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@@ -18,6 +18,7 @@ require('api/tripal_analysis.api.inc');
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require('includes/tripal_analysis_privacy.inc');
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require('includes/tripal_analysis.admin.inc');
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require('includes/tripal_analysis.form.inc');
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+require('includes/tripal_analysis.sync.inc');
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/**
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@@ -57,40 +58,45 @@ function tripal_analysis_node_info() {
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function tripal_analysis_menu() {
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//Sync analysis
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$items['chado_sync_analyses'] = array(
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- 'title' => 'Sync Data',
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- 'page callback' => 'tripal_analysis_sync_analyses',
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- 'access arguments' => array('administer tripal analyses'),
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- 'type' => MENU_CALLBACK
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+ 'title' => 'Sync Data',
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+ 'page callback' => 'tripal_analysis_sync_analyses',
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+ 'access arguments' => array('administer tripal analyses'),
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+ 'type' => MENU_CALLBACK
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);
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// Tripal Analysis administrative settings
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$items['admin/tripal/chado/tripal_analysis'] = array(
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- 'title' => 'Analyses',
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- 'description' => 'A bioinformatics analysis producing features.',
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- 'access arguments' => array('administer tripal analyses'),
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- 'type' => MENU_NORMAL_ITEM,
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+ 'title' => 'Analyses',
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+ 'description' => 'A bioinformatics analysis producing features.',
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+ 'access arguments' => array('administer tripal analyses'),
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+ 'type' => MENU_NORMAL_ITEM,
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);
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$items['admin/tripal/chado/tripal_analysis/help'] = array(
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- 'title' => 'Help',
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- 'description' => "A description of the Tripal Analysis module including a short description of it's usage.",
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- 'page callback' => 'theme',
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- 'page arguments' => array('tripal_analysis_help'),
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- 'access arguments' => array('administer tripal analyses'),
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- 'type' => MENU_NORMAL_ITEM,
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- 'file' => 'includes/tripal_analysis.admin.inc',
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- 'weight' => 10
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+ 'title' => 'Help',
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+ 'description' => "A description of the Tripal Analysis module including a short description of it's usage.",
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+ 'page callback' => 'theme',
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+ 'page arguments' => array('tripal_analysis_help'),
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+ 'access arguments' => array('administer tripal analyses'),
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+ 'type' => MENU_NORMAL_ITEM,
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);
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$items['admin/tripal/chado/tripal_analysis/configuration'] = array(
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- 'title' => 'Configuration',
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- 'description' => 'Settings for the displays of analysis results.',
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- 'page callback' => 'drupal_get_form',
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- 'page arguments' => array('tripal_analysis_help'),
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- 'access arguments' => array('administer tripal analyses'),
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- 'type' => MENU_NORMAL_ITEM,
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- 'file' => 'includes/tripal_analysis.admin.inc',
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+ 'title' => 'Configuration',
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+ 'description' => 'Settings for the displays of analysis results.',
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+ 'page callback' => 'drupal_get_form',
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+ 'page arguments' => array('tripal_analysis_admin'),
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+ 'access arguments' => array('administer tripal analyses'),
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+ 'type' => MENU_NORMAL_ITEM,
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+ );
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+
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+ $items['admin/tripal/chado/tripal_analysis/sync'] = array(
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+ 'title' => 'Sync Analyses',
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+ 'description' => 'Sync Chado analyses with Drupal.',
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+ 'page callback' => 'drupal_get_form',
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+ 'page arguments' => array('tripal_analysis_sync_form'),
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+ 'access arguments' => array('administer tripal analyses'),
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+ 'type' => MENU_NORMAL_ITEM,
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);
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-
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$items['tripal_analysis/properties/minus/%/%'] = array(
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'page callback' => 'tripal_analysis_property_delete',
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@@ -114,34 +120,197 @@ function tripal_analysis_help ($path, $arg) {
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}
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/**
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- * When a new chado_analysis node is created we also need to add information
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- * to our chado_analysis table. This function is called on insert of a new
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- * node of type 'chado_analysis' and inserts the necessary information.
