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@@ -1,4 +1,4 @@
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-<?php
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+<?php
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/**
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@@ -27,9 +27,9 @@ function tripal_feature_preprocess_tripal_feature_sequence(&$variables) {
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// now extract the sequences
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$featureloc_sequences = tripal_feature_load_featureloc_sequences($feature->feature_id, $ffeaturelocs);
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$feature->featureloc_sequences = $featureloc_sequences;
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-
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+
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// if this feature has associated protein sequences (or others via relationships
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- // then we want to make sure the relationships are added so that we can
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+ // then we want to make sure the relationships are added so that we can
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// show the protein sequences
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if (!$feature->all_relationships) {
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$feature->all_relationships = tripal_feature_get_feature_relationships($feature);
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@@ -145,7 +145,7 @@ function tripal_feature_load_featureloc_sequences($feature_id, $featurelocs) {
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$args = array(':feature_id' => $featureloc->srcfeature_id->feature_id);
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$start = $featureloc->fmin + 1;
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$size = $featureloc->fmax - $featureloc->fmin;
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-
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+
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// TODO: fix the hard coded $start and $size
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// the $start and $size variables are hard-coded in the SQL statement
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// because the db_query function places quotes around all placeholders
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@@ -852,11 +852,11 @@ function tripal_feature_get_feature_relationships($feature) {
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}
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}
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$rel->record = $relationship;
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-
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+
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// get the relationship and child types
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$rel_type = t(preg_replace('/_/', " ", $relationship->type_id->name));
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$child_type = $relationship->subject_id->type_id->name;
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-
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+
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// get the node id of the subject
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$sql = "SELECT nid FROM {chado_feature} WHERE feature_id = :feature_id";
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$n = db_query($sql, array(':feature_id' => $relationship->subject_id->feature_id))->fetchObject();
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@@ -893,14 +893,14 @@ function tripal_feature_get_feature_relationships($feature) {
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$rel->record = $relationship;
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$rel_type = t(preg_replace('/_/', " ", $relationship->type_id->name));
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$parent_type = $relationship->object_id->type_id->name;
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-
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+
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// get the node id of the subject
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$sql = "SELECT nid FROM {chado_feature} WHERE feature_id = :feature_id";
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$n = db_query($sql, array(':feature_id' => $relationship->object_id->feature_id))->fetchObject();
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if ($n) {
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$rel->record->nid = $n->nid;
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}
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-
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+
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if (!array_key_exists($rel_type, $relationships['subject'])) {
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$relationships['subject'][$rel_type] = array();
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}
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@@ -912,3 +912,116 @@ function tripal_feature_get_feature_relationships($feature) {
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}
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return $relationships;
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}
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+
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+/**
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+ *
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+ */
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+function tripal_feature_preprocess_tripal_feature_bar_chart_type_organism_summary(&$vars) {
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+
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+ // Add in all the javascript/css files.
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+ tripal_add_d3js();
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+ drupal_add_css(drupal_get_path('module','tripal_feature') . '/theme/css/tripal_feature.css');
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+ drupal_add_js(drupal_get_path('module','tripal_feature') . '/theme/js/tripalFeature.adminChart.js');
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+
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+ // Retrieve and process all the data and save it as javascript settings.
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+ //'''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''
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+
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+ // We are using the organism_feature_count materialized view as the source for our data.
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+ // Thus grab all the records from this materialized view.
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+ $organism_feature_count = chado_select_record(
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+ 'organism_feature_count',
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+ array('*'),
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+ array(),
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+ array('order_by' => array('genus' => 'ASC', 'species' => 'ASC', 'feature_type' => 'ASC', 'num_features' => 'DESC'))
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+ );
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+
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+ // Initialize variables.
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+ $chart = array();
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+ $type_names = array();
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+ $organism_names = array();
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+ $max_bar_height = 0;
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+
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+ // Process each row of the materialzied view into the chart array.
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+ // Note: it's first keyed by type since each type will be a bar. Each type will have
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+ // a "bars" array with the start (y0) and end (y1) height on the bar for a given
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+ // organism. Finally we keep a record of the names of the types & organisms
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+ // for axis' and legend generation respectively.
