From 2cba79ccf103009af80ba7af981ee8ac6e294c1d Mon Sep 17 00:00:00 2001
From: Nick Booher <njbooher@iastate.edu>
Date: Thu, 16 Jan 2020 13:21:54 -0600
Subject: [PATCH] Add options to disable genes and transcripts tarcks

---
 tripal_jbrowse_api.admin.inc | 44 ++++++++++++++++++++++
 tripal_jbrowse_api.module    | 72 ++++++++++++++++++++++++------------
 2 files changed, 92 insertions(+), 24 deletions(-)
 create mode 100644 tripal_jbrowse_api.admin.inc

diff --git a/tripal_jbrowse_api.admin.inc b/tripal_jbrowse_api.admin.inc
new file mode 100644
index 0000000..71bfd97
--- /dev/null
+++ b/tripal_jbrowse_api.admin.inc
@@ -0,0 +1,44 @@
+<?php
+
+require_once 'includes/tripal_jbrowse_api.queries.inc';
+
+/**
+ * @file
+ * Admin page callbacks for the tripal_jbrowse_api module.
+ */
+
+function tripal_jbrowse_api_settings() {
+
+  $results = chado_query(TRIPAL_JBROWSE_API_QUERY_ALL_ORGANISMS)->fetchAll(PDO::FETCH_ASSOC);
+
+  foreach ($results as $row) {
+    $prefix = 'tripal_jbrowse_api_' . $row['organism_id'] . '_';
+    $form['organism_' . $row['organism_id']] = array(
+      '#type' => 'fieldset',
+      '#title' => sprintf('%s %s (%s)', $row['genus'], $row['species'], $row['common_name'])
+    );
+    $form['organism_' . $row['organism_id']][$prefix . 'show_genes'] = array(
+      '#type' => 'checkbox',
+      '#title' => t('Expose genes as an available track for this organism'),
+      '#default_value' => variable_get($prefix . 'show_genes', TRUE),
+    );
+    $form['organism_' . $row['organism_id']][$prefix . 'genes_is_default'] = array(
+      '#type' => 'checkbox',
+      '#title' => t('Load genes track by default when viewing this organism'),
+      '#default_value' => variable_get($prefix . 'genes_is_default', TRUE),
+    );
+    $form['organism_' . $row['organism_id']][$prefix . 'show_transcripts'] = array(
+      '#type' => 'checkbox',
+      '#title' => t('Expose transcripts as an available track for this organism'),
+      '#default_value' => variable_get($prefix . 'show_transcripts', TRUE),
+    );
+    $form['organism_' . $row['organism_id']][$prefix . 'transcripts_is_default'] = array(
+      '#type' => 'checkbox',
+      '#title' => t('Load transcripts track by default when viewing this organism'),
+      '#default_value' => variable_get($prefix . 'transcripts_is_default', TRUE),
+    );
+  }
+
+  return system_settings_form($form);
+
+}
\ No newline at end of file
diff --git a/tripal_jbrowse_api.module b/tripal_jbrowse_api.module
index b15c840..2a1f46f 100644
--- a/tripal_jbrowse_api.module
+++ b/tripal_jbrowse_api.module
@@ -19,6 +19,15 @@ function tripal_jbrowse_api_permission() {
  */
 function tripal_jbrowse_api_menu() {
 
+  $items['admin/tripal/extension/tripal_jbrowse_api'] = array(
+    'title' => 'Tripal JBrowse API',
+    'description' => 'Configure settings for the Tripal JBrowse API module.',
+    'page callback' => 'drupal_get_form',
+    'page arguments' => array('tripal_jbrowse_api_settings'),
+    'access arguments' => array('administer tripal'),
+    'file' => 'tripal_jbrowse_api.admin.inc',
+  );
+
   $base = array(
     'type' => MENU_CALLBACK,
     'access callback' => 'user_access',
@@ -190,6 +199,8 @@ function tripal_jbrowse_api_callback_tracklist($organism) {
 
   $tracks = array();
 
+  $default_tracks = array();
+
   $tracks[] =  array(
     'category' => 'Assembly - ' . $organism->common_name,
     'useAsRefSeqStore' => TRUE,
@@ -203,30 +214,43 @@ function tripal_jbrowse_api_callback_tracklist($organism) {
     ),
   );
 
-  $tracks[] = array(
-    'category' => 'Genes',
-    'label' => 'genes',
-    'key' => $organism->common_name . ' gene models',
-    'type' => 'JBrowse/View/Track/CanvasFeatures',
-    'trackType' => 'JBrowse/View/Track/CanvasFeatures',
-    'storeClass' => 'JBrowse/Store/SeqFeature/REST',
-    'style' => array(
-      '_defaultLabelScale' => 120,
-    ),
-  );
+  $default_tracks[] = 'refseq';
+
+  if (variable_get('tripal_jbrowse_api_' . $organism->organism_id. '_show_genes', TRUE)) {
+    $tracks[] = array(
+      'category' => 'Genes',
+      'label' => 'genes',
+      'key' => $organism->common_name . ' gene models',
+      'type' => 'JBrowse/View/Track/CanvasFeatures',
+      'trackType' => 'JBrowse/View/Track/CanvasFeatures',
+      'storeClass' => 'JBrowse/Store/SeqFeature/REST',
+      'style' => array(
+        '_defaultLabelScale' => 120,
+      ),
+    );
+    if (variable_get('tripal_jbrowse_api_' . $organism->organism_id. '_genes_is_default', TRUE)) {
+      $default_tracks[] = 'genes';
+    }
 
-  $tracks[] = array(
-    'category' => 'Transcripts',
-    'label' => 'transcripts',
-    'transcriptType' => 'transcript',
-    'key' => $organism->common_name . ' transcript models',
-    'type' => 'JBrowse/View/Track/CanvasFeatures',
-    'trackType' => 'JBrowse/View/Track/CanvasFeatures',
-    'storeClass' => 'JBrowse/Store/SeqFeature/REST',
-    'style' => array(
-      '_defaultLabelScale' => 120,
-    ),
-  );
+  }
+
+  if (variable_get('tripal_jbrowse_api_' . $organism->organism_id. '_show_transcripts', TRUE)) {
+    $tracks[] = array(
+      'category' => 'Transcripts',
+      'label' => 'transcripts',
+      'transcriptType' => 'transcript',
+      'key' => $organism->common_name . ' transcript models',
+      'type' => 'JBrowse/View/Track/CanvasFeatures',
+      'trackType' => 'JBrowse/View/Track/CanvasFeatures',
+      'storeClass' => 'JBrowse/Store/SeqFeature/REST',
+      'style' => array(
+        '_defaultLabelScale' => 120,
+      ),
+    );
+    if (variable_get('tripal_jbrowse_api_' . $organism->organism_id. '_transcripts_is_default', TRUE)) {
+      $default_tracks[] = 'transcripts';
+    }
+  }
 
   $other_tracks = module_invoke_all('jbrowse_tracks', $organism);
 
@@ -234,7 +258,7 @@ function tripal_jbrowse_api_callback_tracklist($organism) {
 
   $data = array(
     'dataset_id' => $organism->organism_id,
-    'defaultTracks' => 'refseq,genes,transcripts',
+    'defaultTracks' => implode(',', $default_tracks),
     'names' => array(
       'type' => 'REST',
       'url' => $GLOBALS['base_url'] . '/api/jbrowse/' . $organism->organism_id . '/names',