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+ * Set the permission types that the chado module uses. Essentially we
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+ * want permissionis that protect creation, editing and deleting of chado
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+ * data objects
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*
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* @ingroup tripal_analysis
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*/
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-function chado_analysis_insert($node) {
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- global $user;
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+function tripal_analysis_permission() {
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+ return array(
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+ 'access chado_analysis content' => array(
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+ 'title' => t('View Analyses'),
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+ 'description' => t('Allow users to view analysis pages.'),
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+ ),
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+ 'create chado_analysis content' => array(
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+ 'title' => t('Create Analyses'),
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+ 'description' => t('Allow users to create new analysis pages.'),
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+ ),
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+ 'delete chado_analysis content' => array(
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+ 'title' => t('Delete Analyses'),
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+ 'description' => t('Allow users to delete analysis pages.'),
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+ ),
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+ 'edit chado_analysis content' => array(
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+ 'title' => t('Edit Analyses'),
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+ 'description' => t('Allow users to edit analysis pages.'),
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+ ),
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+ 'adminster tripal analysis' => array(
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+ 'title' => t('Administer Analyses'),
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+ 'description' => t('Allow users to administer all analyses.'),
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+ ),
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+ );
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+}
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- // Create a timestamp so we can insert it into the chado database
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- $time = $node->timeexecuted;
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- $month = $time['month'];
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- $day = $time['day'];
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- $year = $time['year'];
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- $timestamp = $month . '/' . $day . '/' . $year;
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+/**
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+ * We need to let drupal know about our theme functions and their arguments.
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+ * We create theme functions to allow users of the module to customize the
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+ * look and feel of the output generated in this module
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+ *
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+ * @ingroup tripal_analysis
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+ */
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+function tripal_analysis_theme($existing, $type, $theme, $path) {
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+ $core_path = drupal_get_path('module', 'tripal_core');
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+
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+ $theme_path = drupal_get_path('module', 'tripal_analysis') . '/theme';
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+ $items = array(
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+ 'node__chado_analysis' => array(
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+ 'template' => 'node--chado-generic',
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+ 'render element' => 'node',
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+ 'base hook' => 'node',
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+ 'path' => "$core_path/theme",
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+ ),
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+ 'tripal_analysis_base' => array(
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+ 'variables' => array('node' => NULL),
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+ 'template' => 'tripal_analysis_base',
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+ 'path' => "$path/theme/tripal_analysis",
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+ ),
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+ 'tripal_feature_analyses' => array(
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+ 'template' => 'tripal_feature_analyses',
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+ 'variables' => array('node' => NULL),
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+ 'path' => "$path/theme/tripal_analysis",
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+ ),
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+ 'tripal_analysis_properties' => array(
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+ 'variables' => array('node' => NULL),
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+ 'path' => "$path/theme/tripal_analysis",
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+ ),
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+ 'tripal_analysis_help' => array(
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+ 'template' => 'tripal_analysis_help',
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+ 'variables' => array(NULL),
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+ 'path' => "$path/theme",
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+ ),
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+ 'chado_analysis_node_form' => array(
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+ 'variables' => array('form'),
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+ 'path' => $theme_path,
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+ ),
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+ );
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+
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+ return $items;
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+}
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+/**
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+ *
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+ *
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+ * @ingroup tripal_analysis
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+ */
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+function tripal_analysis_block_info() {
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+ $blocks['base']['info'] = t('Tripal Analysis Details');
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+ $blocks['base']['cache'] = DRUPAL_NO_CACHE;
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+
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+ $blocks['featureblast']['info'] = t('Tripal Feature Analyses');
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+ $blocks['featureblast']['cache'] = DRUPAL_NO_CACHE;
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+
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+ return $blocks;
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+}
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+
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+/**
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+ *
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+ *
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+ * @ingroup tripal_analysis
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+ */
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+function tripal_analysis_block_view($delta = '') {
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+
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+ if (user_access('access chado_analysis content') and arg(0) == 'node' and is_numeric(arg(1))) {
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+ $nid = arg(1);
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+ $node = node_load($nid);
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- // If this analysis already exists then don't recreate it in chado
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- $analysis_id = $node->analysis_id;
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- if ($analysis_id) {
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- $values = array('analysis_id' => $node->analysis_id);
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- $result = tripal_core_chado_select('analysis', array('analysis_id'), $values);
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- if ($result and count($result) > 0) {
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- $analysis = $result[0];
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+ $block = array();