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+ foreach ($organism_feature_count as $row) {
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+
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+ // Build up the easy details for the current row's type. These will be overridden
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+ // multiple times but that's more efficient than checking each time.
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+ $chart[$row->cvterm_id]['cvterm_id'] = $row->cvterm_id;
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+ $chart[$row->cvterm_id]['name'] = str_replace('_', ' ', $row->feature_type);
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+
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+ // Save the name of the type and organism into their respective arrays
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+ // for generation of axis' and legends for the chart.
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+ $type_names[$row->cvterm_id] = $row->feature_type;
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+ $organism_names[$row->organism_id] = $row->genus . ' ' . $row->species;
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+
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+ // Save information about the current organism. This isn't actually used by the
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+ // chart but can be used to debug the bar generation to follow.
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+ $chart[$row->cvterm_id]['organisms'][] = array(
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+ 'name' => $row->genus . ' ' . $row->species,
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+ 'value' => (int) $row->num_features
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+ );
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+
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+ // Now to build the bar array with the start (y0) and end (y1) height on the
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+ // bar for a given organism.
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+ // NOTE: we cannot assume the types are all in order so store y0 & y1 in the
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+ // $chart[type] array.
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+ // If y0 has not yet been set for this type then we're starting with the first
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+ // chunk (organism) on the bar.
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+ if (!isset($chart[$row->cvterm_id]['y0'])) {
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+ $chart[$row->cvterm_id]['y0'] = 0;
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+ $chart[$row->cvterm_id]['y1'] = $row->num_features;
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+ }
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+ // Otherwise, add the next chunk (organism) on top of the pre-existing bar.
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+ else {
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+ $chart[$row->cvterm_id]['y0'] = $chart[$row->cvterm_id]['y1'];
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+ $chart[$row->cvterm_id]['y1'] = $chart[$row->cvterm_id]['y0'] + $row->num_features;
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+ }
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+ // Now save the bar chunk we just determined.
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+ $chart[$row->cvterm_id]['bars'][] = array(
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+ 'name' => $row->genus . ' ' . $row->species,
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+ 'y0' => $chart[$row->cvterm_id]['y0'],
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+ 'y1' => $chart[$row->cvterm_id]['y1'],
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+ );
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+
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+ // We also need to keep track of the total number of features for a single bar (Type).
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+ $chart[$row->cvterm_id]['total_features'] = (int) $chart[$row->cvterm_id]['y1'];
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+ // And the maximum "height" for all bars.
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+ if ($max_bar_height < $chart[$row->cvterm_id]['total_features']) {
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+ $max_bar_height = (int) $chart[$row->cvterm_id]['total_features'];
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+ }
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+ }
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+
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+ // Sort based on the total number of features.
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+ // NOTE: This changes the keys so it's no longer the organism/type_id.
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+ usort($chart, 'tripal_feature_admin_summary_sort');
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+ sort($type_names);
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+ sort($organism_names);
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+
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+ // We also need to add information about the materialized views
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+ // so that admin can update it and know how recent the data is.
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+ $mview = db_query('
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+ SELECT mview_id, name, last_update
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+ FROM tripal_mviews
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+ WHERE mv_table=:mv_table',
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+ array(':mv_table' => 'organism_feature_count')
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+ )->fetchObject();
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+
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+ $vars['chart_details'] = array(
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+ 'summary' => $chart,
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+ 'types' => $type_names,
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+ 'organisms' => $organism_names,
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+ 'legendPosition' => 'top',
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+ 'maxBarHeight' => $max_bar_height,
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+ 'mviewUrl' => url('admin/tripal/schema/mviews/update/' . $mview->mview_id),
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+ 'mviewTable' => $mview->name,
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+ 'mviewLastUpdate' => $mview->last_update ? format_date($mview->last_update) : '',
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+ );
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+
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+ // Save everything we just determined as a Drupal JS settings so that we have access to
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+ // it in our js script.
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+ drupal_add_js(array('tripalFeature' => array('admin' => $vars['chart_details'])), 'setting');
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+}
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Stephen Ficklin