(
|
|
|
+ '#type' => 'submit',
|
|
|
+ '#name' => 'add',
|
|
|
+ '#value' => 'Add',
|
|
|
+ '#ajax' => array(
|
|
|
+ 'callback' => "tripal_phylogeny_default_plots_form_ajax_callback",
|
|
|
+ 'wrapper' => 'tripal_phylogeny_default_plots_form',
|
|
|
+ 'effect' => 'fade',
|
|
|
+ 'method' => 'replace',
|
|
|
+ ),
|
|
|
+ );
|
|
|
+ $form['node_settings']['org_table']['remove'] = array(
|
|
|
+ '#type' => 'submit',
|
|
|
+ '#name' => 'remove',
|
|
|
+ '#value' => 'Remove',
|
|
|
+ '#ajax' => array(
|
|
|
+ 'callback' => "tripal_phylogeny_default_plots_form_ajax_callback",
|
|
|
+ 'wrapper' => 'tripal_phylogeny_default_plots_form',
|
|
|
+ 'effect' => 'fade',
|
|
|
+ 'method' => 'replace',
|
|
|
+ ),
|
|
|
+ );
|
|
|
+ $form['node_settings']['org_table']['#theme'] = 'tripal_phylogeny_admin_org_color_tables';
|
|
|
+ $form['node_settings']['org_table']['#prefix'] = '<div id="tripal_phylogeny_default_plots_form">';
|
|
|
+ $form['node_settings']['org_table']['#suffix'] = '</div>';
|
|
|
+
|
|
|
+ $form['submit'] = array(
|
|
|
+ '#type' => 'submit',
|
|
|
+ '#name' => 'submit',
|
|
|
+ '#value' => 'Save Configuration',
|
|
|
+ );
|
|
|
+
|
|
|
+ $form['#submit'][] = 'tripal_phylogeny_default_plots_form_submit';
|
|
|
+
|
|
|
+ return $form;
|
|
|
+}
|
|
|
+
|
|
|
+/**
|
|
|
+ * Validate the phylotree settings forms
|
|
|
+ *
|
|
|
+ * @ingroup tripal_phylogeny
|
|
|
+ */
|
|
|
+function tripal_phylogeny_default_plots_form_validate($form, &$form_state) {
|
|
|
+
|
|
|
+}
|
|
|
+/**
|
|
|
+ *
|
|
|
+ * @param unknown $form
|
|
|
+ * @param unknown $form_state
|
|
|
+ */
|
|
|
+function tripal_phylogeny_default_plots_form_submit($form, &$form_state) {
|
|
|
+ // Rebuild this form after submission so that any changes are reflected in
|
|
|
+ // the flat tables.
|
|
|
+ $form_state['rebuild'] = TRUE;
|
|
|
+
|
|
|
+ if ($form_state['clicked_button']['#name'] == 'submit') {
|
|
|
+ variable_set('tripal_phylogeny_default_phylogram_width', $form_state['values']['phylogram_width']);
|
|
|
+
|
|
|
+ variable_set('tripal_phylogeny_default_root_node_size', $form_state['values']['root_node_size']);
|
|
|
+ variable_set('tripal_phylogeny_default_interior_node_size', $form_state['values']['interior_node_size']);
|
|
|
+ variable_set('tripal_phylogeny_default_leaf_node_size', $form_state['values']['leaf_node_size']);
|
|
|
+
|
|
|
+ $num_orgs = $form_state['values']['num_orgs'];
|
|
|
+ variable_set("tripal_phylogeny_num_orgs", $num_orgs);
|
|
|
+ $colors = array();
|
|
|
+ for ($i = 0; $i < $num_orgs ;$i++) {
|
|
|
+ $colors[$i] = array(
|
|
|
+ 'organism' => $form_state['values']['organism_' . $i],
|
|
|
+ 'color' => $form_state['values']['color_' . $i]
|
|
|
+ );
|
|
|
+ }
|
|
|
+ variable_set("tripal_phylogeny_org_colors", $colors);
|
|
|
+ }
|
|
|
+ if ($form_state['clicked_button']['#name'] == 'add') {
|
|
|
+ $form_state['values']['num_orgs']++;
|
|
|
+ }
|
|
|
+ if ($form_state['clicked_button']['#name'] == 'remove') {
|
|
|
+ $form_state['values']['num_orgs']--;
|
|
|
+ }
|
|
|
+}
|
|
|
+
|
|
|
+/**
|
|
|
+ *
|
|
|
+ * @param unknown $variables
|
|
|
+ */
|
|
|
+function theme_tripal_phylogeny_admin_org_color_tables($variables){
|
|
|
+ $fields = $variables['element'];
|
|
|
+ $num_orgs = $fields['num_orgs']['#value'];
|
|
|
+ $headers = array('Organism', 'Color', '');
|
|
|
+ $rows = array();
|
|
|
+ for ($i = 0; $i < $num_orgs; $i++) {
|
|
|
+ $add_button = ($i == $num_orgs - 1) ? drupal_render($fields['add']) : '';
|
|
|
+ $del_button = ($i == $num_orgs - 1 and $i != 0) ? drupal_render($fields['remove']) : '';
|
|
|
+ $rows[] = array(
|
|
|
+ drupal_render($fields['organism_' . $i]),
|
|
|
+ drupal_render($fields['color_' . $i]),
|
|
|
+ $add_button . $del_button,
|
|
|
+ );
|
|
|
+ }
|
|
|
+ $table_vars = array(
|
|
|
+ 'header' => $headers,
|
|
|
+ 'rows' => $rows,
|
|
|
+ 'attributes' => array(),
|
|
|
+ 'sticky' => FALSE,
|
|
|
+ 'colgroups' => array(),
|
|
|
+ 'empty' => '',
|
|
|
+ );
|
|
|
+ $form['orgs']['num_orgs'] = $fields['num_orgs'];
|
|
|
+ return theme('table', $table_vars);
|
|
|
+}
|
|
|
+
|
|
|
+
|
|
|
+/**
|
|
|
+ * Ajax callback function for the gensas_job_view_panel_form.
|
|
|
+ *
|
|
|
+ * @param $form
|
|
|
+ * @param $form_state
|
|
|
+ */
|
|
|
+function tripal_phylogeny_default_plots_form_ajax_callback($form, $form_state) {
|
|
|
+
|
|
|
+ return $form['node_settings']['org_table'];
|
|
|
+}
|
Stephen Ficklin