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+ switch ($delta) {
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+ case 'base':
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+ $block['subject'] = t('Analysis Details');
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+ $block['content'] = theme('tripal_analysis_base', $node);
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+ break;
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+ case 'tripal_feature_analyses':
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+ $block['subject'] = t('Feature Analyses');
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+ $block['content'] = theme('tripal_feature_analyses', $node);
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+ break;
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+ default :
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}
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+ return $block;
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}
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+}
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+
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+/**
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+ *
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+ * @ingroup tripal_feature
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+ */
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+function tripal_analysis_node_view($node, $view_mode, $langcode) {
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+ switch ($node->type) {
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+ case 'chado_analysis':
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+ // Show feature browser and counts
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+ if ($view_mode == 'full') {
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+ $node->content['tripal_analysis_base'] = array(
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+ '#value' => theme('tripal_analysis_base', array('node' => $node)),
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+ );
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+ $node->content['tripal_analysis_properties'] = array(
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+ '#value' => theme('tripal_analysis_properties', array('node' => $node)),
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+ );
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+ }
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+ break;
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+ }
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+}
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+/**
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+ * Implements hook_views_api()
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+ * Purpose: Essentially this hook tells drupal that there is views support for
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+ * for this module which then includes tripal_analysis.views.inc where all the
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+ * views integration code is
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+ *
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+ * @ingroup tripal_analysis
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+ */
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+function tripal_analysis_views_api() {
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+ return array(
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+ 'api' => 2.0,
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+ );
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+}
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+
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+
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+
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+
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+/*
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+ *
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+*/
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+function tripal_analysis_form_alter(&$form, &$form_state, $form_id) {
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+ if ($form_id == "chado_analysis_node_form") {
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+ }
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+}
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+/**
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+ * When a new chado_analysis node is created we also need to add information
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+ * to our chado_analysis table. This function is called on insert of a new
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+ * node of type 'chado_analysis' and inserts the necessary information.
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+ *
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+ * @ingroup tripal_analysis
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+ */
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+function chado_analysis_insert($node) {
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- // If the analysis doesn't exist then let's create it in chado.
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- if (!$analysis) {
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+ $node->analysisname = trim($node->analysisname);
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+ $node->description = trim($node->description);
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+ $node->program = trim($node->program);
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+ $node->programversion = trim($node->programversion);
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+ $node->algorithm = trim($node->algorithm);
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+ $node->sourcename = trim($node->sourcename);
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+ $node->sourceversion = trim($node->sourceversion);
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+ $node->sourceuri = trim($node->sourceuri);
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+
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+ // if there is an analysis_id in the $node object then this must be a sync so
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+ // we can skip adding the analysis as it is already there, although
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+ // we do need to proceed with the rest of the insert
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+ if (!property_exists($node,'analysis_id')) {
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+
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+ // Create a timestamp so we can insert it into the chado database
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+ $time = $node->timeexecuted;
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+ $month = $time['month'];
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+ $day = $time['day'];
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+ $year = $time['year'];
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+ $timestamp = $month . '/' . $day . '/' . $year;
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+
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// insert and then get the newly inserted analysis record
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$values = array(
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'name' => $node->analysisname,
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@@ -154,37 +323,28 @@ function chado_analysis_insert($node) {
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'sourceuri' => $node->sourceuri,
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'timeexecuted' => $timestamp
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);
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- if (tripal_core_chado_insert('analysis', $values)) {
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- $analysis = tripal_core_chado_select('analysis', array('*'), $values);
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- $analysis_id = $analysis[0]->analysis_id;
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+ $analysis = tripal_core_chado_insert('analysis', $values);
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+ if (!$analysis) {
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+ drupal_set_message(t('Unable to add analysis.', 'warning'));
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+ watchdog('tripal_analysis', 'Insert analysis: Unable to create analysis where values:%values',
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+ array('%values' => print_r($values, TRUE)), WATCHDOG_ERROR);
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+ return;
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}
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+ $analysis_id = $analysis['analysis_id'];
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}
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-
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+ else {
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+ $analysis_id = $node->analysis_id;
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+ }
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+
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// Make sure the entry for this analysis doesn't already exist in the
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// chado_analysis table if it doesn't exist then we want to add it.
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- $node_check_sql = "SELECT * FROM {chado_analysis} " .
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- "WHERE analysis_id = :analysis_id";
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- $node_check = db_query($node_check_sql, array(':analysis_id' => $analysis_id))->fetchObject();
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- if (!$node_check) {
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- // next add the item to the drupal table
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- $sql = "INSERT INTO {chado_analysis} (nid, vid, analysis_id) " .
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- "VALUES (:nid, :vid, :analysis_id)";
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- db_query($sql, array(':nid' => $node->nid, ':vid' => $node->vid, ':analysis_id' => $analysis_id));
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- // Create a title for the analysis node using the unique keys so when the
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- // node is saved, it will have a title
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+ $check_org_id = chado_get_id_for_node('analysis', $node->nid);
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+ if (!$check_org_id) {
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$record = new stdClass();
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- // If the analysis has a name, use it as the node title. If not, construct
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- // the title using program, programversion, and sourcename
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- if ($node->analysisname) {
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- $record->title = $node->analysisname;
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- }
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- else {
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- //Construct node title as "program (version)
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- $record->title = "$node->program ($node->programversion)";
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- }
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$record->nid = $node->nid;
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- drupal_write_record('node', $record, 'nid');
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- drupal_write_record('node_revisions', $record, 'nid');
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+ $record->vid = $node->vid;
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+ $record->analysis_id = $analysis_id;
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+ drupal_write_record('chado_analysis', $record);
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}
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// add the analysis to the node object for
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@@ -261,17 +421,11 @@ function chado_analysis_delete($node) {
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}
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// Remove data from the {chado_analysis}, {node}, and {node_revisions} tables
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- $sql_del = "DELETE FROM {chado_analysis} " .
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- "WHERE nid = :nid " .
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- "AND vid = :vid";
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+ $sql_del = "DELETE FROM {chado_analysis} WHERE nid = :nid AND vid = :vid";
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db_query($sql_del, array(':nid' => $node->nid, ':vid' => $node->vid));
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- $sql_del = "DELETE FROM {node} " .
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- "WHERE nid = :nid " .
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- "AND vid = :vid";
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+ $sql_del = "DELETE FROM {node} WHERE nid = :nid AND vid = :vid";
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db_query($sql_del, array(':nid' => $node->nid, ':vid' => $node->vid));
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- $sql_del = "DELETE FROM {node_revision} " .
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- "WHERE nid = :nid " .
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- "AND vid = :vid";
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+ $sql_del = "DELETE FROM {node_revision} WHERE nid = :nid AND vid = :vid";
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db_query($sql_del, array(':nid' => $node->nid, ':vid' => $node->vid));
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//Remove from analysis and analysisprop tables of chado database as well
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@@ -287,7 +441,15 @@ function chado_analysis_delete($node) {
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* @ingroup tripal_analysis
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*/
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function chado_analysis_update($node) {
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- global $user;
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+ $node->analysisname = trim($node->analysisname);
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+ $node->description = trim($node->description);
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+ $node->program = trim($node->program);
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+ $node->programversion = trim($node->programversion);
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+ $node->algorithm = trim($node->algorithm);
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+ $node->sourcename = trim($node->sourcename);
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+ $node->sourceversion = trim($node->sourceversion);
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+ $node->sourceuri = trim($node->sourceuri);
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+
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if ($node->revision) {
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// TODO -- decide what to do about revisions
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}
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@@ -429,17 +591,21 @@ function chado_analysis_update($node) {
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*
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* @ingroup tripal_analysis
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*/
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-function chado_analysis_load($node) {
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+function chado_analysis_load($nodes) {
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- // get the feature details from chado
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- $analysis_id = chado_get_id_for_node('analysis', $node->nid);
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+ foreach ($nodes as $nid => $node) {
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+ // find the analysis and add in the details
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+ $analysis_id = chado_get_id_for_node('analysis', $nid);
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- $values = array('analysis_id' => $analysis_id);
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- $analysis = tripal_core_generate_chado_var('analysis', $values);
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+ // build the analysis variable
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+ $values = array('analysis_id' => $analysis_id);
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+ $analysis = tripal_core_generate_chado_var('analysis', $values);
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+
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- $additions = new stdClass();
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- $additions->analysis = $analysis;
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- return $additions;
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+ // add in the description field
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+ $analysis = tripal_core_expand_chado_vars($analysis, 'field', 'analysis.description');
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+ $nodes[$nid]->analysis = $analysis;
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+ }
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}
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/**
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@@ -515,164 +681,3 @@ function chado_analysis_node_access($node, $op, $account) {
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return NULL;
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}
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-/**
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- * Set the permission types that the chado module uses. Essentially we
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- * want permissionis that protect creation, editing and deleting of chado
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- * data objects
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- *
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- * @ingroup tripal_analysis
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- */
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-function tripal_analysis_permission() {
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- return array(
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- 'access chado_analysis content' => array(
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- 'title' => t('View Analyses'),
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- 'description' => t('Allow users to view analysis pages.'),
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- ),
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- 'create chado_analysis content' => array(
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- 'title' => t('Create Analyses'),
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- 'description' => t('Allow users to create new analysis pages.'),
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- ),
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- 'delete chado_analysis content' => array(
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- 'title' => t('Delete Analyses'),
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- 'description' => t('Allow users to delete analysis pages.'),
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- ),
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- 'edit chado_analysis content' => array(
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- 'title' => t('Edit Analyses'),
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- 'description' => t('Allow users to edit analysis pages.'),
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- ),
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- 'adminster tripal analysis' => array(
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- 'title' => t('Administer Analyses'),
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- 'description' => t('Allow users to administer all analyses.'),
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- ),
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- );
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-}
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-
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-/**
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- * We need to let drupal know about our theme functions and their arguments.
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- * We create theme functions to allow users of the module to customize the
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- * look and feel of the output generated in this module
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- *
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- * @ingroup tripal_analysis
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- */
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-function tripal_analysis_theme($existing, $type, $theme, $path) {
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- $core_path = drupal_get_path('module', 'tripal_core');
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-
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- $theme_path = drupal_get_path('module', 'tripal_analysis') . '/theme';
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- $items = array(
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- 'node__chado_analysis' => array(
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|
- 'template' => 'node--chado-generic',
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|
- 'render element' => 'node',
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|
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- 'base hook' => 'node',
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- 'path' => "$core_path/theme",
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- ),
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- 'tripal_analysis_base' => array(
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|
|
- 'variables' => array('node' => NULL),
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|
- 'template' => 'tripal_analysis_base',
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|
- 'path' => "$path/theme/tripal_analysis",
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- ),
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|
|
- 'tripal_feature_analyses' => array(
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|
- 'template' => 'tripal_feature_analyses',
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|
- 'variables' => array('node' => NULL),
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|
- 'path' => "$path/theme/tripal_analysis",
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- ),
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|
- 'tripal_analysis_properties' => array(
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|
- 'variables' => array('node' => NULL),
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|
- 'path' => "$path/theme/tripal_analysis",
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- ),
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|
- 'tripal_analysis_help' => array(
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|
- 'template' => 'tripal_analysis_help',
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|
- 'variables' => array(NULL),
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|
- 'path' => "$path/theme",
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- ),
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|
- 'chado_analysis_node_form' => array(
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|
- 'variables' => array('form'),
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|
- 'path' => $theme_path,
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|
- ),
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|
- );
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|
-
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|
|
- return $items;
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|
|
-}
|
|
|
-/**
|
|
|
- *
|
|
|
- *
|
|
|
- * @ingroup tripal_analysis
|
|
|
- */
|
|
|
-function tripal_analysis_block_info() {
|
|
|
- $blocks['base']['info'] = t('Tripal Analysis Details');
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|
|
- $blocks['base']['cache'] = DRUPAL_NO_CACHE;
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|
|
-
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|
|
- $blocks['featureblast']['info'] = t('Tripal Feature Analyses');
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|
|
- $blocks['featureblast']['cache'] = DRUPAL_NO_CACHE;
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|
|
-
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|
|
- return $blocks;
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|
|
-}
|
|
|
-
|
|
|
-/**
|
|
|
- *
|
|
|
- *
|
|
|
- * @ingroup tripal_analysis
|
|
|
- */
|
|
|
-function tripal_analysis_block_view($delta = '') {
|
|
|
-
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|
|
- if (user_access('access chado_analysis content') and arg(0) == 'node' and is_numeric(arg(1))) {
|
|
|
- $nid = arg(1);
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|
|
- $node = node_load($nid);
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|
|
-
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|
|
- $block = array();
|
|
|
- switch ($delta) {
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|
|
- case 'base':
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|
|
- $block['subject'] = t('Analysis Details');
|
|
|
- $block['content'] = theme('tripal_analysis_base', $node);
|
|
|
- break;
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|
|
- case 'tripal_feature_analyses':
|
|
|
- $block['subject'] = t('Feature Analyses');
|
|
|
- $block['content'] = theme('tripal_feature_analyses', $node);
|
|
|
- break;
|
|
|
- default :
|
|
|
- }
|
|
|
- return $block;
|
|
|
- }
|
|
|
-}
|
|
|
-
|
|
|
-/**
|
|
|
- *
|
|
|
- * Implements hook_node_view()
|
|
|
- */
|
|
|
-function tripal_analysis_node_view($node, $view_mode, $langcode) {
|
|
|
- if ($node->type == 'chado_feature') {
|
|
|
- if ($view_mode == 'search_index') {
|
|
|
- // return results for searching
|
|
|
- }
|
|
|
- if ($view_mode == 'full') {
|
|
|
- // return normal results
|
|
|
- $node->content['tripal_feature_analyses'] = array(
|
|
|
- '#markup' => theme('tripal_feature_analyses', $node),
|
|
|
- );
|
|
|
- }
|
|
|
- }
|
|
|
-}
|
|
|
-
|
|
|
-/**
|
|
|
- * Implements hook_views_api()
|
|
|
- * Purpose: Essentially this hook tells drupal that there is views support for
|
|
|
- * for this module which then includes tripal_analysis.views.inc where all the
|
|
|
- * views integration code is
|
|
|
- *
|
|
|
- * @ingroup tripal_analysis
|
|
|
- */
|
|
|
-function tripal_analysis_views_api() {
|
|
|
- return array(
|
|
|
- 'api' => 2.0,
|
|
|
- );
|
|
|
-}
|
|
|
-
|
|
|
-
|
|
|
-
|
|
|
-
|
|
|
-/*
|
|
|
- *
|
|
|
- */
|
|
|
-function tripal_analysis_form_alter(&$form, &$form_state, $form_id) {
|
|
|
- if ($form_id == "chado_analysis_node_form") {
|
|
|
- }
|
|
|
-}
|
Stephen Ficklin